48: Optic Tectum Decision Threshold

A simple model of decision making uses WTA (winner take all) where the option with the highest evidence takes control. The important part of WTA is the “take-all” part [Mysore and Kothari 2020]. Although the process of representing the highest evidence is well studied, the take-all part is less well studies. Vert little is known about the circuit mechanisms underlying unitary output generation [Mysore and Kothari 2020].

When choosing to turn left or right, the OT (optic tectum) in the midbrain is a central player. In mice the OT has a head-movement motor map where specific regions will turn the head left or right along the yaw, roll, or pitch axis. These output neurons are marked by the pitx2 transcription factor [Masullo et al 2019], [Choi JS et al 2021], [De Malmazet and Tripodi 2023]. Interestingly, these pitx2 head movement neurons receive essentially no visual movement, but receive multimodal input, particularly whisker input in mice [Xie Z et al 2021].

The simulated animal for this essay has only limited visual input, non-image photosensors, restricted to simple phototaxis. It does have a lateral line sense, where in fish senses surrounding water motion to detect obstacles and potential prey. Zebrafish can forage in the dark, which requires the lateral line [Carrillo and McHenry 2015], specifically the head lateral line.

Race to threshold – Mauthner cell

As a simplified example of decision making, the acoustic startle reflect and the hindbrain Mauthner cells in fish. There are two Mauthner cells in R4 (hindbrain rhombomere 4), one on each side. This startle reflex is a very fast (20ms) three-synapse circuit to escape danger. A loud sound drives acoustic sense neurons, which drives the ipsilateral Mauthner cell, which drives contralateral motor neurons to quickly turn in a “C-start” before swimming away [Bátora et al 2021]. This simple circuit is essentially a Braitenberg vehicle [Braitenberg 1984]. The Mauthner cells can also be driven by touch, vestibular, or by OT, and in zebrafish larvae, the head touch connections develop first, before the acoustic inputs [Kohashi et al 2021].

A flowchart illustrating the decision-making process in a neural circuit involving sensory inputs and motor connections, labeled with 'Sense.L', 'Sense.R', 'R4.mc.L', 'R4.mc.R', 'N.mn.L', and 'N.mn.R'.
Core of the Mauthner escape circuit. Sense input such as loud noise drive the Mauthner cell, which accumulates and fires when passing the action potential threshold. The Mauthner cell drives spinal motor neurons, which drive muscles. N.mn (spinal motoneurons), R4.m (Mauthner cell in rhombomere 4).

The above diagram shows the Braitenberg-like circuit of the Mauthner cell. Danger sensing neurons, acoustic, touch, or OT, drive the ipsilateral R4.mc (Mauthner cell in rhombomere 4), which drives contralateral N.mn (spinal motor neurons). This circuit, however, implicitly assumes that a danger sense will be dominated by one side or the other because it can’t compare the left and right signals.

Although touch from the animal bumping into an obstacle is often unilateral, sound is bilateral, which means the decision needs to handle some comparison between the two sides. A simple decision model is a race to threshold [Vickers 1970], but a simple race model is not optimal. Instead it is more efficient to compute differences between alternatives [Bogacz and Gurney 2007]. One of these models has two leaky accumulators with lateral inhibition [Usher and McClelland 2001]. DDM (drift diffusion) is another popular model with only a single accumulator with positive and negative inputs [Ratcliff 1978], but that system doesn’t fit this Mauthner cell circuit. In a race to threshold decision, the first accumulator to reach a threshold wins.

In the Mauthner cell circuit, the cell’s membrane voltage can serve as an accumulator and the neuron’s action potential as the threshold. The first R4.mc to reach the action potential threshold wins. The first graph below shows this race.

Graph showing the race to threshold in a neural decision-making model, illustrating the membrane voltage changes over time for left (v.L, blue) and right (v.R, red) accumulators. Includes sub-graphs for both firing and feedback inhibition dynamics.
Race to threshold simulations for a Mauthner-cell-like leaky accumulator circuit. The second graph shows the losing side (right) also firing its Mauthner-cell. The final graph shows the addition of feedback inhibition where the winner suppresses the loser from firing. ap.L (action potential burst of the left Mauthner cell), v.L (membrane voltage of the left Mauthner cell).

The above graphs show a simple race to threshold model for the Mauthner cells. The second graph shows the main issue: the firing of the winning side doesn’t prevent the losing side from also continuing to accumulate and fire. The models here are purely qualitative toy models for illustration. There is no attempt at accuracy to actual R4.mc values.

The current circuit can’t prevent the losing R4.mc from continue accumulating and firing shortly after, which might muddle the downstream motor neurons, possibly preventing a proper C-start and escape. In the actual Mauthner cell circuit, this conflict is solved by feedback inhibitory neurons that suppress the contralateral R4.mc [Koyama et al 2021]. Interestingly, this suppression is by direction electrical connectivity, not by inhibitory neurotransmitters. This feedback inhibition stop the accumulation of the contralateral R4.mc by hyper polarizing the membrane voltage directly, essentially resetting to zero.

Diagram depicting the Braitenberg-like circuit of the Mauthner cell with sensory inputs (Sense.L and Sense.R), ipsilateral Mauthner cells (R4.mc.L and R4.mc.R), feedback inhibition neurons (fbIN), and contralateral spinal motor neurons (N.mn.L and N.mn.R).
Adding post-firing feedback inhibition. When the winning R4.mc fires, it inhibits the losing R4.mc using a feedback interneuron. fbIN (feedback interneuron), N.mn (motoneuron), R4.mc (Mauthner cell).

The above diagram adds feedback neurons to suppress the losing R4.mc after an event. This suppression needs to be relatively short. The Mauthner cell only fires a brief burst, not an extended sustained output, which means the feedback inhibition only applies to the immediate event. This system may be a sufficient lockout for the highly specialized startle reflex, but a more general decision system may need a more complicated lockout system.

OT locking out for WTA

Let’s consider the OT crossed turning projection, which is used for orienting and seeking, while the OT uncrossed output is used for avoidance. OT decides to turn left or right for many input types, including visual, auditory, lateral line, touch, and even abstract cognitive decisions from cortical inputs. OT.co (OT crossed output) neurons project to R6.rs (mid-hindbrain reticula-spinal), which then projects to N.mn (spinal motoneurons) [Wheatcroft et al 2022]. This R.rs accumulation circuit exists in frog tadpoles, where they receive direct N5 (trigeminal) head touch input [Buhl et al 2015]. This circuit is roughly similar to the Mauthner cell circuit above, where OT.co replaces the sensory neurons, and the contralateral/ipsilateral crossing patterns are different.

Diagram comparing OT crossed turning and OT turning with action lockout in a neural circuit.
Simplified model of OT as input to mid-hindbrain turning to show parallel to Mauthner cell circuit. The second model shows how ongoing actions can disable OT output to turning neurons. H.zi (zona incerta), N.mn (spinal motoneuron), OT (optic tectum), R6.rs (reticulospinal turning neurons in hindbrain R6), Snr (substantia nigra pars reticulata).

So, let’s apply an ongoing-action lockout to the OT turning circuit by disabling OT output when an action is occurring. Unlike the specialized Mauthner cell circuit, which directly inhibited R4.mc, support the lockout suppresses the OT input to the accumulation circuit. In mammals, OT.co are inhibited by Snr (substantia nigra pars reticulata) and H.zi (zona incerta) [Doykos et al 2020]. H.zi is closely associated with movement, which suggests it could be a broad movement corollary / efference copy [Hormigo et al 2023]. H.zi appears to activate after or around movement onset, not during decision making [Hormigo et al 2023]. This timing contrasts with Snr, which drops its suppression just prior to movement. Either Snr or H.zi or a combination of the two is capable of suppressing OT.co during ongoing movement, which would eliminate input from the downstream R6.rs turning neurons.

Along with an inhibition of OT.co, H.zi also inhibits ipsilateral R6.rs chx10 turning neurons [Cregg et al 2020], but that study does not report an Snr input to R6.rs.chx10. That H.zi input could serve as a similar feedback inhibition as the Mauthner cell circuit, but the following simple model only uses the OT.co suppression.

Graph illustrating the OT action lockout mechanism over time, showing the values for left and right outputs.
In this scenario, the winner of the race to threshold cuts off the input to all accumulators. The losing accumulator slowly leaks to zero. ap.L (left action potential), v.L (left accumulator value)

The above chart shows a model of R6.rs turning neurons as leaky integrators for OT.co input, where the value abstractly represents the R6.rs membrane voltage. In this configuration, an action potential for turning left disables the OT input, but does not disable the R6.rs neurons directly. The OT input to R6.rs stops, and the R6.rs neurons leak back to their initial condition.

Increasing gain to avoid metastability

The R4.mc circuit is hyperoptimized for speed, including the feedback lockout circuit, which means it can lock out the loser within a short time, but even the hyper optimized circuit has limits. The Mauthner cell itself takes time to fire, and the feedback neurons also take time to fire. If the lower reaches its AP (action potential) threshold before the feedback inhibition takes hold, both R4.mc will fire, which will disrupt the animal’s escape. This issue of in-between decisions of greater for other decision circuits that aren’t as optimized as the Mauthner cell circuit. In frog tadpoles, disconnecting the midbrain impairs hindbrain decisions because of too many bilateral synchronous firing instead of limiting activation to a single side [Larbi et al 2022]. To improve the response, we need additional circuitry to distinguish the winner from the loser.

FFI (feedforward inhibition) can act as a high-pass filter, moving noise and weak signals from the accumulation in a gated accumulator model [Schall et al 2011]. Contralateral FFI could inhibit the weaker signal, increasing the division between the weaker and the stronger. But contralateral FFI works much better after the addition of lateral disinhibition [Koyama et al 2016].

Diagram depicting a neural circuit for decision-making involving sense inputs (left and right), feedforward inhibition (FFI), and motor neurons (N.mn) guiding actions.
Adding contralateral FFI to distinguish winner from loser in a WTA decision circuit. FFI (feedforward inhibition), N.mn (motoneuron), R4.mc (Mauthner cell).

The above circuit adds FFI neurons to the Mauthner cell escape circuit. A left sensory input will suppress the right Mauthner cell and vice versa. This contralateral inhibition should increase the difference between the two signals. Note, that the diagram has omitted the feedback inhibition because here we’re only interested in the ramp to threshold, not the lockout phase discussed earlier.

Graphs depicting a decision-making model showing plain ramp to threshold, weak contralateral feedforward inhibition (FFI), strong contralateral FFI, and large input difference related to Mauthner cell circuits.
Charts showing the effect of contralateral FFI. The first chart shows plain accumulation with two close inputs. The second and third show weak and strong contralateral FFI. The last shows the circuit when the inputs have a larger difference. ffi.L (value of FFI neurons), v.L (value of accumulator neurons).

The above charts show several scenarios with the FFI added to the circuit. The first chart shows a plain ramp to threshold without any FFI added. The second shows the addition of weak FFI. Weak FFI increases the time difference between threshold crossing at the cost of slowing the decision slightly.

However, increasing the FFI weights further causes the system to break entirely as in the third chart. Because the two signals are nearly equal, and because the FFI is strong, the FFI ends up inhibiting both choices and the decision never reaches threshold [Koyama et al 2016]. This problem is mainly when the inputs are fairly close. As the final chart shows, if the inputs are widely separated, the large FFI inhibition still allows the winner to reach threshold. However, widely separated inputs were never the original problem.

Although this dual output suppression is a problem for the escape circuit because it seeds to make an immediate decision, it could be a benefit in a more leisurely situation where the decision should be postponed until a clear winner emerges. A good deal of decision research considers delayed response time as a measure of conflict.

But for the escape circuit, this dual suppression is a problem. Contralateral inhibition can accentuate the differences, but at the cost of squashing the result entirely. A solution is to add lateral disinhibition between the FFI neurons [Koyama et al 2016]. Only the stronger input can inhibit the contralateral choice.

Diagram illustrating a neural circuit for the Mauthner cell escape reflex, featuring sensory inputs, feedforward inhibition (FFI), and motor output pathways.
Adding lateral disinhibition to the contralateral FFI circuit. FFI (feedforward inhibition), N.mn (spinal motoneuron), R4.mc (Mauthner cell).

The above decision circuit adds lateral disinhibition to the two FFI neurons. If the left sense is stronger, it with both inhibit the right R4.mc and disinhibit the left R4.mc by inhibiting the right FFI neuron. This should minimize the situation where nearly equal inputs inhibit both outputs.

Graph comparing plain ramp to threshold decision-making model on the left and FFI with disinhibition model on the right, showing action potential thresholds over time for left and right inputs.
The right chart shows how the disinhibition circuit widens the difference between the winning input and the lower. ffi.L (value of the left feedforward inhibition neuron), v.L (accumulator value of the left Mauthner cell).

The above chart shows the plain ramp to threshold and the FFI with disinhibition circuit for the same inputs. As the graph on the right shows, the disinhibition circuit greatly amplifies the difference between the inputs, making a clear decision.

This disinhibition pattern can also be modulated by top-down control, creating a two-phased decision [Shen B et al 2023]. Before the top-down disinhibition is activated, the two options accumulate evidence with only a minor suppression of their competitor. Enabling disinhibition quickly forces a WTA choice.

Lamprey optic tectum

While R4.mc supports a specialized escape circuit, OT supports a general orientation decision to turn left or right. As its name suggests, OT receives optical information from the retina, but in mammals it also receives whisker information, in fish it receives lateral-line information, and in lampreys and some fish it receives electrosensory information. The lateral-line and elestrosensory systems are closely related. The question immediately arises for the OT: which sense came first? Larval lampreys do not have image forming retinas, but only ocellus-like photoreceptors [Salas 2016], and the larval lamprey retinal area does not project to OT [Barandela et al 2023]. The larval OT does project to M.rs (midbrain reticulospinal, specifically nMLF – nucleus of the medial lateral fasciculus) [Barandela et al 2023], but I haven’t found any study reporting the inputs to the larval lamprey OT.

A later lamprey metamorphosis expands both the retina and the OT into image supporting systems and connects the two [Barandela et al 2023]. During that metamorphosis OT greatly expands and becomes a seven layered structure comprised of alternating white and grey layers.

A diagram illustrating the integration of optic and electrosensory inputs in the optic tectum (OT), showing pathways to left and right ramp outputs.
Layers and inputs to the OT. Visual inputs connect to the superficial OT.s layer. Lateral-line and electrosensory input connect to the intermediate OT layer. The output OT.co layer combines the visual and electrosensory input.

In adult lampreys the retinal connects to OT.s (superficial layer of OT) and the ELL (electrosensory) connects to OT.i (intermediate layer of OT) with minimal overlap [Kardamakis et al 2016]. The output OT.co (crossed OT output neurons) extend dendrites to both OT.s and OT.i and integrate the two senses [Kardamakis et al 2016].

This essay will focus on the electrosensory path and OT.i. First, because, like the lamprey larva, the simulation animal does not have an image forming eye, but does have a lateral-line sense. Second, because the mammalian OT pitx2 turning area is also in OT.i [Masullo et al 2019], and receives whisker input but minimal or no visual input [Zahler et al 2021], [González-Rueda et al 2024]. Mexican blind cavefish show denser somatosensory in OT with increased somatosensory input [Patton et al 2010].

For OT as a decision circuit, there are two questions: how does any lateral inhibition between the left and right choice connect, and is the inhibition system feedforward like the Mauthner cell or a feedback system? For visual and auditory input, the lateral inhibition uses R.is (nucleus isthmus). In all vertebrates, R.is provides a donut-like center enhancement and surrounding inhibition [Mahajan and Mysore 2022], which includes suppressing contralateral input [Schryver 2021], but does not project contra laterally to the midbrain [Fenk et al 2023]. However, the OT.i lateral line may not use R.is. In lamprey an electrosensory distractor does not suppress a visual stimulus, it doesn’t suppress another electrosensory stimulus [Kardamakis et al 2016]. This suggests that visual and lateral line use different systems for lateral inhibition. In mammals the R.is (R.pbg parabigeminal in mammals) provides ACh to the visual OT.s layer as part of the selection process, but OT.i and OT.d (deep OT) receive ACh from Ppt (pedunculopontine tegmentum) and P.ldt (laterodorsal tegmentum) not from R.is.

The second question is whether the decision sharpening uses feedforward inhibition or feedback inhibition. The R.is circuit seems more of a feedforward inhibition system, because it inhibits based on ongoing input, not sampling from a ramping population of neurons. But the mammalian OT is a central accumulator in a decision loop involving the basal ganglia and cortex [Brody and Hanks 2015], which is only possible as a feedback loop. This feedback loop requires a ramping population of recurrently connected neurons, because an integrate-and-fire system like the Mauthner cell only fires when the final decision is made, but a feedback loop needs intermediate values. OT has recurrent connections in mammals [Basso and May 2017], [Liu Z et al 2016], frogs [Khakhalin et al 2014], [Felch et al 2015], [Jang EV et al 2016], and zebrafish OT shows edge-of-chaos spontaneous avalanche behavior, which likely also requires recurrent connectivity [Zylbertal and Bianco 2023], but I don’t know of any lamprey recurrent connectivity, or whether it exists in OT.i or OT.co. It’s possible that the feedback-based population decision system developed jawed vertebrates after the lamprey split.

Diagram illustrating the decision-making circuit involving electrosensory information and output pathways for turning actions in a neural model.
Lamprey OT decision system, focusing the ELL input to OT.i. Here, Snr is used to inhibit the output, not for lateral inhibition. V.pt DA connectivity as a decision onset amplifier to output neurons. DA (dopamine), OT.co (crossing OT projecting), OT.i (intermediate ELL input layer), R.ovl (hindbrain octavolateral nucleus for electrosense), R.rs (reticulospinal turning neurons), Snr (substantia nigra pars reticulata), V.pt (posterior tuberculum).

The decision output should be isolated from the decision ramping process to prevent premature action. In the Mauthner cell system, the neuron itself provided that isolation because it only fires after the decision is made. But a population ramping system needs additional circuitry to isolate the decision. Like other vertebrates, the lamprey OT.co are inhibited by Snr (substantia nigra pars reticulata), which could prevent a premature decision from driving action by suppressing output while the decision is incomplete. As a parallel decision sharpening system, the lamprey midbrain dopamine system V.pt (posterior tuberculum), believed to be homologous to the mammalian Snc (substantia nigra pars compacts), receives input from OT [Suryanarayana et al 2021] nd enhances locomotor output by projections to MLR [Ryczko et al 2013], [Ryczko et al 2016], [Ryczko and Dubuc 2023] and R.rs [Ryczko et al 2020], [Ryczko and Dubuc 2023], and also projects to OT.co [Pérez-Fernández et al 2017]. In mammals Snr has a phasic increase around action onset. The V.pt DA boost amplifies and extends locomotor output. For decision sharpening, this system would invigorate the action only after the ramping process was complete or near complete while discouraging pre-decision action.

Note, the R.rs output stage can be considered its own accumulator, because the R.rs neurons themselves integrate and fire. Two-stage accumulators have advantages over a single stage [Balsdon et al 2023], [Verdonck et al 2021]. So, this system could be viewed as a two-stage accumulator system.

While the lamprey may have all the pieces to form a decision system using OT, too much is unknown about the lamprey OT to use it as the basis for the simulation. Instead, I’ll incorporate research from the mammalian OT decision system, which is much better studies, but does have the disadvantage of possibly including mammal-specific features. For example, the mammalian OT has both ramping and bursting neurons, suggesting a distinct ramping population from the OT.co output population, unlike the lamprey, which combines ramping and output in a single neuron population.

OT ramping with feedback excitation and inhibition

Consider the OT as a feedback decision system, particularly focusing in OT.i (intermediate layer of OT), because in mice a subpopulation of OT.i marked by pitx2 (a gene transcription factor) turns the head in the yaw, roll, and pitch axes [Liu X et al 2022]. Because the essay animal is fish-like with no neck, and also two dimensional, we can focus on the left-right yaw. This left-right decision is also important singe the bilateral organization of the brain means the left-right circuits are distinct from any unilateral decision, because they require commissural connections.

The mammalian OT has both ramping neurons and bursting neurons [Basso and May 2017], although the exact circuitry is not known. OT.ramp may project to burst neurons such as OT.co that send the action. For this model I’ll assume that the ramping neurons are a subpopulation distinct from the bursting and that OT.co are the bursting neurons, but this assumption is not based on any research I can find.

After a decision commits, the system needs to lockout further decisions until the new action completes. As discussed above, this lockout function is compatible with the known Snr and H.zi suppression of OT.co [Comoli et al 2012]. This lockout function is speculative because I haven’t found research about lockout for OT decisions.

A diagram illustrating the decision-making circuit involving optic tectum (OT) inputs, ramping neurons, crossed outputs, and their connections to downstream motor neurons.
OT decision circuit with ramping and bursting output. The output neurons are suppressed by H.zi and Snr as an action lockout. H.zi (zona incerta), N.sp (spinal motoneurons), OT.co (crossing OT output), OT.ramp (ramping OT neurons), OT.input (ELL input neurons), R.rs (reticulospinal turning neurons).

The above diagram shows the OT decision circuit. In general, OT.input is very flexible and can include abstract input from the cortex in mammals [Thomas et al 2023], as part of the cortex decision circuit. The OT.i.pitx2 neurons for mouse head turning have strong whisker input from N5 (trigeminal cranial nerve), but weak or no visual input [Xie Z et al 2021]. Although this whisker primary and the OT.i.pitx2 head turning could be a novel mammal system, the fish lateral line serves a similar function as mammal whiskers. Zebrafish larvae, for example, can learn to hunt in darkness using the lateral line, despite being primarily visual hunters [Whestphal and O’Malley 2013]. A proto-vertebrate with lateral-line sensors but without an image-forming retina could use this mammalian OT.i.pitx2 circuit for decisions. The OT accumulation and delay sustain are primarily OT.i [Basso et al 2021].

The LCA (leaky competing accumulator) model of decision making [Usher and McClelland 2001], uses a pair of leaky accumulators with feedback lateral inhibition. That model, like other decision models such as DDM (drift-diffusion), are intended to describe higher level decision making, such as modeling human tasks, but the structure is inspired by neural circuits like the OT decision system.

The OT.ramp are likely a population of recurrently connected neurons, unlike the paired Mauthner cell which integrated with its membrane potential and only fired a single AP once the threshold was crossed. OT.ramp are likely to use both membrane integration and recurrent connectivity for their ramping. For simplicity, I’m trading OT.ramp neurons as leaky integrators, which does obscure important details about the firing model, including issues with E/I (excitation/inhibition) balance and edge-of-chaos positive feedback behavior. Because OT.ramp fire during the integration, unlike Mauthner cells, the competition between left and right can use feedback inhibition instead of relying on contralateral, disinhibiting feedforward inhibition.

Diagrams comparing two types of feedback inhibition in a decision-making circuit: Soma feedback inhibition on the left and Dendrite feedback inhibition on the right.
Two models of lateral inhibition. The soma feedback inhibition directly inhibits the accumulator. The dendrite feedback cuts off input from the accumulator. in.L (left OT input), ramp.L (left OT ramping), OT.co.L (left OT crossing output).

The above diagram shows two styles of feedback inhibition: inhibiting the OT.ramp neuron soma directly and inhibiting the OT.ramp input by inhibiting their dendrites. The soma inhibition could also include axon output inhibition. In the cortex SST (somatostatin) interneurons inhibit dendrites, PV (parvalbumin) interneurons inhibit the soma directly, and CCK interneurons inhibit the axon output. PV neurons may not be unique in inhibiting the soma, and the PV role in the cortex is more about E/I balance than lateral inhibition. However, OT neurons and cortex neurons are not developmentally related: all OT neurons derive from OT progenitors [Cheung et al 2024]. The analogy with the cortex is only to illustrate that different inhibitory neurons can target specific areas of the target neuron, and specifically introduce the ability to inhibit input to the neuron.

Let’s take a toy model of OT.ramp, as if they were a single leaky integrator for each side. Unlike real neuron population spiking, these model OT.ramp produce continuous output, which the feedback neurons can use. The purpose is to get a qualitative idea of how FBI (feedback inhibition) might work for soma-targeted inhibition and dendrite-targeted inhibition.

Graphs illustrating decision-making models with feedback inhibition. Top left: No feedback between left (e.L) and right (e.R) choices. Top right: Inhibition at the soma impacting both choices. Bottom left: Inhibition at dendrites affecting left and right choices differently. Bottom right: Combined inhibition at both soma and dendrites, demonstrating decision dynamics across time.
Ramping values for different feedback circuits. Soma inhibition directly inhibits the accumulator. Dendrite inhibition blocks input to the accumulator. e.L (left accumulator value)

The above graphs show the leaky integrator OT.ramp with either no FBI, soma-only FBI, dendrite-only FBI, and both soma and dendrite FBI. Unlike the Mauthner cell FFI, the dendrite input FBI does not drive both OT.ramp to zero, which likely means that the FFI disinhibition circuit is less important. Also, unlike the Mauthner cell simulation, which measured the membrane voltage, the graphed value is a general excitation level.

Graphs illustrating the effects of weak and strong feedback inhibition on left and right neural responses over time.
Varying connectivity strength for the feedback inhibition.

The above graphs show the behavior with variations in FBI strength. The weak FBI shows a significant difference between soma-only and dendrite-only inhibition. Weak soma FBI allows both options to fire, while the weak dendrite FBI clearly distinguishes between the options. Both strong FBI circuits distinguish their outputs.

In the real recurrent neural system, output spikes are not a continuous functions, and the population may be too small to use population encoding to approximate continuity. The input itself isn’t continuous, and includes noise. In addition, recurrent excitation is a positive feedback system, and in combination with normalizing inhibition, can produce chaotic transitions between states. This model does not support edge-of-chaos behavior, which may be important to the actual system. It also doesn’t include detailed timing and oscillatory behavior, and OT is known to produce gamma (25-100Hz) oscillations, and oscillations can interact with feedback, such as for SST neurons in the postsubigulum head direction system [Simonnet et al 2017]. All of these limitations may mean that cases such as the strong FBI or the weak FBI graphs above are physically impossible.

OT feedback commissures

The left/right decision requires contralateral communication, which is relatively rare, and can help isolate some of the decision circuitry. The OT.ramp decision model above required contralateral inhibition, which means commissural feedback paths between the OT sides are particularly important. There are three main contralateral paths in the OT that I’ve found studies for:

  • Direct OT to OT contralateral connections [Doykos et al 2020].
  • R.is (nucleus isthmus) contralateral inhibition in some species [Gambrill et al 2016].
  • Contralateral Snr and Ppt.a (anterior pedunculopontine tegmentum) inhibition, either related to the Sprague effect [Durmer and Rosenquist 2001], or as part of the basal ganglia output [Jiang H et al 2003].

The lamprey has OT input from the contralateral OT, and bilateral M.rf (midbrain reticular formation) [de Arriba and Pombal 2007], which likely includes Snr. The Lamprey OT.co has input from Snr [Kardamakis et al 2015]. Because “midbrain reticular formation” is so broad, these two studies may not contradict each other. The majority of contralateral OT projections is from OT.i with some from OT.s and OT.pv (periventricular aka deep) and more from OT.l than OT.m [de Arriba and Pombal 2007], which could correspond to the mammalian OT.i pitx2 group.

The direct OT to OT connectivity is the simplest for this circuit. OT.i to contralateral OT.i exists in the anterior OT [Doykos et al 2020]. OT.burst have projections to the contralateral OT [Basso and May 2017]. OT to contralateral OT exists for deeper OT.s and deeper of OT.id [Broersen et al 2025]. In lamprey, the majority of OT to contralateral OT is OT.i [de Arriba and Pombal 2007]. OT contralateral projections include competitive inhibition for choice, and OT contralateral projections reflect choice earlier than other decision brain regions [Essig et al 2020]. OT to OT is generally restricted to anterior OT, and about 50% of OT to OT are excitatory and 50% are inhibitory.

Diagram illustrating the circuitry involved in decision-making in the optic tectum, showing connections between various neurons including OT.i.R, OT.i.L, Snr, Ppt.a, and R.is.
Several of the major OT commissures. The core includes direct OT to OT projections and loops including Ppt.a and Snr. The R.is inhibition is important for visual and auditory, but may not be used for lateral-line and touch. Broader contralateral loops use T.pf and the striatum and in mammals T.pf and C.m2. C.m2 (premotor cortex), OT.i.L (left intermediate optic tectum), Ppt.a (anterior pedunculopontine tegmentum), R.is (nucleus isthmi), S.d (dorsal striatum), Snr (substantia nigra pars reticulata), T.pf (parafascicular thalamus)

R.is is critical for visual and auditory competitive choice between targets on a single hemisphere [Kawakami et al 2021]. Disabling R.is.mc (magnocellular R.is) in owls abolishes all competitive OT in a single hemisphere, but that study did not examine contralateral effects [Mysore and Knudsen 2013]. In pigeons, disabling R.is.mc reduces inhibition of R.is.pc (parvocellular R.is) [Marín et al 2007], but again this study was unilateral and did not examine effects on the contralateral OT. In bearded dragons, R.is.mc is required for bilateral competition during REM sleep, but in those animals it does not project to the contralateral midbrain [Fenk et al 2023], which would include OT. The primate R.pbg (parabigeminal), which is the mammal homolog of R.is, does project to the contralateral OT [Deichler et al 2020], but the mammal R.pbg is connected with OT.s (superficial OT) visual lateral particular for ACh (acetylcholine), while OT.id (intermediate and deep OT) receives ACh from Ppt and P.ldt (laterodorsal tegmentum) [Krauzlis et al 2023], [Wolf et al 2015]. I haven’t found a study specifically examining contralateral inhibition from R.is, and while some species do have contralateral connectivity, it doesn’t appear to be directly used for the orienting/head turning decisions for this essay.

OT.i receives contralateral inhibition from a portion of Snr, particularly Snr.al (anterolateral Snr) [Jiang H et al 2003], [Velero-Cabré et al 2020], although most (75%) of Snr inhibition of OT is ipsilateral [Jiang H et al 2003]. Ppt.a and Snr are important for the Sprague effect, where inhibition of unilateral C.vis (visual cortex) input to OT results in hemispheric attentional neglect, but is restored when Ppt.a and/or contralateral Snr projections are also inhibited [Krauzlis et al 2023]. Most Snr.l projections are modulatory and depend on movement direction and modulate choice, and find little evidence for strong Snr suppression of OT.id [Doykos et al 2025], but note that this study specifically examines Snr.dl, but Snr.vm also projects to OT and has a different progenitor origin and functionality. For mice licking tasks, which use OT.l, the Snr to OT.l projection is important for licking accuracy [Lee J and Sabatini 2021]. OT.i.pitx2 projections include Snr [Masullo et al 2019].

There are OT.id projections to Ppt [Coizet et al 2009], [Melleu and Canteras 2024], [Leiras et al 2022], [Tubert et al 2019], major input from OT to Ppt GABA and ACh neurons [Morgenstern and Esposito 2024], and OT.id bidirectional connectivity with Ppt [Comoli et al 2012], [Krauzlis et al 2013], [Melleu and Canteras 2024], [Wu and Zhang 2023]. Ppt correlates with orienting of eyes, body, and limbs [Wolf et al 2015]. In contrast with studies consistently reporting OT projections to Ppt, only a few studies report any direct projections to Snr, but does include a report of OT.i.pitx2 to Snr [Masullo et al 2019]. Note, however, that Snr.p and Ppt.a are contiguous, and Ppt.a GABA can be seen as a continuation of Snr [Mena-Segovia et al 2009], and Ppt is somewhat arbitrarily defined by the location of its ACh neurons [Mena-Segovia et al 2009], which may not precisely define the limits of its glutamate and GABA neurons.

The OT projection through Ppt to Snr could participate in the inhibitory feedback loop, or implement parts of it. Snr, Ppt and the basal ganglia can affect or even determine OT decisions. This modulation could be added to an existing OT decision circuit that only uses OT to OT commissural projections for feedback inhibition, or it could be part of the original feedback inhibition.

ACh sharpening the decision output

The mammalian division between OT.ramp and OT.burst demonstrates an important issue with decisions: downstream areas should see the results of the decision, not the intermediate ramping process leading up to the decision. Mammalian decisions appears to use systems outside of OT like Ppt and Snr to produce sharp, cleanly defined bursts. How might an evolutionary progression for a proto-vertebrate decision sharpening progress, specifically to isolate downstream R.rs from the ramping process?

One potential method is to amplify the output when a decision is made. R.is.pc (parvocellular R.is) is a distinct R.is nucleus with ACh feedback projections to OT. Like the rest of R.is, R.is.pc is a short feedback loop with OT, but unlike the negative feedback in the WTA system, this is positive feedback. In birds an OT projection to T.nr (thalamus nucleus rotundus) requires ACh input to burst. Without the ACh amplification, the OT signal is too weak to drive T.nr [Basso et al 2021].

