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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Essay 29: Sleep and Basal Ganglia

The original impetus for this sleep essay was the idea that the basal ganglia could best be understood as a sleep and wake circuit [Kazmierczak and Nicola 2022]. After reviewing the rest of the brainstem sleep circuitry, it’s time to tackle the original problem.

Snr as a sleep/wake gate

Snr (substantia nigra pars reticulata) is the output node of the basal ganglia. It’s a set of GABA neurons that tonically suppress the majority of all brainstem motor areas including MLR (midbrain locomotor region), OT (optic tectum), and R.rs (hindbrain reticulospinal motor command) with corollary discharge to the thalamus. Snr can inhibit initiation of eating and motion [Rossi et al 2016], but don’t disrupt ongoing actions [Liu et al 2018]. Disruption of Snr can cause hyperactivity and insomnia [Geraschenko et al 2006]. The caudal Snr derives from hindbrain r1 (rhombomere r1 near the midbrain-hindbrain boundary) [Achim et al 2012], [Lahti et al 2015], [Partanen and Achim 2022], suggesting it may be evolutionarily old, possibly older than other basal ganglia regions.

Sleep as gating motive from action or sleep from action. Wake as disinhibiting sleep. Snr (substantia nigra pars reticulata).

As described in part 1 this essay, sleep suppresses senses, motivation and action. To implement this suppression, sleep could disconnect senses and motivation neurons from action neurons. In the above diagram, the gate is conceptual. The circuit could also inhibit the sense or action nodes directly instead of requiring specific gating neurons. This gating architecture has the advantage of simplicity because the sleep circuit can be localized in the gate, while the senses and actions can be mostly free of sleep circuitry.

As a preview, sleep neurotransmitters and peptides in BG (basal ganglia) include AD (adenosine), enk (enkephalin), MOR (μ-opioid receptor), and wake neurotransmitters include DA (dopamine), tac1 (tachykinin 1 aka neurokinin 1 aka substance P), dyn (dynorphin), and DOR (δ-opioid receptor).

If the vertebrate brain follows this architecture, Snr is well-placed to control that gate. Snr.m (medial Snr) projections have many collaterals to distinct motor areas and suppressing the wake-promoting areas covered earlier in this essay, which suggests widespread suppression as opposed to fine-grained control.

Snr.m gad2 connectivity. 60% of Snr.m inputs are from motor, motivation and wake areas. H.l (lateral habenula), H.stn (subthalamic nucleus), H.zi (zona incerta), M.pag (periaqueductal gray), OT.m (medial optic tectum), P.ge (external global pallidus), Ppt (pedunculopontine nucleus), R.rs (reticulospinal motor command), S.d (dorsal striatum), Snr.m (medial substantia nigra pars reticulata).

As the above diagram illustrates, despite its description as basal ganglia output, 60% of the gad2 (genetic marker), Snr.m inputs are outside of the basal ganglia, particularly from the midbrain (30%) and hypothalamus (10%) [Liu et al 2020]. Snr.m has two independent neuron types marked by gad2 and pv (parvalbumin), which are topographically organized with gad2 in Snr.m and pv in Snr.l (lateral Snr). While Snr.l.pv seems to be strictly motor related, Snr.m.gad2 are sleep related [Liu et al 2020]. However, [Lai et al 2021] reports Snr.l as sleep related.

Functional sleep and action requirements. Any ongoing action should suppress sleep, and sleep should suppress all actions.

Snr’s widespread motor and motivation connectivity suggests a possible primitive role in sleep. Sleep needs to suppress all actions, but any ongoing action needs to suppress sleep, because an animal shouldn’t fall asleep while eating or moving. It seems plausible that a primitive proto-vertebrate could have used Snr for sleep regulation without needing the rest of the basal ganglia.

Because astrocytes can integrate inputs spatially and temporally and are associated with sleep, it’s plausible that Snr astrocyte would be involved in this circuit. Interestingly Snr astrocytes are sensitive to dopamine and become hyperactive in the absence of dopamine [Bosson et al 2015] and are sensitive to glutamate from H.stn [Barat et al 2015].

Dopamine D2.i sleep / wake circuit

Although the independent Snr circuit is a functional sleep / wake gating circuit, it tonically inhibits the sense to action circuit, adding noise. An improvement to the circuit enables the gate when a signal is available, using the striatum to selectively open the gate. This circuit uses dopamine to open and close the gate. High dopamine is a wake signal and low dopamine is a sleep signal.

