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 studied. 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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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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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 18: Proto-striatum

A problem with essay 17 was the lack of action stickiness, which became a problem for avoiding obstacles. When the animal hits an obstacle head-on, both touch sensors fire and the animal chooses a direction randomly. Because the decision repeats every tick (30ms) and chooses randomly to break ties, the animal flutters between both choices and remains stuck until enough random choices are in the same direction to escape the obstacle. What’s needed is a stick choice system to keep a direction once it’s selected. In some decision studies, this is a “win-stay” capability.

A previous essay solved this issue with muscle-based timing or a dopamine-based system, but some of the theories of the striatum function suggest it might solve the problem. The core idea uses the dopamine as a feedback enhancer to sway choice to “stay.”

Simplified proton-striatum circuit for “win-stay.” B.ss somatosensory (touch), B.rs reticulospinal motor control, M.lr midbrain locomotive region, S.pv parvalbumin GABA inhibitory interneuron, Snc substantia nigra pars compacta, S.spn striatum spiny projection neuron (aka medium spiny neuron), ACh acetylcholine, DA dopamine.

The circuit is intended not as the full vertebrate basal ganglia, but a possible core function for a pre-vertebrate animal in the early Cambrian. The circuit here represents only the direct path and specifically only the striostome (patch) circuit, and only represents the downstream connections, and ignores the efferent copy and upstream enhancements. Despite being simplified, I think it’s still to complicated as a single evolutionary step.

Simplified proto-circuit

If that simplified striatal circuit is too complicated for an evolutionary step, but lateral inhibition is a reasonable circuit.

Simplified photo-circuit with lateral inhibition.

The above simplified circuit is a simple lateral inhibition circuit with an added reset function from the motor region.

The main path is through the somatosensory touch (B.ss), through the substantia nigra pars compacta (Snc – posterior tubuculum in zebrafish) to the midbrain locomotive region (M.lr). [Derjean et al. 2010] traced a similar path for olfactory information. I’m just replacing odor with touch.

The reset function might be a simple efferent copy from the central pattern generator for timing. In a swimming animal like an eel, the spinal cord controls the oscillation of body undulation, moving the animal forward. Because the cycle is periodic, when the motor system fires at a specific phase such as an initial-segment muscle twitch, it can send a copy of the motor signal upstream as an efferent copy. That signal is periodic, clock-like, something like the theta oscillation in vertebrates, and upper layers can use that clock.

Zebrafish larva swim in discrete bouts, each on the order of 500ms to 2sec. Since the specific mechanism that organizes bouts isn’t known, any model is just a guess, but might motivate some of the striatal circuitry. Specifically, the acetylcholine (ACh) path in the striatum. The motor swimming clock could break movement into bouts with a reset signal.

Since the sense to Snc to M.lr is a known circuit [Derjean et al. 2010], lateral inhibition is a common circuit, and motor efferent copy of central pattern oscillation is also common, this simplified circuit seems like a plausible evolutionary step.

Improved circuit

Some problems in the simplified circuit lead to improvements in the full circuit. The simplified circuit is susceptible to noise, leading to twitchy behavior, because sensors and nerves are noisy. Secondly, when two options compete, a weaker signal might win the competition if it arrives first. An accumulator system that averages the signals will give better comparisons.

To improve the decisions, the new circuit adds a single pair of inhibition neurons, specializes the existing neurons, and changes the connections.

Circuit improving noise and decision.

To improve decision making, the S.spn neurons are now accumulators, averaging inputs over 100ms or so, just long enough to reduce noise without harming response time too much. As an implementation detail, the S.spn neurons might either accumulate calcium (Ca) itself, or a partner astrocyte might accumulate Ca.

To improve noise behavior, the added Snc inhibition neurons tonically inhibit the Snc neurons, so a stray signal from B.ss to Snc won’t inadvertently trigger the action before the decision. The dual inhibition is a slightly complicated circuit which reduces noise because an active path (disinhibited) has only sense inputs; the modulatory signals are taken away.

The dopamine feedback has the benefit of being a modulator instead of a pure feedback signal. Because it’s a multiplicative modulator, dopamine doesn’t trigger the cycle itself. When the signal ends, the dopamine feedback doesn’t continue a ghost reverberation signal.

Choice decisions: drift diffusion

Psychologists, economists, and neuroscientists have several useful models for decision making, primarily deriving from the drift diffusion model [Ratcliff and McKoon 2008], which extends a random walk model to decision-making. While most of the research appears to be centered on visual choice in the cortical (C) visual system, such as the lateral intraparietal area (C.lip), the concepts are general and the circuits simple, which could apply to many neural circuits, even outside of the mammalian cortex.

Drift-diffusion is a variation of a random walk. Each new datum adds a vector to an accumulator, walking a step, until the result crosses a threshold.

Circuits for leaky competing accumulator (LCA) and feed-forward models of two-choice decision.

One simple model is the leaky competing accumulator (LCA) of [Usher and McClelland 2001], where each choice has an accumulator, and the accumulators inhibit each other laterally. Another model use feedforward inhibition instead of lateral inhibition, where each sense inhibits its competitors. For this essay, these models seem a good, simple options for the simulation.

In the context of the striatum, [Bogacz and Gurney 2007] analyze the basal ganglia and cortex as a choice-based decision system. They interpret the direct path (S.d1) as the primary accumulator, and the indirect path (S.d2 / P.ge / H.stn) as feed-forward inhibition. They suggest that the basal ganglia could produce near-optimal decision in the two-choice task.

References

Bogacz R, Gurney K. The basal ganglia and cortex implement optimal decision making between alternative actions. Neural Comput. 2007;19:442–477

Derjean D, Moussaddy A, Atallah E, St-Pierre M, Auclair F, Chang S, Ren X, Zielinski B, Dubuc R. A novel neural substrate for the transformation of olfactory inputs into motor output. PLoS Biol. 2010 Dec 21

Ratcliff, R., & Childers, R. (2015). Individual differences and fitting methods for the two-choice diffusion model of decision making. Decision, 2(4), 237.

Usher, M., & McClelland, J. L. (2001). On the time course of perceptual choice: The leaky competing accumulator model. Psychological Review, 108, 550–592.

Wang, X.-J. (2002). Probabilistic decision making by slow reverberation in cortical circuits. Neuron, 36, 1–20.