The mammalian OT.i.pitx2 turning region receives ACh from Ppt and P.ldt. The mammalian R.pbg is considered homologous to the first and bird R.is, but mammalian R.pbg ACh appears to be specific to the OT.s visual layers [Krauzlis et al 2013]. R.pb and Ppt/P.ldt are sibling neural areas, produced by the same progenitor pool in R1 at different development times [Volkman et al 2010]. Unfortunately, although R.is is well-studied for fish and bits, Ppt is not, so I don’t know if the mammalian Ppt/P.ldt ACh projection to OT orientation neurons is ancestral but simplified in fish and birds, or if the R.is ACh is ancestral and the Ppt/P.ldt ACh is a mammalian adaptation. OT varies widely among species because it’s a major visual system under strong evolutionary pressure. Even considering the basic layering, the lamprey OT has 7 layers [Basso et al 2021], the mammalian OT has 6 layers, the bird OT has 15 layers [Basso et al 2021], and the first OT is divided into paraventricular soma and a large neuropil layer, where the neuropil itself can be divided into layers. Because the essays have uses the non-visual-first model of OT evolution, I’ll use the mammalian model as ancestral and R.is/R.pbg as later refinements after image-forming vision developed.

A diagram illustrating the relationship between the Ppt area and OT.ramp neurons, showing connections to the OT.co neurons and R.rs.m turn actions, with ACh signaling highlighted.
Ppt as providing an ACh boost to output nodes after a decision is made. ACh (acetylcholine), OT.co (crossing output of the optic tectum), OT.ramp (OT ramping neurons), Ppt (pedunculopontine tegmentum), R.rs.m (mid-hindbrain reticulospinal turning neurons)

In the above model, Ppt acts as a high-pass filter. A distinct OT ramping population produces a non-choice-selective measure of the decision progress [Horwitz and Newsome 1999], which projects weakly to Ppt. This model uses individually weak projections from OT.ramp are insufficient to drive Ppt ACh until they are collectively and possibly synchronously active. Only higher level input will drive ACh, when then boosts OT.co output and enabling boosting. The OT.id threat-avoidance system uses a similar architecture of individually weak and unreliable projections that require simultaneous activation to drive threat escape to M.pag.d (dorsal periaqueductal grey) [Evans et al 2018]. The OT.co turning system might use a similar circuit with Ppt. Note also that Ppt intrinsically produces gamma oscillations [Garcia-Rill et al 2018], which could synchronize output neurons, providing a stronger burst. Ppt could enhance OT.co bursting not only from ACh release, but also by entraining gamma oscillations in OT.

H.stn sharpening decisions by inhibiting OT.co

Another method for sharpening the R.rs decision signal is disabling the OT.co output while a decision is in progress. In larval zebrafish, swimming occurs in bouts of about 500ms, primate saccades are carefully timed around 200ms, and in rodents, stimulating OT produces step-like saccade-like head movements at around 350ms, instead of a continuous turning motion [Masullo et al 2019]. This saccade-like process around 200ms to 350ms suggests a gating system, either internally or externally driven.

As mentioned in the lockout discussion, Snr and H.zi are responsible for OT.co inhibition [Doykos et al 2020]. At the onset of primary saccades, tonic Snr suppression pauses to allow OT bursting. Snr itself is driven by H.stn (subthalamic nucleus), which itself is driven by OT [Al Tanner et al 2023], [Ricci et al 2024]. H.stn is also driven by Ppt [Al Tanner et al 2023], which is strongly interconnected by OT. When OT is activated, it can increase H.stn tonic firing from 27Hz to 45Hz [Coizet et al 2009]. Interestingly, bursting input to H.stn can produce long-lasting H.stn output over several hundred milliseconds [Ammari et al 2010]. Putting this together, OT.ramp could use H.stn to inhibit its OT.co output while the decision is in progression, possibly using H.stn as a 200ms to 300ms timing mechanism as an initial internal-only ramping period.

Diagram illustrating the feedback circuit involving H.stn, Snr, Ppt, OT.ramp, and OT.co, showing how these components connect in a decision-making process for motor control.
Output gating system using H.stn and Snr to suppress OT.co output until the ramping completes. H.stn (subthalamic nucleus), OT.co (optic tectum crossing output), OT.ramp (OT ramping neurons), Ppt (pedunculopontine tegmentum), R.rs (mid-hindbrain reticulospinal turning), Snr (substantia nigra pars reticulata)

The above diagram shows the basic flow. When a decision starts, OT.ramp signals H.sth, which inhibits OT.co using Snr. Note that this diagram is primarily for a proto-vertebrate, although these connections exist in mammals. In mammals, the full circuit would include the rest of the basal ganglia and the cortex.

Wei W et al propose a sharpening function for H.stn using the full basal ganglia to sharpen cortical decisions [Wei W et al 2015]. In their model, ramping input to S.d (dorsal striatum) suppresses spontaneous P.d (external globus pallidus) activity, which increases H.stn, which then cancels out the primary S.d1 (striatum projection neuron with D1 dopamine receptor) to Snr disinhibition. Because P.d can only be suppressed to zero, the H.stn suppression of the decision is also limited, and eventually the decision ramp overcomes the suppression [Wei W et al 2015].

A diagram illustrating the decision-making circuit in the optic tectum, showing connections between various components including OT.ramp, OT.co, H.stn, and Snr.
H.stn and the basal ganglia as suppressing incomplete decisions. The S.d1 and S.d2 paths compete, but the S.d2 is limited by P.d and eventually loses. H.stn (subthalamic nucleus), OT.co (OT crossing output), OT.ramp (OT accumulator neurons), P.d (dorsal pallidum), R.rs (mid-hindbrain reticulospinal turning), S.d1 (striatum projection neuron with D1.s dopamine receptor), S.d2 (striatum projection neuron with D2.i dopamine receptor), T.pf (parafascicular thalamus)

The above diagram shows a reinterpretation of the Wei W et al sharpening model, with their cortex focus replace by this essay’s OT focus. The oppositional paths of S.d1 (striatum projection neuron with D1.s dopamine receptor) and S.d2 (striatum projection neuron with D1.i dopamine receptor) prevent the OT.co output from firing while the decision is in progress. Because the S.d2 indirect path is limited by P.d, which can only be inhibited to zero, it eventually saturates, and limits H.stn activity, allowing the S.d1 path to continue increasing and eventually overcome the H.stn inhibition. This model is compatible with the view of H.stn as a decision slowing circuit during conflict [Frank 2006].

H.stn neuron activity is diverse with some studies showing at least three clusters of decision-related responses [Branam et al 2024], one of which is compatible with the Wei W et al model. This cluster of H.stn responses shows an early, sharp rise during the initial stimulus with a gradual decline until action onset.

Dopamine for sharpening and sustaining decisions

Midbrain dopamin in Snc (substantia nigra pars compacta) may play a role in further sharpening and sustaining the decision. Vertebrates have a descending Snc DA projection to MLR (midbrain locomotor region) for lamprey [Ryczko et al 2013], [Grätsch 2018], [Beauséjour et al 2025], salamander and rat [Ryczko et al 2016] and R.rs for lamprey [Ryczko and Dubuc 2017], [Beauséjour et al 2024], which enhances locomotor vigor [Ryczko et al 2016], [Ryczko and Dubuc 2017], [Grätsch 2018]. In lamprey, this descending DA projection outnumbers ascending projections to the basal ganglia by eleven to one [Ryczko et al 2013]. In zebrafish larvae, the basal ganglia primarily receives DA from local forebrain dopamine regions with either minimal or no V.da (midbrain dopamine) input [Rimmer 2020]. For a proto-vertebrate, it seems reasonable to focus on the descending DA projection instead of the smaller ascending one to the basal ganglia.

A diagram illustrating the neural circuitry involved in the decision-making process, showing OT.ramp and OT.co as components influencing the R.rs.m turn, with DA input from the Snc.v area.
Descending dopamine for decision sharpening and sustaining. DA (dopamine), OT.co (OT crossed output), OT.ramp (OT accumulation), R.rs (mid-hindbrain reticulospinal turning), Snc.v (substantia nigra pars compacta, ventral area).

In lamprey, salient input from OT projects to V.pt (posterior tuberculum) DA neurons, considered an Snc homolog [Suryanarayana et al 2022]. V.pt DA projects to R.rs [Beauséjour et al 2024], and OT also receives V.pt input [de Arriba and Pombal 2007]. These projections enhance the activity of the downstream neurons.

In the context of decision sharpening, DA activity around movement onset would activate downstream action activity, distinguishing that action from the pre-decision ramping time.

In mammals, OT projects both to Snc [Huang M et al 2021], [Masullo et al 2019] and to the contralateral V.rmtg (rostromedial tegmentum) [Pradel et al 2021], [Guillamón-Vivancos et al 2024], which inhibits Snc. These projections collectively support turning, but not increase locomotion, place preference, or learning [Poisson et al 2024].

Diagram illustrating the structure of the OT ramp decision circuit, showing connections between OT left and right ramping neurons, dopamine inputs from Snc.v, and projections to R.rs.
OT projections to midbrain dopamine, considered as enhancing turning decisions. DA (dopamine), OT (optic tectum), R.rs (mid-hindbrain reticulospinal turning), Snc.v (substantia nigra pars compacta, ventral part), V.rmtg (rostromedial tegemenum).

The above diagram has been organized to emphasize its similarity to the Mauthner cell FFI decision circuit. In the Mauthner cell circuit with contralateral FFI, a simultaneous left and right input would suppress both outputs. For that escape circuit, this dual suppression was bad because it suppressed escape, but for DA decision sharpening, the dual suppression is perfect because it inhibits partial decisions. As long as the left and right accumulators are active, the contralateral FFI circuit suppresses DA output. When one choice decisively wins, the output is disinhibited and quickly reports the decision.

Graph depicting the ramping activities of left (ramp.L) and right (ramp.R) optic tectum (OT) signals, along with dopamine (DA) levels for left (DA.L) and right (DA.R) choices over time.
Time course of a decision. The red and blue graphs show the left and right accumulators. As long as the accumulators are sufficiently close, they suppress the DA output with the contralateral FFI. When the left choice decisively wins, the DA output is disinhibited and quickly rises. DA (dopamine), DA.L (left DA), FFI (feedforward inhibition), ramp.L (left accumulator)

The above graph shows the time course of the decision. The amber DA choice is suppressed while the left and right accumulators are in conflict. Once the conflict resolves, the DA quickly rises. In this simulation, the FFI contralateral suppression is 2:1, so the DA is release once the winner is twice the loser. The unshackled DA will now enhanced the downstream turning R.rs, committing the decision.

The V.da neurons here are the non-food-related motor DA in Snc.v, marked by aldh1a1 in mammals, and likely the specific subgroup marked by anx1a. Broadly speaking, V.da can be split into three groups: and eating and food seeking group, an action-only group, and a threat and avoidance group. An Snc.v group (aldh1a1 /anxa1) which produces movement, but does not respond to food or produce food conditioning [Seiler et al 2024], [Azcorra et al 2023], [Hadjas et al 2025]. It seems likely that the OT projection to Snc.v would be to this aldh1a1/anxa1 group, but I don’t have a paper that shows that specific connection.

Simulation

The simulations added a simple electrosense for food, which produces left and right signals depending on the heading with some noise. When the simulated animal heads directly toward the food, the left and right inputs have equal values. When the food is to one side, the closer side has a stronger signal.

Although the simulation itself didn’t produce anything particularly interesting, it did raise two larger questions about the decision making. First, whether the 2AFC (two alternative forced choice) model makes any sense at all for this evolutionary stage. Second, more questions about timing, particularly with rapid movements, and aborted choices.

2AFC (two alternative forced choice)

2AFC is a popular experiment for studying decision making. Typically, the experiment has a central cue: sound, visual, tactile (whisker), or odor for mice, and the mice must move to a left or right door port to get food, or lick to a left or right spout to water. In primate experiments, a monkey might see drifting dot patterns and must saccade to a left or right target to signal if the drift is more to the left or to the right. In these experiments, two nearly equal cues still produce a strong left or right action.

But in the electrosense simulation, two nearly equal left and right inputs would generally mean the food is straight ahead. If the food is straight ahead, the animal should make smaller turns to center the turn, not side decision-like turns. The OT is organized to make this kind of adjustment decision. Turning in the anterior OT are smaller than the wide turns in the posterior OT, and the anterior OT shows more activity as the animal moves toward the target [Essig and Felsen 2021].

If two food sources were equally distance from the animal, or their signal/distance matched, a left or right choice would be better than moving straight, but that situation would be metastable and likely resolve itself without additional decision circuitry. If the animal drifted to one side by chance, one food source would be nearer, and the animal would approach it.

Obviously, mammals have the ability to make two 2AFC decisions, but it’s not clear when that ability would be an evolutionary advantage for simpler animals. The 2AFC experiments are artificial cued situations that don’t resemble natural foraging. Although mammals can solve these situations, it seems more likely this is a byproduct of advantages aimed at a more direction situation, but generalized enough to cover the odd experiment.

Some decision researchers argue that real world options are generally sequential [Ballesta and Pado-Shioppa 2019]. Some argue that sequential decisions contrast the current option with the background, as opposed to drift-diffusion with two opposing actions, and contrast tug of war models vs sequential models [Kacelnik et al 2012]. Pure 2AFC is rare in nature [Ellerby 2028]. Reality includes competition with rivals and the potential for resources to accumulate and deplete.

Dynamic environment and slow accumulation

The second issue the simulation raised was when the animal’s situation changed more quickly than the accumulator. The dynamic environment produces obsolete partial data [Piet et al 2018]. In the simulation, the underlying non-decision behavior is a random walk. The new decision system overrides the random walk when it has a result, but the random walk does not stop for the decision. So, the random walk can turn sharply and reverse the left and right accumulators. If the accumulators are sufficiently slow, or insufficiently leaky, the partial results are now a mixture of invalid data from the past and new valid data.

There are a few immediate improvements. Shortening the accumulation or increasing the leak would shorten the timescale to minimize corruption. In mice, the midbrain accumulation timescale appears to have a τ=250ms delay time with longer integration requiring the cortex [Khilkevich et al 2024]. Rats can dynamically change the integration timescale when the environment becomes more unreliable [Piet et al 2018].

In theory, the animal could avoid making movements while it’s deciding to avoid corrupting the data, such as pausing random-walk turns by disabling the ARTR (anterior hindbrain turning region) in zebrafish. But this doesn’t seem to be a general solution because the animal would be continually pausing as it’s making a decision.

Another solution could reset the accumulators at any action, including non-decision actions like the random walk. The OT.s visual system does have a reset using V.lc (locus coeruleus) Ne (norepinephrine) to OT astrocytes [Uribe-Arias et al 2023], as a response to an escape action. In the cortex, movement preparation collapses at movement onset for that decision as a reset [Khilkevich et al 2024].

Animals rarely miss choices [Lu W and Wan X 2025], possibly suggesting an urgency signal [Cisek et al 2009], [Thura et al 2012]. An efference copy from the random walk ARTR, or a shared efference copy from the swimming CPG might force the turn decision circuit to curtail its evidence accumulation to make a decision before the random walk.

But again, I don’t know if these are general solutions. Research experiments generally work to reduce dynamic activity, such as head-fixed mice, or reporting neural activity after the animal has overtrained to produce stereotyped behavior, and introducing delays to separate neural signals to better distinguish which brain areas are active in each time period of a decision. But those necessary simplifications also erase any measurement of how the decision systems deal with dynamism [Gordon et al 2021]. Some research in auditory streaming does support dynamic decision making [Cao R et al 2021], although that study is for the cortex, and it’s unclear if those results apply to OT.

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47: Striatum as a mosaic of broken mirrors

The mosaic of broken mirrors is an analogy for the striatum in the basal ganglia [Da Cunha et al 2009]. The striatum represents a vertebrate’s actions and environment in a broken and overlapping fashion. While actions have focal projections to the striatum, the contextual input is broad and diffuse [Fee MS 2012]. While the hippocampus represents the environment globally, the striatum depends on piecewise representation. This means striatal learning is unable to generalize, because mosaic fragments lack a global perspective [Da Cunha et al 2009].

In the essays I’ve used the striatum as a timeout for food seek from an odor plume. When a food odor doesn’t have any food, or the odor is behind a barrier, the animal needs some sort of timeout to give up seeking the odor, turn away from the false odor, and search else where. However, the current simulation only uses the seek action for the timeout; it lacks environment context.

A simple illustration depicting two circular shapes; one has a blue and red figure inside, while the other contains a green star-like shape.
Simulation screenshot showing the model animal trapped into perseverating seek in the center of a false odor plume. Circles represent odor plumes and the star represents food.

The above simulation screenshot shows the general problem. The circles represent food odor plumes and the star represents food. The animal has followed a false odor plume and will continue circling the center until the striatum timeout. However, there is a nearby valid odor plume with food in it. The animal should avoid the false odor plume and search the correct odor plume, but currently it can’t distinguish the two, because it’s only using its own seek action as a key. If the animal could detect environmental context differences between the two plumes, it could search more effectively.

As a context, odor neighborhoods [Jacobs 2022], [Marin et al 2021] can represent a primitive representation of place. If each place has a different set of odor molecules, the animal can use that odor scene to distinguish false odor plumes from true food odor sources.

Striatum as timeout

In the essays I’ve used the striatum as a timeout mechanism to prevent perseveration, specifically the S.d2 (striatum projection neurons with D2.i Gi inhibiting dopamine receptor), which use A2a.s (adenosine Gs stimulating receptor) to measure the buildup of Ado (adenosine). The striatum’s projection neurons are roughly evenly divided between S.d1 (D1.s Gs stimulating dopamine receptor) and S.d2. For long stimulations, S.d1 generally motivate the current action and S.d2 opposes the action and produces avoidance [Soares-Cunha et al 2020], but for short stimulations both are active for action initiation [Cui G et al 2013].

Ado signaling limits swimming in frog tadpoles [Dale 1998]. In the striatum A2a.s receptors in S.d2 projection neurons also detect Ado buildup from neuron activity and from astrocytes that monitor neuron activity [Kang S et al 2020]. The Ado buildup activates S.d2 neurons and increases its internal PKA (protein kinase A) [Ma L et al 2022]. PKG slowly builds up during activity with a buildup time constant on the order of 10-20s and a decay constant on the order of 70s [Ma L et al 2022], but the increase appears to be log or sigmoid-like, not linear, suggesting that longer timeouts would be possible with high thresholds or opposition from S.d1. In S.d2, the PKA buildup enables the release of the opioid enkephalin [Konradi et al 2003], [Hook et al 2008], which activates the DOR.i (δ-opioid inhibitory receptor), which is necessary for the inhibitory/avoidance behavior for S.d2 [Soares-Cunha et al 2020].

Because the essay simulation needs a timeout to limit food seek perseveration, and the Ado and S.d2 avoidance chain could plausibly implement that timeout, I’ve been using it as the basis for the simulation’s timeout. This function seems evolutionarily plausible, because avoiding perseveration is important to keep the animal from unproductive seeking, and the implementation is fairly straightforward, only requiring already existing Ado timeout sensing and S.d2, without needing the entire basal ganglia. However, up to this point, that timeout has only used the action as a key, and has not included any context. Essay 15 and 16 did cover odor seek timeout in the context of associative habituation, but on the context of the fruit fly mushroom body.

Action and context as striatum inputs

S.pn (striatum projection neurons: both S.d1 and S.d2) are often called medium spiny neurons because their extensive dendrites are covered with spines. Spines are small dendrite compartments that receive axon inputs. Spines can compartmentalize Ca2+ (calcium) transients [Fang LZ and Creed 2024], meaning S.pn activation is not necessarily global across the entire dendrite tree, but compartmentalized. In S.d (dorsal striatum), cortical axons attach to S.pn spines, while T.pf (parafascicular thalamus) connects to the dendrite shaft [Fee MS 2012]. T.pf signals include ongoing action feedback and efference copies from the hindbrain and midbrain, including OT (optic tectum), while the cortex provides environmental context.

Diagram illustrating the connection between cortical inputs (C), thalamic inputs (T.pf), and striatum projection neurons (S.pn) via dendritic spines.
Rough diagram of inputs to S.pn dendrites. Cortical input is to distal dendrites and spines, while T.pf is more proximal and to dendrite shaft. C (cortex), S.pn (striatum projection neuron), T.pf (parafascicular thalamus).

Songbirds have a portion of the basal ganglia devoted to singing called Area X [Kornfeld et al 2020]. Area X receives song action variability information from C.lman (lateral nucleus of anterior nidopallum) and timing context from C.hvc, which are areas of the songbird cortex. C.lman provides an action efference copy of the variation actions [Fee MS 2014]. The majority (85%) of C.hvc input is on S.pn spines, while 55% of the C.lman action information is on the dendrite shafts [Kornfeld et al 2020]. The action efferent copy input to S.pn are not plastic, while the contextual input on the shafts is plastic [Fee MS 2012]. The context drives S.pn activation to an Up state, gating the core action driver [Fee MS 2012]. Action input to the striatum is focuses, while contextual information is diffuse [Fee MS 2012].

S.pn inputs can differ in their attachment to spines or dendrite shafts, and they can also differ in triggering behavior and for Up states. S.pn are normally hyper polarized, meaning they are normally especially difficult to trigger. Some inputs can shift S.pn into an Up state, where they are more easily triggered. In S.v (ventral striatum), inputs from E.sub.v (ventral subiculum in the hippocampal complex) can shift S.pn into an Up state for hundreds of millisecond [O’Donnell and Grace 1995], [Sesack and Grace 2010]. When E.sub.v is disable, S.v spontaneous or bistable activity halts, and other inputs such as F.pfc (prefrontal cortex) can’t trigger action potentials [O’Donnell and Grace 1995]. Up state transitions can be facilitated by dopamine [Fang LZ and Creed 2024], [Lahiri and Bevan 2020] and astrocyte sensing of glutamate activity [D’Ascenzo et al 2007], [Yu X et al 2018].

For the purposes of the essay simulation, these differences in striatum input suggest it’s plausible to treat action input and contextual input as distinct types of input, following [Fee MS 2012]. Specifically, that the combination of an action input and a context is required to drive the striatum timeout. This means that a seek timeout can be specific to a context and not overflow to other contexts.

Innate and contextual odors

In vertebrates, O.sn (odor sensory neurons) axons project to O.gl (glomerules) in Ob (olfactory bulb), where they connect with O.pn (odor projection neuron: mitral and tufted cells in mammals) dendrites. Each O.gl is a large neuropil (axon and dendrite connection area) where multiple O.sn and O.pn combine. In mammals, each O.gn responds to a single O.sn odor feature. Each O.gl typically responds to several odor molecules, and each odor molecule drives multiple O.gl [Wilson and Mainen 2006], [Weiss 2020]. In other vertebrates, each O.gl can combine inputs from multiple O.sn. Insect odor processing also uses glomerules, but this shared structure is independent evolution not homology because even the underlying odor detection receptors are unrelated between insects and vertebrates [Weiss 2020]. The glomeruli structure is likely simply an effective way of connecting multiple O.sn to O.pn.

As an analogy that the simulation uses, consider phonemes in a syllable, where each syllable is like an odor molecule and each phoneme is like a glomeruli. The syllable “cat” consists of “c-“, “-a-“, and “-t”, corresponding to three glomerules, and “c-” is driven by many different syllables. So, O.gl doesn’t identify the whole odor, but only a feature of the odor, like “c-“, but the features can be recombined to identify the odor.

The odor glomerules in vertebrates are divided into a smaller innate group and a larger contextual group. Most mammals have distinct Ob and O.a (accessory olfactory bulb). The lamprey Ob.m (medial Ob) projects directly to the midbrain, including Hb.m (medial habenula) and V.pt (posterior tuberculum) [Derjean et al 2010], [Beauséjour et al 2022], while the Ob.l (lateral Ob) projects to Pa (pallium/cortex) and basal ganglia [Beauséjour et al 2022], [Beauséjour et al 2024], [Suryanarayana et al 2021].

Previous essays have only used the innate Ob.m projection and ignored the Ob.l projection. This essays adds the Ob.l context projection to S.o t(olfactory tubercle), which is a part of S.v (ventral striatum) with large, direct olfactory input, and output to H.l (lateral hypothalamus) and Pv (ventral pallidum). The Ob.l context may represent odor neighborhoods, introducing a notion of place.

Odor neighborhoods

Odors rarely occur in isolation, are dynamic in space and time [Marin et al 2021], and form spatial neighborhoods [Jacobs 2022]. Olfactory curs influence E.hc (hippocampus) place fields, and place cells in blind rats are similar to sighted rats [Marin et al 2021]. In O.pir.p (posterior piriform cortex/olfactory cortex), place can be decoded to 90% accuracy with 240 neurons [Poo C et al 2022]. The olfactory spatial hypothesis considers odor are more for navigation than for identification [Jacobs 2012], where an odor neighborhood is a local area of odor mixtures.

It seems plausible that an early proto-vertebrate could use a combination of odor features from O.gl in an early S.v to restrict a seek timeout to a local place. The circuit is a straightforward extension of existing Ado timeout circuitry.

Seek striatum

For the essay’s simulation, I’m using odor context from Ob.l as a neighborhood detector. The striatum has two inputs: an action that enables the striatum during a seek and a place context identified by odor to restrict the search.

A simulation screenshot depicting various spatial representations of sensory inputs, including graphs and spatial maps related to odor detection and processing mechanisms.
Screenshot of the seek task blocked by a U-shaped barrier with odor neighborhoods represented by color and pattern. The local odor “rat” is represented by odor glomerules for “r-“, “-a-“, and “-t”.

The above screenshot shows the animal after its timeout from a failed odor seek when blocked by a barrier. The star represents food and the circle is an odor plume. Each pattern in the arena represents an odor neighborhood. The right side of the screenshot shows the active glomerules for the neighborhood, represented by “r-“, “-a-” and “-t”. I’m using syllables to represent odor molecules and phonemes to represent odor features detected by Ob glomerules.

Fruit fly mushroom body and Kenyon cells

Because the hypothetical proto-vertebrate would have a much simpler striatum than the mammal striatum, consider the comparison with the fruit fly MB (mushroom body) and its KC (Kenyon cells), which has a similar structure to the Sv projections to Pv, but has a much smaller scale. The mushroom body is highly conserved among insects and possibly predates all arthropods [Fiala and Kaun 2024], and serves as an odor pattern detector. In fruit flies, 52 O.pn project to ~2000 KC [Chan ICW et al 2024], which project to 24 MBON (mushroom body output neurons) [Seki et al 2017]. Each KC has three to seven claws [Zheng et al 2022], which are essentially single-connection dendrites.

A diagram illustrating the connectivity of Kenyon cells (KCs) in the fruit fly mushroom body, showing olfactory sensory neuron (OSN) inputs, projection neurons (PNs), and connections to mushroom body output neurons (MBONs) with their neurotransmitter types.
Architecture of the Drosophila mushroom body, adapted from [Aso Y et al 2014]. For this essay, only the left side projections of PN to KC are important. KC (Kenyon cell), PN (olfactory projection neuron), OSN (olfactory sensory neuron)

The above diagram shows the fruit fly mushroom body, but only the KC on the left are relevant for this essay. The MBON on the right would correspond to Pv (ventral pallidum) in this analogy. Each of the 2000 KC receive essentially random olfactory input from the O.pn, where each KC receives 3-7 O.pn inputs.

This mushroom body structure roughly corresponds to vertebrate O.pn projections to S.ot (ventral striatum olfactory tubercle), which projects to Pv. Although the connectivity pattern is similar, the two structures are not homologous in any fashion. Insect O.sn and vertebrate O.sn use entirely separate olfactory receptor families, and KCs use ACh (acetylcholine) as a neurotransmitter, while S.pn use GABA and vertebrate-specific opioids. The point of the analogy here is only to compare the scale of the O.gl and S.ot for a possible proto-vertebrate because the mammal S.ot is vastly too large to be plausible for that ancestor.

The MB has been compared to vertebrate CB-like (cerebellum-like) structures in the hindbrain [Farris 2011], suggesting that both serve as adaptive sensory filters. CB-like structures have dual inputs: one is sensory-specific input and the other is multimodal contextual. The MB also serves as a brake on insect locomotion, because fruit flies with MB lesions are less likely to stop locomotion once begun moving. This locomotion stopping is similar to the seek perseveration timeout in this essay.

Diagram comparing the olfactory processing pathways in insects and vertebrates. The insect mushroom body pathway includes odor sensory neurons (O.sn), odor projection neurons (O.pn), Kenyon cells (KC), and mushroom body output neurons (MBON), leading to seek/avoid responses. The vertebrate pathway similarly includes O.sn, O.pn, striatal projection neurons (S.pn), and the ventral pallidum (Pv), also leading to seek/avoid responses.
Analogy between the insect mushroom body and the vertebrate ventral basal ganglia. KC (Kenyon cells), MBON (mushroom body output neuron), O.pn (olfactory projection neuron), O.sn (olfactory sensory neuron), Pv (ventral pallidum), S.pn (striatum projection neuron)

For scale, consider using the lamprey Ob during the syllable analogy. The lamprey has approximately 40 olfactory receptor genes [Beauséjour et al 2020]. If we exclude about 10 innate from Ob.m, the 30 are contextual odors in Ob.l Consider splitting each odor as a syllable into three odor features as pheromones. If the 30 lamprey O.gl were organized like phonemes, then it might have 10 initial consonants, 10 vowels, and 10 final consonants. Suppose each S.pn receives three inputs from O.pn: one of 10 initial consonants, one of 10 vowels, and one of 10 final consonant. The 1000 S.pn would cover the possible syllables, expanding the dimensionality from 30 odor phonemes to 1000 odor syllables. Analogously, the Drosophila 52 O.pn phonemes expand to ~2000 KC syllables, roughly the same order of magnitude. Of course, the olfactory neighborhoods aren’t actually nicely ordered into convenient human-readable syllables, but it’s a convenience analogy, particularly for the simulation.

Returning to the original metaphor of the mosaic of broken mirrors [Da Cunha et al 2009], the O.pn breaks odor molecules (syllables and unbroken mirror) into a broken set of odor features (phonemes and mosaic tessera), and randomly reassembles the features in S.pn like tessera in a mosaic, partially recovering the original syllable structure, albeit lossy. Because the features are broken pieces stripped from their original odor molecule identity, the system could add other modalities, such as lateral line or whisker sensing, or temperature, or color fragments, before combining them, Although the fruit fly KCs primarily combine odor inputs, they also include a smaller number of non-odor inputs such as visual, gustatory, mechanosensory, and proprioceptive inputs [Farris 2011].

S.core seek and S.msh roam

So far I’ve used the striatum as a timeout to avoid seek perseveration, giving up on a failed food odor. Adding an odor neighborhood context improves the accuracy of seek perseveration control. Now that odor neighborhoods are available, the animal could also avoid neighborhoods that it’s already searched, essentially creating a memory breadcrumb, as explored in essay 44.

A diagram showcasing a grid with labeled sections including 'dm,' 'dl,' 'msh.d,' 'msh.v,' 'core,' 'lsh,' 'mot,' and 'lot,' indicating different components or regions.
Rough topographic divisions of the striatum. The blue S.msh.d is used for roam, and the amber S.core and S.lsh are used for seek. S.core (Sv core), S.dl (dorsolateral striatum), S.dm (dorsomedial striatum), S.lot (lateral S.ot – olfactory tubercle of Sv), S.lsh (lateral shell of Sv), S.mot (medial S.ot), S.msh.d (medial shell of Sv, dorsal part), S.msh.v (medial shell of Sv, ventral part), Sv (ventral striatum aka nucleus accumbens)

Sv (ventral striatum) is divided into S.core (Sv core) and S.sh (S shell), where S.core surrounds the anterior commissure, which connects Ob and amygdala. The shell further divides into S.msh (medial shell) and S.lsh (lateral shell), with S.ot also dividing into S.mot (medial S.ot) and S.lot (lateral S.lot). S.msh itself divides into S.msh.d (dorsal S.msh) and S.msh.v (ventral S.msh). These regions have distinct genetic transcription factor types and connectivity, and S.msh may be even more complicated with further genetically defined subtypes [Chen R et al 2021].

Functionally, S.lsh and S.core are more similar, related to cues and seek [Floresco 2015], [Chen G et al 2023], [Ding YD et al 2022], [Dobrovitsky 2017], while S.msh is distinct and related to place [Al-Hasani et al 2015], [Humphries and Prescott 2010], but not cues [Domingues et al 2025]. S.sh is important for place habituation: avoiding places already visited [Floresco 2015]. S.core is more associated with seek actions, and S.msh associated with place preference and avoidance [Fisher et al 2025]. S.ot is less studied, but is strongly Ob and O.pir related. Assigning S.lot to the same group as S.lsh and S.mot with S.msh is not well supported functionally, but does have some transcriptional support [Chen R et al 2021]. S.msh.d generally supports RTPP (real-time place preference) and S.msh.v RTPA (real-time place avoidance) [Ding YD et al 2022], [D’Aquila 2024], [Faget et al 2024], but because other studies report S.msh.d as necessary for cued avoidance [Ramirez et al 2015], the S.msh function may not be as simple as a clear RTPA/RTPP difference. Sv has three-dimensional aspects as well, with S.msh.a (anterior S.msh) and S.msh.p (posterior S.msh) having opposing seek and avoid motivation [Castro et al 2015], [Berridge 2019], [Bond et al 2020], [Marinescu and Labouesse 2024], with differing projections to locomotion vs eating regions [Richard and Berridge 2011].