In the above diagram, Snr and S.d2 (D2.i associated striatum projection neurons) are sleep-promoting regions and S.d1 (D1.s associated striatum projection neurons) is a wake-promoting region. D2.i (inhibitory Gi-protein dopamine receptor) disconnects inputs, as opposed to inhibiting a neuron directly. When DA is available, S.d2 is disconnected, and S.d1 inhibits Snr, opening the gate. When DA is low, S.d2 is active, which inhibits S.d1, disinhibiting Snr, closing the gate and producing sleep. The D2i between S.d2 and S.d1 is from [Dobbs et al 2016].

The idea of the circuit is that the sense signal disinhibits itself during wake, but sleep prevents sense from disinhibiting itself. The minimal system only requires D2i circuits [Oishi et al 2017]. Wake enables the gate, and sleep disables the gate. Although I’ll cover D1s later, D2i is more fundamental because disabling D1s can be reversed by sufficient arousal, but disabling D2i can’t [Kazmierczak and Nicola 2022].

Note the diagram is somewhat incorrect, because direct S.d2 to S.d1 connection is weak [Tepper 2008]. Instead, S.d2 GABA inhibits S.d1 input at distal dendrites as opposed to inhibiting the neuron soma itself.

P.v ventral pallidum and S.core

While S.d2 neurons in model above suppresses motor for sleep, S.d2 in S.core (ventral striatum core aka nucleus accumbens) can produce sleep pressure by inhibiting the wake supporting P.v (ventral pallidum) [Oishi et al 2017]. P.v is a tonically active, wake-promoting nucleus, primarily inhibiting sleep areas or disinhibiting wake areas.

Sleep/wake control adding P.v as a tonic wake producing node. DA (dopamine), D2i (inhibitory Gi-coupled dopamine receptor), H.l (lateral hypothalamus), Hb.l (lateral habenula), M.pag (periaqueductal gray), Ppt (pedunculopontine nucleus – ACh), P.v (ventral pallidum), S.d1 (D1-associated striatum projection neuron), S.d2 (D2-associated striatum projection neuron), Snr (substantia nigra pars reticulata), V.mr (median raphe – serotonin), Vta (ventral tegmental area – dopamine).

P.v fill a similar wake-promoting role as S.d1, but unlike S.d1 it’s tonically active and affects the motivation loop of H.l, Hb.l, and Vta instead of gating sense from action. Where P.v supports general wake, S.d1 supports specific wake for an action. Like the previous basal ganglia sub-circuit, this sub-circuit only requires D2i receptors.

P.v promotes wake by inhibiting Hb.l sleep-producing system [Li et al 2023]. It also promotes wake through Vta by disinhibiting GABA interneurons [Li et al 2021]. (It could also disinhibit H.l orexin but I don’t have a reference).

In the model above, stimulating S.d2 inhibits wake-producing P.v, which disinhibits sleep-producing areas like Hb.l and inhibits wake-producing areas like H.l and Vta through GABA interneurons. Conversely, stimulating the D2i receptor by high DA inhibits S.d2, which disinhibits Pv, allowing it so promote wake. Disabling the D2i receptor activates S.d2, promoting sleep even with high dopamine [Qu et al 2010].

Note that S.d1 also connects to P.v and can produce wake [Zhang et al 2023]. P.v has multiple sub-populations with opposing functions. For example, it has both a hedonic hot spot for liked food and a cold spot for disliked food [Castro et al 2015]. For the sake of simplicity the diagram only shows a sleep-promoting path through S.d2, but there may be a wake-promoting path through S.d2 to an opposing P.v subpopulation.

D1s – stimulator dopamine receptors

Although using only D2i as a mode switch to the sleep path is functional, it can be improved by also enhancing the wake path with D1s (stimulatory Gs-coupled dopamine receptor).

D1s as enhancing the basal ganglia wake path. DA (dopamine), D1s (stimulatory Gs-coupled dopamine receptor), D2i (inhibitory Gi-coupled dopamine receptor), S.d1 (D1-associated striatum projection neuron), S.d2 (D2-associated striatum projection neuron), Snc (substantia nigra pars compacta – dopamine), Snr (substantia nigra pars reticulata).

The improved circuit works exactly like the D2i-only circuit but enhances the wake path when DA is available. Dopamine boosts both the signals from the sense to S.d1 and the signal from S.d1 to Snr [Salvatore 2024], [Kliem 2007], [Rice and Patel 2015]. When dopamine is available, it boots the sense to S.d1 signal with D1s, which more strongly disinhibits the gate by inhibiting Snr, which is also boosted by D1s.