As a complication for reading the research, because the heterogeneity of Sv regions was relatively recently discovered, many papers report results for S.sh without distinguishing between S.lsh, S.msh.d, or S.msh.v, despite these regions having different or even opposing functions. Older papers often simply report results for Sv without even distinguishing S.core from S.sh. Another complication is that Sv is also important for eating, not simply dedicated to seek or avoidance. Stimulating S.sh.a immediately stops eating [Reed et al 2018]. However, eating and roaming/seeking are related because they’re mutually exclusive: the animal needs ot stop roaming or seeking to eat. In case cases eating circuits may actually be stop-moving circuits, since 70% of S.sh are inhibited while eating and 30% are short lived excite while eating [Marinescu and Labouesse 2024]. Note that although the divisions in S.v are broadly topographic, some sub-functions could be mixed salt-and-pepper style, particularly in the complicated S.msh region.

So, the essay can add S.msh place habituation to avoid places already visited [Floresco 2015]. This seems likely to be S.msh.d because S.msh.v is more associated with threat avoidance [Ding YD et al 2022].

Odor neighborhoods for roaming

The odor spatial hypothesis suggests that the vertebrate Ob (olfactory bulb) is used more for spatial navigation than odor identification [Jacobs 2012]. Odors form spatial neighborhoods [Jacobs 2022], and the mammalian E.hc (hippocampus) place fields are driven by odor [Jacobs 2022]. Odors are rarely in isolation, but are dynamic in space and time. Place cells in blind rats are similar to sighted rats [Marin et al 2021]. A very old model of E.hc called it the rhinencephalon (nose brain), which was displaced by the discovery of spatial place fields, but if place is grounded by an old odor neighborhood circuit, then rhinencephalon may be accurate [Jacobs 2022].

For the essay simulation I’ve created two parallel basal ganglia paths for seek and roam. The seek path is only activated when the animal is following a food odor plume. The roam path is more broadly activated when the animal is searching for food. For specific paths, S.core and S.lsh appear specific to seek [Dobrovitsky 2017], [Soares-Cunha et al 2020], [Walle et al 2024]. Sv research doesn’t investigate roam circuits per se, but RTPA (real-time place avoidance) and RTPP (real-time place preference) and conditioned place preference are centered on S.msh [Britt et al 2012], [Marinescu and Labouesse 2024].

Flowchart illustrating the pathways in the basal ganglia for seeking and roaming behaviors in response to olfactory signals. Left side shows 'Ob.l place' input leading to seek and roam pathways, including interactions between various neural regions.
Paths used by the simulation for seek timeout and roam timeout with odor neighborhood context. H.l (lateral hypothalamus), Hb.lm (lateral habenula, medial part), MLR (midbrain locomotor region), Ob.l (lateral olfactory bulb), Pv.dl (ventral pallidum, dorsolateral part), Pv.vm (ventral pallidum, ventromedial part), R1.a (anterior hindbrain locomotor region), R5.rs (mid-hindbrain turning region), S.core (ventral striatum core), S.msh.d (striatum medial shell, dorsal part), T.pf (parafascicular thalamus), V.rn (raphe nuclei)

The above diagram shows a hypothetical dual seek and roam circuit. S.core uses seek action feedback / efference copy to enable a seek timeout to avoid perseveration. S.msh.d uses H.l (lateral hypothalamus) roaming driver to enable place habituation to avoid searching places already visited.

A screenshot of a simulation showing an animal's movement in a patterned arena with various sections representing different odor neighborhoods. Circles denote active olfactory stimuli and a star marks the location of food. Syllables and phonemes are used to represent odor features.
Screenshot of the simulation with the animal leaving an area it’s already explored. The phonemes “d-“, “-o-“, and “-g” represent the current odor neighborhood.

The above screenshot shows the simulation for roaming odor neighborhood. Each pattern represents a different odor neighborhood. The phonemes on the right — “d-“, “-o-“, and “-g” — represent odor features of the neighborhood. The animal is avoiding the bottom neighborhood marked by blue horizontal lines because roaming has timed out for that neighborhood.

Box plot and violin plot comparing the distances traveled in an open field for two groups: with 'PvRoam' and without 'PvRoam'.
Monte Carlo simulation of the animal’s search. PvRoam represents roaming with timeout enabled. No PvRoam representing roaming without timeout.

As a test to verify that avoiding place repetition improves food search, I ran 300 Monte Carlo simulations for both the roam timeout enabled and disabled. In the simulation code, the timeout circuit is organized by its Pv projection, which owns the corresponding Sv. So enabling the roaming timeout means enabling PvRoam. The results suggest that avoiding place repetition improves performance by regarding the long-search tail of the distribution.

Discussion: multimodal feature inputs

The essay’s simulation only used odor features as striatum inputs for identifying neighborhoods, but the mosaic model can work with multimodal inputs. For example the lateral line sense can detect a barrier to the right of the animal, That signal can be added to the striatum mosaic to distinguish odor neighborhoods bordered by a reef from a neighborhood over sand. Temperature sensors can distinguish cold and warm neighborhoods. Similarly, even simple, non-imaging photoreceptors tuned to multiple colors could help distinguish sand from reef or deep blue ocean from shallow waters. Three or four bits of visual information could help distinguish neighborhoods without needing complicated visual processing.

Similarly, although the fruit fly mushroom body mainly has odor inputs, it also includes some visual, gustatory, and thermosensory input [Chan ICW et al 2024]. Like a striatum mosaic, the visual processing in the mushroom body isn’t complex, but it can distinguish environments.

Insect mushroom body as a cerebellum-like structure

An interesting comparison between the insect MB (mushroom body) and vertebrate CB-like (cerebellum-like) structures suggests that both act as adaptive sensory filters [Farris 2011]. Vertebrate CB-like structures, mainly in the hindbrain, use anti-Hebbian plasticity to predict and erase self-motion from sensor data [Bell et al 2008], [Montgomery et al 2012].

For example, the aquatic lateral-in sense uses water motion sensors to detect objects and prey. If the animal is swimming near an obstacle to the right, the relative water motion produces a curl around the animal, which a relatively simple circuit can decode to infer the barrier [Oteiza et al 2017]. Because the animal’s own swimming also produces water movement, a CB-like organ R.mon (medial octavo lateral nucleus) subtracts the self signal, enabling more accurate obstacle and prey detection.

Similar to the striatum context and action architecture explored in this essay, CB-like structures have a context formed by parallel fibers, which encodes multimodal combination of self-action and proprioceptive input, and a primary sensory input, which the context modulates. Also similar to this essay’s striatum model, repeated activation is anti-Hebbian: suppressing repeated activation.

There are major differences between the striatum and CB-like functionality, of course. CB-like structures form an adaptive filter to produce a more useful signal, while the striatum timeout in this essay avoid repeating search areas, and it’s hard to find any commonality in those two functions other than the very general avoidance of repetition.

Possible cortex enhancements

Because the simulation is a tow model, it hides the noise and signal problems. Odors in particular are difficult and messy sensor input because odors in water are clumpy, not the clean odor gradients and neighborhoods of the model. Real odor signals will appear and disappear, and neuron signals are generally short, between 3ms for fast AMPA receptors and 100ms NMDA receptors, but the odor needs much longer sustain, on the order of several seconds.

Cortical pyramidal neurons can activate a sustained ADP (afterdepolarization) model lasting on the order of 6-8 seconds when activated by ACh (acetylcholine) activating mACh.q (Gq coupled acetylcholine receptor). This sustained activity could stretch an odor neighborhood signal across the gaps in spotty odor receptor signal. A proto-vertebrate improvement could use a simple proton-cortical circuit as short term memory.

A more complicated improvement is associative pattern recognition. The mosaic striatum model can detect simple patterns, but it can’t generalize, and may be susceptible to noise and distractor signals. Typically, an odor scene will have multiple odor molecules, unlike the simulation’s simplified model. Cortex circuits could filter the noisy inputs and produce a more reliable input to the striatum, replacing direct Ob input with more conceptual O.pir (piriform cortex) engrams.

Odor and place

Although odors can form neighborhoods, they aren’t necessarily precise or reliable. One complicated improvement is dedicated cortical regions devoted to identifying place. O.pir ish the main olfactory cortex in mammals with homologous olfactory cortexes in other vertebrates. In mammals, O.pir.a (anterior O.pir) idenfieis odors, and O.pir.p (posterior O.pir) detects place [Poo C et al 2022]. The neuronal connectivity of O.pir.p resembles parts of E.hc, which is well-known to encode place.

Consider an evolutionary sequence of improvements that starts from a simple striatum mosaic that detects odor neighborhoods, then improves that primitive place detection with more sophisticated cortical place in O.pir.p. That single-mode odor place detection could then combine with other sensory modes using egocentric and allocentric inputs like head direction and landmarks into a more reliable place detection in E.hc.

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Ventral Pallidum for Sustain and Timeout

Previous essays have used Pv (ventral pallidum) as part of the seek and avoidance circuit without exploring it in detail. For this essay, I’m revisiting Pv in more detail for two purposes: first, to check that the simulation’s seek and avoid model is compatible with scientific results about Pv, and second, to understand more on how those internal circuits work.

Timeouts are critical for the food-odor seek circuit to prevent the animal from getting stuck in a trap where it either can’t reach the food, or the food odor has no food. A timeout could simply disable seek and return to the default roaming random walk, or it could actively avoid the current area. When the seek times out, an active avoidance phase is more effective than returning to roaming, because the avoidance moves away from the current false cues and into a distant area more likely to have a new food source.

Diagram illustrating the seek and avoid circuit related to food detection, showing phases of roaming, detecting odor, seeking food, timing out, and avoiding false cues.
State machine for seeking food. When the animal detects an odor, it follows the odor gradient until the animal either finds food or an internal timeout shifts the seek to avoid.

The simulation uses the basal ganglia as a timeout system, specifically Sv (ventral striatum) with Pv that’s interconnected with food-seek motivation based in H.l (lateral hypothalamus). The model uses Ado (adenosine) as a timeout neurotransmitter and S.d2 (striatum projection neuron with D2.i receptor) to signal the timeout. Essay 31 covered the adenosine-S.d2 system in more detail. Essentially, neural activity produces Ado from neurons and neighboring astrocytes. The Ado then activates A2a.s (adenosine G-s coupled receptors) on S.d2, which potentiates S.d2 and increases internal activity in an PKA (protein kinase A) activation chain. As Ado builds up over time, S.d2 activity increases until it triggers a switch from seek to avoid in Pv.

A flowchart illustrating the seek and timeout process in a neural simulation, showing the interactions between 'Ob', 'H.I seek', and 'R1.a' with a 'S.ot/Pv timeout' indicator.
The current simulation model uses the Sv/Pv to timeout seek motivation. H.l (lateral hypothalamus), Ob (olfactory bulb), Pv (ventral pallium), R1.a (anterior hindbrain motor area), S.ot (olfactory tubercule portion of Sv)

The above diagram shows how the current simulation model uses Sv/Pv as a timeout. H.l (lateral hypothalamus) is responsible for seek motivation based on odor input from Ob (olfactory bulb) and it drives roaming search to R1.a (anterior hindbrain motor region). The basal ganglia, represented by S.ot (olfactory tubercle, an olfactory region of Sv) and Pv serve as the timeout function. This essay aims to expand that simple model into a more accurate representation of the Sv/Pv timeout.

Seek and avoid

In neuroscience, seek and avoid are measured with RTPP (real-time place preference) and RTPA (real-time place avoidance) experiments, although these measurements are often interpreted as “valence” instead of actions. Circuits that produce RTPP could contribute to the seek action, and circuits that produced RTPA could produce avoidance. For example, Hb.lm (lateral habenula, medial part) produces RTPA when stimulated and RTPP when inhibited [Stamatakis et al 2016], and Sv, Pv, and H.l produce either RTPP or RTPA, depending on which neurons are stimulated. In Sv, S.d1 (striatum projection neuron with D1.s dopamine receptor) produces RTPP [Soares-Cunha et al 2020], [Tan et al 2024], while S.d2 produces RTPA [Bonnavion et al 2024], but only when stimulated for longer times [Soares-Cunha et al 2020]. Different regions of Sv have flipped seek and avoidance, between S.msh.d (medial shell of Sv, dorsal) and S.msh.v (medial shell of Sv, ventral) [Yao Y et al 2021]. In Pv, glutamate neurons produce RTPA and GABA neurons produce RTPP [Stephenson-Jones et al 2020], which matches H.l, where glutamate produces RTPA [Stamatakis et al 2016] and GABA produces RTPP [Jennings et al 2015], [Siemian et al 2021].

Diagram illustrating the neural circuits involved in the seek and avoid behavior in the brain, showing connections between various components like S.ot, Pv, H.l, Ob, and R1.a.
Simplified seek and avoid timeout circuit. The seek circuit uses H.l as the subthalamic motor region to the R1.a anterior hindbrain motor region. The avoid circuit uses Hb.lm to V.rn raphe also to R1.a. The Sv and Pv basal ganglia switch between the circuits. H.l (lateral hypothalamus), Hb.lm (lateral habenula, medial part), Ob (olfactory bulb), Pv (ventral pallidum), R1.a (anterior hindbrain motor region), S.ot (olfactory tubercle), V.rn (raphe nuclei).

The above diagram shows a simplified timeout and avoid circuit. The blue arrows show the proposed timeout avoid path. The greyed arrows show related connectivity, which are either contextual or for other actions. For example, the H.l glutamate to Hb.lm avoidance is necessary for predator and toxin avoidance such as a looming response from OT (optic tectum) [Lecca et al 2017] or pain responses from R.pb.l (lateral parabrachium) [Phua et al 2021]. Although the H.l is RTPA and also uses Hb.lm as an avoidance action path, it seems less likely to be a seek-timeout path. Because the Sv, Pv, and H.l circuit is also an eating circuit, some of the locomotion is stopping to eat. Some of the Sv and Pv projections to H.l are eating circuits [Root et al 2015], and eating also inhibits Hb.lm avoidance [Hu H et al 2020] because the animal shouldn’t move away from its food.

Hb.lm is a key action node for avoidance, using V.rn (raphe nuclei) to drive avoidance. In zebrafish, this path is exclusively V.mr (median raphe) because the zebrafish Hb.lm only connects to V.mr [Agetsuma et al 2010]. In mammals, the target of Hb.lm is less clear cut because both V.mr and V.dr (dorsal raphe) receive Hb.lm output [Baker et al 2015] and could participate in avoidance.

Pv as a heterogenous area

In this model, Pv is a key decision node. It receives seek-driving input from H.l and A.bl (basolateral amygdala) [Giardino et al 2018], [Heinsbroek et al 2020] and decision and timeout information from S.ot. Pv is defined by the projection of Sv, specifically using tac1 (tachykinin 1 for substance-p neurotransmitter), which S.d1 neurons exhibit. However, the neuron types and origins are heterogenous [Ottenheimer et al 2024], and derive from neighboring regions. In part, Pv derives from Po.l (lateral preoptic area) and H.l neuron types, in part it derives from P.bst (bed nucleus of the stria terminalis, extended amygdala), in part it derives from Pd (global pallidus external) [Ottenheimer et al 2024], and it has some functionality more similar to P.bf (basal forebrain), including ACh (acetylcholine) attention projections.

A diagram illustrating the connections and circuits involved in attention, avoidance, and decision-making within the brain, specifically highlighting the ventral pallidum (Pv), lateral hypothalamus (H.l), and other neural components.
Multiple circuits in Pv, including attention, avoidance, wake, seek, eat, avoidance, selection, and feedback to Sv. A.bl (basolateral amygdala), H.l (lateral hypothalamus), H.stn (sub thalamic nucleus), Hb.lm (lateral habenula, medial), P.epn (entopeduncular nucleus), Pv (ventral pallidum), Pv.a (anterior Pv), Pv.p (posterior Pv), Pv.dl (dorsolateral Pv), Pv.vm (ventromedial Pv), S.d1 (striatum projection neuron with D1.s receptor), S.d2 (striatum projection neuron with D2.i receptor), S.pv (striatum parvalbumin inhibitory neuron), Snr (substantia nigra pars reticulata).

The above diagram shows some of the difficulty by categorizing Pv functions by its output projections. Pv ACh (acetylcholine) projections particularly to A.bl to sustain attention, such as enabling odor seek [Kim R et al 2024], which is a P.bf function. Separate Pv glutamate and GABA projections to Hb.lm produce RTPP and RTPA [Stephenson-Jones et al 2020], which matches theH.l and Po.l function. Projections to H.l are more complex, producing wake [Luo YJ et al 2023] and eating [Palmer et al 2024]. Pv has choice-related output to Vta (ventral tegmentum) [Faget et al 2018], [Palmer et al 2024], which drives seek but is not motivational. Pv also has similar connections to the basal ganglia, similar to the S.d (dorsal striatum) and Pd (dorsal pallidum aka globus pallidus external) connections to H.stn (subthalamic nucleus), Snr (substantia nigra pars reticulata) and P.epn (entopeduncular nucleus aka globus pallidus internal) [Root et al 2015]. However, those Pd-like circuits are restricted to a particular part of Pv.dl (dorsolateral Pv). Finally, like Pd, Pv has “arkypallidal” feedback connections to Sv [Vachez et al 2021].

Decision: selection and commitment

Decision can be decomposed into a selection function and a commitment function. Selection chooses between competing options, such as left or right. Commitment ensures that the selection follows through and is not immediately distracted. Commitment is more important because without commitment, a selection isn’t a decision, while a random selection or a first-arriving selection is a workable decision. In a WTA (winner-take-all) process, the key part is the “take-all” part. Random take-all would also work. The commitment function needs a lockout function (“take-all”) but also a timeout function,e ach of which may be separate circuits.

A flow diagram illustrating the relationship between Sv (ventral striatum) and Pv (ventral pallidum) in a neural circuit, highlighting components like Vta select, Sv lockout, and Hb.lm timeout.
Possible circuit decomposition of decision between selection, lockout, and timeout. Hb.lm (lateral habenula, medial), Pv (ventral pallidum), Sv (ventral striatum), Vta (ventral tegmentum).

The above diagram shows a possible functional decomposition for Pv and decision-making. The Pv to Vta projection is important for the selection process [Palmer et al 2024]. More speculatively, the Pv feedback connection to Pv could provide a lockout function by inhibiting new selections through Sv. A similar circuit may exist in H.sth, which also projects directly to S.d [Williams 2024]. The Pv to Hb.lm projection is more clearly established as an avoidance pathway [Faget et al 2018].

One neuron, two functions

Although selection isn’t the focus of the essay, some learning theory results and some neuroscience measurements show that single S.d2 neurons are possibly serving opposite roles: selecting an action, but then opposing that same action [Hodge and Yttri 2025], [Soares-Cunha et al 2020], or terminating the current activity [Tecuapetla et al 2016]. In the classical model of basal ganglia selection, S.d1 and S.d2 are oppositional: S.d1 promotes an action and S.d2 either opposes the action or promotes an opposite action [Bariselli et al 2019]. In the learning model where DA (dopamine) serves as a teaching signal, DA enhances selected actions when successful and suppresses unsuccessful actions. However, some scientists argue that this learning model doesn’t work for S.d2 if S.d1 and S.d2 are selection with no other function [Lindsey et al 2025]. Some proposals to rescue the learning models include sustaining S.d2 activity after selection [Lindsey et al 2025]

Some prominent results show both S.d1 and S.d2 selecting the winning option [Cui G et al 2013], not opposing each other. However, studies consistently show the stimulating S.d1 makes contralateral turns but stimulating S.d2 makes ipsilateral turns [Conde-Berriozabal et al 2025], which is clearly oppositional. Possibly resolving this conflict, stimulating S.d2 shows a short 1s period of inhibiting Pv and exciting Vta while longer 2s stimulation excites Pv and inhibits Vta [Soares-Cunha et al 2020]. Another study shows short 350ms S.d2 as not producing RTPA, but 2s long S.d2 stimulus does produce RTPA [Hodge and Yttri 2025].

S.d2 neurons produce both GABA and the opioid enkephalin as neurotransmitters [Dai KZ et al 2022]. GABA is a fast neurotransmitter on the order of 3-5ms and only requires electrical AP (action potentials). Enkephalin is a much slower neuropeptide and is released when internal Ca2+ (calcium) and PKA (protein kinase A) levels have risen [Konradi et al 2023], [Hook et al 2008]. PKA levels rise in response to G-s protein coupled receptors like A2a.s (adenosine G-s coupled receptor). Enkephalin requires both action potentials and PKA, likely triggered by A2a.s. This A2a.s PKA signaling needs to overcome D2.i, which inhibits the PKA pathway. Technically, D2.i inhibits AC (adenylyl cyclase), which prevents cAMP accumulation, which prevents PKA. One result of this longer chain is that enkephalin signaling is much slower than GABA and is modulated by other neurotransmitters like DA and Ado.

This dual transmitter system means that a short stimulus might release GABA, while a longer stimulus would release enkephalin. In addition, S.d2 axons contain DOR.i (δ-opioid inhibitory receptor), which can self-inhibit its own GABA release [Steiner and Gerfen 1998]. The longer enkephalin path may disable the faster GABA path. Prolonged S.d2 stimulation produces RTPA and requires active DOR.i in Pv [Soares-Cunha et al 2020]. A similar oppositional fast vs slow transmitter system exists in the H.l to Vta connection, where GABA provides fast inhibition but a slower neurotensin neurotransmitter excites [Patterson et al 2015].

Diagram illustrating the functional decomposition of the ventral pallidum (Pv) and its role in timeout and decision-making circuits, involving interactions with the lateral habenula (Hb.lm) and ventral tegmental area (Vta).
Hypothetical fast and slow multiplexing circuit. The fast path uses GABA through Pv.g to activate DA in Vta for a selection. The slow path uses enkephalin to disinhibit an avoidance action path using Pv glutamate and Hb.lm. DA (dopamine), glu (glutamate), Hb.lm (lateral habenula, medial), Pv (ventral pallidum), Pv.g (Pv GABA neuron), S.d2 (striatum projection neuron with D2.i receptor), Vta (ventral tegmentum).

The above diagram shows hypothetical fast and slow multiplexing circuit with GABA driving the fast selection path and enkephalin driving the slow avoidance path. The fast S.d2 GABA path disinhibits Vta by inhibiting a tonically active Pv GABA interneuron. The slow S.d2 enkephalin path inhibits a distinct tonically active Pv GABA interneuron, which disinhibits the Pv glutamate to Hb.lm avoidance path, and re-inhibits Vta DA. Re-inhibition of Vta DA serves as a lockout of subsequence decisions. Disinhibition of the Hb.lm avoidance enables timeout avoidance. With this temporal multiplexing system, a single S.d2 neuron can serve all three decision functions: selection, lockout, and timeout.

Pv glutamate inputs vs tonic activity

The most prominent Pv inputs from Sv are inhibitory, which raises the question: what are they inhibiting? Either it is inhibiting an excitatory input or it’s inhibiting tonically active neurons. So, the glutamate inputs have an outsized importance because without glutamate or tonic activity, the inhibition has nothing to work against.

In studying the Pv projection to Hb.lm, [Stephenson-Jones et al 2020] inhibited glutamate and GABA neurons to explore the tonic behavior. Inhibiting glutamate did not produce an effect, either RTPP or RTPA, and inhibiting GABA also did not produce an effect. This result suggests that the Pv output neurons are not tonically active, either from their own activity or other internal Pv activity. Without tonic activity, glutamate inputs are necessary to drive output.

The major glutamate inputs are from A.bl, H.l, and H.stn, but the H.stn input is specific to the Pd-like area in Pv.dl [Root et al 2015], so for the purpose of this essay I’m assuming H.stn is restricted to a specific Pv subarea with dorsal basal ganglia function and does not apply to the rest of Pv.

A diagram illustrating the neural connections involving the lateral hypothalamus (H.l), striatal projection neurons (S.d1 and S.d2), and the ventral pallidum (Pv), highlighting their roles in the seek and avoid circuits.
H.l glutamate as powering the Pv. Without H.l input the system is unpowered and has no output. Enk (enkephalin), Glu (glutamate), H.l.ox (lateral hypothalamus orexin), Hb.lm (lateral habenula, medial), Pv.g (ventral pallidum GABA output), Pv.glu (Pv glutamate), S.d1 (striatum projection neuron with D1.s dopamine receptor), S.d2 (striatum projection neuron with D1.i dopamine receptor).

The above diagram shows an hypothetical circuit using H.l.ox (orexin neurons of H.l) as a food search signal that drives both roaming random walk and directed, targeted seek. When the animal is not seeking food because it’s sated or eating, H.l.ox is silent, which unpowers the circuit. My choice of H.l.ox as a glutamate source is hypothetical. H.l has at least 17 glutamate populations [Wang Y et al 2021], including one that implements SLR (subthalamic locomotor region) [Ji C et al 2024], some that project to Hb.lm directly for aversion [Lecca et al 2017], as well as eating-related neurons, and H.l.ox.

I’ve used the enkephalin output from S.d2 because the Hb.lm is the avoidance circuit. The enkephalins receptor DOR.i (δ-opioid receptor) is coupled to inhibitory G-protein and acts primarily presynaptically but does act postsynaptically in Pv [Neuhofer and Kalivas 2023], [Rysztak and Jutkiewicz 2020]. In Pv, stimulating DOR.i inhibits 24% of Pv neurons and excites 13% [Root et al 215]. In an alternative circuit, the S.d2 enkephalin-triggered DOR.i receptor is presynaptic on the glutamate input to Pv.g. Without that glutamate input, the Pv.g neuron is inhibited, which disinhibits the Pv.glu path.

A diagram showing neural pathways related to ventral pallidum circuits. The diagram is divided into four sections with representations of different neuron types and their interactions, including S.d1 neurons interacting with GABA and enkephalin, as well as their connections to the lateral habenula.
Several possible hypothetical slow RTPP and RTPA circuits, focusing on S.d1 opposition to RTPA. S.d1 could directly oppose Pv.glu avoidance with GABA, it could enhance inhibitory interneurons with substance P, or it could inhibit Pv.glu RTPA with dynorphin. Dyn (dynorphin opioid), enk (enkephalin opioid), glu (glutamate), H.l.ox (lateral hypothalamus orexin), Hb.lm (lateral habenula, medial), Pv (ventral pallidum), Pv.g (Pv GABA), Pv.glu (Pv glutamate), S.d1 (striatum projection neuron with D1.s receptor), S.d2 (striatum projection neuron with D2.i receptor), SP (substance-P neurotransmitter), tac1 (tachykinin 1 transcription factor for SP),

Unfortunately, the exact details of the circuits aren’t known yet. It seems reasonable to assume that the S.d1 RTPP path opposes the S.d2 RTPA path using peptides or opioids instead of GABA, but S.d1 produces two additional outputs: the opioid dynorphin with its inhibitory KOR.i (κ-opioid receptor) and the peptide SP (substance P) with its excretory NK1.q (neurokinin 1 with PLC/PKC path). Like enkephalin’s DOR.i receptor, dynorphin’s KOR.i is primarily presynaptic. The above diagram shows three hypothetical circuits, but other more complicated possible circuits exist, including using more tonically active inhibitory GABA interneurons. In particular, S.d1 and S.d2 have auto-receptors for dynorphin and enkephalin respectively, which inhibits their own release of the opioids. Dynorphin is known to self-inhibit S.d1 neurons in Pv [Steiner and Gerfen 1998], which may be its main function. Although I’ve focused on S.d1 and S.d2 neurotransmitters for the slow circuit, another possibility is that a distinct internal Pv mechanism drives the slow avoidance circuit, independent of S.d2 enkephalin and S.d2 dynorphin or SP.

A.bl glutamate

I used H.l.ox as the source of glutamate above, but A.bl is also an important source of glutamate, and inhibiting A.bl can turn odor seek into avoid [Kim R et al 2024], which is exactly the situation here. A.bl is a cortical area, which means it’s more complicated, but has the advantage of supporting sustained, working-memory output. A.bl receives olfactory input from Ob and O.pir (piriform cortex) and outputs glutamate to Pv and to Sv. A.bl has both seek and avoid outputs with distinct projections [Sniffen et al 2024]. A.bl is necessary for conflicting seek and threat, but disabling A.bl does not prevent seek [Hernández-Jaramillo et al 2024]. In addition A.bl receives ACh input from Pv [Root et al 2015]. For this circuit, I’m using the A.bl seek output to serve the same function as H.l did in the previous description. Without A.bl seek input, the seek collapses and turns to avoidance [Kim R et al 2024].

Diagram illustrating the role of the A.bl region in glutamate signaling and its connections to various structures including the olfactory bulb (Ob), ventral pallidum (Pv), and habenula (Hb.lm).
Using A.bl as the primary glutamate source to power the Pv seek and avoidance circuit. A.bl itself is powered by ACh from Pv. A.bl (basolateral amygdala), ACh (acetylcholine), H.l (lateral hypothalamus), Hb.lm (lateral habenula, medial), Ob (olfactory bulb), P.bst (bed nucleus of the stria terminalis, extended amygdala), Pv (ventral pallidum), Pv.g (Pv GABA), Pv.glu (Pv glutamate), Sa (central amygdala), S.d1 (striatum projection neuron with D1.s receptor), S.d2 (striatum projection neuron with D1.i receptor), Sv (ventral striatum).

The ACh input from Pv to A.bl is important to sustaining attention. ACh acts on m1.q (ACh metabotropic G-q coupled receptor) in the A.bl PY (pyramidal) neurons [Unal et al 2015]. Activating m1.q turns the PY neurons into a sustained excitation with an ADP (after-depolarization potential) after receiving both ACh and an AP (action potential) [Unal et al 2015]. ADP turns the PY neuron into an Up state for 7-10 seconds, meaning it’s more easily activated by inputs than its base state. Essentially, ACh converts A.bl firing into working memory or sustained attention.

The Pv ACh neuron inputs include H.l, Sv, and Sa (central amygdala) and P.bst (bed nucleus of the stria terminalis, external amygdala) [Schlingloff et al 2025]. This ACh modulation gives another opportunity to control seek to an odor target. An initial odor detection on the order of 500ms might only trigger sustained seek if ACh is activated by a food-seek drive from H.l and not suppressed by Sv, Sa, or P.bst. Working memory or sustained attention for the odor would require food motivation and an absence of habituation.

Simulation

The main seek path is almost entirely disconnected from the Pv timeout circuitry discussed in the essay. The main seek path is a short, fast path from Ob to V.pt (posterior tuberculum) to MLR (midbrain locomotor region) to R5.rs (mid-hindbrain reticulospinal turning area), represented by Ob to MidSeek to HindMove.

A flowchart illustrating the pathway from the olfactory bulb (Ob) to a central decision-making node ('MidSeek') that connects to the midbrain locomotor region (V.pt-MLR) and subsequently to the hindbrain region (R5.rs) for movement control.
Simulation model for the direct seek path. Ob (olfactory bulb), MLR (midbrain locomotor region), R5.rs (mid-hindbrain reticulospinal motor), V.pt (posterior tuberculum).

An earlier simulation model used S.d as a timeout for an OT orientation circuit, but the S.d lacks the direct avoidance action that Sv has with Hb.lm. However, the Pv and Hb.lm circuit is almost entirely disconnected from the V.pt-MLR, which means that the Pv modulation is quite convoluted.

A diagram illustrating a neural circuit model showing connections between various brain regions, including the olfactory bulb (Ob), midbrain (MidSeek), ventral pallidum (Pv), and areas involved in seeking and avoiding behaviors.
Convoluted avoidance path from PvSeek through HbAvoid to suppress the MidSeek action. A.bl (basolateral amygdala), Ob (olfactory bulb), Pv (ventral pallidum), R1.a (anterior hindbrain motor region), R5.rs (mid-hindbrain motor region), S.ot (olfactory tubercle).

In the avoid circuit, HbAvoid is the key avoidance node, which PvSeek uses for avoidance. An avoidance action needs to stop ongoing action, and to enable a reversal of the current seek direction. In the simulation, MidSeek can reverse its direction if it received an avoid signal. However, I don’t know if any midbrain circuit can reverse direction with an external modulating signal. The most plausible path is from V.mr as the main target of Hb.lm.

If this seek to avoid reversal circuit does exist, it might exist in OT, which does handle both seek and avoid, is used for general left vs right decisions, and receives V.rn input. But for the sake of this essay, I’m avoiding the complexity of revisiting OT and instead assuming that MidSeek can reverse direction on its own.

An alternative is more of a switchboard configuration, where avoidance disables the seek path and enables an odor avoidance path. In animals like the lamprey and fish, Ob directly drives Hb.m for odor chemotaxis, although that path does not exist for mammals, because hippocampus output drives their Hb.m. Using that switchboard model, Pv would use V.rn as the controller to switch between the V.pt seek circuit and the Hb.m odor avoidance chemotaxis. V.rn is essentially part of the Hb.m and R1.a motor circuit, and can project to essentially the entire brain the serotonin and non-serotonin projections.