The D1s in Snr and dopamine may be more important for motor suppression than dopamine in the striatum [Salvatore 2024]. In Parkinson’s disease and also normal aging, bradykinesia (slow movement) correlates with dopamine in Snr more closely than dopamine in the striatum. Motor symptoms in Parkinson’s disease don’t generally occur until striatal dopamine is reduced by 80%, but the effect on Snr is more immediate with only a small drop of dopamine.

Note that the Snc (substantia nigra pars compacta) to Snr dopamine comes from somatodendritic broadcast, not from an axon synapse. Snc dendrites in Snr produce dopamine to enhance the S.d1 to Snr connection.

Although the previous diagrams show the basic logic of the circuit, the basal ganglia use adenosine as a sleep-producing neurotransmitter, competing with dopamine.

Adenosine in striatum sleep

Adenosine is a product of the energy molecule ATP and is produced by neural activity, and also as a astrocyte transmission molecule. Although adenosine can accumulate in a circadian manner, particularly in P.bf (basal forebrain), it’s typically a shorter term sleep pressure. Caffeine is wake promoting by suppressing adenosine receptors.

Dopamine and adenosine are paired, opposing neurotransmitters in the basal ganglia: dopamine produces wake and adenosine promotes sleep. As an opposing signal to dopamine, the adenosine circuit is a flip version of the dopamine circuit.

Parallel adenosine sleep circuit in the basal ganglia. AD (adenosine), A1i (inhibitory Gi-coupled adenosine receptor), A2a.s (stimulatory Gs-coupled adenosine receptor), S.d1 (D1-associated striatum projection neuron), S.d2 (D2-associated striatum projection neuron), Snr (substantia nigra pars reticulata).

When adenosine is active in the above circuit, it cuts off S.d1 input and output and enhances S.d2’s suppression of S.d1. With S.d2 fully suppressed, Snr is free to suppress the gate and therefore suppress sleeping action.

Since adenosine is low in the morning, sleep is suppressed, which is enhanced by high ultradian morning dopamine. If A2a.s (stimulating Gs-coupled adenosine receptor) are stimulated in the striatum, the animal is more likely to sleep even in the morning [Yuan et al 2017], specifically in S.core not S.sh (ventral striatum shell aka nucleus accumbens) [Oishi et al 2017].

The dual signal system allows for interesting combinations at the boundary between sleep and wake. If adenosine is high with sleep pressing, then a large amount of dopamine motivation is required to continue wake. In fact, sleep deprivation down regulates D2i receptors, moving from the neuron membrane to the interior [Volkow et al 2012], which tips the balance toward sleep by diminishing the D2i-mediated wake signal. Caffeine inhibits both the A1i (inhibitory Gi-coupled adenosine receptor) and A2a.s receptors, tipping the balance to dopamine wake.

Dorsal striatum indirect path

The full S.d (dorsal striatum) path includes an indirect path, but this path may be more related to pure motor control, not sleep. As mentioned above, Snr divides into two populations Snr.l with pv neurons and Snr.m with gad2 neurons, and the Snr.l neurons are motor related, not sleep related [Liu et al 2020]. Similarly, the indirect path including P.ge (external globus pallidus) and H.stn (sub thalamic nucleus) may not be sleep related. Nevertheless, I’ll include it here, in case it is sleep related.

S.d model with indirect path included. DA (dopamine), D1s (stimulatory Gs-coupled dopamine receptor), D2i (inhibitory Gi-coupled dopamine receptor), H.stn (subthalamic nucleus), P.ge (external globus pallidus), S.d1 (D1-associated striatum projection neuron), S.d2 (D2-associated striatum projection neuron), Snc (substantia nigra pars compacta), Snr (substantia nigra pars reticulata).

Note that both P.ge and H.stn are tonically active, and they oscillate together at beta frequencies (roughly 10hz), which suppresses action. An excessive beta oscillation in this P.ge and H.stn circuit is a Parkinson’s disease symptom that suppresses motion and can also interrupt sleep. D2i receptors in H.stn mean that dopamine suppresses H.stn output [Shen et al 2012].

One significant experiment showed that lesioning P.ge increased wake by 40%, particularly eliminating normal circadian night-time sleep, replacing it with day-time like napping [Qiu et al 2016], which would suggest that P.ge is a major sleep center like Po.vl (ventrolateral preoptic area) [Vetrivelan et al 2010]. Note that this analysis would suggest that my basal ganglia sleep diagram is entirely wrong, because P.ge as a sleep center is basically incompatible with its position in the circuit.

P.ge – external globus pallidus

Lesioning P.ge increases wake by 40%, almost entirely eliminating circadian sleep [Qiu et al 2016]. However, this produces hyperactive chewing, weight loss, abnormal motor behavior and death in 3-4 weeks [Vetrivelan et al 2010]. Other manipulations of P.ge produce hyperactivity, abnormal movement, and odd stereotypical behavior [Gittis et al 2014]. So, it’s unclear to me that P.ge is a sleep center, but removing P.ge produces excessive action which then suppresses sleep.

In addition, P.ge is a heterogenous area with at least three major cell types with distinct projections and roles. Arkypallidal neurons project strongly and exclusively to the striatum. Lhx6 neurons project strongly to Snc and to some areas of H.stn, excluding the center. Pv neurons project to all of H.stn and also to T.pf (parafascical thalamus) [Gittis et al 2014].

Distinct projection neuron types of P.ge. H.stn (subthalamic nucleus), P.ge (external globus pallidus), Snc (substantia nigra pars compacta), Snr (substantia nigra pars reticulata), Spn (striatal projection neuron), Spv (pv marked striatum interneuron), T.pf (parafascicular thalamus).

With three projection types, it’s possible that they have entirely separate functions. For example, the lhx6 projections are functionally compatible with a sleep promoting role, and lhx6 neurons in H.zi (zona incerta) are sleep promoting [Liu et al 2017].

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Essay 27: Feeding State Machine

Essay 27 returns to feeding, which essay 23 had an earlier sketch of. While the animal in earlier essays could eat while moving, like snails and worms, this essay will add the requirement of stopping before eating, which requires extra control mechanisms to manage the state transition.

A filter feeder like amphioxus, a non-vertebrate chordate that may hint at pre-vertebrate feeding, might move to find a better feeding zone, but then settles down as a static filter feeder. Tunicates, which are more closely related to vertebrates settle down permanently as adults and dissolve their brain as no longer needed. Because I want to keep the essay simple, I’m imaging something more like licking, which is more studied in rodents, as opposed to a more alien filter feeding. The main problem for the essay to introduce locomotion and eating as distinct actions.

As a contrast to further explore the idea of states and state transitions, the essays also explores the transition between roaming and dwelling: global wide-ranging search vs area restricted search. Roaming and dwelling are more amorphous motivational states as opposed to the strict motor division between moving and eating.

Feeding states

Below is a more detailed diagram of the foraging and feeding states, revolving around the core foraging task. The animal passively roams until is finds an odor cue for a food target, which starts a seek to the target. If it finds food, the animal sops and eats.

In this model, the roam state and dwell state can be separate from seeking a target, depending on the animal’s environmental niche. A seek can start in a roam state or a dwell state, and seek cues may or may not initiate dwell state. For example, dwell state might only start when the animal eats nutritious food, indicating that food is nearby.

Feeding state diagram for the essay. ach (acetylcholine neurotransmitter) agrp (hunger peptide), ARS (area restricted search), cgrp (alarm/bitter taste peptide), da (dopamine), glp-1 (satiety/sickness peptide), ox (orexin wakefulness/action peptide), set (somatostatin peptide), V.dr (dorsal raphe), 5HT (serotonin)

The diagram includes important failure states. If seeking fails, the animal gives up and leaves the area, and must ignore the last cue to avoid perseveration. If the taste is bitter or toxic, the animal rejects the food. For now, I’m postponing longer failure states like the food lacking nutritional value or causing food poisoning.

To avoid perseveration, seeking the failed cue forever, the avoid state moves the animal away from the failed cue and ignores seek cues. A more sophisticated brain could remember the failed cue for a short time, but the current essays lack short term memory.

Eating here means specifically licking or filter feeding. I’m being precise here because the simulation requires it, and more vague neuroscience terms like “reward” are often unclear about exactly what it’s relation to actual eating are.

The connection between the dwell state and serotonin is from [Flavell et al 2013], [Ji et al 2021] which founds serotonin marking the dwell state in the flatworm C. elegans, and [Marques et al 2020] finding serotonin for a zebrafish dwell (“exploit”) state.

Roaming and dwelling

Food search phases have multiple strategies, broadly divided into roaming and dwelling. Roaming is a broader, more general search without a specific area or target. Dwelling or ARS (area restricted search) is slower, with tighter turning, where the current area is believed to be more likely to have food. [Horstick et al 2017] describes dwell as four properties: reduction in travel distance, increased change in orientation, increased path complexity, and a directional bias.

For this essay, dwelling is a motivational drive not a motor command, meaning it can overlap with other motivations and doesn’t provide a strict action state requirement. For example, dwell isn’t required to seek a target, which can occur in the roaming state, for example in C. elegans [Ji et al 2021].