Hysteresis

The simulation raised the problem of hysteresis again. This time partially because of its simplified PKA and enkephalin model. In this case, the simulation uses a single threshold for deciding to avoid, using PKA and enkephalin rising above a threshold. Unfortunately, when avoidance occurs, the simulation immediately decays the PKA, which drops it below the threshold, curtailing the avoidance and allowing the animal to reenter the failed odor plume. Because the simulation is a program, this problem could be easily fixed by adding a second threshold to disable avoidance, but how could Pv accomplish this hysteresis?

One solution could have Pv blocking any new decision to seek an odor. The S.d2 fast selection phase could be inhibited by low levels of enkephalin. When a new odor triggers S.d2, it would release some level of enkephalin because of the remaining PKA, which might be enough to block a new decision. An alternative solution could use the ACh to A.bl attention circuit. If the lower enkephalin level was still high enough to block ACh attention, it would block a new seek action. This A.bl solution would work especially well if A.bl habituates to an odor if it has no ACh.

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45: Basal Ganglia as Consensus

I’m returning to decision making from essay 42, because I think it can be simplified by restricting it further to concentrate on the hindbrain parts of BG (basal ganglia) without needing the forebrain S.d (striatum) or P.ge (external globus pallidus). [Kamali Sarvestani et al 2011] suggest a BG functional split between a brainstem arbitration system with Snr (substantia nigra pars reticulata), H.stn (subthalamus), and P.ge; and an extension system focused on S.d. Because I’m still focused on left vs right turning decisions, which is part of the bilaterian physical structure [Braitenberg 1984], P.ge can also be dropped. Snr and H.stn form short subcortical BG loops such as Snr, H.stn, and OT (optic tectum); or Snr, H.stn, and R.pb (parabrachial nucleus); or Snr, H.stn, and M.pag (midbrain periaqueductal gray) [Coizet et al 2024]. For the essay simulation, these short BG loops can connect brainstem action paths into a consensus circuit.

Decision, coordination, and consensus

The simulation represents has several independent brainstem locomotion action paths that currently combine in the spinal cord: temporal chemotaxis and phototaxis in the Hb.mv (habenula, medial ventral) to R.ip (interpeduncular nucleus) to R1.a (anterior hindbrain motor area) path, spatial chemical seek in the V.pt (posterior tuberculum) to MLR (midbrain locomotor region) path, and obstacle avoidance in the M.pt (pretectum) to M.nmlf (nucleus of the median lateral fasciculus – midbrain motor area). If the simulation implemented ASR (acoustic startle reflex), it would implement the N8 (acoustic nerve) to R4.rs.mc (Mauthner cell) to N.sp (spinal cord) 3-neuron reflex action path. If the simulation implemented looming defense, it would need the OT to R5.rs (mid-hindbrain turning reticulospinal) path. With the exception of MLR and OT, which both use the hindbrain R5.rs, these each use different reticulospinal driving neurons, resolved only in the spinal cord.

A diagram illustrating neural pathways for chemotaxis (klnotaxis) and odor seek (tropotaxis) actions in a brain simulation, highlighting connections between specific brain regions.
Two action paths for chemotaxis (odor seeking). The top habenula path uses self-motion and time differences to locate the odor (klinotaxis). The bottom bilateral seek path compares left and right odors to determine the location (tropotaxis). In the current simulation, these paths are only resolved in the spinal cord. Hb.mv (medial habenula, ventral part), MLR (midbrain locomotor region), N.sp (spinal cord), Ob (olfactory bulb), Ppt (pedunculopontine tegmentum), R1.a (anterior hindbrain motor region), R5.rs (mid-hindbrain reticulospinal), V.pt (posterior tuberculum).

The above diagram shows two of the chemotaxis (odor seeking) paths in the current simulation. In the lamprey, Ob.m (medial olfactory bulb) projects to Hb.mv in the midbrain roof [Stephenson-Jones et al 2012], and to V.pt in the midbrain tegmentum (floor) [Derjean et al 2010]. The Hb.mv to R.ip system is used for chemotaxis [Chen WY et al 2019], phototaxis [Chen X and Engert 2014], and thermotaxis [Palieri et al 2024], using self-motion and temporal gradient measurement to determine direction [Chen X and Engert 2014], [Palieri et al 2024]. The V.pt path drives MLR locomotion [Derjean et al 2010], and I’m using this path as a tropotaxis seek, but without a study backing it up, other than V.pt being involved with turning [Barrios et al 2020], [Horstick et al 2020]. Both paths are chemotaxis paths, but they are entirely separate except for their Ob input and N.sp final output. Currently, any differences are resolved by a strict priority where R5.rs from the MLR/OT path strictly overrides R1.a (aka R.pn.o pontine oxalis) from the Hb.mv – R.ip.m path. A better solution would combine the two chemotaxis estimates, improving the accuracy and avoiding conflicts. This combination would be part of a consensus decision system, which essay 30 introduced as a place holder in the context of RTPA (real-time place avoidance).

A diagram illustrating multiple 'drive' inputs converging into a 'consensus' decision-making process, leading to a 'motor' output.
Hypothetical consensus loop to combine independent action paths into a single motor decision.

This consensus loop could be implemented by the short brainstem BG loops described by [Kamali Sarvestani et al 2011] and [Coizet et al 2024]. A key node in MLR, Ppt (pedunculopontine tegmentum), is tightly connected with the entire BG. R1.a (aka R.pn.o) is both an input to BG using T.pf (parafascicular thalamus) [Gonzalo-Martín et al 2024] and driven by Snr [McElvain et al 2021].

MLR seek

To introduce the BG, consider a simplified role as lateral inhibition between a left vs right decision for the MLR seek circuit. Essay 40 discussed the Sprague effect, which uncovered contralateral inhibition between OT involving Snr and Ppt [Durmer and Rosenquist 2001], [Jiang H et al 2003], [Krauzlis et al 2013], [Valero-Cabré et al 2020]. GABA neurons in Ppt.a (anterior Ppt) are essentially a continuation of the adjacent Snr.p [Mena-Segovia and Bolam 2017], [Hormigo et al 2018]. Glutamate neurons in Ppt.p are part of the MLR and produce locomotion, extending into the adjacent M.cnf (uniform nucleus) part of MLR [Mena-Segovia and Bolam 2017]. Both Ppt and Snr.p derive from R1 (hindbrain rhombomere 1) [Waite 2012], [Lahti et al 2016], [Morello et al 2020].

Diagram illustrating the chemotaxis paths in a simulation, highlighting connections from the medial olfactory bulb (Ob.m) and posterior tuberculum (V.pt) to the midbrain locomotor region (MLR) and reticulospinal pathways (R5.rs) for right and left decision making.
Hypothetical bilateral odor seek circuit using Snr and Ppt.a for lateral inhibition. MLR (midbrain locomotor region), Ob.m (medial olfactory bulb), Ppt (pedunculopontine tegmentum), R5.rs (mid-hindbrain reticulospinal turning), Snr (substantia nigra pars reticulata), V.pt (posterior tuberculum).

A possible early proto-vertebrate could use Snr simply for lateral inhibition when deciding to turn left or right in the MLR seek circuit. In the above circuit based on the Sprague effect circuit, Snr acts both as a feedforward inhibition from V.pt to Ppt and feedback inhibition from Ppt to the contralateral Ppt.

For simplicity, I’ve used Ppt for both forward motion [Brocard et al 2010] and turning [Assous et al 2019], [Dautan 2023], [Huang Y et al 2024] omitting the highly related OT turning. Although Ppt does have directional neurons [Huang Y et al 2024], turning is more closely associated with OT, which both Ppt and Snr are reciprocally connected to [Comoli et al 2012], [Valero-Cabré et al 2020]. It’s possible that a proto-vertebrate seek circuit always used OT as its primary turning node with Ppt as modulatory for attention and persistence.

T.pf parafascicular thalamus

The Hb.mv → R.ip → R1.a chemotaxis circuit connects to BG with T.pf (parafascicular thalamus) [Gonzalo-Martín et al 2024], which directly connects to Snr and H.stn [Hanini-Daoud et al 2022]. T.pf is a unique thalamus nucleus both morphologically and electrophysically [Phelan et al 2005]. T.pf receives input from several brainstem motor regions, including R1.a (R.pn.o) [Gonzalo-Martín et al 2024], and it outputs to most of the cortex, strongly to S.d, and also directly to H.stn and S.nr [Gonzalo-Martín et al 2024], [Hanini-Daoud et al 2022]. This path from R1.a → T.pf → Snr lets the Hb.mv – R.ip.m chemotaxis path influence the V.pt → MLR chemotaxis seek path. Stimulating T.pf produces ipsiversive head turning, prolonged stimulation produces full body turns, and stimulation and restore movement during DA depletion such as in Parkinson’s disease [Fallon et al 2023].

Diagram illustrating chemotaxis and odor seek pathways in a neural simulation, highlighting connections between the medial olfactory bulb (Ob), habenula (Hb.mv), interpeduncular nucleus (R.ip), R1.a, parafascicular thalamus (T.pf), substantia nigra (Snr), midbrain locomotor region (MLR), and nucleus of the spinal cord (N.sp).
Habenula chemotaxis path to influence the MLR chemotaxis path via T.pf and Snr. Hb.mv (medial Hb, ventral part), MLR (midbrain locomotor region), N.sp (spinal cord), Ob (olfactory bulb), Ppt (pedunculopontine tegmentum), R.ip (interpeduncular nucleus), R1.a (anterior hindbrain motor area aka R.pn.o), R5.rs (mid-hindbrain reticulospinal), Snr (substantia nigra pars reticulata), T.pf (parafascicular thalamus), V.pt (posterior tuberculum).

The above diagrams shows the R1.a temporal chemotaxis path influencing the MLR spatial chemotaxis path via T.pf, where Snr is already a left vs right decision for MLR, now modulated by R1.a → T.pf input. T.pf itself can provide an integrative role, but for not it has only a single input. This T.pf connection could either serve as an efferent copy: preventing MLR from interfering with an R1.a decision, or a consensus planning input before the turning decision commits.

The thalamus is a new system in vertebrates, not present in other chordates. It developed in the same prosomere (brainstem segment) as Hb and the pineal gland. If the thalamus defining tcf7l2 genetic transcription factor is changed, the thalamus acquires Hb properties [Roberson and Halperin 2018]. Tcf7l2 is also a regulator for nACh function [Srivastava et al 2023], with other effects including the GLP-1 metabolic pathway. The thalamus is modulated by ACh (acetylcholine), which transforms most of the thalamus from a sleep-mode bursting pattern to an attentive tonic bursting pattern [Ye M et al 2009], but many T.pf neurons respond differently to ACh without the more typical bursting vs tonic thalamus pattern. Thalamus ACh comes from Ppt and P.ldt (laterodorsal tegmentum) [Ye M et al 2009]. One possibly motivation for a proto-vertebrate adding the thalamus as a relay is its reaction to ACh as a sleep and attention gating mechanism.

Diagram illustrating the connections between various brain regions, including T.pf, Hb.mv, R.ip.m, R1.a, S.nr, and MLR, with annotations indicating neurotransmitter types.
Highly speculative justification for adding T.pf as a relay node in a consensus circuit. The habenula-pineal area is a circadian system, and melatonin from the pineal gland and ACh from Hb.mv could gate a T.pf relay in a proto-vertebrate. ACh (acetylcholine), Hb.fr (fasciculus retroflex), Hb.mv (medial habenula, ventral part), MLR (midbrain locomotor region), nACh (nicotinic ACh receptor), Ppt (pedunculopontine tegmentum), R1.a (anterior hindbrain motor region), R.ip.m (interpeduncular nucleus), Snr (substantia nigra pars reticulata), T.pf (parafascicular thalamus).

As a speculation, Hb.mv is interesting in this context because T.pf is called “parafasciclar” because it encircles the Hb projection Hb.fr (fasciculus retroflex) and because Hb.mv is a major ACh source that appears to be driven by local ACh release [Chung L et al 2016]. As far as I know, there is no evidence that ACh from Hb.mv affects T.pf in modern vertebrates. To motivate a proto-vertebrate creating a T.pf relay instead of directly contacting Snr, note that both ACh and the Hb-pineal complex are associated with the sleep-wake cycle. The pineal gland and habenula serve as a circadian clock [Vatine et al 2011], [Baño-Otálora et al 2017], and pineal producing melatonin [Aranda-Martínez et al 2023], and Hb providing a role in sleep [Hikosaka 2010], [Aizawa et al 2013]. However, this is entirely speculative, because the initial reason for the thalamus is known. In some vertebrates like fish, parts of the thalamus have an entirely different origin and organization with a similar function [Butler 2008], [Mueller 2012]. Speculative origin aside, adding T.pf as a gated relay to the decision commitment circuit adds value by making the circuit responsive to sleep and attention modulation.

Ppt as attention center like R.is

While the R1.a temporal chemotaxis modulation of the MLR spatial chemotaxis is relatively straightforward, the opposite direction is complicated by the complexity of Ppt, which is not purely motor but integrative [Gut and Winn 2016], [Noga and Whelan 2022], with some arguing that Ppt should not be considered as MLR [Gut and Winn 1016], [Opris et al 2019]. Ppt has a role in attention and as a central BG node. Connectivity from MLR/Ppt to R1.a may not be a locomotive consensus circuit, but an independent attention/modulatory function. To illustrate a possible attention/modulatory role for Ppt independent of MLR, consider the analogy with a sibling nucleus R.is (nucleus isthmi, aka parabigeminal in mammals).

R.is is a developmental sibling to Ppt, produced from the same progenitors in R1, but at a different development time [Volkmann et al 2010], [Wullimann et al 2011]. It is well-studied for visual attention in the OT [Henriques et al 2019], and unlike Ppt it has a clear and straightforward function. Like Ppt, R.is contains ACh and GABA neurons, but these are separated into distinct nuclei in R.is. The ACh neurons sustain visual attention in zebrafish to maintain focus on a hunting target [Henriques et al 2019], [Krauzlis et al 2013], [Marín et al 2007]. The GABA neurons form a long-distance lateral inhibition network to suppress distractors [Marín et al 2007]. R.is is visually topographic: each R.is area corresponds to a visual area in OT. If OT receives a visual stimulus near the horizon, it excites a corresponding R.is area, which in turn sustains attention to the reciprocal OT area with ACh and suppresses other visual areas with GABA.

Diagram illustrating the left topographic connection between the R.is (nucleus isthmi) and the optic tectum (OT), highlighting cholinergic (ACh) signaling pathways.
Simplified two-area model of the OT and R.is attention circuit. R.is.pc uses ACh to sustain attention in the matching OT area. R.is.mc uses GABA to suppress distant visual areas that may contain distractors. ACh (acetylcholine), OT (optic tectum), R.is.mc (nucleus isthmi, magnocellular part), R.is.pc (R.is, parvocellular part).

The above diagram shows the R.is visual attention circuit for OT.s (superficial OT – visual), simplified to two regions, such as the upper or lower visual field. Importantly, this is a unilateral circuit: it does not have contralateral inhibition of the opposite side, unlike the focus of this essay. However, note that the circuit structure is similar to the Ppt, Snr and OT.d (deep OT – motor) circuit, where Ppt provides ACh and Snr provides GABA to select OT.d motor actions. So, consider Ppt as if it played a similar role as R.is, but selected attention to left and right motor decisions instead of visual attention, and where ACh sustains attention to the current selected motor action and Snr inhibition suppresses distractors.

Diagram illustrating two neural circuits for attention modulation in left and right motor decisions, showing connections between Ppt, S.nr, OT, and R5.rs.
Motor-decision attention circuit using Ppt and Snr as analogous to R.is.pc and R.is.mc for visual attention. Ppt.p provides ACh for sustained attention to a motor decision. Ppt.a and Snr provide lateral inhibition to suppress the contralateral decision. ACh (acetylcholine), OT (optic tectum), Ppt.a (anterior pedunculopontine tegmentum), Ppt.p (posterior Ppt), R5.rs (mid-hindbrain reticulospinal turning), Snr (substantia nigra pars reticulata).

In the above diagram, the left and right OT are weighing a decision to turn left or right for seeking. The mammalian OT.l (lateral OT) has crossed seek output to mid-hindbrain R5.rs turning neurons [Melleu and Canteras 2024]. Ppt.a (anterior Ppt) and Snr provide lateral inhibition for the OT decision, while Ppt.p (posterior Ppt) provides ACh to sustain attention to the currently selected side.

Diagram illustrating the neural pathways involved in chemotaxis and odor seeking in the brain, highlighting key brain structures such as Hb.mv, R.ip, R1.a, Snr, T.pf, MLR, OT, and Ppt.
Odor seek path modulating the habenula chemotaxis path via T.pf and Snr. Hb.mv (medial habenula, ventral), MLR (midbrain locomotor region), N.sp (spinal cord), Ob (olfactory bulb), OT (optic tectum), Ppt (pedunculopontine tegmentum), R1.a (anterior hindbrain motor), R5.rs (mid-hindbrain reticulospinal), Snr (substantia nigra pars reticulata), T.pf (parafascicular thalamus), V.pt (posterior tuberculum).

To complete the consensus loop, Snr also projects to R1.a (R.pn.o) [Delgado-Zabalza et al 2023], and Ppt projects to T.pf, including ACh and non-ACh projections [Ye M et al 2009], [Gonzalo-Martín et al 2024]. To simplify the diagram, I’ve merged the OT and Ppt. OT projects heavily to T.pf [Fallon et al 2023], [Gonzalo-Martín et al 2024].

As a caveat, the Snr projections to OT and R1.a are largely disjoint, although both collateralize to Ppt [McElvain et al 2021]. So, Snr may not provide a single shared left vs right decision between OT and R1.a but may instead facilitate reciprocal consensus with each making its final decision.

H.stn inheritance from chordate ancestor

The preceding discussion uses systems derived from R1 or from the midbrain for OT, which are on opposite sides of the MHB (midbrain-hindbrain boundary). H.stn (subthalamic nucleus) is a hypothalamus-derived region [Barbier and Risold 2021] of BG, adjacent to H.pstn (para-subthalamic nucleus) and H.l (lateral hypothalamus), which are all interconnected with R.pb. Unlike the all-GABA Snr, H.stn is almost entirely glutamate, and is part of the indirect BG path from S.d and the hyperdirect path from the cortex [Cavanagh et al 2011], but also from R.pb and Ppt [Jia T et al 2022], [Pautrat et al 2018]. H.stn enables stopping from the cortex hyperdirect path [Fischer et al 2017], [Ricci et al 2024] and also for delaying decision making in difficult situations [Frank 2006]. H.stn can also produce movement [Watson et al 2021], [Ricci et al 2024] with projections to Ppt and Snc (substantia nigra pars compacta).

The question here is why would the midbrain-hindbrain BG circuits above add a hypothalamus node to an existing consensus circuit in the hindbrain? One natural possibility is to gate food-seek by hunger, which is a major hypothalamus function. R.pb, H.l and R.nst (nucleus of the solitary tract) are all hunger and eating related nuclei. Alternatively, action paths through the hypothalamus may have been original chordate circuits, preceding the Ppt-Snr circuits described above.

The chordate tunicate ascidian Ciona has a larval stage that swims for about 12 hours before setting on a feeding spot, dissolving its tail and locomotor brain, and transforming into a sessile filter feeder [Anselmi et al 2024]. The larval brain is highly asymmetrical with a single gravity sensor, and two one-sided photoreceptor regions for separate phototaxis and dimming avoidance paths [Borba et al 2024], with functional similarities to the Hb.m-R.ip phototaxis and M.pt (pretectum)-OT dimming circuits. The transformation to sessile filter-feeding adult is triggered by chemical and mechanical neurons in three papillae at the front of the animal, which trigger a shutdown of locomotion [Hoyer et al 2024].

A diagram illustrating the neural circuitry connecting the retina and pineal gland to various brain regions, including the habenula (Hb), subthalamic nucleus (H.stn), substantia nigra (S.nr), mesencephalic locomotor region (MLR), and anterior hindbrain (R1.a), with annotations indicating acetylcholine (ACh) influences.
Partial circuitry of the Ciona nervous system, showing the phototaxis path and the papillae stop-metamorphosis path. The associated vertebrate areas are functional analogs, not homologs. AMG (ascending motor ganglia), CB (cerebellum), Hb (habenula), H.stn (sub thalamus), MGIN (motor ganglia interneuron), MN (motor neuron), PNIN (peripheral interneuron), PNRN (peripheral relay), PNS (papillae neurons), PR-1 (photoreceptor group 1), PRRN (photoreceptor relay), RTEN (rostral trunk epidermal neuron)

The above diagram shows the Ciona phototaxis path [Borba et al 2024], the papillae stop and metamorphosis path [Hoyer et al 2024], and some of the hindbrain [Ryan et al 2016], [Ryan and Meinertzhagen 2019]. I’ve added vertebrate areas as analogies, but these are not homologous. Genetic studies have suggested that aBV (anterior brain vesicle), pBV (posterior BV), and MG (motor ganglia) are homologous to the vertebrate forebrain, midbrain and hindbrain [Negrón-Piñeiro et al 2020]. Coronet cells in Ciona forebrain have been associated with hypothalamic DA cells [Lemaire et al 2021] or retina DA amacrine cells [Negrón-Piñeiro et al 2020], and relay cells of the coronet as genetically related to H.mb (hypothalamic mammillary body) [Lemaire et al 2021]. AMG (ascending motor ganglia) is genetically related to CB (cerebellum) [Kourakis et al 2024]. However, there is no evidence for homology in the functional analogies I’ve added for H.stn, Snr and MLR.

The additional vertebrate analogies in the diagram, including H.stn, Snr, MLR, Hb are for illustration only and are not homologous. However, the Ciona circuit does show that chordate action paths through the hypothalamus to the midbrain and hindbrain predate vertebrates. So, a proto-vertebrate could have built the proto-BG starting from a hypothalamus action path, instead of H.stn being added later to a hindbrain circuit. In this explanation, a single, asymmetrical H.stn and Snr could be primitive with a single, asymmetrical Ppt/MLR and only later adding bilateral inhibition and consensus with the phototaxis/chemotaxis path in Hb-R.ip.

The H.stn hyperdirect path

In keeping with H.stn is a primitive component of the BG circuit, consider the hyperdirect BG path, which is named following the conventions of the direct and indirect paths in the striatum. In mammals the hyperdirect path is often studies from C.mo (motor cortex) and F.pfc (prefrontal cortex) as a stop signal [Cavanagh et al 2011]. A path from OT.l (lateral OT) to H.stn is a stop signal for surprising visual events [Coizet et al 2009]. A path involving R.pb is involved with pain responses [Pautrat et al 2018], [Luan et al 2020], [Ricci et al 2024]. H.stn is also associated with prolonged decision-making under uncertainty [Frank 2006], slowing the decision process itself.

Diagram illustrating the connections between various brain regions, including H.stn, Snr, MLR, and Ppt, and their influence on locomotion pathways such as R5.rs.
The H.stn hyperdirect path. C.mo (motor cortex), H.stn (sub thalamus), MLR (midbrain locomotor region), OT.l (lateral optic tectum), R5.rs (mid-hindbrain reticulospinal turning), R.pb (parabrachial nucleus), Snr (substantia nigra pars reticulata), T.pf (parafascicular thalamus).

H.stn is heterogenous both topographically and mixed salt-and-pepper for connectivity and genetically [Haynes and Haber 2013], [Prasad and Wallén-Mackenzie 2024]. Functionally, it is highly involved with decision making, particularly premature and impulsive responses, perseveration, and motivation [Baunez and Lardeax 2011]. Along with its Snr projection, H.stn projects to MLR/Ppt [Smith et al 1990], [Watson et al 2021] and to Snc [Lobb et al 2010], [Ledonne et al 2012], and can initiate movement and turns, not only stopping movement. Importantly for this essay, unilateral H.stn stimulation produces ipsilateral turning [Freestone et al 2015], [Zhou J et al 2025], and stimulation of T.pf → H.stn connection produces locomotion or ipsilateral turning [Watson et al 2021].

Diagram illustrating chemotaxis and odor seeking pathways, including neural connections from the olfactory bulb (Ob) to various brain areas involved in food location and movement decisions.
Basal ganglia consensus circuit incorporating chemotaxis modulation of the odor seek path and food-zone stopping using H.stn. Hb.mv (medial habenula, ventral), H.stn (sub thalamus), MLR (mid-brain locomotor region), N.sp (spinal cord), Ob (olfactory bulb), Ppt (pedunculopontine tegmentum), Snr (substantia nigra pars reticulata), R1.a (anterior hindbrain motor region), R5.rs (mid-hindbrain reticulospinal turning), T.pf (parafascicular thalamus), V.pt (posterior tuberculum).

The above diagram incorporates H.stn into the consensus circuit between the Hb → R.ip temporal chemotaxis and the V.pt → MLR spatial odor seek circuit. H.stn signals stop when the filter-feeding animal reaches an appropriate feeding spot. For simplicity, the diagram only shows the influence Hb→R.ip on the MLR/Ppt circuit, but the opposite direction includes Ppt to T.pf modulation of the R1.a output of the Hb→R.ip path. Because H.stn also receives input from the entire R.pb [Williams 2024], [Jia T et al 2022] and from OT.l [Al Tanner et al 2024], it can incorporate visual, somatosensory, and lateral-line stop signals from OT, and incorporate R.pb pain and irritation signals into the left vs right decision loop [Al Tanner et al 2023].

Asymmetry

So far, the essay has assumed a Braitenberg-like bilateral circuit [Braitenberg 1986] for the left vs right decision, but the ascidian Ciona forebrain and midbrain are asymmetrical, with single asymmetrical ganglia as opposed to bilateral paired ganglia. This asymmetry may help explain some of the circuitry in Snr and in OT.l, where each side contains decision variables for both ipsilateral and contralateral turning.

Although the Ciona hindbrain is primarily symmetrical in general connectivity, its AMPA (glutamate receptor) pattern is asymmetrically biased toward the left, driven by the left-bias pitx2 transcription factor [Kourakis et al 2021]. The nodal/pitx transcription factor chain produces left-based asymmetry, affecting Hb [Lagadec et al 2015] and non-neural systems including the heart [Waite 2012]. This pitx2 path is also important for forming the pituitary and stomeodeum (mouth opening) [Waite 2012]. H.stn and OT.i orientation neurons are both marked by a symmetrical pitx2 isoform in mammals, despite being symmetrical, but zebrafish only have an asymmetrical form of pitx2 [Waite 2012].

So, let’s consider an asymmetrical implementation of this left vs right decision. A reason to examine asymmetry is the internal structure of both Snr and OT.l, where each side has both ipsilateral and contralateral turning information [Brown et al 2014], [Báez-Cordero et al 2020], [Hanini-Daoud et al 2022], [Duan et al 2021], [Doykos et al 2025], [Essig et al 2020], which means each side is capable of a turning decision without needing a contralateral decision.

A diagram illustrating neural circuitry for decision-making involving left and right movement in a biological context. The circuit includes components such as T.pf, Snr, MLR, and R5.rs, with separate paths for contralateral and ipsilateral signals for left and right decisions.
Hypothetical proto-vertebrate asymmetrical ipsilateral vs contralateral decision using only one side of Snr. MLR (midbrain locomotor region), Ppt (pedunculopontine tegmentum), R5.rs (mid-hindbrain reticulospinal turning), Snr (substantia nigra pars reticulata).

The above diagram shows an asymmetrical left vs right decision using Snr. When T.pf→Snr is stimulated, of the 28% of Snr that respond, ~50% are excited and ~50% are biphasic inhibited followed by excited [Hanini-Daoud et al 2022]. Similarly, when T.pf→H.stn is stimulated, 50% of Snr are excited and 50% inhibited. Similarly, the OT turning system has both ipsilateral and contralateral neurons for decision-making [Essig et al 2020], [Duan et al 2021].

Diagram illustrating the decision-making process in turning left or right, highlighting the roles of the subthalamic nucleus (Snr) and parafascicular thalamus (T.pf) in coordinating lateral movement.
Snr left vs right decision circuit showing both the ipsi vs contralateral decision on each side and both sides combining to a decision. MLR (midbrain locomotor region), Ppt (pedunculopontine tegmentum), Snr (substantia nigra pars reticulata), T.pf (parafascicular thalamus).

In vertebrates, H.stn, Snr and OT.l as symmetrical, despite H.stn and OT.l having asymmetrical pitx2 markers, and despite these ganglia having the capability of deciding using only a single side. It’s possible that an original single-sided system later became duplicated, similar to the single eye of Amphioxus and Ciona developing into the paired vertebrate eye.

Snr internal lateral disinhibition

The above asymmetry discussion is largely a motivation for the Snr internal circuitry and behavior, which contains both ipsilateral and contralateral turning responses [Báez-Cordero et al 2020]. Snr neurons are essentially all projection neurons with no interneurons, but the projection neurons contain weak collaterals to other Snr neurons [Brown et al 2014]. Because Snr is tonically active, the collaterals are also tonically active, but the net tonic effect is minimal or nonexistent, because Snr neuron neuron firing is desynchronized [Brown et al 2014], [Higgs and Wilson 2016], suggesting that Snr collaterals may primarily enforce desynchronization [Higgs and Wilson 2016]. Alternatively, the weak Snr collaterals may require a synchronous input to significantly disinhibit other Snr, similar to lateral inhibition for contrast [Brown et al 2014] or serve as divisive gain control as feedback inhibition not lateral inhibition [Yttri and Dudman 2018].

Diagram illustrating the connections between H.stn, Snr, and OT with decision-making components labeled A, B, and C. The Snr is shown with various outputs (a1, a2, b1, b2, c1, c2) impacting the decision process.
Snr disinhibition circuit with weak inhibition. Weak or asynchronous signals have little or no effect, but a strong and synchronous inhibition of choice B disinhibits both choice A and choice C. If both B and C are simultaneously inhibited, the third choice A gains additional disinhibition. H.stn (sub thalamus), OT (optic tectum), Snr (substantia nigra pars reticulata).

T.pf and H.stn stimulation can drive both inhibition and excitation in S.nr [Hanini-Daoud et al 2022], possibly using this disinhibition circuit. An inhibition of one option disinhibits other options. The above diagram shows how this lateral disinhibition could scale beyond two options. Inhibiting option B disinhibits both open A and C. Inhibition both options B and C more strongly disinhibits option A. In this context, H.stn could encode “move-away,” leaving contralateral space, not encoding a direct motor action [Zhou J et al 2025].

This need for synchronous input resembles the looming circuit between OT.m and M.pag [Evans 2017] and amphibian hindbrain decision circuits [Buhl et 2012]. An advantage of this kind of weak, consensus input circuit is resistance to noise or other spurious input, because the animal will only react to a strong stimulus that drives many inputs simultaneously. In Parkinson’s disease, one of the causes of movement impairment is a synchronous H.stn↔P.ge (globus pallidus, external) oscillation at beta frequencies [Deffains et al 2016]. A treatment for Parkinson’s disease is DBS (deep brain stimulation) of H.stn, which breaks up abnormal beta [Pelloux et al 2014], although the exact mechanism of DBS stimulation is still unclear.

Simulation: comparison with previous conflict resolution

The previous essay 44 also had to resolve conflicts between the Hb→R.ip path and the Seek-MLR path. In that essay, I used a sibling of Ppt, P.ldt (laterodorsal tegmentum), to inhibit midbrain DA (dopamine) to inhibit the seek path. However, that DA control assumes an already existing BG circuit, and in a sense I’m going backwards to rebuild foundational control.

A flowchart illustrating neural pathways related to limbic and tectal functions, depicting connections between components such as HbTax, R1.a, V.pt, and others in the context of locomotion and sensory behavior.
Previous essay modulation of the tectal seek path by the Hb taxis path using P.ldt to disable dopamine required by the seek path. Hb.mv (medial habenula, ventral), MLR (midbrain locomotor region), N.sp (spinal cord), Ob.m (medial olfactory bulb), P.ldt (laterodorsal tegmentum), R1.a (anterior hindbrain motor), R5.chx10 (mid-hindbrain turning), R.ip (interpeduncular nucleus), V.pt (posterior tuberculum).

The plan for the current essay is functionally similar: R1.a chemical avoidance inhibits MLR odor seek, but the implementation now uses BG H.stn→S.nr inhibition instead of inhibition DA as a way of disabling seek. The previous implementation was a bit hand-wavy because it assumed a fully-functioning DA and BG system already existed. In this essay, I’m starting to assemble the core of a BG system itself.

Flowchart illustrating the chemotaxis and seek pathways in a neural network with various brain regions including the olfactory bulb (Ob), habenula (Hb), and midbrain locomotor region (MLR).
Simulation model for the odor-avoiding Hb to R1.a path to inhibit the odor-seeking V.pt to MLR path. Hb (habenula), MLR (midbrain locomotor region), N.sp (spinal cord), Ob (olfactory bulb), OT.co (optic tectum, crossing output), Ppt (pedunculopontine tegmentum), R1.a (anterior hindbrain motor), R5.rs (mid-hindbrain turning), Snr (substantia nigra pars reticulata), T.pf (parafascicular thalamus), V.pt (posterior tuberculum).