In the C. elegans the dwell state is associated with serotonin and the roam state with PDF (pigment dispensing factor) [Flavell et al 2013]. In zebrafish the dwell state is associated with V.dr (dorsal raphe) serotonin [Marques et al 2020], the roam state is associated with SST (somatostatin peptide) [Horstick et al 2017]. While arousal isn’t quite the same as well, [Lovett-Barron et al 2017] found SST as a low-arousal marker, while CART, ACh (acetylcholine), NE (norepinephrine), serotonin, dopamine and NPY (neuropeptide Y) as signs of high arousal.

Triggers for the dwell state depend on the animal’s species [Dorfman et al 2020]. In C. elegans, which feeds on bacteria, nutritional feedback extends the dwell state [Ben Arous et al 2009]. In some animals a food cue triggers dwell, while in others only eating nutritious food triggers dwell. In zebrafish lack of a food cue causes H.c (caudal hypothalamus) activation decay [Wee et al 2019].

Reflexive eating

This essay models reflexive eating as a hindbrain system controlled by B.pb (parabrachial nucleus) with downstream motor and sensory in B.nts (nuclei tractus solitarius), M.mdd (reticular medulla), and B.3g (trigeminal – orofacial sensorimotor). The simulation isn’t as detailed, treating the hindbrain eating as a single low-level module.

Hindbrain modules involved in reflexive eating. B.3g (trigeminal), B.mdd (reticular medulla), B.nts (nucleus tractus solitarius), B.pb (parabrachial nucleus).

This innate circuit can with without input from higher areas [Watts et al 2022]. For example if rodents lack any dopamine, they won’t move or eat and will starve even if food is near them. However, if food or water is placed at their lips, which activates the innate circuit, the rodents will eat [Rossi et al 2016].

The B.pb area also processes sweet, bitter or salt, and can reject food without requiring higher areas. The higher areas modulate B.pb behavior, such as suppressing B.pb’s innate rejection of sour when drinking lemonade.

Because the B.pb innate eating and the MLR (midbrain locomotor region) are independent, some system much coordinate switching between moving and eating.

The illusion of state machine atomicity

The feeding state diagram suggests a simple atomic transition from seeking food to eating the food, but this transition needs management from some neural circuits. For example, when braking during driving, drivers need to pay attention to the stopping distance. Braking stops a car, but the state transition isn’t a simple atomic transition. For this essay’s eating task, some neural circuit must keep track of the animal’s stopping after seeking and only allow eating when locomotion has stopped.

State transition from seeking to eating, emphasizing the stopping state. H.pstn (parasubthalamic nucleus), H.stn (subthalamic nucleus).

H.stn (subthalamic nucleus) is involved with stopping, waiting, and switching tasks [Isoda and Hikosaka 2008]. Since H.stn also receives motor efference copies via T.pf (thalamus parafascicular nucleus) and Ppt (peduncular pontine nucleus), H.stn is in a good position to manage the stopping transition and can prevent eating until the locomotion has ended. The diagrams shows H.pstn (parasubthalamic nucleus) as a parallel area for gaiting eating, following [Barbier et al 2021].

H.stn and H.pstn state transition circuit

H.stn and H.pstn are well-placed to fulfill the transitions between seeking and eating. To flesh this idea out, here’s a simplified model of the seal to eat state transition circuit.

The main action paths are horizontal: moving is from H.stn to MLR to B.rs (reticulospinal motor neurons) and eating is from H.pstn to B.nts to orofacial licking motor neurons. The rest of the circuit manages the transition between the two states.

State transition circuit for move state to eat state. B.nts (nucleus tractus solidarus), fb (feedback), H.pstn (parasubthalamic nucleus), H.stn (subthalamic nucleus), MLR (midbrain locomotor region), Snr (substantia nigra pars reticulata), T.cl (centrolateral thalamus), T.pf (parafascicular thalamus).

Control over the transition comes from S.nr (substantia nigra pars reticulata), which inhibits eating when the animal is moving, and inhibits moving while the animal is eating. To know when the animal has stopped moving, H.stn receives motor efferent copies from T.cl and T.pf (centrolateral and parafascicular thalamus, aka intralaminar). As a note, T.cl contains cerebellum output, so H.stn may receive fine-grained motor timing feedback. H.pstn receives parallel eating efferent copies from B.pb and B.nts to know when the animal has stopped eating.

This circuit has the same structure as a lateral inhibition decision circuit, but the function is about handling timing and transition, not deciding between competing options.

Note: [Shah et al 2022] suggest H.pstn is more specific to suppressing feeding for aversive situations like food poisoning or a predator threat, but not the motor control as described here.