For the sake of the simulation, I’m splitting turning from forward drive, where Tectum handles turning and MidMove handles forward. This functional division has vertebrate correlates because unilateral MLR stimulation produces bilateral forward movement without turns [Brocard et al 2010]. However, as discussed above, Ppt does have turning information. For simplicity, however, I’m combining that function into OT as the main turning system. In reality MLR/Ppt likely has turning functionality, but for the simulation it’s difficult to distinguish the Ppt turning role from the OT turning role. Instead, I’m treating Ppt as modulatory/attention for OT-based turning, similar to R.is attention circuit for vision.

Issues with M.pt

There is an issue with how M.pt (pretectum) obstacle avoidance fits into this H.stn-Snr model. In non-mammals, particularly in amphibians, M.pt is the main visual obstacle avoidance [Krauzlis et al 2018], while OT is for orientation, such as hunting prey, and M.pt inhibits OT.co (crossed-output OT) directly [Krauzlis et al 2018]. However, this direct M.pt inhibition of OT.co is counter to this essay’s model of H.stn-Snr as the central node in a consensus circuit. In fact, in non-mammals a major striatum output is both directly from S.d and through P.epn.a (entopeduncular nucleus) to M.pt and from P.epn.a and M.pt to OT [Marin et al 1997]. While P.epn.a has similar functionality to Snr, it is derived from the forebrain, not from R1 like part of Snr.

Flowchart illustrating the interaction between different neural pathways involved in obstacle avoidance and seeking behaviors, highlighting connections between S.d, P.epn.a, M.pt, V.pt, OT.co, and S.nr.
Pretectum obstacle avoidance inhibiting OT object seek directly without using Snr. ACh (acetylcholine), M.pt (pretectum), OT.co (optic tectum, crossed output), P.epn.a (entopeduncular nucleus, anterior), Ppt (pedunculopontine tegmentum), S.d (striatum), Snr (substantia nigra pars reticulata), V.pt (posterior tuberculum)

With this system, which exists in reptiles, birds, and frogs but not mammals [Krauzlis et al 2018], Ppt/MLR cannot be the final left vs right integration center. M.pt and OT.d do project to Snr [Liu D et al 2020], specifically the gad2 subpopulation. Lamprey M.pt is directly connected with OT [Capantini et al 2017], and it receives P.gi inhibition [Capantini et al 2017], where P.gi is functionally similar to Snr but derives from forebrain progenitors. The amphibian S.d to S.nr to M.pt to OT path inhibits obstacle avoidance to disinhibit hunting [Krauzlis et al 2018]. In amphibians, the striatum has two major pathways, the above S.d to M.pt to OT, and a tegmental S.d to M.tg (midbrain tegmentum) as a possible Snr homolog [Krauzlis et al 2018].

In itself, M.pt inhibition of OT isn’t a major issue, because I can treat it as an exception, but it does illustrate a problem with envisioning a general system for locomotion consensus. Although a general system may be a cleaner model, it doesn’t necessarily match evolution’s actual implementation. The striatum is explicitly outside of the scope of this essay, but the direct S.d to M.pt connectivity does show the benefit of splitting the BG into parts, because that S.d to M.pt function can presumably function without the rest of BG.

Issues with Ppt

Ppt is proving difficult to model because it’s not performing a single coherent function (or that I’m not seeing it.) Instead, it’s performing a set of semi-related functions. Partly, Ppt is performing MLR functions with glutamate neurons that extend to M.cnf [Mena-Segovia and Bolam 2017], which is more purely MLR. Some researchers consider Ppt as entirely separate from MLR [Gut and Winn 2016], which would simplify the model. Partly, Ppt is performing Snr-like functionality with the Ppt.a GABA population that extends from Snr.p [Mena-Segovia and Bolam 2017]. Partly, it seems to have R.is-like functionality with its ACh population, providing attention for OT, thalamus, P.bf (basal forebrain), S.d, and several hypothalamic, midbrain and hindbrain areas. But Ppt also has independent decision functions, including triggering a final decision with Snc bursting [Redila et al 2015] and C.m2 (premotor cortex) transition from planning to execution [Inagaki et al 2022].

This diagram illustrates the neural circuits resembling BG-like, R.is-like, Decision-making, and MLR-like systems, showing connections between different neuron populations involved in various decision-making processes.
Some of the functional roles of Ppt. C.m2 (premotor cortex), M.cnf (cuneiform nucleus), MLR (midbrain locomotor region), OT (optic tectum), Ppt (pedunculopontine tegmentum), Snc (substantia nigra pars compacta), Snr (substantia nigra pars reticulata)

Although Ppt can be studied in terms of its ACh, glutamate, and GABA neurotransmitters, even the neurotransmitter types oversimplifies the problem. For example, Ppt.p contains a distinct GABA cluster unrelated to the Snr extension in Ppt.a [Mena-Sevogia et al 2009]. Ppt contains non-MLR glu that signals decision threshold to Snc [Nishimaru et al 2023], [Ryczko 2024] and to C.mo via the thalamus [Inagaki et al 2022]. The Ppt decision functionality is related to neighboring M.rn (midbrain reticular nucleus). Ppt heavily influences T and S.d, particular S.cin (acetylcholine interneurons of S.d) with ACh and glutamate projections [Morgenstern and Esposito 2024]. Contrariwise, Ppt ACh signals deviation from exception [Zhang S et al 2024]. Because Ppt is highly internal connected with all ACh, glutamate, and GABA [Hormigo et al 2018], these sub-functions don’t appear to be independent modules.

Simulation

The simulation update itself turned out to be fairly minor, without any externally visible effects. Essentially, it ended up refactoring updates from the Hb-R.ip avoidance path through T.pf and the H.stn-Snr complex. Although it’s a significant architectural change, at least currently with the simple left vs right decisions, there’s no real functional change.

One question is whether the simulated H.stn-Snr circuit is for commitment or for choice. The actual H.stn-Snr is used for both, but the sub-functions may use different circuits. As I explored in essay 42, commitment is more primitive because commitment without a sophisticated choice system is useful, but choice without the ability to commit is useless.

It’s tempting to use Ppt as a central critical node, because it’s at the intersection of multiple functionality, but Ppt can be lesioned without eliminating decision. So it may be important in a modulatory sense, but it is not essential for functionality.

In the current simulation, H.stn and Snr are functionally indistinguishable. There’s currently no reason to have separate modules that distinguish between them. This may be because the current decision is simply right vs left, and later complexity will show the need for distinct areas. Alternatively, it may be that at the level of abstraction for the simulation, there is no need to separate the two into separate modules.

Discussion

The essay has two main aims: see if BG could be broken apart into simpler, but still useful subregions, preferably with more local developmental origins instead of the sprawling multi-region mammal BG; and see if BG could form the foundation of a consensus circuit linking disjoint action paths. This basic idea seems solid, but there are many interesting open questions about the details, because there are almost too many potential kernels of a proto-vertebrate BG, and it’s unclear how to select which ones are more likely.

The [Kamali Sarvestani et al 2011] model splits the BG into a striatum domain and a H.stn, Snr, and Pge arbitration domain centered on H.stn. That paper considered evidence from the mammalian BG, and I think the anamniote (amphibian, lamprey, and fish) BG adds supporting evidence to their model. Although missing in mammals, a major S.d output in anamniotes modulates M.pt obstacle avoidance and OT visual hunting without involving H.stn, Snr, or Ppt [Marin et al 1997]. This second striatum output path raises the possibility of the S.d to M.pt to OT being primitive, and the S.d to H.stn, Snr as a secondary improvement.

The [Coizet et al 2024] model examines even smaller subcortical BG loops with Snr and H.stn as joining with OT, R.pb, and M.pag as independent loops. In this essay, I focused more on the Hb-R.ip and R1.a temporal chemotaxis path and V.pt to MLR spatial chemotaxis paths, because the simulation uses those action paths more prominently. The general idea seems solid, despite the change in focus nodes. Simpler brainstem loops with a subset of BG.

The consensus aspect of the essay has fewer studies that I’ve found so far. [Jeon H et al 2022] studied cortical BG loops, focusing on H.stn as a central integrating hub, describing the system as “everyone talks and everyone listens.” I think the same description could apply to subcortical loops. For the essay simulation, the consensus circuit is the more driving need. As I mentioned in the previous essay 44, the integration of multiple action paths, including hypothalamic food-zone drivers, seek action paths, distinct avoidance-of-return paths, and obstacle avoidance was becoming increasingly ad hoc, even for a relatively simple animal. A consensus system allows better integration and likely more extensibility.

Snr complications

Although the essay uses Snr as part of the consensus system, the Snr output is mostly disjoint, not collateralized. [McElvain et al 2021] find disjoint output pools, including distinct OT.m (medial OT), OT.c (central OT), OT, R.pn.o (aka R1.a), R.my (medulla reticulum), V.dr (dorsal raphe), M.ic (inferior colliculus – auditory and lateral line). They find that all these pools do collateralize with Ppt, T.il (including T.pf), and T.mo (motor thalamus), but not across pools. For the essay, this result argues against a general “turn left” (or “avoid right”) consensus Snr, and more for individual “turn left” for R1.a and OT.

Additionally, the mammalian Snr is itself a chimera formed from both R1 hindbrain progenitors and midbrain progenitors [Partanen and Achim 2022], [Mendelsohn et al 2024]. These multiple Snr types have different origins and distinct genetic transcription factor development, and each type has multiple subtypes.

Somewhat independently, Snr can be divided into gad2 and PV subtypes. The Snr gad2 subpopulation drives more connected to midbrain and hindbrain motor areas and receives more input from non-BG sources (only 38% of inputs from BG) [Liu D et al 2020]. Gad2 is also associated with sleep and rest [Liu D et al 2020]. So an additional potential Snr origin story could be sleep neurons appropriated by decision systems. The Snr PV subpopulation is more specifically driven by BG (75% of inputs) and its output is more focused on midbrain and thalamus [Liu D et al 2020]. OT.l (crossed) has more Snr PV input and OT→H.stn connection is only from OT.l, not OT.m.

Presumably, the proto-vertebrate had only a single Snr system. The hindbrain R1 and gad2 seems more likely, with midbrain and PV as enhancing decision-making. Unfortunately, there’s no data to support that speculation. Because the majority of studies are mammalian, some of these Snr systems may be mammalian innovations, obscuring a simpler proto-vertebrate system.

Mammalian bias for H.stn, Snr, and Ppt

Almost all of the studies for the essay are mammalian studies of H.stn, Snr, and Ppt. When the aim of the essay is exploring proto-vertebrate origins of BG, excluding data from anamniotes: amphibian tadpoles, fish, or lampreys is a major flaw. Homologues for H.stn, Snr, and Ppt exist for those animals, but they are either poorly studied, or I just haven’t found the studies. This absence is important for both Snr and Ppt.

As mentioned above, the mammal Ppt is playing too many roles to understand what its core, original function might have been. An attention system like R.is, or a MLR function, a lateral inhibition like Snr, or even a decision threshold system connected to DA are all plausible. Ppt studies from lampreys, amphibian tadpoles, and fish might show a single, simpler function or at least a smaller system like an MLR with an associated ACh attention system.

The mammalian Snr is also highly heterogenous both in development and function. Studies from lampreys, tadpoles, or fish might distinguish conserved Snr areas from mammalian innovations. The distinct M.pt to OT path in anamniotes might mean that the Snr-like path is simpler than mammals and possibly more functionally focused.

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44: Breadcrumb odor search

In the simulation, food search has two phases: a roaming phase, which is a correlated random walk, and a seek phase which climbs an odor gradient to food. Seek is very efficient, although it does require a timeout to handle false odor plumes, but roaming is essentially a random walk, leaving lots of opportunities for improvement. One possible improvement is reducing repeated search by avoiding already searched areas.

Evolutionary own-trail avoidance

Some of the earliest bilaterian fossil trails show the crawling animals avoiding crossing their own trail [Sims and Kiverstein 2022], suggesting this optimization existed in even the earliest bilaterians. The fossil trails also show wall-following (thigmotaxis). By combining own-trail avoidance, wall-following, and u-turns the bilaterians generated spiral-like paths that efficiently searched the local area.

The communal unicellular slime mold Physarum polycephalum leaves a trail of slime as it moves and the slime mold avoids its own trail [Reid et al 2012]. Physarum has been studied as solving complex search like the traveling salesman problem and maze escape. Even a simple animal can implement own-trail avoidance. Robot navigation and mapping has experimented with own-trail avoidance [Balch 1993]. Ants use pheromones to make trails to food [Jackson et al 2006], which is essentially an external memory for navigation.

The simulated animal represents a chordate proto-vertebrate, and the proto-vertebrates were freely swimming filter feeders, which essentially precludes leaving an odor trail because water currents would immediately disturb the odors. For the sake of this essay, I’m ignoring this practical implausibility, because I’m interested in how memory might use existing proto-vertebrate avoidance circuits. Using breadcrumbs as external memory can be a prelude to neural internal memory [Sims and Kiverstein 2022].

Odor avoidance

Odor trail avoidance could use at least two direct action paths in the proto-vertebrate brainstem. One path goes through Hb.mv (medial ventral habenula) to R1.a (anterior hindbrain motor area), and another path goes through V.pt (posterior tuberculum) to MLR (midbrain locomotor region) to R5.rs (hindbrain reticulospinal motor). Hb.mv, R1.a, MLR, and R5.rs are all highly conserved areas in vertebrates, while V.pt is likely conserved as the equivalent to mammalian midbrain dopamine Vta (ventral tegmental area) and Snc (substantia nigra pars compacta). Other action paths exist using the cortex, but to keep the animal simple, I’m still postponing all cortical circuits.

In lampreys, the Ob.m (medial olfactory bulb) projects direction to Hb.m (medial habenula) [Stephenson-Jones et al 2012], [Suryanarayana et al 2021]. Zebrafish Ob also projects to right Hb.d (Hb.mv in mammals) to R.ip.v (ventral interpeduncular nucleus, R.ip.m medial R.ip for mammals) [Miyasaka et al 2014], [Choi JH et al 2021], [Krishnan et al 2014], [Turner 2016] which can support chemotaxis to avoid odors [Choi JH et al 2021], [Krishnan et al 2014].

The R.ip.v (R.ip.m for mammals) is interconnected with R1.a for motor and can drive taxis avoidance, including chemotaxis [Chen WY et al 2019], phototaxis [Chen X and Engert 2014], and chemotaxis [Palieri et al 2024].

Diagram illustrating neural circuitry involving the olfactory bulb (Ob.m), medial habenula (Hb.mv), interpeduncular nucleus (R.ip.m), ventral raphe (V.mr), and anterior hindbrain motor area (R1.a) for sensory processing and motor output.
Possible negative chemotaxis for breadcrumb avoidance using the lamprey odor to habenula path. Hb.mv (medial ventral habenula), Ob.m (medial olfactory bulb), R1.a (anterior hindbrain motor area), R.ip.m (median interpeduncular nucleus), V.mr (median raphe).

Tetrapods do not have a direct Ob to Hb connection, in contrast to the lamprey and possibly fish. In a the fire-bellied toad, a basal amphibian, the Ob only projects to the habenular commissure but not to Hb itself [Freudenmacher et al 2020]. Similarly, mammals do not have a direct Ob projection to Hb.mv. Instead, Hb.mv is almost entirely driven by posterior P.se (septum) [Viswanath et al 2014], [Yamaguchi et al 2013], [Choi K et al 2016], which is mainly driven by E.hc (hippocampus). This mammalian upgrade from direct Ob sensory input to cognitive E.hc input is a major reason I’m using this Hb.mv to R.ip.m path for the essay.

V.mr (median raphe) will be important fr this essay to detect transition from roaming to avoidance, allowing U-turns or directional turns only at border crossings. When the animal first enters the avoidance odor plume, it should turn away, but it shouldn’t continue turning while it’s inside the plume.

Odor seek

I’m treating the section path through V.pt as a seek action path because of its resemblance to the Vta/Snc connectivity with MLR, and the Ob to V.pt can drive movement [Derjean et al 2014], but I haven’t seen a study showing seek functionality. In lampreys Ob.m projects to V.pt [Derjean et al 2014], which drives MLR, which drives R5.rs (hindbrain reticulospinal motor neurons) [Beauséjour et al 2022]. Zebrafish Ob.m projects to V.pt [Imamura et al 2020].

A diagram illustrating the neural pathways involved in olfactory processing and locomotion, highlighting connections between various brain regions including Ob.m, V.pt, MLR, and R.rs.
Possible odor-seek path in lampreys and fish. MLR (midbrain locomotor), Ob.m (medial olfactory bulb), OT (optic tectum), R.rs (mid-hindbrain reticulospinal motor), V.pt (posterior tuberculum).

For this essay, I’m interpreting this circuit as a seek system to approach food odors. Because MLR is highly interconnected with OT (optic tectum), I’m considering this system as “tectal” although I’m not actually using OT for this essay.

An alternative breadcrumb path

An alternative path for memory could use Hb.lm (medial Hb.l – lateral habenula), which projects to V.mr.glu (glutamate V.mr) and Vta.pm (posterior-medial Vta). Vta.pm drives RTPA (real time place avoidance through S.msh.v (ventral S.msh – medial shell of the ventral striatum). V.mr.glu drives E.hc (hippocampus) theta through P.msdb (median septum and diagonal band), which can also drive RTPA itself.

Memory for avoiding repetition is the underlying goal here, but this essay is focused on a fictional breadcrumb odor, in part because the path is simpler. Although Hb.lm produces avoidance like Hb.mv, it’s more complicated to explain where the Hb.lm signal comes from. In contrast the lamprey Hb.mv is directly driven by Ob.m.

A diagram illustrating the neural circuit involving the medial habenula (Hb.lm), ventral tegmental area (Vta.pm), and associated pathways, depicting connections to regions such as V.mr.glu and E.hc.
Possible memory avoidance paths using the habenula, hippocampus and basal ganglia. E.hc (hippocampus), Hb.lm (medial lateral habenula), P.msdb (median septum and diagonal band), S.msh.v (ventral medial shell of the ventral striatum), V.mr.glu (median raphe glutamate projection), Vta.pm (posterior medial ventral tegmental area).

The above diagram shows a possible mammalian path for memory-based avoidance. Hb.lm is driven by S.msh (medial shell of the ventral striatum), which is associated with place preference and avoidance. Because the animal is avoiding already explored areas, this is a possible action path for mammals. However, that memory-based system requires far more neural machinery than the essay’s proto-vertebrate allows.

Medial habenula

For context (but not strictly needed for this essay), Hb.m has two areas with distinct circuits, although in mammals these two areas further subdivide into five subareas. In lampreys and fish Hb.d (mammal Hb.m) is asymmetrical. In fish, odor goes to the right Hb.m, and light input goes to the left Hb.m. The right odor input is used for chemotaxis [Chen R et al 2023], [Chen WY et al 2019], such as food seeking or avoiding predators. The light input is used as a landmark for body and head direction [Lavian et al 2024], such as using the sun as a compass.

A diagram illustrating the neural circuitry related to navigation, including connections between the habenula, direction pathways, and avoidance systems, with inputs from light and odor.
Median habenula divisions dorsal and ventral with their respective inputs and outputs. The dorsal Hb.m is for landmarks and head direction and the ventral Hb.m is for taxis, including chemotaxis and thermotaxis. Hb.md (dorsal Hb.m – medial habenula), Hb.mv (ventral Hb.m), P.bac (bed nucleus of the anterior commissure), P.ldt (laterodorsal tegmental area), P.ts (triangular septum), R1.a (anterior hindbrain motor area), R.dta (dorsal tegmental area), R.dtg-vtg (dorsal tegmental area of Gudden, ventral tegmental area of Gudden), R.ip.l (lateral R.ip – interpeduncular nucleus), R.ip.m (median R.ip), R.nin (nucleus incertus), V.mr (median raphe).

Taxis and landmark information use different areas of R.ip. Taxis uses R.ip.m (median R.ip in mammals, ventral R.ip in fish) [Krishnan et al 2014], and direction uses R.ip.l (lateral R.ip in mammals, dorsal R.ip in fish) [Lavian et al 2024]. R.ip.l and R.ip.m correspondingly project differently. R.ip.l is interconnected with directional nuclei in R.dta (dorsal tegmental area) such as R.dtg (dorsal tegmental nucleus of Gudden) for head direction, R.vtg (ventral tegmental nucleus of Gudden), and R.nin (nucleus incertus) for eye direction. R.ip.m is connected with motivational areas such as V.mr, P.ldt (laterodorsal tegmentum) and the motor R1.a.

In mammals, Hb.m only receives input from the posterior septum, specifically P.bac (bed nucleus of the anterior commissure), P.ts (triangular septum), P.sf (septofimbrial nucleus), and P.ms (median septum) [Juárez-Leal et al 2022]. These septal areas are largely driven by E.hc. This indirect, cognitive hippocampal input for mammals contrasts with the direct sensory input for fish and lampreys.

Full habenula

For further context, Hb.l (lateral habenula) also divides into two major areas, which further subdivide into nine subnuclei. Hb.lm (medial Hb.l) will likely be important soon because it’s an avoidance path that projections directly to V.mr and Vta.pm motivational avoidance areas, but it’s not yet important for this essay. Hb.lm is important for avoidance and Hb.ll (lateral Hb.l) for failure. Hb.ll.ov (oval sub nucleus of Hb.ll) is highly studied for its role in dopamine motivation and learning, and its inputs are specific to Hb.ll.ov, which contrasts with other Hb.l inputs that are more diffuse.

Zebrafish Hb.v (Hb.l in mammals) only projects to the serotonin are V.mr, but not to dopamine areas [Agetsuma et al 2010]. Because lamprey Hb.l does project to dopamine as well as serotonin areas [Stephenson-Jones et al 2012], the zebrafish may be a secondary loss, but it does suggest that V.mr is more critical to Hb.l than the dopamine projection.

A diagram illustrating the neural circuits involved in memory-based avoidance and navigation in a proto-vertebrate, including various pathways related to odor, light, and direction, with connections to specific brain areas such as the habenula and reticular formation.
Functional connectivity of the habenula. H.l.glu (lateral habenula glutamate projection), Hb.ll (oval nucleus of the lateral Hb.l – lateral habenula), Hb.lm (medial Hb.l), Hb.md (dorsal Hb.m – medial habenula), Hb.mv (ventral Hb.m), P.bac (bed nucleus of the anterior commissure), P.epn (endopeduncular nucleus), P.ldt (laterodorsal tegmental area), P.ts (triangular septum), R1.a (anterior hindbrain motor area), R.dta (dorsal tegmental area), R.dtg-vtg (dorsal and ventral tegmental nuclei of Gudden), R.ip.l (lateral R.ip – interpeduncular nucleus), R.ip.m (medial R.ip), V.mr (median raphe), Vta.l (lateral Vta – ventral tegmental area), Vta.pm (posteromedial Vta).

The above diagram shows a functional diagram of Hb and some of its inputs and outputs. This essay uses Hb.mv avoidance taxis for avoid the breadcrumb odor. The next essay may use Hb.lm avoidance (non-taxis avoidance) for place avoidance memory. Hb.md landmark and Hb.ll failure are not currently used in the simulation, but may become important soon.

Simulation

The essay’s simulation has the animal searching for food using a correlated random walk as its base search strategy. Adding breadcrumbs for the animal’s own path could potentially improve the search by avoiding re-searching old areas. The simulation uses an Ob to Hb.m path, which then drives R1.a motor area. If the animal detects a breadcrumb, it turns away from its current path.

Diagram illustrating the neural pathways involved in navigation and motor control, featuring connections from the olfactory bulb to the habenula, raphe area, and hindbrain motor areas.
Simulation modules for the breadcrumb negative taxis. Hb.mv (ventral Hb-m – medial habenula), Ob.m (medial olfactory bulb), R1.a (anterior hindbrain motor area), R.ip (interpeduncular nucleus), V.mr (median raphe).

The above diagram shows the simulation modules in this breadcrumb avoidance action path. HbTaxis includes both Hb.m and R.ip. The Raphe module represents V.mr and stores the current for a short time on the order of a second. The animal should only make a U-turn if it newly encounter its trail. If it’s already avoiding the trail, it should move ballistically. The Raphe module maintains the current avoidance action to enable boundary-only turns.

A simulation diagram showing a purple blob representing a moving object, with a food target (green star) in the center of a bounded area. A red trajectory indicates the path taken by the object.
Screenshot of the animal seeking food in an open field. The teal star represents food, the teal circle represents its odor plume, and the purple circles represent the breadcrumb trail.

Simulation roam

Roaming is driven by circadian wake and by a FoodZone detection, as used in essay 43. Parts of H.l respond to the animal entering a food zone [Jennings et al 2015]. For this essay, H.l HypMove drives roam when outside a food zone and pauses inside a food zone for filter feeding. HypMove represents the SLR (subthalamic / hypothalamic locomotor region), which is part of H.l [Ji C et al 2024].

Flowchart illustrating signal pathways in a simulation model for a food-seeking behavior in a fictional proto-vertebrate, showing inputs like 'FoodZone' and motor outputs.
Simulation modules for roaming. Wake and hunger drives roaming, which stops when the animal reaches a food zone. H.l (lateral hypothalamus), H.scn (suprachiasmatic nucleus – circadian), N.sp (spinal cord), P.bst (bed nucleus of the stria terminalis), SLR (subthalamic motor region), S.ls (lateral septum), R1.a (anterior hindbrain motor area).

Importantly, the roaming signal needs to disable breadcrumb avoid. If the animal is in a food zone, any roaming optimization needs to stop when roaming stops. In the essay’s stimulation, I’m using R1.a HindMove as an integration point for roaming motivation with the chemotaxis.

Simulation seek

The breadcrumb avoidance needs to coordinate with the Seek module. Seek follows a target odor toward food, essentially chemotaxis. The Seek module implements a bilateral, directional seek. In lamprey the V.pt receives direct input from Ob and projects to MLR [Derjean et al 2010], [Beauséjour et al 2022], [Beauséjour et al 2024], which drives locomotion through R5.rs.chx10 (mid-hindbrain reticulospinal) [Cregg et al 2020]. The Seek module is enabled by HypMove, which represents H.l, in particular its roaming signal.

A flowchart illustrating the neural pathways involved in seeking behavior, detailing connections from the olfactory bulb (ObGlom) to various motor control centers, including Striatum, MidMove, and HindMove.
Simulation modules for the seek action path, directly driven by olfactory input. H.l (lateral habenula), MLR (midbrain locomotor region), N.sp (spinal cord), Ob.m (medial olfactory bulb), S.lsh (lateral shell of the ventral striatum), R5.chx10 (mid-hindbrain locomotor region), V.pt (posterior tuberculum).

The Seek module uses an entirely different locomotion action path than the breadcrumb’s avoid action path. Seek drives MidMove, representing MLR, which projects to R5.rs.chx10 (mid-hindbrain reticulospinal motor area), which is distinct form the R1.a motor area. In contrast the breadcrumb taxis used HbTaxis to the HindMove R1.a module. These two action paths only directly interact at the spinal cord motoneurons. Because there’s not central node that manages these two action paths, they need to inhibit each other as a distributed system.

Importantly, the Seek module needs a timeout to avoid perseveration. I’m using the striatum as a timeout system, as I’ve done in that last few essays. The striatum region would likely correspond to the mammalian S.lsh (lateral shell of S.v – ventral striatum) or S.core (core of S.v) because those are involved with seeking, as opposed S.msh (medial shell of S.v), which is more involved with place.

A diagram showing a simulated animal's path in a maze-like environment, including a dark area, an odor plume highlighted in light blue, and a food target represented by a teal star.
Screenshot of the U-trap scenario as the animal times out its seek. The teal star represents the food zone and the teal disk represents its odor plume.

The above screenshot shows the animal just after the striatum timeout expire. The circular teal area is an odor plume, the teal star is the food zone, and the beige walls are barriers. While Seek is active, the animal struggles against the barrier to try to follow the odor plume. When the striatum expires, the animal returns to its roaming.

Monte Carlo results

I updated the simulation framework to enable Monte Carlo experiments without using the graphical view. Each scenario timed the animal searching, finding, and eating food with success defined as nutrients in the animal’s gut. The scenarios executed 200 times. The two scenarios maps were an open field and a U-shaped trap. Each map had a scenarios with a large seek odor plume and a scenario without an odor plume.

Box plot comparing results for roaming and trail strategies in an open field and trap scenarios, with additional histogram for open field roam.
Monte Carlo results comparing roaming without breadcrumb avoidance against trail avoidance.

Although the breadcrumb trail shows a small improvement in the open field, it’s a minor difference. For this simple implementation there isn’t a huge gain with the breadcrumbs. It’s possible that a better implementation would improve the results, but this essay was looking for large gains from a simple change.

The breadcrumb strategy did avoid crossing the animal’s trail more than the roaming-only strategy, but often the breadcrumbs pushed the animal away from the goal. If the animal made a mistaken turn away from the goal, the trail-avoidance would exacerbate that mistake by driving the animal to search further away from the goal. In contrast the default roam would often reverse its mistake.

The seek trap scenario found that striatum timeout with avoid was better than timeout that just disabled seek. If that result generalizes, it might help explain why the S.v (ventral striatum) output region P.v (ventral pallidum) produces avoidance when triggered by S.d2 (striatum projection neurons with D2.i inhibitory dopamine receptors) indirect path.

The seek trap also showed the need for progressively increasing timeout. Because the timeout recovery time is currently fixed, the animal could restart seeking before exiting the trap, producing a cycle of seek and timeout. The current striatum timeout matches the adenosine building on the timeframe of 120s to 180s, but it doesn’t include longer term plasticity. Plasticity would progressively increase the timeout on the order of 20 minutes to an hour.

Issues raised by the simulation

The simulation raised several issues because it integrated multiple action paths that I’d previously implemented independently.

  • The breadcrumb avoid in Hb-R.ip should respect the roam and food zone calculated in H.l.
  • The breadcrumb avoid is distinct from chemotaxis avoid such as avoiding predator odor, which is also in the Hb-R.ip circuit.
  • How does the breadcrumb avoid interact with ARTR (anterior hindbrain turning region)?
  • How does the R.pb (parabrachial) toxic-environment avoid interact with the Hb-R.ip taxis avoid?
  • How does V.rn (serotonin raphe nuclei) interact with Hb-R.ip and R1.a? These regions are highly interconnected.
  • Avoid itself should have a timeout. S.msh.v and Vta.pm are activated for avoidance and could serve as an avoidance timeout.
  • Seek (V.pt) uses a different MLR action path and mid-hindbrain R5.rs than the anterior hindbrain R1.a motor output used by SLR roam and Hb-R.ip avoidance. How is this conflict managed? In the lamprey, inhibiting SLR does not affect the Ob to MLR to R5.rs action path [Derjean et al 2010].
  • Seek needs to stop when roaming stops for a food zone.
  • Seek timeout needs to progressively increase when the initial timeout is insufficient to escape the U-trap.

Roam vs seek action paths

I’m treating the roam action path as distinct from the seek path. Roam uses Hb.m → R.ip → R1.a using SLR, but seek uses V.pt → MLR → R5.rs.chx10. These two paths use similar input from innate-odor Ob.m and final output N.sp (spinal motoneurons), but everything else is independent. I’m associating the roaming path with limbic areas and seek path with tectal-associated areas, but OT (optic tectum) is not part of the essay’s simulation. The important issue here is how the two paths interact.

For the seek path I’m using the lamprey V.pt as a proto-vertebrate seek precursor to the mammalian Vta.l and S.lsh seek system.

Flowchart illustrating the interaction between the roam and seek modules in a neurobiological simulation. It shows connections between brain regions responsible for navigation and movement, labeled with abbreviations for specific circuits and pathways.
Subcircuit showing the distinct action paths for roaming and seeking. Roaming is associated with SLR and limbic areas, and seeking is associated with MLR and tectal-associated areas. Hb.mv (ventral medial habenula), MLR (midbrain locomotor region), N.sp (spinal motoneurons), Ob.m (medial olfactory bulb), P.ldt (laterodorsal tegmental area), R1.a (anterior hindbrain motor region), R5.chx10 (mid-hindbrain motor region), V.pt (posterior tuberculum).

Studies involving nicotine addiction have identified an inhibitory path in mammals from R.ip avoidance via P.ldt (laterodorsal tegmentum) and the Vta to S.lsh circuit [Wolfman et al 2018], [Kim K and Picciotto 2023]. R.ip ⊣ P.ldt → Vta.l → S.lsh. R.ip inhibits P.ldt, which inhibits Vta.l phasic dopamine, which inhibits seek.

For the simulation, I’m using P.ldt as an inhibitory path from HbTaxis to inhibit Seek. In mammals P.ldt and Ppt (pedunculo-pontine tegmentum) are distinct but related areas, but non-mammal studies do not show distinct areas, at least for the studies I’ve read. I’m assuming a proto-vertebrate would have a single Ppt/P.ldt complex. Ppt is either part of the MLR or at least highly associated with it, and Ppt is highly interconnected with OT.

Simulation model

The Hb.m roam and V.pt seek action paths described above need to interact with the hunger and food-zone driving input from H.l HypMove. In this system, H.l HypMove drives both R1.a and V.pt. In mammals H.l as SLR drives R1.a for roaming [Ji C et al 2024]. Mammalian H.l is also strongly interconnected with Vta.