A note on this model: the actual neural circuit isn’t as clean, parallel and logical, because evolution isn’t an intelligent designer. Furthermore, this brain region is part of the neuropeptide core, where neuropeptide broadcast-like signaling can be more important than point-to-point circuit diagrams. Specifically, the disinhibition of B.pb eating is more likely peptides from the hypothalamus, not S.nr tonic inhibition.

H.l food zone

Studies on H.l (lateral hypothalamus) show two interesting results relevant here [Jennings et al 2015]:

  • Two distinct GABA neuron populations gate eating and seeking.
  • Two distinct neuron populations are active in a food zone or outside a food zone.

The food zone neurons partially explain how H.l decides between seeking and eating. How does this animal knows when it’s reached the food? In C. elegans there are dopamine chemosensory neurons that sense when the animal passes over food bacteria, and signals the animal to slow [Sawin et al 2000]. Dopamine chemosensory neurons also signal for the animal to turn more when leaving food (dwell-like state) [Hills et al 2004]. For this essay, using B.pb and B.nts to sense nearby food seems like a reasonable simplification because the simulation animal is aquatic and aquatic taste is a chemosensory system, similar to a close-range olfaction.

Food zone modulation of seeking and eating. fz (food zone), H.l (lateral hypothalamus).

The essay uses a signal when the animal is in a food zone or not in a food zone. The food zone signal inhibits eating or seeking actions when the animal is in a non-appropriate place. The essay uses a signal from B.pb as mentioned above.

In mammals H.l receives input from more sophisticated location systems than a bare chemosensory signal, such as E.sub.d (dorsal subiculum of hippocampus), S.ls (lateral septum, which processes hippocampal output), A.bl (basolateral amygdala, highly connected to hippocampus), S.msh (medial shell striatum receiving large hippocampus input) as well as the bare B.pb as for the simulation. All these areas incorporate more complicated environmental context. When the essays start investigating environmental context, I’ll need to revisit the H.l food zone with more sophisticated input.

H.sum as driving seek

Fleshing out the drivers of the seek circuit, consider H.sum (supramammillary nucleus, aka retromammillary) and its role in exploring (roaming and seeking). [Ferrell et al 2021] study a subset of H.sum neurons that express tac1 peptide (tachykinin, aka substance-P or neurokinin). These H.sum neurons correlate highly with movement velocity, a second before the action. Since they precede action, they’re upstream in the locomotive path.

H.sum is also involved in wakefulness [Liang et al 2023], [Plaisier et al 2020], motivation [Kesner et al 2021], and specifically food motivation [Le May et al 2019], and is modulated by hunger peptides like GLP-1 [Vogel et al 2016], [López-Ferreras et al 2018].

H.sum also participates in threat avoidance [Escobedo et al 2023], but that circuit is through Poa (preoptic area) and is outside this essay, although it would be interesting if any of the downstream circuitry is shared. H.sum is also well know for its role in hippocampal theta oscillations, novelty [Chen et al 2020], temporal and spatial memory [Cui et al 2013], and social memory, although those are outside the scope of this essay.

The diagram below shows a possible explore-related path of mammalian H.sum via the tac1 neurons.

Exploration locomotion driven through H.sum. H.l (lateral hypothalamus), H.sum (supramammillary nuleus), Hb.l (lateral habenula), MLR (midbrain locomotor region), M.pag (periaqueductal gray), P.ms (medial septum), V.dr (dorsal raphe – serotonin), Vta (ventral tegmental area – dopamine)

It may be important that H.sum and Vta (ventral tegmental area) are both neighbors and H.sum includes dopamine neurons and those dopamine neurons are sometimes considered an extension of the Vta [Yetnikoff et al 2014].

The following diagram gives an extremely rough idea of the adjacency of these areas. In a smaller primitive pre-vertebrate, these might not only be neighbors but mingled earlier functionality. The diagram includes H.zi (zona incerta) because it’s a neighbor, and also because H.zi is a food-seeking area [Ye et al 2023], but I’m postponing consideration of H.zi to a future essay.

Neighbors of the lateral habenula and supramammillary nucleus. H.l (lateral hypothalamus), H.pstn (parasubthalamic nucleus), H.stn (subthalamic nucleus), H.sum (supramammillary nucleus), H.zi (zona incerta), MLR (midbrain locomotive region), Ppt (Pedunculopontine pontine nucleus), Snc (substantia nigra pars compacta – dopamine), Snr (substantia nigra pars reticulata), Vta (ventral tegmental nucleus – dopamine), ZLI (zona limitans intrathalamica).

In addition, the rostral part of Vta nearest H.sum is part of p3 in the prosomeric embryonic model, which is a source of hypothalamic cells [Kim et al 2022]. For pre-vertebrates in this essay, then, there might not be a distinct between H.sum and Vta / posterior tuberculum, particularly since the essays are currently focusing on downstream connections, not upstream dopamine to a future striatum. Zebrafish downstream dopamine circuits directly modulate locomotor movement [Ryczko et al 2020], [Reinig et al 2017]. I think it’s reasonable to simplify this circuit for now and consider H.sum as directly projecting to MLR.

State transition circuit for seek to eat

Putting these ideas together yields something like the diagram below. Like the earlier simplified diagram, horizontal paths drive core seeking and eating behavior, and other circuits manage the state transition. Seeking uses the top path from H.l to H.sum to MLR to B.rs, which produces the final locomotion. Eating uses the bottom path from H.l to H.pstn to B.nts, which controls reflexive eating.

State management circuit for seek to eat transition. B.nts (nucleus tracts solitarius), fb (feedback), fz (food zone), H.l (lateral hypothalamus), H.pstn (parasubthalamic nucleus), H.stn (subthalamic nucleus), H.sum (supramammillary nucleus), MLR (midbrain locomotor region), T.cl (centrolateral thalamus), T.pf (parafascicular thalamus).

The left contains motivational drivers. The food zone and non food zone systems restrict seeking and eating, only allowing seeking and eating in appropriate locations.

In the center H.stn and its parallel H.stn enforce a smooth transition between seeking and eating, using motor efferent copies to pause transition until active motor stops. The smooth transition creates the illusion of an atomic state transition.

As a diagram note, I’ve used red for the H.l inhibitory neurons that gate seek and eat because they’re playing the same role as Snr neurons. Technically they should be blue, if following normal essay conventions.

Modulation of eating

The eating and feeding modulation systems are complicated and overlapping, which is too detailed for this essay, but two part are interesting. First, B.pb tonically inhibits eating with the CGRP peptide to B.nts. To enable eating, H.arc (hypothalamus arcuate) disinhibits B.nts eating by sending AgRP (a hunger peptide) to B.pb [Campos et al 2016].

Modulation of reflexive eating. AgRP (a hunger peptide), B.nts (nucleus of the solitary tract), B.pb (parabrachial nucleus), CGRP (an anti-eating peptide), H.arc (hypothalamus arcuate).

Although the essays have used the disinhibition pattern before, the pattern has generally ben GABA disinhibition, while this feeding disinhibition uses peptide signaling. As mentioned above, there are many feeding-related peptides that inhibit, excite, and modulate the feeding system without using connection based synapses.

As a parallel, a drinking modulation path goes through the basal ganglia Snr and OT (optic tectum) [Rossi et al 2016]. This path though the basal ganglia and OT coordinates anticipatory licking, while the earlier B.nts path is reflexive eating.

Control of anticipatory licking. B.mdd (medulla licking motor), OT.dl (deep, lateral optic tectum), Snr.l (lateral substantia nigra pars reticulata)

Another drinking path involves S.a (central/striatal amygdala), midbrain, and hindbrain circuits [Zheng et al 2022]. M.dp (deep mesencephalic nucleus) extends licking but doesn’t initiate it. So M.dp might extend eating after tasting. Similarly B.plc extends eating [Gong et al 2020]. S.a sst (somatostatin peptide) neurons promote eating and drinking [Kim et al 2017].

Sustained eating with an amygdala circuit. B.mdd (medulla motor eating), B.pb (parabrachial nucleus), M.dp (deep mesencephalic nucleus), S.a.sst (set-expressing neurons of the central amygdala).

Another path for tasting and eating runs through S.v (ventral striatum). [Sandoval-Rodríguez et al 2023] founds S.v directly controlling feeding using hindbrain taste input to extend eating, and using hindbrain GLP-1 (anti-eating peptide) to inhibit eating. Unlike most striatum circuits, these striatum neurons project directly to the hindbrain motor areas.

Ventral striatum taste exciting and food inhibition circuit with the hindbrain. B.ap (area postrema – nutrient sensing), B.mdd (medulla motor), B.nts (nucleus of the solitary tract), B.pb (parabrachial nucleus), Sv (ventral striatum / nucleus accumbens).

Because this essay is already complicated enough, this simulation isn’t covering all of these details. For simplicity, the simulation will use a simple continuation circuit inspired by the central amygdala and postpone other control circuits for later exploration.

Simplified eating continuation circuit with the central amygdala. B.mdd (medulla motor), B.pb (parabrachial nucleus), Sa.sst (central amygdala, sst projecting neurons)

The important point for now is that eating modulation uses multiple paths, some controlled through synaptic circuits and others through broadcast motivational peptides. The system is not one or the other, but a messy combination. To model this messiness, the simulation needs to handle both systems.