Diagram illustrating the interaction between roam and seek action paths in a simulated animal searching for food, highlighting motor areas and sensory inputs.
Roaming and seek action path interaction in the simulation. H.l (lateral hypothalamus), Hb.mv (ventral Hb.m – medial Habenula), MLR (midbrain locomotor region), N.sp (spinal cord motoneurons), Ob.m (medial olfactory bulb), OT (optic tectum), P.ldt (laterodorsal tegmentum), R1.a (anterior hindbrain motor), R5.chx10 (mid-hindbrain motor), R.pb.l (lateral parabrachial), SLR (subthalamic locomotor region), S.lsh (lateral shell of S.v – ventral striatum).

The R.pb.l tactile toxic avoidance needs to interact with the R1.a roaming circuit. The simulation’s R.pb.l RpbAvoid drives avoiding in R1.a HindMove, which is almost certainly incorrect. R.pb drives avoidance for place-specific irritations like itch. This R.pb itch-avoidance projection is to hypothalamic nuclei such as H.pv and H.l, and is distinct from R.pb projections for S.a (central amygdala), and P.bst (bed nucleus of the stria terminalis), which functionally handles food-related issues like sickness. In the diagram, the dotted line from RpbAvoid to HypMove does not currently exist in the simulation, but I will need to change that connectivity in a later essay.

Discussion

The experiment explored if a simple breadcrumb odor could improve searching for food. The breadcrumb odor drives an avoidance circuit in R1.a using the same avoidance action path as for predator odors with Hb.m to R.ip. The essay’s implementation did not show a significant improvement from roaming random walk.

One possibility is that this result is accurate and a simple breadcrumb trail is not an improvement over random walk for this scenario. The breadcrumb avoids crossing the animal’s own path. When the animal makes a wrong choice away from the food, this avoidance can exacerbate the error by forcing the animal to continue searching further away instead of crossing the trail to correct the mistake.

Another possibility is that the essay’s implementation is too simplistic or is broken. While possible or even likely, I’d have expected that if breadcrumbs provide an immediate large improvement, that even a flawed implementation would show significant gains.

The most significant improvement for seeking was the timeout and subsequent avoidance when the animal gave up seeking the odor. This timeout avoidance was more effective than the breadcrumb avoidance of the seek, and both were more effective with giving up and resuming roam without an avoidance phase. The striatum as a timeout and memory device is both simpler than a complicated mental breadcrumb system and potentially more effective.

References

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Chen R, Xu X, Wang XY, Jia WB, Zhao DS, Liu N, Pang Z, Liu XQ, Zhang Y. The lateral habenula nucleus regulates pruritic sensation and emotion. Mol Brain. 2023 Jun 27;16(1):54. 

Chen WY, Peng XL, Deng QS, Chen MJ, Du JL, Zhang BB. Role of Olfactorily Responsive Neurons in the Right Dorsal Habenula-Ventral Interpeduncular Nucleus Pathway in Food-Seeking Behaviors of Larval Zebrafish. Neuroscience. 2019 Apr 15;404:259-267.

Chen X, Engert F. Navigational strategies underlying phototaxis in larval zebrafish. Front Syst Neurosci. 2014 Mar 25;8:39. 

Choi JH, Duboue ER, Macurak M, Chanchu JM, Halpern ME. Specialized neurons in the right habenula mediate response to aversive olfactory cues. Elife. 2021 Dec 8;10:e72345.

Choi K, Lee Y, Lee C, Hong S, Lee S, Kang SJ, Shin KS. Optogenetic activation of septal GABAergic afferents entrains neuronal firing in the medial habenula. Sci Rep. 2016 Oct 5;6:34800. 

Cregg JM, Leiras R, Montalant A, Wanken P, Wickersham IR, Kiehn O. Brainstem neurons that command mammalian locomotor asymmetries. Nat Neurosci. 2020 Jun;23(6):730-740. 

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Freudenmacher, L., Schauer, M., Walkowiak, W., & von Twickel, A. (2020). Refinement of the dopaminergic system of anuran amphibians based on connectivity with habenula, basal ganglia, limbic system, pallium, and spinal cord. Journal of Comparative Neurology, 528(6), 972-988.

Imamura F, Ito A, LaFever BJ. Subpopulations of Projection Neurons in the Olfactory Bulb. Front Neural Circuits. 2020 Aug 28;14:561822. 

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Jennings JH, Ung RL, Resendez SL, Stamatakis AM, Taylor JG, Huang J, Veleta K, Kantak PA, Aita M, Shilling-Scrivo K, Ramakrishnan C, Deisseroth K, Otte S, Stuber GD. Visualizing hypothalamic network dynamics for appetitive and consummatory behaviors. Cell. 2015 Jan 29;160(3):516-27. 

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43: Filter-feeding and Roaming

I’m revisiting feeding, because it’s central to the vertebrate brain’s organization, redoing essay 23: feeding, essay 27: feeding state machine, essay 36: R.pb as tunicate brain, and essay 38: food zone. For this essay, I’m leaning harder into the proto-vertebrate as a filter feeder [Mallat 2021], similar to the chordate amphioxus [Chung J et al 2023]. Proto-vertebrate filter feeding is essentially breathing, and vertebrate breathing itself developed from filter feeding [Li S and Wang F 2021]. This filter feeding circuitry is distinct from the jawed vertebrate searching for small morsels of food and quickly eating them, which is a more action-oriented process.

I’m focusing again on the transition between locomotion and feeding, but this time using the DLR (diencephalic locomotor region) and introducing opioids as a feeding signal. To keep the system manageable, I’m disabling the seek system, such as chemotaxis, and only using a simple random walk roaming search. The whole system can then be reduced to switching between a roaming search phase and a resting, filter-feeding stage.

Filter-feeding state machine

Consider a simple proto-vertebrate filter-feeder, similar to amphioxus [Chung J et al 2023] or an ascidian that continued locomotion through adulthood. Unlike ascidians that lose locomotion [Osugi et al 2017], the proto-vertebrate would alternate filter feeding in a location with moving to a new location. The animal might move because the filter feeding didn’t produce any nutrients or because of a noxious environment or to avoid a predator.

Because the proto-vertebrate is no simple, it might use the same system as ascidians to choose a filter feeding place: either finding odor, taste, and touch that indicates a good place to stop, or timing out and settling for the current place if it hasn’t found an ideal place.

Minimal filter feeding behavior, switching between a locomotor search phase and a sedentary filter feeding stage. The labelled neuropeptides are suggestions for managing the state transitions. A2a.s (adenosine Gs receptor), DA (dopamine), DOR.i (δ-opioid Gi receptor), MOR.i (μ-opioid Gi receptor), npy (neuropeptide Y), tac1.q (tachykinin 1 Gq receptor).

The above state diagram shows a minimal behavior for a simple filter feeder. The search for food can time out with A2a.s (adenosine receptor), or it can halt earlier if a food zone is found with DOR.i (δ-opioid Gi inhibiting receptor for enkephalin). Filter feeding ends continues as long as the feeding produces food, signaled by MOR.i (μ-opioid Gi receptor). The animal leaves the feeding place and filter feeding ends if the environment is hazardous with tac1.q (tachykinin 1 Gq receptor for substance P) or when filter feeding doesn’t produce food, and the animal remains hungry, signaled by NPY (neuropeptide Y). Similarly, if the search state has a promising seek target, DA (dopamine) extends the search.

Expanding the filter feeding state machine

The filter feeding state can be the main state, such as tunicate ascidians committing to sessile filter feeding as adults. Since adult ascidians are sessile, filter feeding is the only state. The proto-vertebrate may have similarly spent almost all of its time filter feeding or resting, only moving when necessary to avoid environment hazards, or predators, or if the filter feeding is unsuccessful.

Simple filter feeding behavior.

I’ve distinguished the avoiding path from the give-up path because they have very different internal logic. Avoidance is driven by external senses, but giving up is internal, comparing expected food intake with the actual eating results. Because an initial sampling phase does not yet generate nutrients, the system must sustain the sampling phase even without feeding back, but it must also timeout eventually if the feeding place is unsuccessful.

Opioids as suppressing search

The opioid peptides and receptors are a vertebrate novelty. Neither amphioxus nor tunicates show either the opioids or their receptors, and invertebrates also lack these [Dreborg et al 2008], [Huang et al 2022]. The four opioid peptides and receptors (pomc with MOR, penk with DOR, pdyn with KOR, pnoc with NOR) exist in all vertebrates and likely divided from a single opioid paired with a single receptor [Larhammar et al 2015], [Stevens 2009] during the two whole genome duplication events between tunicates and vertebrates [Dreborg et al 2008].

In mammals the MOR.i receptor exists across the entire brain [Le Merrer et al 2009] and is broadcast in ventricle CSF (cortical spinal fluid) [Veening et al 2012] and the bloodstream through the pituitary [Veening et al 2012]. However, the matching opioid β-endorphin is only produced in three places, H.arc (hypothalamus arcuate nucleus), H.pit (pituitary gland), R.nst (nucleus of the solitary tract in hindbrain). Before the genome duplication events, the proto-vertebrate likely had only a single opioid and paired receptor. The timing for β-endorphin is seconds to minutes in CSF and 30 minutes or more for peripheral [Veening et al 2012].

For the purposes of filter feeding, I think it’s reasonable to treat proto-vertebrate MOR as mainly through CSF with a relatively long time of minutes to an hour. Because the proto-vertebrate brain would have been smaller, many or most of brain areas would be adjacent to the CSF [Vígh et al 2004] and might use MOR as a broadcast peptide.

Many locomotor regions are inhibited by eating and often have MOR.i receptors. H.sum (supramammillary nucleus) is associated with movement, exploration, and avoidance and is suppressed while eating. Subsets of H.l.g (lateral hypothalamus gaba neurons) sensitive to leptin (a fat-sensing satiation peptide) is suppressed while eating [Petzold et al 2023]. H.l.ox (lateral hypothalamus orexin area) is associated with arousal and seeking and is suppressed while eating. H.arc AgRP (arcuate with AgRP peptide) is active before feeding, associated with hunter, and suppressed at contact with food [Altafi et al 2024]. V.lc (locus coerulus – noradrenaline source) is suppressed during mammal licking [Fan W et al 2024]. S.v (ventral striatum) is inhibited while eating and inhibiting S.v increases eating. H.l may be a central node in the transition between seeking and eating [Kongstorp et al 2025]. Food presentation suppresses R.pb CGRP (parabrachial nucleus CGRP alarm peptide) [Carter et al 2013].

Roaming drive from H.arc AgRP/NPY

A voluntary search for food needs to be driven by some specific process. While hunger is a driving force, the circadian rhythm seems to be the primary driver, modulated by hunger [Sayar-Atasoy et al 2023]. In the mammal hypothalamus, H.scn (suprachiasmatic nucleus) is the main circadian driver, with H.dm (dorsomedial hypothalamic nucleus) and H.l orexin as other important nodes. For the hunger circuit, circadian drives the hunger circuits in H.arc and H.pv (paraventricular hypothalamus). These circadian and hunger systems drive roaming circuits in H.l and eating circuits in R.pb.

Circadian and hunger circuit driving food search and eating. Nuclei above are loosely grouped into circadian, hunger, roaming food search, and eating circuits. H.arc.agrp (arcuate hypothalamus), H.dm (dorsomedial hypothalamus), H.l (lateral hypothalamus), H.scn (suprachiasmatic nucleus), H.pv (paraventricular hypothalamus), R1.a (anterior hindbrain), R.pb.l (lateral parabrachial nucleus), R.nst (nucleus of the solitary tract).

The above diagram shows major nodes in the circadian, hunger, roaming food search, and eating circuits. The H.l subarea corresponds to the DLR, driving R1.a (anterior hindbrain) roaming. R.pb.l (lateral parabrachial nucleus) is a key hindbrain nucleus for managing feeding and alarm. R1.a essentially implements the roaming random walk search for food. R.nst is a key hindbrain eating nucleus.

Roaming and DLR

Roaming needs locomotor circuitry because it’s a locomotor action. The DLR (diencephalon motor region) and MLR (midbrain locomotor region) are locomotor areas above the hindbrain that exist in all vertebrates, including the lamprey [Ménard and Grillner 2008], [Robertson et al 2014]. Although the MLR is well-studied, less is known about the DLR. MLR is strongly driven by OT (optic tectum) [Kim LH et al 2017], and basal ganglia, and may be part of an olfactory seek path in lamprey that does not use DLR [Derjean et al 2018]. In mammals, DLR appears be be in H.l.p (posterior H.l), directly driving R1.a (anterior hindbrain, pontine oralis area) [Ji C et al 2024] with a possible corresponding locomotor region for zebrafish in H.v (ventral hypothalamus) [Farrell et al 2021]. The following diagram shows potential related areas and connectivity with H.l.p as DLR.

Possible connectivity with posterior lateral hypothalamus as the DLR. DLR (diencephalon motor region), H.l.p (posterior lateral hypothalamus), H.sum (supramammillary nucleus), Po.l (lateral preoptic area), P.ms (median septum), R1.a (anterior hindbrain, locomotor).

Exploration is associated with several highly interconnected regions, including H.sum (supramammillary nucleus) [Farrell et al 2021], P.ms (median septum) [Köhler and Srebro 1980], [Kuhn et al 2024], [Mocellin and Mikulovic 2021], Po.l (lateral preoptic area) [Subramanian et al 2018], and H.l [Altafi et al 2024]. I’m interpreting exploration as roaming food search, but “exploration” is often used in distinct and specialized contexts, such as information gathering. These exploration areas are also associated with RTPA (real-time place avoidance), such as the H.sum projections to Po.l [Escobedo et al 2023]. P.ms projections to Hb.l are RTPA, but P.ms projections to Po.l are locomotive without avoidance [Zhang GW et al 2018]. Although it’s possible that Po.l is strictly an avoidance node, which would not help this essay’s need for roaming, it’s also possible that sub-circuits within Po.l, P.ms, and H.sum are dedicated to avoidance, while others are used for roaming. For example, one study shows H.sum to Po.l as strictly avoidance [Escobedo et al 2023], while another shows H.sum tac1 (substance P) as correlated with all voluntary locomotion, not only avoidance [Farrell et al 2021].

P.ms may be particularly important for roaming as an integrator of spatial information and food drive [Tsanov 2022]. For the DLR, H.sum, H.pv and Poa stimulation all produce locomotion, but these areas require P.ms [Fuhrman et al 2015]. Some of these studies suggest that P.msdb.glu to Vta produces locomotion, which would be more to the seek circuit than for roaming. P.ms.glu activity sustains for several seconds after the stimulation ends, likely from intrinsic neuron mechanisms, because blocking internal neurotransmission does not curtail the sustained activity [Korvasová et al 2021].

Timing issues with giving up

As discussed in essay 38, a circuit for giving up on a feeding place conflicts with the circuit for starting feeding, because both have a shared threshold for giving up. The animal gives up on a feeding place if it isn’t receiving nutrients, but when it starts eating, it also doesn’t receive any nutrients. In particularly, filter feeding has a long delay between starting to feed and nutrients in the gut, as opposed to relatively quick feeding for mammals. The MOR.i receptor might manage successful feeding, but β-endorphin might be released only after minutes. To solve this dilemma, some mechanisms is necessary to spend enough time sampling the new place before giving up one it.

Bridging sustain with startup enthusiasm for a give-up time.
Illustration of the need for starting enthusiasm before long-term sustained gut nutrients are available.

The above graph shows the difficulty. The horizontal dotted line represents the threshold for giving up. When feeding starts, the received nutrients are below the threshold at zero. A naive implementation would immediately give up. Successful feeding has a delay (1 minute here) before its signal for MOR.i is available. To give the potential feeding place a chance, the animal either needs to be actively stopped with a starting enthusiasm period, or stopped for resting. Because filter-feeding and resting are essentially identical for the proto-vertebrate, a resting stop could be sufficient without needing a starting enthusiasm system.

Taste and dopamine is a possible intermediate to give time for MOR to kick in. If the animal tastes food in the filter-feeding branchial arches before the food is digested, that early signal could trigger dopamine to extend a food-zone waiting period and allow filter feeding to continue. This temporary dopamine signal might habituate relatively quickly to avoid perseveration. In mammals, Vta dopamine extends eating rich food [Zhu Z et al 2025].

Food-zone stopping

Essay 38 covered the H.l support for food zone from [Jennings et al 2015]. The core of the food zone is food odor. The ascidian larva has a simple odor and tactile circuit in the ascidian palps that help decide where the larva should settle. The genetic transcription factors for ascidian palps are similar to the vertebrate forebrain, specifically foxg1, which marks the vertebrate forebrain [Cao C et al 2019]. Looking at the vertebrate circuit, the path from Ob (olfactory bulb) to S.ot (olfactory tubercle) to Pv (ventral pallidum) to H.l can serve the food zone function.

Potential food-zone circuit for stopping in a likely filter-feeding spot. H.l (lateral hypothalamus), Ob (olfactory bulb), Pv (ventral pallidum), R1.a (anterior hindbrain), S.ot (olfactory tubercle).

From [Bernat et al 2024], the S.ot to P.v to H.l path is the main S.ot path through P.v. Let’s consider this as the food-zone stop circuit. When the animal senses a food odor, the S.ot to H.l circuit will activate, detecting a food zone, which drives the animal to stop roaming and settle for feeding.

Importantly, S.o has the same adenosine timeout capability as the rest of the striatum, with A2a. (adenosine Gs receptor) and penk (enkephalin) marking the timeout indirect path. Enkephaline is the opioid ligand for DOR.i, but it also activates MOR.i, which is expressed in Pv [Neuhofer and Kalivas 2023], [Le Merrer et al 2009] and increases eating. This A2a.i and DOR.i circuit is the transition marker for the state machine above.

A dopamine taste signal might extend the food zone timeout [Zhu Z et al 2025]. The S.ot adenosine timeout neuron has a D2.i (dopamine Gi inhibitory) receptor, which inhibits the timeout without suppressing it entirely, essentially extending it.

Roaming timeout as filter-feeding sample

Anther possibly simpler sampling strategy is to use resting as a sampling phase. The roaming action itself could time out after a few minutes, resting for another few minutes before starting roaming again. In rodents the locomotion bouts are fairly short. Obviously, rodents are not filter feeders, but a proto-vertebrate filter-feeder could use a similar roaming-resting rhythm to periodically sample potential feeding zones without needing any odor place-detection circuit.

Roaming with timeout. H.l is the main roaming circuit. The S.sh and Pv loop is a timeout circuit to curtail roaming time. H.l (lateral hypothalamus), Pv (ventral pallidum), R1.a (anterior hindbrain), S.sh (ventral striatum shell).

The above circuit shows roaming driven by H.l with a timeout circuit suing S.sh (ventral striatum shell) and Pv. As in the odor timeout, roaming uses an A2a.s circuit as a timeout, with a time of a few minutes. Because filter feeding and resting are essentially equivalent, this resting phase can find a feeding spot without explicitly detecting a food zone.

Simulation

The simulation roughly follows the circuits outlines above, centered on H.l as a roaming driver. The main change from previous essays is in HypMove which represents H.l. This essay simplifies H.l, because H.l has almost no internal connections [Burdakov et al 2020], mantling that HypMove needs to essentially implement a single neural layer. It can combine the main circadian driver with hunger and suppressive elements like FoodZone or a morphine suppressor from HypEat, where the animal shouldn’t move if it’s successfully filter feeding. H.l has strong MOR.i, which can inhibit the driving hunger signal. H.l uses a timeout with a S.msh model in RoamTimeout to timeout the roaming. This timeout produces a periodic rest time while the timeout recovers, which then defaults to filter feeding.

Block diagram of the major feeding modules of the simulation. HypMove is the central node. It combines information from several sources to produce a roam-drive signal to HindMove.

The above diagram shows the roaming sub circuit, focused on HypMove. FoodZone is equivalent to S.ot in this simulation, while in mammals the food zone likely includes S.ls (lateral septum), S.v (ventral striatum), and P.bst (bed nucleus of the stria terminalis). HypEat is equivalent to the morphine and satiation circuits, which includes H.arc and H.pv, but also includes broadcast feeding receptors like leptin and glucose receptors that are on H.l neurons directly without needing separate interoception neurons.

HypMove roaming drives HindMove, the R1.a model. As in the DLR H.l to R1.a connection, this connection is slow (~1s) and weak in HindMove and can be overridden by essentially anything else in the hindbrain.

Filter feeding is likewise weak and not driven by upstream modules outside of the hindbrain. This passive eating without higher control is unlike mammal eating. HindEat is not driven by hypothalamus or forebrain inputs. If the animal has stopped moving, the hindbrain will start filter feeding after a short time (~1s). If the filter feeding is successful, gut nutrients will trigger MOR release in HypEat, which will continue to suppress roaming.

Screenshot showing the animal paused while filter feeding.

The above screenshot shows the animal stopped in a food zone (the teal stars), eating and receiving gut nutrient feedback, which drives MOR to suppress roaming.

References

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42: Optic Tectum Decision

The key element of decision making is the commitment to an action: all-or-none, both sustaining a decision and locking out competing action. In contrast, the choice part of decision-making is less important. Even a simple random choice or first choice is an effective decision mechanism, but losing out the all-or-none means the decision isn’t a decision. The key is ensuring that once a choice is made, the animal sticks to that choice. The losing action should not interfere with the winner. Specifically a decision suppresses dithering: switching between competition actions [Redgrave et al 1999].

This essay uses wall-following from essay 41 as the decision. If the animal detects a wall to the right, it will follow that wall for a time, improving search over random walk by reducing the search to a single dimension. In this case, the choice is left or right, which particularly matters because the choice requires communication between the two sides, which requires specific circuits because commissures are relatively rare.

Decision: two-phase commit

Decision-making has two main components: the choice (preparation) and commitment. A decision that doesn’t sustain or that doesn’t lock out competing stimuli isn’t a decision. Decision-making can split into a preparation / selection phase, which compare options — taking time if necessary, followed by a commit winner-take-all phase where the winning action goes forward and any losing action is locked out.

Decision as a two-phase process

Most decision research is focused on the preparation phase because people are interested in choosing A vs B, and much less research on the commitment implementation, the timeout and lock-out. For the essay simulation, the commitment is more important and needs to be implemented first. Without the commitment, a losing option can continually interrupt the animal, distracting it from its goals. The requirements for commitment are something like:

  • Sustain
  • Timeout: prevent the sustain from becoming perseveration
  • Lockout: prevent competing actions

Orientation and wall-following

For a decision, this essay uses wall-following (thigmotaxis), continuing from essay 41. Wall-following needs to be treated as a decision beyond a single swimming cycle. Consider the alternative where a lateral-line sense is a simple sensory-action reflex for each swimming cycle. Without a longer conception of the decision, the animal can’t avoid perseveration: it would circle a pillar or a convex arena endlessly. Any timeout needs to curtail wall-following, not right turns. Similarly, without persistence the animal might alternate left and right wall-following in a crowded environment, where both the left and right lateral-line indicates obstacles. Of the two, the timeout issue is more critical, but the ability to continue an action, is necessary to enable a “win-stay” strategy.

Because the research hasn’t located the circuit for wall following, these essays need to choose a brain location for it. The previous essay proposed R1.a (anterior hindbrain) as the driver of thingmotaxis, but an alternative uses OT (optic tectum) as an orientation center for thigmotaxis. Because OT receives lateral-line input via M.ts (torus semicircularis / inferior colliculus) [Zeymer et al 2018], it has the sensory information needed to turn toward a wall. OT is known as an orientation center. When a surprising or salient sensation appears, the animal turns toward it. If we imagine the proto-vertebrate as non-cortical, then that orient is likely OT. Even in mammals with a strongly developed cortex that can provide orientation functionality, OT is perhaps the strongest [Schall 2019].

Two architectures for orientation decisions. On the left, the orientation sustains its own decisions and is directly modulated by timeout. On the right, a separate module is responsible for sustaining the decision, possibly incorporating motor efference copies as part of the sustain system.

One immediate question is if the orientation also implements sustain. Compare the left and right model. In the left model, the orientation system implements sustain itself, driving and sustaining a turn action. The right model has a distinct sustain system, which may be driven by motor efference copies. The known connectivity of OT could support either model.

OT has independent sustaining capabilities, in part due to sodium channel modulation [Ghitani et al 2016], [Thompson AC and Aizenman 2023]. OT also has a loop with T.pf (parafascicular thalamus) and S.d (dorsal striatum), which can implement the timeout using A2a.s (adenosine G-s coupled stimulatory receptor) and adenosine accumulation. Although the left model is possible, several studies report OT burst neurons activate at the decision point [Lintz et al 2019], [Stine et al 2023], with ramping neurons before the decision and action [Munoz and Wurtz 1995], [Lintz et al 2019], not after the decision, suggesting the model on the right. Ppt (pedunculopontine tegmental nucleus) is well-suited as a central node of the sustain role. Ppt maintains activity from one decision to another in tasks that repeat decisions [Thompson JA et al 2016]. It also receives widespread input from hindbrain motor areas, including R1.a and R5.my.gi (medulla giganocellular chx10 turning neurons) [Huerta-Ocampo et al 2021].

If wall-following uses the midbrain orientation circuitry, then a combination of OT and Ppt is plausible following the model on the right. Note, though, that the sustain may not be only Ppt, but could also include other anterior hindbrain systems like R1.a, V.rn (serotonin Raphé nuclei), and possibly R.ip (interpeduncular nucleus), because all of these are associated with brainstem sustained attention network [Alves et al 2022].

S.nr tri-value logic

S.nr (substantia nigra pars reticulata) is a key player in commitment. S.nr provides tonic suppression over essentially every voluntary action. For this essay, consider S.nr as a tri-value logic. The tonic, middle level of S.nr allows ongoing actions to continue, but inhibits starting a new action. A low S.nr value, the classic disinhibition model, allows new actions to start. A high S.nr value stops ongoing actions. The tonic level itself might be adjustable. For decision-making, this tri-value S.nr can support the commitment requirements of sustain, timeout (Stop), and lockout (passive inhibition with overriding Go).

S.nr as a tri-value system. The tonic activation allows sustain of an ongoing action. A Go signal disinhibits an action, allowing it to start. A Stop signal inhibits an ongoing action.

In the diagram above, the tonic S.nr inhibits new actions, but ongoing actions would continue, or a sufficiently strong sense input could start an action. An explicit Go signal would allow a weak sensory input to start an action. An explicit Stop signal would stop all action, regardless of the sense strength. The adjustable tonic level can be influenced by sleep and wake pressure, since S.nr.m is associated with sleep [Liu D et al 2020]. As the animal grows tired, a higher tonic S.nr would discourage new actions and encourage stopping of sustained actions, but the sleep pressure would not outright prevent action.

In the context of decision commitment, disabling S.nr eliminates orientation selectivity: mice are unable to resist orienting to any object in the whisker field [Redgrave et al 1999]. In PD (Parkinson’s disease) an overly-active S.nr produces bradykinesia (slow movements) and akinesia (lack of voluntary movement), and inhibiting S.nr can reduce akinesia and bradykinesia [Hu Y et al 2023], [Lin C et al 2024]. However, an underactive S.nr can produce dyskinesia (twisted postures) where opposing actions activate at the same time, and stimulating S.nr can reduce dyskinesia [Hu Y et al 2023].

Action sustain and timeout

An immediate consequence of commitment is timeout. Without a timeout, an unending commitment can lock an animal into a decision forever. A previous essay already covered a possible timeout circuit using adenosine as a timing neurotransmitter. The S.d2 (striatum with D2 dopamine-receptor) projection neuron have A2a.s (adenosine G-s coupled stimulatory) receptors, and some studies use A2a.s receptors to identify the S.d2 neurons as S.a2a as opposed to the S.d2 convention in the essays. Adenosine builds up around active neurons, partially produced by astrocytes that monitor glutamate activity [Ma et al 2022]. This adenosine progressively activates S.d2 neurons, which stops action using the indirect path.

Basal ganglia timeout circuit. Ongoing left wall-following provides an efference copy to S.d2. As time continues, adenosine enables S.d2, and eventually activates the indirect path to stop the left action. H.stn (subthalamic nucleus), P.ge (globus pallidus, external), S.d2 (striatum D2-receptor projection neuron), S.nr (substantia nigra pars reticulata), T.pf (parafascicular thalamus).

The above diagram shows a possible timeout circuit for thigmotaxis following a left wall. During the left wall-following, an efference copy via T.pf (parafascicular thalamus) drives glutamate to S.d2 in the striatum. Sustained glutamate in S.d2 produces adenosine, which progressively activates S.d2, which then inhibits the current action using the indirect path of P.ge (external globus pallidus) to H.stn (subthalamic nucleus) to S.nr to stop the left action.

Note that the P.ge / H.stn circuit is complex and oscillatory. This path isn’t necessarily a straight chain as the above diagram would suggest. For example, S.d2 to H.stn / P.ge can switch the mode from irregular, unsynchronized firing to a regular oscillation [Terman et al 2002], or switch from a gamma (~80Hz) to a beta (~20Hz) frequency [Wang Y et al 2024].

Interrupting sustained action

Sometimes sustained actions need to be interrupted, either for dramatic reasons like a predator attack or more mundane situations like stubbing a toe. These interrupts need to be fully general, halting the current action, no matter which action path happens to be active. Note the similarity to sleep, where sleep needs to halt any action.

Two ways of halting action are either a direct halt signal or a deadman’s switch. In a deadman’s switch, a tonic signal maintains normal behavior, and the absence of the signal stops the action. The brain uses this pattern with several instances of high-affinity Gi (G-protein coupled inhibitory) receptors that saturate in normal, tonic activity, but disengage when the neurotransmitter drops. In particular the D2.i (dopamine G-i inhibitory) receptor is high affinity, quickly saturating, that is fully active at normal tonic levels of dopamine and only shuts off when dopamine levels drop.

Adding a dopamine deadman’s switch to the timeout circuit. An interruption drops DA, which immediately activates the timeout circuit from S.d2. H.stn (subthalamic nucleus), P.ge (external globus pallidus), S.d2 (striatum D2 projection neuron), S.nr (substantia nigra pars reticulata), T.pf (parafasciculus thalamus), V.da (midbrain dopamine), V.rmtg (rostral medial tegmentum).

The diagram above adds a dopamine deadman’s switch to the timeout circuit. Tonic dopamine from V.da (midbrain dopamine) normally inhibits S.d2, allowing for a normal timeout. Because D2.i is a high affinity receptor, a low tonic level of dopamine activates it and quickly saturates the receptor. When dopamine drops below a threshold, the D2.i receptor will deactivate and disinhibit the S.d2 neuron, which rapidly fires the timeout using the indirect path, stopping the action. Dopamine will drop if V.rmtg (rostromedial tegmental) activates. V.rmtg is activated by pain or itch sensations and by many more general failure or disappointment systems.

Lockout and the Sprague effect

The commitment phase needs to lockout alternative distractors. I haven’t found any research on this specific scenario. Decision research generally studies artificial forced-choice scenarios, where each choice is separated by several seconds from another choice, and is forced by a single decision point, like a T-maze or Y-maze, or turning left or right from a central cue port. The design of the typical experiment removes the scenario of sequential, continuous choices. Because of the lack of direct studies, the following discussion is more speculative. Attention is a related, but distinct research area to decision-making. Sustained attention is similar to this commitment issue.

The Sprague effect is related to OT attention. In mammals OT receives excitatory input from C.vis (visual cortex). If the left C.vis is lesioned, the animal will ignore items in contralateral, right visual field. Paradoxically, a following lesion to contralateral, right OT will restore attention to the left visual field [Gambrill et al 2018], [Gebhardt et al 2019], [Jiang et al 2003], [Krauzlis et al 2013]. Further studies have shown this effect with the second lesion to the tectal commissure [Gambrill et al 2018] or to the specific area of contralateral S.nr [Krauzlis et al 2013] or to the entire contralateral Ppt [Valero-Cabré et al 2020].

In frogs there is a direct OT to contralateral OT connection. Unilateral OT legion impairs bilateral visual behavior regardless of looming direction [Gambrill et al 2018]. In contrast unilateral OT lesion deficit in behavior only in lesioned hemifield [Gambrill et al 2018].

Possible Sprague effect circuit, showing lockout of contralateral wall-following. OT.d (deep layers of optic tectum), Ppt.a (anterior pedunculopontine tegmental nucleus), Ppt.p (posterior Ppt), S.nr (substantia nigra pars reticulata).

This above diagram shows a potential circuit for the Sprague effect. (For simplicity, straightening out crossed output to the motor.) Once a decision to follow a right wall has been made, the ongoing motor action sends an efferent copy to Ppt [Caggiano et al 2018], which projects to S.nr [Durmer and Rosenquist 2001], which inhibits the contralateral OT.d [Durmer and Rosenquist 2001]. Similarly, a motor efferent copy to Ppt also projects to the ipsilateral OT.d [Valero-Cabré et al 2020], which enhances attention to continue following the right wall.

This Ppt sustained attention circuit is similar to the R.is (nucleus isthmus / parabigeminal) circuit in fish [Henriques et al 2019] and birds [Marín et al 2007], covered in essay 19. Like Ppt, R.is has both ACh and GABA components, although in Ppt the components are mixed salt-and-pepper, while R.is has distinct nuclei. Ppt and R.is are sibling areas, both generated from the same progenitors in R1 (hindbrain rhombomere 1), but one is generated before the other [Morello et al 2020]. R.is is better understood because it has simpler connectivity than Ppt. When zebrafish hunt paramecia, R.is sustains attention to a target prey and inhibits attention to other visual areas [Henriques et al 2019]. R.is provides a similar effect in birds [Knudsen 2011], [Marín et al 2007], [Mysore and Knudsen 2011], [Reynaert et al 2023].

Although Ppt has much more complicated connectivity and function, like R.is, it has reciprocal connectivity with OT. Ppt is also active during actions, and it highly heterogenous, and connected with much of the hindbrain motor, both R.pn (pons, anterior hindbrain) and R.my (medulla, central and posterior hindbrain). Like R.is, Ppt proves ACh attention to OT [Isa et al 2021], [Mena-Segovia et al 2008], [Mena-Segovia et al 2017], [Krauzlis et al 2013], [Wolf et al 2015] and as the Sprague studies show, it inhibits the contralateral OT via S.nr.

At the time of choice, many Ppt reflect previous action and outcome. Ppt lesions reduce influence of recent experience on action selection. The Ppt ACh input to OT is possible as a Bayesian prior [Thompson et al 2016].

Passive lockout

An alternative to an active of alternative actions is a passive lockout, which inhibits actions without needing input from a sustain system. Once an action commits, the passive lockout prevents new action. A possible passive lockout involves the H.stn / P.ge pair, which is hyperactive in PD. Akinesia like PD is exactly what’s needed for passive lockout.

H.stn / P.ge as a passive lockout system. H.stn (subthalamic nucleus), P.ge (external globus pallidus), S.nr (substantia nigra pars reticulata).

In the above circuit, H.stn and P.ge form a spontaneously oscillating circuit at beta frequencies. In PD, this circuit is hyperactive, oscillating at beta frequencies, providing broad movement inhibition [Fischer et al 2017]. This circuit drives S.nr, which inhibits the action.

This description vastly oversimplifies the P.ge / H.stn circuit. The P.ge / H.stn circuit can operate in at least two modes: inhibitory at beta frequencies (H.stn exciting S.nr), and excitatory at gamma (P.ge inhibiting S.nr) [Fisher et al 2017], [Terman et al 2002]. H.stn also has distinct subregions, with H.stn.vm (venture-medial) as almost an extension of H.l [Haynes and Haber 2013], while H.stn.l as distinct functionality [Baunez and Lardeux 2011], [Pasquereau and Turner 2017].

Studies seem to divide on whether H.stn is suitable for a commitment function. H.stn activity terminates at onset of movement [Espinosa-Parrilla et al 2013], which would argue against passive lockout. H.stn gamma increases during movement for humans [Fischer et al 2017], but others point out that H.stn beta are brief bursts, not sustained [Feingold et al 2015], and H.stn beta in humans is active for acute stopping [Wessel et al 2016].

A second passive lockout is in the striatum itself, discouraging new actions by default. S.pn (striatum projection neurons), both S.d1 (D1 receptor S.pn) and S.d2, are hyper polarized, making them harder to drive than most neurons. Secondarily, new actions are inhibited by the feedforward, fast-spiking S.pv (parvalbumin) neurons, which inhibit S.d1 and S.d2 before they can be activated. S.pv activates before S.d1 and S.d2 [Gage et al 2010], [Lee C et al 2019], [O’Hare et al 2017], [Yim et al 2011].

Striatum passive lockout using the inhibitory S.pv neurons. Once an action starts, an endocannibinoid sub circuit disinhibits the action, allowing sustained activity. eCB (endocannibinoid neurotransmitter), S.d1 (striatum D1-receptor neurons), S.d2 (striatum D2-receptor neurons), S.pv (striatum parvalbumin inhibitory neuron), T.pf (parafascicular thalamus).

This S.pv inhibition is suppressed by sustained action using a retrograde eCB (endocannabinoid) system that disinhibits both S.d1 and S.d2 by inhibiting GABA release from S.pv [Narushima et al 2006], [Adermark et al 2009], [Mathur and Lovinger 2012].

Active initialization

A passive lockout system needs to be paired with an active initialization. If new actions are passively inhibited by default, a new action needs extra effort to cross the barrier. Possible active initialization nodes include OT, Ppt, as well as the S.d1 direct path.

The following diagram shows a possible active initialization. The passive lockout subcircuit is the same as before. The active initialization would logically use the S.d1 path. Phasic dopamine activates the Go path, both by enabling the S.d1 input and their output, because D1.s receptors are on inputs to S.d1 and on the axons in S.nr, which enables the direct path to disinhibit the S.nr.

Explicit active Go circuit to override the passive lockout circuit. H.stn (subthalamic nucleus), LL (lateral-line), OT (optic tectum), P.ge (external globus pallidus), Ppt (pedunculopontine tegmentum), S.d1 (D1-receptor striatum), S.nr (substantia nigra pars reticulata), T.pf (parafascicular thalamus), V.da (midbrain dopamine).

This Go circuit is for wall-following, which uses the lateral-line as a wall distance sensor. The lateral line sense is input to the OT orientation circuit, which excites both the S.d1 path via T.pf and the V.da path, which will add a phasic DA burst to enhance the S.d1 circuit, giving it an extra boost to overcome the barriers.

Note that OT / Ppt also inhibits contralateral OT as described in the Sprague effect system, and the OT to V.da excitation is ipsilateral, but OT also inhibits the contralateral V.da via V.rmtg [Pradel et al 2021]. So this circuit is also part of the active lockout system.

Consider the striatum passive lockout circuit again, which discouraged new actions but enabled sustained actions. That passive lockout implies the necessity of an extra push for new actions. Phasic dopamine bursts could provide that extra push. A burst of dopamine activates the low-affinity D1.s receptors in S.d1, allowing S.d1 to override its intrinsic hyperpolarization and the feedforward S.pv inhibition and initiate a new action.

Striatum passive lockout circuit with sustain from eCB disinhibition and new actions enabled by DA burst. DA (dopamine), eCB (endocannabinoid), S.d1 (D1-receptor striatum projection neuron), S.d2 (D1-receptor striatum projection neuron), S.pv (striatum parvalbumin inhibiting interneuron), T.pf (parafascicular thalamus).

Pretectum suppression of OT

This essay uses the aquatic-only lateral-line for thigmotaxis. Thigmotaxis is an interesting system because the animal must be weakly attracted to the wall but simultaneously repelled by the wall to avoid collision. M.pt (pretectum) is an obstacle avoidance system in the midbrain and OT is an orienting system. In non-mammalian vertebrates (reptiles, birds, frogs), the striatum projects directly to M.pt, which inhibits OT [Krauzlis et al 2018]. If the animal gets too close to the wall, M.pt should inhibit the OT orientation and avoid the wall, but if the animal is far enough from the wall, it should approach the wall with thigmotaxis, suppressing the avoidance circuit.

Thigmotaxis balancing attraction from OT orientation and avoidance from M.pt obstacle avoidance. LL (lateral line), M.pt (pretectum), OT (optic tectum), S (striatum), T.pf (parafascicular thalamus).

The above circuit shows this potential thigmotaxis circuit. Normally, M.pt avoids the wall and suppresses OT to keep any OT orientation from running into the wall. But during thigmotaxis, the S circuit will suppress M.pt to allow the animal to get closer to the wall.

Simulation

The simulation divides thigmotaxis into several systems. An obstacle system roughly corresponds to M.pt and keeps the animal from running into a wall. An orientation system provides an attractive drive toward the wall. These two systems are now designed as independent and general, where sensory input is external. For example, the lateral line drives both the obstacle and orient systems, but the code for obstacle and orient systems are ignorant of the lateral line itself.

Outline of simulation modules for lateral-line thigmotaxis.

The decision commitment uses a loop with a sustain module and a striatum module. The sustain roughly corresponds to Ppt with possible associated areas like V.dr and R1.a, because the simulation is more abstract than directly implementing each neural ganglia. The striatum module provides with timeout function with an adenosine-lie timeout. The sustain also provides an active inhibitory lockout function, following the Sprague effect studies.

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Essay 41: Thigmotaxis

Thigmotaxis is wall-following locomotion, as opposed to random-walk exploring open areas. Thigmotaxis is almost entirely studied as an indicator of anxiety, under the model that anxiety is driven by distant, learned fear. Under this model, wall-following is driven by trying to avoid threat. However, for this essay I’m treating thigmotaxis as a navigational strategy, an addition to the random walk, area-restricted search, and targeted seek that previous essays have simulated. Because thigmotaxis is essentially never studied in itself (or at least I haven’t found any studies yet), even the regions that implement thigmotaxis is not studied.

Simulated thigmotaxis

Because I haven’t found research into the underlying mechanisms of thigmotaxis, the following motivation and implementation is speculative, but may be useful in exploring the non-defensive value of thigmotaxis.

When navigating a maze, wall-following using the right hand rule is a highly effective technique. Although this simple rule doesn’t work on all mazes, it works on a large number. Importantly, even a simple nervous system could implement this rule, since this technique doesn’t require any memory. The following screenshot shows some of the searching value of thigmotaxis.

Simulation of thigmotaxis behavior showing an animal navigating a maze using wall-following techniques.
Screenshot of thigmotaxis where the animal follows the wall to the right to explore an island in the maze.

In the screenshot above, the animal is turning using thigmotaxis to explore the isolate island. A random walk about bound off the island and spend more time in open areas. Similar, wall-following naturally moves from section to second in the rest of the maze, such as following the corridor between the main areas to the left and right. In contrast, while random motion can also cross the passage if the trajectory happens to match, the probability is lower. Wall-following will always read the new section, but random search will only probabilistically have the proper trajectory to enter.

State and stateless thigmotaxis

For thigmotaxis, using the lateral-line sense seems to be the most direct with fewest requirements. Lateral-line is a new sense in vertebrates not present in tunicates, the closest non-vertebrates. The lateral line sense is a series of hair cells that measure water flow around the animal. This sense detects nearby objects and obstacles like a passive sonar at a distance approximately the animal’s own length. The lateral line sense has disjoint head and trunk systems and is lateralized into distinct left and right. The essay simulation approximates the lateral line by combining sense data points into these four combined areas with no finer details to approximate the information available to a simple proto-vertebrate.

A simple, stateless thigmotaxis tries to keep the head lateral-line in a middle range. If the head is too far from the wall, the animals turns toward the wall. If the head is too near the wall, the animal turns away from the wall. Because the lateral-line sense is lost beyond the animal’s own length, if the head loses the signal but the trunk still senses a wall, the animal can turn toward the trunk side to regain a head sense.

Stateless thigmotaxis is likely to lose the wall if the animal doesn’t turn quickly enough or the wall changes are too sharp, as in the post-like wall in the above screenshot. In the simulation, stateless thigmotaxis very quickly loses the wall and almost never follows sharp turns. In the animal loses the wall, thigmotaxis turns off and the animal reverts to random walk. Adding state to the system remembers the wall’s side. Even a short memory like a second or two can improve thigmotaxis performance. If the animal is following a wall to the right as above and the lateral line sense is lost, but the animal remembers that the wall is on the right, it can turn right, most likely restoring contact with the wall.

Based on running the simulation, short term memory is likely important to thigmotaxis, almost as important as the distance sense itself. In trying to understand which brain area might implement thigmotaxis, having access to simple short term memory is likely important.

Improving ascidian cement-gland search

As several essays have covered, the ascidian tunicate larva searches for a permanent adult filter-feeding settling place with a combination of phototaxis and geotaxis. When the ascidian larva finds a landing spot, it will attach with a cement gland. Geotaxis drives the ascidian larva up and phototaxis drives it away from light [Anselmi et al 2024]. This combination prefers overhanging ledges, which are both dark and upward, but the animal will settle on flat ground if it can’t find a ledge. This cement gland and phototaxis combination still exists in some fish and amphibian tadpoles. Consider a proto-vertebrate that adds thigmotaxis to this cement-gland strategy. Because the thigmotaxis animal spends more time near walls than random search would, it’s more likely to find an overhand.

As a search strategy, thigmotaxis could improve over random walk if the search target is near walls. In a reef-like ecosystem, better food sources might be near the reef and more marginal feeding in open sand. Along with potential improved defense of sticking near walls, thigmotaxis may improve search, both by preferring richer areas near walls or reefs, and improving maze-like navigation, where the maze here is the reef itself.

Arguments against thigmotaxis

There is an argument against thigmotaxis as a specific locomotor strategy, increase arguing that thigmotaxis is an epiphenomenon [Horstick et al 2016]. Circular arenas are common in scientific experiments. In a circular arena, the animal will appear to stick to the wall if the animal simply moves forward ballistically while avoiding barriers. The diagram on the left below shows this illusionary thigmotaxis. In contrast, the diagram on the right shows genuine thigmotaxis, where wall-following is needed to produce the trajectory.

Diagram comparing two maze navigation strategies: thigmotaxis (left) and a circular path (right).
Illusionary thigmotaxis on the left, where wall-following appears from a combination of ballistic motion and obstacle avoidance. In contrast, the right shows actual thigmotaxis where wall-following is necessary to produce the trajectory.

In a mouse experiment (that I can’t find the reference to), driving MLR (midbrain locomotor region), a low-level locomotor area, drives the animal forward, but obstacle avoidance keeps the animal from running into the walls. The resulting path is circular, running around and around the experimental area following the walls, which appears exactly as thigmotaxis, but in this case there is not thigmotaxis system at all. The apparent thigmotaxis is an epiphenomena from the combination of the shape of the arena, forward motion, and wall avoidance.

Note that the epiphenomenon depends on the arena shape [Horstick et al 2017]. If part of the arena is convex instead of concave, the ballistic motion will avoid the wall, bound off it, and the apparent thigmotaxis will disappear. The screenshot above shows that situation, where a distance thigmotaxis system is required to follow the wall.

Motor-driven taxis

Since I can’t find any direct thigmotaxis study, using related studies seems like the best approach. Thermotaxis is the avoidance of too-hot or too-cold areas. In fish the Hb.d (dorsal habenula; Hb.m in mammals) to R.ip (interpeduncular nucleus in the anterior hindbrain) circuit is central to thermotaxis [Paoli et al 2025]. This thermotaxis is movement-driven, as opposed to sensory-driven. Movement organizes the circuit. When the fish turns to the right, the circuit remembers the movement direction, and if heat increases, the circuit determines that heat is toward the right. The circuit needs two pieces of state. First is needs to remember that it turned to the right for a second or two. If the temperature increases, the circuit now knows the hotter area is toward the right. The second memory saves the “right is too hot” for a few seconds so the animal can avoid the right side. The important thing here is that a motor efference copy drives the hold system. The system is motor-driven with a coincidence detection of the motor turn with a sensory change.

The specific brain area for this thermotaxis circuit is the anterior hindbrain. The motor detection is in R1.a (anterior hindbrain, rhombomere 1) in the R1.dta (dorsal tegmental area). The thermal gradient signal is from the right Hb.d. The habenula is asymmetric in most vertebrates with the right and left having different functions. Taxis is primarily right Hb.d. The motor direction and sensory gradient are compared in R.ip.i (interpeduncular nucleus, intermediate part), which is in the basal R1. R.ip.i is primarily neuropil [Dragomir 2019] with axons and dendrites from R1.a and R.ip itself only has a relatively few neurons, a structure similar to Ob (olfactory bulb) glomeruli.

An interesting effect of this system is that only the signal valence matters, not the identity. A too-hot signal, or too-cold, or too-dark, or predator odor signal doesn’t need to be distinguished in the circuit. All of these result in avoiding the right if they increase after the animal turns right. This means that all kinds of threat signals can use the same circuit. In frogs the right Hb.d is organized around a single neuropil [Concha and Wilson 2001], suggesting that multiple senses lose their identity in the right Hb.d. Similarly, attraction can use the same system by switching left and right. The fish R.ip.v appears to have a gradient where more dorsal areas are attractive and more ventral areas are avoidant [Chen WY et al 2019].

Thigmotaxis and anxiety

Although thigmotaxis is not studied in itself, it is heavily studied as a marker for anxiety. Although anxiety research is aimed at understanding human anxiety, animal studies typically use “anxiety-like” to make clear that animal results may not match human anxiety. The main anxiety-like measures in mice are OFT (open field test), which directly measures thigmotaxis and EPM (elevated plus maze), which measures mice avoiding corridors above the ground.

Much of the anxiety study focuses on the forebrain, particularly sub-areas of P.bst (bed nucleus of the stria terminalis) and E.hc.v (ventral hippocampus), but there is significant anxiety research in the hindbrain, particularly research into nicotine addition and anxiety from nicotine withdrawal. The hindbrain areas most associated with anxiety-like behavior are Hb.m, R.ip and V.mr (median raphe).

Motor-driven taxis

The simulated thigmotaxis outlined earlier was sensor-driven: the animal’s movement was purely an output. But zebrafish studies about thermotaxis (avoiding too hot or too cold areas) suggest that the animal’s self movement drives the data collection and decision [Paoli et al 2025]. The thermotaxis circuit is movement-driven. The animal first moves to the right or the left, and only after the movement does the circuit measure change in temperature. If the fish turns to the right and heat increases, the circuit stores state about heat to the right. If the heat is too hot, the fish can turn to the left to avoid the heat.

This thermotaxis circuit needs to pieces of state. First it needs to remember that it turn to the right for a second or two, allowing a later temperature increase to show that the right side is hotter. Secondly once it has determined that the right side is hotter, it needs to store that information so it can avoid the right for a time. These two state variables are on the order of a second to a few seconds. The important thing here is that a motor efference copy drives the system. It’s a coincidence detection of the motor turn with changes in a sense like temperature.

The implementation area is in the anterior hindbrain. The motor direction state is in R1.a (anterior hindbrain) in R1.dta (dorsal tegmental area). The thermal gradient signal arrives from the right Hb.d (dorsal habenula in fish, medial habenula in mammals). The two data are combined in R.ip.i (interpeduncular nucleus, intermediate part), which is in the basal R1. R.ip.i is primarily neuropil [Dragomir 2019], [Wu et al 2024] with axons and dendrites from R1.a and Hb.d and only a relatively few neurons, similar to the structure of olfactory bulb glomeruli.

A second interesting effect of motor-driven behavior is that only the signal valence matters, not the identity. A too-hot signal, or too-cold, or too-dark, or a predator odor signal doesn’t need to be distinguished in the circuit, because all of these result in avoiding the dangerous right side. This means that all kinds of threat signals can use the same circuit. In frogs the right Hb.d is organized around a single neuropil [Concha and Wilson 2001], suggesting multiple senses lose their identity in the right Hb.d. Similarly attraction is a simple change in direction, so the bulk of the circuit can be the same. The first R.ip.v appears to have a gradient where more dorsal areas are attractive and more ventral areas are avoidant [Chen WY et al 2019].

Habenula and thigmotaxis

Research into anxiety and nicotine addition have consistently shown correlations with right Hb.d (Hb.mv in mammals), R.ip.d and anxiety-like behaviors, prominently including thigmotaxis. In studies anxiogenic (anxiety producing) or anxiolytic (anxiety inhibiting) is measured by changes in thigmotaxis in measurements like the OFT (open field test). Which raises the question of whether these studies are measuring anxiety as defined in human psychology or something else that merely resembles anxiety, but may have a different underlying purpose. Studies generally use “anxiety-like” instead of “anxiety” to make it clear that “anxiety-like” might not be the same as the normal use of anxiety. For example exploration-based task can’t distinguish anxiolytic from novelty seeking, exploration, or impulsive approach [Calhoon and Tye 2015]. Some anxiety researchers criticize using thigmotaxis tests like OFT and EPM for anxiety [Headley et al 2019]. The majority of anxiety studies are definitely measuring thigmotaxis (OFT) but may not be measuring anxiety.

For these studies, I’m treating Hb.m (Hb.d in fish), R.ip, and V.mr (median raphe) as part of a single interconnected system, with V.dr (dorsal raphe) as a possibly interconnected region.

Left Hb.d does not appear to be anxiety related [Agetsuma et al 2010], but several studies suggest right Hb.d in fish, Hb.mv in mammals as anxiety related. Hb.mv / right Hb.d are associated with ACh and in particular the nACh (nicotinic receptor) which is named after nicotine’s stimulatory effect in this region, and Hb.m and R.ip are in a center in nicotine addition and anxiety-like withdrawal symptoms [Jonkman et al 2017], [Molas et al 2017], [Pang et al 2016], [Klenowski et al 2023], [Matos-Ocasio et al 2021], [Wills et al 2022], [Zhao-Shea et al 2015]. Disabling Hb.d increases anxiety baseline [Bühler et al 2021]. Disabling of Grp151 (a genetic transcription factor) in Hb and impairs habituation to novelty [Broms et al 2017]. Disruption of Hb asymmetry in development is anxiogenic [Corradi and Filosa 2021]. Hb.m is associated with nicotine, novelty, anxiety and fear in mammals [Hashikawa et al 2020]. Disabling Hb can be anxiolytic, particularly when stressed [Jacinto et al 2017], but disabling the Hb.mv to R.ip connection can be anxiolytic, and disabling the P.ts to Hb.mv input can be anxiolytic [Okamoto and Aizawa 2013], [McLaughlin et al 2017], [Yamaguchi et al 2013]. Disabling Hb.m reduces ACh in R.ip, producing many side effects including increase in anxiety [Mathuru and Jesuthasan 2013] and failure to habituate to novel area [Kobayashi et al 2013]. Hb.mv nACh activation can be anxiogenic in nicotine mice, although with a lesser effect in naive mice [Pang et al 2016]. A reminder here that anxiogenic and anxiolytic here is always measured by thigmotaxis, in combination with non-thigmotaxis anxiety-like tests.

R.ip is highly connected with Hb.m and it is essentially defined as the target of Hb.m axons, but R.ip has an independent identity comprised of a strong connection with the anterior hindbrain is modulated by Vta. Importantly here, Vta is heterogeneous. One DA from section from Vta.pn-if (paranigral area, interfascicular) to R.ipc is anxiolytic [DeGroot et al 2020], another projection from Vta.p associated with CRF (corticotropin releasing factor peptide), associated with stress, is anxiogenic [Grieder et al 2014], [Calpari et al 2020], [Wills et al 2022]. CRF in R.ip potentiates Hb.mv to R.ip [Zhao-Shea et al 2015]. R.ip receives anxiety-modulating input from both Hb.mv and from Vta and is strong associated with anxiety produced by nicotine withdrawal [Matos-Ocasio et al 2021], [Zhao-Shea et al 2015].

V.mr (median raphe) is a major 5HT (serotonin) region, tightly connected with R.ip and with E.hc (hippocampus). Physically V.mr is adjacent to R.ip, immediately posterior and dorsal to R.ip. V.mr 5HT is anxiogenic with projections to E.hc.d [Abela et al 2020], [Andrade et al 2013]. Since many studies are highly focused on the forebrain, ascending connections are often overemphasized. More studies focus on the V.mr connections to the forebrain and few study connections to the more local hindbrain. V.mr 5HT is anxiogenic [Dos Santos et al 2015], [Ohmura et al 2014] 5HT anxiety is only R1-derived 5HT but not R2, R3/R5 [Kim et al 2009].

Although more studies report Hb.m ACh areas as anxiogenic, some studies also report Hb.l affecting anxiety. Because Hb.l does project to both V.mr and V.dr, this circuit may feed into the same circuit mentioned above, but more directed to V.mr and not to R.ip. Disabling Hb.l is anxiolytic [Cui et al 2020]. Interestingly V.lc (locus coeruleus) to Hb.l is anxiogenic [Pereira et al 2023], and anxiety is correlated with Hb.l astrocyte activation [Tan et al 2022], and V.lc and R.my (medulla) norepinephrine are strongly related to astrocyte activation.

Habenula, R.ip, and anterior hindbrain

This essay assumes that thigmotaxis is somewhere in the anterior hindbrain and strongly connected to Hb.m, R.ip.v, and V.mr. The following diagram shows current studies of relevant hindbrain connections and emphasizes an ambiguity relevant to the essay, namely the relation of R.ip.v to anterior hindbrain motor areas, particularly R2.artr.

A diagram illustrating neural connections involving the habenula (Hb.m), interpeduncular nucleus (R.ip), and median raphe (V.mr), indicating potential links in anxiety and navigation-related circuits.
The medial habenula to interpeduncular nucleus circuit, which this essay uses as a possible location for thigmotaxis. Hb.m (medial habenula), R1.a (anterior hindbrain), R2.artr (anterior hindbrain turning region), R.ip.d (interpeduncular nucleus, dorsal), R.ip.v (R.ip, ventral), V.mr (median raphe).

R.ipd and R1.a are connected to form a head direction circuit [Petrucco et al 2023], [Petrucco 2024] and landmark navigation [Lavian et al 2024]. This sub circuit does not appear to be anxiety or thigmotaxis because R.ip.d and Hb.md (left Hb.d) are not associated with anxiety, in contrast to Hb.mv (right Hb.d) and R.ipv, which are strongly associated with anxiety and thigmotaxis.

R.ip.v is strongly correlated with chemotaxis [Chen WY et al 2019], thermotaxis [Palieri et al 2024], [Paoli et al 2025], and OMR [Dragomir et al 2020] and necessarily needs to connect with motor regions [Wu et al 2024].

R2-R3 ARTR (anterior hindbrain turning region) is strongly associated with turning direction [Chen X et al 2018], [Dunn et al 2016], and phototaxis [Karpenko et al 2020], [Wolf et al 2017], and OMR [Chen X et al 2018], [Naumann et al 2016].

However, none of the R2.artr studies mention any connection with R.ip.v or V.mr, and none of the R.ip.v studies mention R2.artr. While is seems plausible that R2.artr and the unnamed R1.a motor area are the same area, but the science doesn’t say anything at all, neither confirming the identity as R2.artr with the unnamed R.ip pair or establishing a separate anterior hindbrain area. For the sake of the essay and simulation, I’m treating R2.artr as being the partner of R.ip.v, because that option is simpler, with fewer moving parts.

Discussion

Here I’ve approached thigmotaxis primarily as a navigation strategy, adding to earlier essays that used random walk and target seek and avoid (taxis) that previous essays have used. Here the wall-following is a strategy that reduces search from a two dimensional problem to a one dimensional problem. In addition it increases the time spent searching near wall-like areas as like a reef in coastal water, which may have been important to proton-vertebrates as they searched for filter-feeding locations.

However scientific studies don’t currently study thigmotaxis as a separate behavior, which makes this essay particularly speculative. Essentially all of the information about thigmotaxis is from studies that use thigmotaxis as a measure of anxiety. Because anxiety is a major research topic, thigmotaxis has a large amount of indirect research. In a sense it’s a well-studied topic, but that research doesn’t cover how the motor circuit for thigmotaxis works.

From the other direction, there is significant research for locomotion for seeking and other taxis [Palieri et al 2024], random walks [Dunn et al 2016], klinotaxis [Karpenko et al 2020], optic-flow locomotion [Chen X et al 2020], and details on swimming primitives like enumerating several swimming types and turn types [Marques et al 2018]. But I haven’t found a study that treats thigmotaxis as a locomotion primitive that needs explaining.

Because thigmotaxis can be implemented fairly simply using the lateral line with some short-term memory, both of which are available in the hindbrain, and because the anterior hindbrain Hb.m / R.ip / V.mr system is an anxiety (thigmotaxis) center, placing thigmotaxis in the anterior hindbrain seems reasonable. Recent research has started to explain anterior hindbrain locomotion [Paoli et al 2025], [Dragomir et al 2020], [Naumann et al 2016]. However there appears to be two lines of research, one centered on the Hb / R.ip circuit and another studying the R2.artr circuit, but I haven’t yet found a study that connects the two lines of research, which makes it unknown whether the Rb – R.ip and R2.artr are two separate circuits or part of a single circuit. If they’re two adjacent circuits, then presumably they communicate, but this is also unknown. Again the essay simulation needs to make a decision in the absence of scientific data. Because treating the two circuits as one larger circuit is simpler, the essay uses that model.

If thigmotaxis is part of a search strategy: reducing search dimensionality from two to one, then some of the ascending connections from this circuit, including from V.mr, R.dtg, and R.nin (nucleus incepts, a target of R.ip) to E.hc (hippocampus) could be spatial and navigational, not just anxiogenic. Lesions to those connections produce spatial navigational deficits in tests like the Morris water maze.

Although this essay has focused on anxiety studies that target the hindbrain, there are many studies that show forebrain anxiety circuits. In particularly P.bst.ov (bed nucleus of the stria terminals, oval nucleus), part of the extended amygdala and E.hc (ventral hippocampus) are strong anxiety-like centers [Han et al 2024]. Furthermore the combination of E.hc.v, A.bl (basolateral amygdala), and F.m (medial prefrontal cortex) [Padilla-Coreano et al 2016] is also a strong anxiety-like center. Again where “anxiety-like” is measured as modulating thigmotaxis. R.ip – V.mr are anxiety-related, but not directly implementing the thigmotaxis motor action.

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Essay 39: Hindbrain

Early studies described the hindbrain as a “reticular formation,” which means that under the microscope it looks like a find netlike structure, as if it was an undifferentiated, impenetrable mass. However, using modern genetic tools, the hindbrain shows a strongly hierarchical organization [Vishwanathan et al 2024]. The hindbrain is capable of action decision-making on its own, in opposition to a theory that forebrain systems like the basal ganglia are primary for action decision [Humphries et al 2007].

The vertebrate hindbrain can also be explored as a sequence of evolutionary additions, where early hindbrain provides locomotion but not other functions, as in the non-vertebrate chordate Amphioxus. The subcircuits of the hindbrain could be describes as a sequence:

  • Locomotion – exists in Amphioxus
  • Filer feeding – added in tunicates like the ascidian Ciona
  • Vestibular corrections for locomotion (“posture”) – lamprey larva
  • Vestibular stabilization for image vision – lamprey adult

In this essay I’m reviewing the hindbrain as this sequence of evolutionary steps and using it to introduce decision-making circuit patterns and also to clarify the hindbrain capabilities, which allow higher areas to use its fundamental abilities.

Xenopus tadpole

As a study animal the Xenopus (African clawed frog) tadpole has advantages of a simple nervous system and the additional advantage of similar behaviors to the chordate ascidian tadpole, believed to be the closest chordates to the vertebrates. The ascidian tadpole swims for only a few hours before permanently attaching to a rock or overhang using a cement gland on its palps (basically head) and settling permanently as a sessile filter feeder. It uses a simple photoreceptor ocellus for phototaxis and a gravity-sensing otolith for geotaxis to first swim up, then down if necessary, but preferably swimming up to a shadow-producing ledge. The Xenopus tadpole in an early stage also swims upward beneath a shadow to attach its cement gland to the underside of a leaf [Jamieson and Roberts 2000], [Roberts et al 2000], [Nokhbatolfoghahai and Downie 2005], [Rétaux and Pottin 2011] and some amphibian species tadpoles filter feed [Pryor 2014], but at a later development stage.

Amphibian locomotor CPG

The swimming CPG (central pattern generator) produces the alternating left and right muscle movements that progresses toward the tail along the trunk segments. The caudal hindbrain (R5-R8) can sustain swimming oscillations, even if more rostral areas are lesioned [Soffe et al 2009]. In contrast to the rhythmic caudal hindbrain, the rostral hindbrain has only loose rhythm and not synchronized to swimming [Soffe et al 2009]. So, along with locomotion, this circuit can demonstrate persistent neural activity as in working memory and show that persistence does not necessarily imply a single attractor state.

The caudal hindbrain (R5-R7, aka medulla) and N.sp (spinal cord) locomotor circuits have a simple organization with four neuron types [Soffe et al 2009].

  • N.mn (motor neuron) drives the muscle
  • R.din (descending interneuron) pattern generator and premotor
  • R.cin (commissural interneuron) inhibits opposite side to organize anti-phase oscillation
  • R.ain (ascending interneuron) lateral inhibition of sensory input [Roberts et al 2010]
Xenopus swimming central pattern generator. aIN (ascending interneuron), cIN (commissural interneuron), dIN (descending interneuron), MN (motoneuron)

R.din is the primary premotor neuron and its cellular properties support oscillations both intrinsically and with rebound firing after inhibition. R.din are the most medial and ventral stripe in the hindbrain and are marked by genetic transcription factor chx10 [Li WC and Soffe 2019]. The chx10 locomotor neurons are strongly conserved in vertebrates. In mammals chx10 hindbrain neurons contribute to locomotion, stopping [Bouvier et al 2015] and turning [Huang et al 2013], [Cregg et al 2020].

R.din fire rhythmically for swimming and fire early in the swimming cycle [Soffe et al 2009]. R.din initiate swimming and drive the rest of the CPG [Ferrario et al 2021]. R.din typically fire a single AP (action potential) on each swimming cycle alternative left and right [Li WC and Soffe 2019]. The early tadpole R.din population size is approximately 50 neurons [Soffe et al 2009].

R.din can oscillate through a combination of:

The R.din intrinsic NMDA-dependent oscillation can produce membrane oscillations even when APs are blocked [Li WC et al 2010], likely dependent on sodium leak currents [Svensson et al 2017]. Leak currents modulate AHP (afterhyperpolarization) and ADP (afterdepolarization), which regulates the membrane potential after an AP, which either makes subsequent APs harder to fire or easier to fire. So, cell properties can either encourage persistent firing or force only a single AP spike with a long refractory period. For R.din these properties promote oscillation, which differs from the other neurons in this circuit, which do not promote oscillations.

R.din intrinsic oscillation appears to be a secondary effect, not the main CPG driver [Bubnys et al 2019]. Rebound firing after R.cin inhibition is a stronger effect [Soffe et al 2009], [Moult and Cottrell 2013]. Although R.din oscillate independently, they will typically fire a single AP on each swimming cycle, alternating left and right [Li WC and Soffe 2019]. In the lamprey, there is a debate whether the commissural couple of the CPG is necessary for oscillation or if each side is an independent oscillator [Cangiano and Grillner 2018], [McClellan 2018]. Stimulating single R.din neurons in tadpoles rarely initiates swimming, with exceptions when the hindbrain is disconnected from the midbrain [Li WC and Soffe 2019], suggesting that the population of R.din is essential.

R.ci inhibits the contralateral R.din to coordinate the paired oscillators to fire in opposite phases. In Xenopus R.cin are glycine interneurons. As described above, the R.cin inhibition of R.din drives the oscillator by promoting rebound APs.

R.ain are inhibitory interneurons that suppress sensory input [Roberts et al 2010]. These form lateral inhibition with other CPGs, blocking sensory input to discourage competing actions. While the tadpole is swimming, it will respond less to touching of the trunk and tail.

While the CPGs for swimming are relatively simple, coordinating the multiple limbs for tetrapods is more complicated, particularly with the added challenge of gravity. For mammals and likely all tetrapods, the rhythmic generators are correspondingly more complicated. The exact coupling of rhythm generators and multiple pattern generators is a debated [McCrea and Rybak 2008].

A few things to take away here. First, the feedback inhibition in this CPG produces oscillation, which will be important for later WTA (winner-take-all) decision-making, because decision-making uses a similar structure. Second, the oscillatory sustaining behavior is dependent on intrinsic cell properties, not simply circuit connectivity. The R.din intrinsic oscillation and inhibition rebound are specific properties that neighboring neurons lack. They are specifically designed for their roles in driving oscillation.

Swimming eigenshapes

Borrowing from linear algebra, movement for simple bilateral animals can be described by a small number of basic vectors that encode basic shapes “eigenshapes,” implying that swimming actions are low dimensional. Almost all (95%) locomotion for the flatworm C. elegans can be described by four dimensions [Stephens et al 2008], almost all (96%) of ascidian tadpole swimming can be described by six vectors [Athira et al 2022] and 96% of zebrafish larva swimming is captured by three vectors [Girdhar et al 2015]. These basis vectors encode the lateral displacement of each body segment from the midline and a linear combination of the vectors produces the majority of posture shapes while swimming.

The zebrafish larva has fewer dimensions because it has a stiff spine that limits posture variability [Girdhar et al 2015]. In zebrafish larva, two of the three dimensions encode the swimming oscillation and the third encodes an initial turn. After an initial turn, zebrafish settle into a stereotypical swimming pattern. Most of the variation in swimming bouts is attributable to the depth of the initial of the initial turn.

The low dimensionality of vertebrate swimming suggests that it uses relatively simple circuits. The swimming CPG already covers two of the three basis shapes with variation in the initial turn using distinct action paths. This division between a stereotyped forward movement modulated by distinct turning circuits persists in tetrapods. The MLR (midbrain locomotor region) produces forward motion whether it’s stimulated unilaterally or bilaterally in mammals [Brocard et al 2010] and salamanders [Ryczko et al 2016], while separate turning systems drive chx10 R.rs (reticulospinal) neurons in the central hindbrain [Cregg et al 2020].

Tadpole locomotion action paths

At hatching tadpoles have limited senses, which simplifies understanding their action paths. Tadpoles have touch sensitivity, light sensitivity from the pineal eye, and possibly water movement from the lateral line [Roberts et al 2010]. The lateral eyes are not functional until a few days later.

Tadpoles have four major action paths [Borisyuk et al 2017];

Beside the four main action paths, tadpoles have a few additional action paths:

Xenopus tadpole action paths. Each column is an action path. ain (ascending interneuron), din (descending interneuron), dla (dorsal lateral ascending), dlc (dorsal lateral commissural), in5 (trigeminal interneuron), M.dmd (diencephalon/mesencephalon descending), mhr (mid-hindbrain GABA inhibitory), mn (motoneuron), M.pineal (pineal eye), N.rb (Rohon-Beard trunk touch), N5 (trigeminal touch), xin (hindbrain extension neurons)

The above diagram shows the action paths and their implementing circuits. Each box represents a small collection of functionally-similar neurons. As a general pattern, primary sensory neurons like N5 (trigeminal head touch, 5th cranial nerve) drive a collection of relay neurons like R.in5 (trigeminal interneurons), which spatially integrate the sensory evidence and drive decision pre-motor areas like the CPG R.din neurons or feed into an evidence integrator like the proposed R.xin (extended hindbrain interneurons).

Head press stop

The tadpole has different reactions to head press than for head touch. While head touch drives swimming, head press stops the tadpole when it reaches an attachment site, like the chordate ascidian tadpole [Johnson et al 2024]. Xenopus tadpoles have a cement gland on their head [Nokhbatolfoghahai et al 2005], which they use to attach to the bottom of ledges, lily pads, or the water surface. Similarly the ascidian sensory neurons in the palp area trigger stopping and settling, when the ascidian settles down to its adult sessile filter feeding form. However, the ascidian palp are chemosensory as well as mechanosensory [Ryan et al 2016], [Hoyer et al 2024] and have forebrain transcription factors [Cao et al 2019], [Liu and Satou 2019], but the Xenopus tadpole is purely mechanosensory using hindbrain N5 (trigeminal) [Roberts et al 2010] and no forebrain olfactory input. In addition, the vertebrate N5 trigeminal placode does not exist in tunicates. These differences make it unclear if the prototypical vertebrate was more like the ascidian tadpole or the amphibian tadpole.

Head press neurons are N5 that contact R6.mhr (mid-hindbrain GABA inhibitory) neurons that contact R6.din swimming CPG [Roberts et al 2010]. R6.mhr fire at very low rates without stimulation. R6.mhr cell bodies that respond to head press are in approximately R6-R8 with short dorsal dendrites and long ventral dendrites [Perrins et al 2002]. A single R6.mhr can halt swimming, but single neuron firing is rare because a head press activates all R6.mhr [Ferrario et al 2021]. R6.mhr are rhythmically inhibited by swimming [Perrins et al 2002].

The Xenopus tadpole is non-feeding at this stage, and it loses the head press shortly afterward. Although some amphibian tadpoles do have a filter feeding stage, I haven’t read of any that use the cement gland as part of their filter feeding. The missing chemo sensation and associated forebrain input is not necessary if the animal doesn’t use that information for filter feeding.

Head touch

The tadpole head touch is a distinct action path from the head press. Head touch produces swimming in a random direction. A head touch activates 70 N5 neurons that active R2.in5 (trigeminal interneurons) in R2 and R3, which then activate proposed integrating neurons R.xin [Buhl et al 2012], [Buhl et al 2015]. The R2.in5 are not specific to a head location but integrate from most touch neurons across the ipsilateral head. When the signal is strong enough, nearly all R2.in5 spike at least once. Each R2.in5 connection to R6.din is weak, with a small EPSP and unreliable 49% probability of glutamate. However, because the population does strongly converge to R5.din, simultaneous population firing will drive R5.din and swimming, but a single noisy R5.in5 will not trigger a false alarm.

Even a reflex action requires some nuance. Because individual neurons are noisy and the world itself is noisy, a small or noisy sensation shouldn’t trigger an expensive escape. In the tadpole, N5 head touch strongly converges on R2.in5 simultaneously [Buhl et al 2012].

The swimming direction from a head touch is more complicated than a reflex [Buhl et al 2015]. A strong touch will drive fast 25ms ipsilateral swimming that is reflex-like with a higher threshold and immediate decay, but weaker touches will drive a longer bilateral integration that ramps from 25ms to 50ms, possibly using the proposed R.xin neurons [Koutsikou et al 2018], [Ferrario et al 2021].

Trunk touch

Tadpole trunk touch also drives swimming and is functionally similar to head touch, but is a distinct action path. Head touch neurons are from the trigeminal placode through the N5 cranial nerve, while trunk touch are non-placode Rohon-Beard touch cells that travel through the spine. The trunk sensory pathway goes through N.sp.dlc (dorsolateral commissural) and N.sp.dla (dorsolateral ascending) neurons and then to R.xin integrating neurons, which activates R.din swimming CPG [Borisyuk et al 2017]. N.sp.dlc produces weak, long NMDA excitation of all contralateral neuron types, including motoneurons [Roberts et al 2010]. The swimming direction is unpredictable even if the midbrain is disconnected by a MHB lesion [Ferrario et al 2021].

Although N.sp.dla and N.sp.dlc trunk touch neurons have fast responses that decay rapidly, the R.din CPG neurons show a slow ramping EPSC, which is too long to come only from the trunk sensory neurons [Koutsikou et al 2018]. N.sp.dlc does not appear to contact R.din directly, and N.sp.dlc has a short response on the order of 60ms to 160ms, but R.din shows ramping EPSC for nearly 1s before reaching firing threshold. A hypothetical population of R.xin neurons are proposed to produce the sustained and ramping input. The slower excitation allows time for temporal summation and integration with other inputs such as the pineal eye or head touch, and enables random swimming direction, which improves escape from predators by reducing predictability. These neurons have not yet been identified, but they appear to be hindbrain-specific because a MHB lesion does not eliminate the ramping behavior.

This kind of ramp-to-threshold decision making is commonly modeled as a DDM (drift diffusion model) and studied for decision making in the cortex and OT (optic tectum). The R.xin neurons, when they are identified, could provide insights into cortical decision making by providing a simpler but complete hindbrain circuit in contrast to the more complex, distributed OT and cortex model, which includes complex loops with the thalamus and basal ganglia.

Dimming response

The early Xenopus tadpole (stage 37) doesn’t have retina vision until lateral development (stage 44) after a few days. Until the paired eyes are available, light response uses the single pineal eye, which is closely related to the adjacent habenula. Dimming from M.pineal (pineal eye) causes upward swimming [Jamieson and Roberts 2000]. Upward swimming is in a spiral, like ascidian swimming. The Xenopus tadpole’s upward swimming is like ascidian tadpole upward swimming response to dimming [Bostwick et al 2020], which uses a combination of geotaxis from an otolith and phototaxis from photoreceptors [Olivo et al 2021]. M.pineal drives sensory relay M.dmd (diencephalic/mesencephalic descending neurons), which drives R6.din [Borisyuk et al 2017].

The probability of tadpole responding to light dimming is low. Swimming and reattachment of the cement gland can be quick (8s) but also longer (61s). At stage 44 tadpoles swim continuously, but the pineal eye persists beyond stage 44. At stage 45 lateral eyes become functional. Because young tadpoles do not feed at this stage [Jamieson and Roberts 2000], this swimming and cement-gland attachment is defensive, not for filter feeding.

The Xenopus tadpole also has UV light avoidance using deep UV photoreceptors near the hypothalamus. These photoreceptors are not related to either the retina or to the pineal eye. The action path uses neurons in the caudal hindbrain (R6 area) [Currie et al 2016].

Struggle

Struggle is a distinction motion from swimming, used to escape predator grasp. In Xenopus the structure circuit has a similar structure to a swimming CPG but is a distinct neuron population [Borisyuk et al 2017], [Roberts et al 2010]. While the struggle network is active, the R.din swimming network is inactive.

ATP-based stopping

The previous actions paths covered swimming, but a control system is also necessary for stopping. ATP and adenosine are natural for timing because neural activity uses ATP, which degrades into adenosine. As activity continues adenosine builds up. An adenosine receptor can then inhibit swimming after adenosine builds up. In Xenopus stopping of swimming uses this adenosine/ATP timing system [Dale 1998], [Dale 2002]. When adenosine receptors are disabled, swimming extends from 215s to 600s.

Zebrafish locomotion

The zebrafish larva has additional hindbrain locomotion systems that illustrate hindbrain decision making. The zebrafish hindbrain locomotion sorts into three major clusters: forward translation, left turns, and right turns [Feierstein et al 2023]. Turning uses a common set of chx10 neurons in R.rs.v (ventral reticulospinal) for phototaxis, OMR (optomotor reflex), dark-flash, and spontaneous turns [Huang et al 2013]. Fast escape and slow swimming use distinct circuits, which parallels the fast and slow swimming circuits of the chordate Amphioxus [Lacalli and Candiani 2017]. Neurons in the fast path are more ventral and are born earlier than slower swimming circuits [Agha et al 2024].

The zebrafish escape has at least two independent circuits [Marquart et al 2019]

  • R4.mc (Mauthner cell) escape SLC (short-latency C-start)
  • R1.llc (long latency C-start)

The R4.mc are giant, easily identified neurons in R4, which are part of the ASR (acoustic startle response), where N8 (auditory nerve) directly drives R4.mc, which directly drive N.sp.mn (spinal motoneurons) in a fast, three synapse escape reflex to loud sounds. Although R4.mc is most studied for its acoustic response, it also drives escape for looming threats from OT [Martorell and Medan 2022], and touch from the trunk and head [Bhattacharyya et al 2017]. Early in development, head touch neurons are the first R4.mc input [Kohashi et al 2012].

R1.llc are a set of R1 neurons that respond to slower environmental threats and also produce escape swimming [Marquart et al 2019]. While R4.mc are extremely well-studied, the connectivity and function of R1.llc is less known beyond their response to lower priority threats. The threshold between R4.mc SLC and slower R1.llc LLC is modulated by many factors, including specific calcium ion receptors in R6.dc [Shoenhard et al 2022].

The ascidian tadpole has ddN cells, which are proposed as homologous to R4.mc. ddN cells are the only descending and decussating (commissural) cells in Ciona [Ryan et al 2017].

In zebrafish larva locomotion also initiates from M.nmlf (nucleus of the medial lateral fasciculus). The mlf is the main locomotion and oculomotor nerve tract through the hindbrain. M.nmlf is closely tied to M.pt (pretectum) and OT (optic tectum) and drives movement for optic flow, dimming, and hunting. M.nmlf is also activated by head touch [Sankrithi et al 2010], serving a similar function to the Xenopus R.in5 neurons.

Mauthner cell – decision with FFI

The R4.mc (Mauthner cell) escape circuit is a good illustration of decision making, because the circuit rapidly chooses between turning left or right. R4.mc escape circuit is only three synapses long, with the N8 (acoustic) sensory neurons, R4.mc premotor neurons, and the final N.sp.mn (spinal) motoneurons. R4.mc choose an initial turn direction, suggesting that only one of the two R4.mc cells should activate to avoid delays from competing, simultaneous left and right activation. Although touch may be a simple, non-conflicting system, where touching the left of the head drives a right turn, the direction of other senses like sound, vision, or lateral-line can be more ambiguous. Both left and right sensors can suggest a threat or obstacle to avoid. The system needs a WTA (winner-take-all) circuit.

In the diagram below a sound to the left drives a swimming muscle contraction on the right (‘C-bend’) followed by bilateral swimming and the reverse for a sound to the right. In the R4.mc circuit, the crossing is downstream of the R4.mc neuron.

Winner-take-all circuits for left/right escape decisions. The left panel shows a circuit with simple FFI (feedforward inhibition), and the right panel adds competing disinhibition of the contralateral FFI. IN (FFI interneuron), N8 (acoustic nerve), R4.mcell (Mauthner cell).

As a first attempt at this WTA circuit, consider FFI (feedforward inhibition). A left sound drives the right choice and suppresses the left choice using an inhibitory GABA interneuron, and the flipped circuit for a right sound. The left diagram above shows this circuit. When one side significantly outweighs the other, the WTA circuit works by suppressing the other side, and we have the basis of a decision circuit.

However, this circuit runs into trouble when both sides are nearly equal or are equal. Because of the mutual inhibition, the choice neurons may not register any choice at all [Koyama et al 2016]. In some situations like avoiding an obstacle, stopping may be a reasonable outcome, but continuing to move forward without turning is not. In other cases like escaping a predator, not acting can be fatal. What we need is a true WTA circuit, not a circuit that fails for nearly equal input.

One solution is to add disinhibition to the FFI [Koyama et al 2016]. The diagram on the right shows the addition of FFI disinhibition. Each inhibitory neuron also inhibits its opposing peer with the effect of disinhibiting its primary sensor. The Koyama study examined these FFI circuits with and without disinhibition, showing that the disinhibition circuit sharpens the choice, making a better WTA circuit with a minimal zone of indecision.

Habenula and R.ip in R1

The R1 area near the MHB also includes Hb (Habenula) input to the hindbrain, projecting to both R1.ip (interpeduncular nucleus) and V.dr (dorsal raphe), both derived from ventral R1, and to V.mr (median raphe) derived from ventral R2-R3. Hb is the main input to R1.ip. Hb is derived form the M.pineal area and is involved with phototaxis [Chen X and Engert 2014], chemotaxis [Chen WY et al 2019], thermotaxis [Palieri 2023], and CO2 avoidance [Koide et al 2018], essentially a gradient-following system. The projections from R1.ip are less well understood, but R1.ip.r (rostral R1.ip) appears to be part of the head direction circuit [Petrucco et al 2023], and R1.ip.c (caudal R1.ip) is strongly left vs right directional [Dragomir et al 2020]. The location and function of R1.ip.c is similar to R2.artr (anterior rhombocephalon turning region), but no studies have explored whether they are connected areas or independent.

Unfortunately, the detailed action output path has not been detailed, although logically the Hb-R1.ip driven taxis behavior must connect with the locomotion motor somehow.

Filter feeding

The second major hindbrain system develops to support filter feeding and digestion. Since early aquatic vertebrates don’t need to distinguish filter feeding from breathing, a relatively simple system suffices. Adding filter feeding as an addition to locomotion introduces major decisions between the two systems, because the animal needs to decide when to filter feed and when to move.

While the locomotor hindbrain is similar to earlier chordate Amphioxus locomotion, the Amphioxus filter feeding differs from ascidian and vertebrate feeding because Amphioxus uses cilia for water flow and ascidian and early vertebrates actively pump water through pharyngeal arches [Li S and Wang 2021]. The ascidian filter feeding and digestion neurons are marked by the phox2 transcription factor [Gigante et al 2023]. In vertebrates, phox2 marks the visceral nervous system including branchial arch muscles like the face, jaw, neck, and pharynx, with corresponding hindbrain areas R.nst (nucleus of the solitary tract), N5 (trigeminal jaw), N7 (facial nerve), R.na (nucleus ambiguus), R.m10 (dorsal vagus motor), N10 [Dufour et al 2006].

Vertebrate hindbrain feeding and breathing is a two phase pumping system [Li S and Wang 2021]. The buccal cavity (mouth area) bounded by lips. In lamprey, the N5 muscles in R2-R3 expel water from the buccal cavity and rebound, passive recoil brings food and water into the mouth. A second phase drives the water through the pharyngeal slits, into a posterior operculum area, which is emptied by N7 muscles in R4-R5.

Early vertebrate filter feeding circuit using a dual phase system. Water first flows into the mouth/buccal cavity using N5 trigeminal premotor in R2-R3, which also drives the water through the pharyngeal slits. Water is accepted on the other side in the operculum and expelled using N7 premotor in R4-R5. Digestion premotor is handled by R.nts and R.m10. N5 (trigeminal cranial nerve), N7 (facial nerve), N10 (vagal nerve), R.nts (nucleus of the solitary tract), R1.pb (parabrachial nucleus).

Amphioxus breathing is mostly through the skin and the pharyngeal slits are exclusively for filter feeding. The muscular filter feeding improved feeding, which opened a space to use the pharyngeal slits for a second purpose of breathing [Li S and Wang 2021]. The introduction of the jaw introduced new feeding opportunities beyond filter feeding, which adapted the older system to new requirements. Similarly, air breathing adapted some of the same circuits. The lamprey respiratory rhythm generator is in R2.m7 similar in location and function to the mammalian pre-Bötzinger area.

Filter feeding vs locomotion

Because sedentary filter feeding is mutually exclusive with locomotion, a sedentary filter feeder needs to stop filter feeding when moving away from a threat or because of low food yields, and start after arriving at a new food spot. Feeding can fail for several reasons, either from lack of available food, toxic food or digestion problems, or environmental hazards that trigger itch-like nociceptors, or possible predator threats. If sand becomes lodged in the pharyngeal slit filter, the animal can stop normal filter feeding and instead pump water in the opposite direction to clear the debris. For any of these problems, the animal needs to stop filter feeding, and often should move from the current location and find a new place to feed.

As part of the circuit for these decisions, the rostral R1.pb (parabrachial nucleus) is strongly tied to the more caudal R.nst (nucleus of the solitary tract) feeding and digestion areas. Unlike the areas discussed above, R1.pb is not primarily a rhythmic CPG center, although it is involved in breathing [Arthurs et al 2023]. It integrates a broad range of feeding, digestive, and visceral information, including taste, both positive like sweet and negative like bitter, and digestive signals like the detection of toxins in the gut. R1.pb also includes nociceptive signals from both N5 and N.sp, including itch. R1.pb CGRP (an alarm peptide) controls meal termination [Campos et al 2016] and signals danger [Campos et al 2018], essentially acting like a general alarm [Palmiter 2018], and suppressing feeding from threat [Yang et al 2021].

Other R1 areas are also involved in a decision to stop filter feeding, and move to avoid the area. V.lc (locus coerulus source of noradrenaline), also in R1, is a phox2a region that can suppress feeding and encourage place avoidance [Yang et al 2021]. Similarly, the serotonin V.mr (median raphe) from R2-R3, mentioned above in connection with Hb, is also associated with avoidance.

The point for this essay is to show that the hindbrain includes higher-level decision making between two systems as well as decision making within hindbrain systems [Cisek 2022].

Sleep

The hindbrain is also associated with sleep. The area around R1.pb and V.lc is strongly associated with waking [Ao et al 2021] and is one of the only areas where a single lesion can produce a coma [Fuller et al 2011]. One the sleep-promoting side, an area near N7 (R5-R6) region, named R5.pf (prefacial) is associated with sleep [Anaclet et al 2014], [Anaclet and Fuller 2017], [Chen MC et al 2020]. The two regions are interconnected with R5.pf suppressing the wake-generating region in R1.

Vestibular locomotion

Unlike crawling on the sea floor, vertebrate swimming is three dimensional, which greatly complicates stability, especially considering external forces, currents, and wave motion. Pre-vertebrate chordates like the ascidian tadpole swim in a helical pattern [McHenry and Strother 2003], which provides some swimming stability, but impairs the directionality of any sensing and navigation system. Amphibian tadpoles also swim in a spiral pattern [Jamieson and Roberts 2000], but adult swimming is stabilized as their vestibular and visual systems develop.

The vestibular system of early zebrafish larva is simplified with only one of the otoliths (the utricle) and none of the semicircular canals have developed [Bianco 2012]. Early development suggests pitch and roll posture correction near R4 [Straka and Baker 2013]. Still, this one system is critical for the larva’s survival and corrects errors in pitch, allowing the larva to consistently choose up or down using R4.tan (tangential nucleus near R4) [Straka and Baker 2013]. These corrections are a combination of the vestibular system in the hindbrain and optic flow from M.pt (pretectum), which are relayed to pitch-specific posture systems in the hindbrain [Wang K et al 2019]. Because the otolith can’t distinguish forward acceleration from the head tilting backward, the optic flow is critical for distinguishing the forward movement until the semicircular canals develop [Bianco et al 2012].

Vestibular system for locomotion posture control.

Vestibular information uses N8 (vestibuloauditory nerve), which arrives at R4, near the R4.mc Mauthner acoustic escape cells. Vestibular information is split according to direction (pitch, roll, yaw) into specialized nuclei, which covers almost the entire hindbrain [Straka and Baker 2013]. The lamprey divisions include rostral R.aon and caudal R.pon for semicircular canal processing and an intermediary R.ion for otolith processing. These areas are also interconnected, providing more complex capabilities than simple reflexes. The vestibular system is organized by motor output, not by vestibular input [Straka and Baker 2013]. So, the pitch area receives vestibular input from N8 and optic flow from M.pt and combines them to produce corrective swimming. The information from optic flow to the vestibular system uses mlf (medial longitudinal fasciculus).

To control swimming, the lamprey’s swimming systems are organized into four columns along the caudal hindbrain. Different combinations of the columns provide different corrective motions such as rolling left or right, or pitching up or down [Deliagina et al 2014]. The system is organized by motor output, so rolling to the right is handled by a specific R.rs group. 68% of R.rs that respond to vestibular input respond only in one plane (yaw, pitch, roll), and 25% respond to rotation in more than one plane. This system is handled by the hindbrain. With a unilateral vestibular lesion, the lamprey continuously rolls [Deliagina and Fegerstedt 2000]. Lamprey swimming can be continuously modulated to control direction, speed, and posture (pitch and roll) [Sankrithi and O’Malley 2010].

Note that non-image-forming photoreceptors can help posture and stability, even without optic flow. Like the simple phototaxis of zooplankton [Randel and Jékely 2016], when the lamprey is rolled to one side, the photoreceptor on the lower side will report less light than the one pointing toward the surface, and the posture system can use this different to roll the animal to match the light from both eyes. In fish this is called the dorsal righting reflex.

Although the ascidian tadpole has a gravity-sensing otolith, which is used for geotaxis, this otolith is not homologous to the vertebrate vestibular system.

Cerebellum-like regions

The vestibular senses have an immediate issue that the animal’s own motion produces vestibular signals, which would cause problems for posture control such as pitch adaptation. The larva zebrafish is a good example because only the otolith utricle part of the vestibular system is available, but it can’t distinguish forward acceleration from pitch tilting [Bianco et al 2012]. A naive posture correction might drive the animal up or down simply because the animal moved forward. As an improvement the system needs to take the animal’s own movement into account, which is a function of the cerebellum in R1.

The cerebellum and cerebellum-like structures are adaptive filters that learn how the animal’s own movement affects sensory input, including the lateral line and vestibular system [Bell et al 2008], [Montgomery et al 2012].

The cerebellum and cerebellum-like systems are too complex to cover in detail, but they’re important to mention because they’re connected with all the systems in the hindbrain.

Vestibular optic stabilization

The hindbrain also includes stabilization for the image-forming eye, both using VOR (vestibular-optomotor reflex), where vestibular data stabilizes the visual image using eye movements, OKR (optokinetic reflex), where optic flow stabilizes the image using eye movements, and OMR (optomotor reflex), where optic flow drives body movements to stabilize the image. OKR and OMR are widely studied reflexes.

However, since these image-stabilization reflexes assume the animal has already evolved an image-forming eye that uses stable images, these reflexes must have developed after the eye. The image-forming eye drives the evolution of muscles to stabilize the image. But note that stability is not absolutely required for vision because optic flow can provide information even with a fixed eye.

This late development may explain the apparent disorganization of the eye movement system. Horizontal eye movement in one direction uses motor neurons in the caudal hindbrain N6 (abducens) near N5, but the opposing movement is in the midbrain N3 (oculomotor nerve) near the OT and M.pt.

Optic stabilization network. M.m3 (oculomotor in midbrain), N8 (vestibuloacoustic nerve), R1.m4 (oculomotor in R1), R6.N6 (abducens oculomotor in R6), R.vn (vestibular nuclei) in the hindbrain.

In the larval zebrafish the semicircular canals are not available, relying only on the utricle otolith, but that input for pitch VOR is ambiguous, because forward motion and pitch rotation produce the same information. Optic flow information from M.pt can disambiguate between the two, and eye stabilization uses a combination of vestibular and optical information [Bianco et al 2012]. Roll stabilization also uses vestibular and optical data.

Saccades

The hindbrain generates spontaneous saccades with the generator in ventral R2-R3 [Ramirez and Aksay 2021], which may correspond to R2.artr [Leyden et al 2021]. Saccades intersperse with fixation [Ramirez and Aksay 2021], where the eye maintains a consistent remembered position. 19% of spontaneous active hindbrain are saccade related. Although the OT is studied as a saccade center, the hindbrain can generate saccades on its own, although it can’t target them like the OT can.

R.vpni eye position integrator

The target eye position is managed by R.vnpi (vestibular position integrator) in the hindbrain near R6 that maintains the fixation eye position as the animal moves, updated by VOR or OKR [Aksay et al 2007], [Gonçalves et al 2014], [Lee MM et al 2015], [Miri et al 2011]. The velocity to position integrator has a long persistent time decay between 10s and 100s. It’s used as an example of a recurrent line attractor [Seung 1996], but the cells of R.vpni have multiple persistence times across neurons, varying from 2.5s to 14s [Miri et al 2011], contrary to the precise homogeneity of the canonical line attractor.

Hindbrain summary

The point of this essay is to demonstrate the hindbrain as an evolution of successive capabilities and to show how it is self-sufficient to control its own actions. Its action selection is determined as a hindbrain circuits with feedforward and feedback inhibition and even making decisions by integrate-to-threshold processes similar to the cortex and OT. As the [Borisyuk et al 2017] study suggests, the selection of the action paths can be generated from a simple neural model. In particular these action selections do not require midbrain or forebrain systems like the OT or basal ganglia.

[Humphries et al 2007] make a similar argument with the hindbrain “reticular formation,” pointing out that basal ganglia lesions do not completely impair behavior, even if the animal is decerebrate, where all of the brain anterior to the OT is removed, although the hindbrain-only behavior is limited. They point out that both descending and ascending information is available as an electrical bus like system, where each cluster can sample and send information to and from the bus. The more detailed tadpole studies described here with R.din/chx10 receives widespread inputs [Huang et al 2013] and R.ain provides widespread lateral feedback inhibition, while R.cin provides contralateral inhibition and R.din clusters provide recurrent excitation.

Despite the older “reticular” description, the hindbrain has a strongly modular hierarchical organization [Vishwanathan et al 2024]. For posture control, the lamprey has four organized motoneuron pools that fire differently to manage forward swimming, turns, pitch, and roll [Zelenin et al 2001]. As covered above, the hindbrain is highly structured both by its segmentation into functionally distinct rhombomeres and columns. The hindbrain is arranged into stripes of broad neuron classes (glutamate, glycine, gaba, serotonin), and within regions neurons are stacked according to age [Koyama et al 2011]. The genetic stripes of alternating excitatory (glutamate) and inhibitory (gaba and glycine) stripes [Soffe et al 2009], [Feierstein et al 2023], [Severi et al 2018] with the ventral locomotor marked by chx10 [Agha et al 2024].

The major hindbrain division of locomotor vs feeding/breathing is marked by different transcription factors. The ascidian-derived filter feeding system is marked by phox2b, while locomotor systems are typified by lhx3 [Mazzoni et al 2023].

The point isn’t to say that the hindbrain is independent of the rest of the brain. It’s more that the rest of the brain builds on basic decision making from the hindbrain. Now, an interesting detail from [Humphries et al 2007] is that they contrast the hindbrain to a decerebrate lesion anterior to OT, not the intact animal to a MHB (midbrain-hindbrain boundary) lesion. So, their argument leaves open the interesting question of the caudal midbrain.

Missing

This essay doesn’t explain Ppt (pedunculopontine tegmental), P.ldt (laterodorsal tegmental), S.nr (substantia nigra pars reticulata), V.rn (serotonin raphe nuclei), V.rmtg (gaba inhibition of Vta), and Vta.g (also gaba inhibition of Vta), all of which derive from the hindbrain, specifically R1. Most of these are important components of the basal ganglia, which has critical components in the forebrain and midbrain.

Midbrain additions to hindbrain functions

Understanding how the hindbrain works by itself can provide suggestions for understanding other areas like the midbrain. [Larbi et al 2022] studied the trunk touch escape swimming, focusing on MHB lesions disconnecting the hindbrain from the midbrain. Lesioning the midbrain did not eliminate the trunk escape, but it did slow the response and impair the WTA left vs right decision. With the MHB lesion, more touches produces simultaneous left and right premotor drives, which slowed the response by conflict. When the midbrain was allowed to participate, more decisions were clearly left or right. The midbrain then improves decision-making accuracy, even if it’s not absolutely required.

Similarly, without the midbrain the tadpole stopped swimming 23s after trunk stimulation, but with the midbrain the tadpole stopped swimming in 3s. The trunk to M.dmd connections is not sufficient to explain the results [Larbi et al 2022]. This suggests that the stopping decision has important components in the midbrain and/or forebrain.

Knowledge of the hindbrain to improve study of the midbrain. The midbrain could be studied as driving the hindbrain, with the hindbrain as motor output, or the midbrain could be studied as modulating existing hindbrain capabilities. The difference between these approaches might simplify understanding of the midbrain.

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