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Essay 22: Subthalamic Nucleus

After essay 21 changed the animal’s default movement to a Lévy exploration, it’s immediate to ask whether that random search is a full action, just like a seek turn or an avoid turn. An if exploration is a controlled action, then the model needs to treat exploration as a full action, like approach or avoid.

Exploration as a full locomotive system at the level of approach and avoid.

[Cisek 2020] identifies a vertebrate system for exploration, including the hippocampus (E.hc) and its associated nuclei such as the retromammilary hypothalamus (H.rm aka supramammilary). Essay 22 considers the idea of treating the subthalamic nucleus (H.stn) as part of the exploration circuit.

Subthalamic nucleus

H.stn is a hypothalamic nucleus from the same area as H.rm, which is part of the hippocampal theta circuit, which synchronizes exploration and spatial memory and learning. However, H.stn is part of the basal ganglia and not directly connected with the exploration system.

[Watson et al. 2021] finds a locomotive function of H.stn, where specific stimulation by the parafascicular thalamus (T.pf) to H.stn starts locomotion. If the stimulation is one-sided, the animal moves forward with a wide turn to the contralateral side. T.pf includes efference copies of motor actions from the MLR as well as from other midbrain actions.

Locomotion induced in the H.stn by T.pf stimulation. H.stn sub thalamic nucleus, T.pf parafascicular nucleus, MLR midbrain locomotor region.

For essay 22, let’s consider the H.stn locomotion as exploration. Since H.stn is part of the basal ganglia, the bulk of essay 22 is considering how exploration might fit into the proto-striatum model of essay 18.

Striatal attention and persistence

Since the current essay simulation animal is an early Cambrian proto-vertebrate, it doesn’t have a full basal ganglia. Evolutionarily, the full basal ganglia architecture could not have sprung into being fully formed; it must have developed in smaller step. Following a hypothetical evolutionary path, the essays are only implementing a simplified striatal model, adding features step-by-step. Unfortunately, because there’s no living species with a partial basal ganglia — all vertebrates have the full system — the essay’s steps are pure invention.

The initial striatum of essay 18 was a partial solution to a simulation problem: persistence. When the animal hit a wall head on, activating both touch sensors, it would choose randomly left or right, but because the simulation is real-time not turn-based, at the next tick both sensors remained active and the animal would choose randomly again, jittering at the wall until enough turns of the same direction escaped the barrier.

proto-striatum circuit for persistence by attention.
Proto-striatum for persistence by attention. Action feedback biases the choice to the last option: win-stay. B.rs reticulospinal motor command, Ob olfactory bulb, MLR midbrain locomotor region, Snc substantia nigra pars compacta (posterior tuberculum).

The main sense-to-action path is from the olfactory bulb (O.b) through the substantia nigra (Snc aka posterior tuberculum in zebrafish) to the midbrain locomotor region (MLR) and to the reticulospinal motor command neurons (B.rs), following the tracing and locomotive study of [Derjean et al. 2010] in zebrafish and Vta/Snc control of locomotion in [Ryczko et al. 2017]. The proto-striatum circuit is built around that olfactory-seeking circuit, acting persistent attention.

The proto-striatal model uses an efference copy of the last action from the MLR to bias the choice of the next action via a MLR to T.pf to striatum path. The model biases the choice through removing inhibition of the odor to action path. If the last action as left, the left odor is disinhibited, making it more likely to win.

The striatal system uses disinhibition for noise reasons. [Cohen et al. 2009] studied attention in the visual system and found that attention removed coherent noise by removing inhibition. By removing inhibition, the attended circuit is less affected by the controlling circuit’s noise.

Note: essay 19 considered an alternative solution to the attention issue by following the nucleus isthmi system in zebrafish as studied in [Grubert et al. 2006], where the attention to the win-stay odor used acetylcholine (ACh) amplification to bias the choice.

Striatal columns: approach and avoid

An immediate difficulty with the simple proto-striatal model is the lack of priority. Although left vs right have equal priority, avoiding a predator is more important than seeking a potential food source. Unfortunately, the proto-striatum treats all options equally. As a solution, essay 18 split the striatum into columns, where each column resolves an internal conflict without priority (“within-system”) and the columns are compared separately (“between-systems”), where “within-system” and “between-system” are from [Cisek 2019].

Proto-striatum columns for maintaining attention.
Dual striatum column for approach and avoid, where MLR resolves the final conflict. B.rs reticulospinal command neuron, B.ss somatosensory (touch), MLR midbrain locomotive region, M.pag periaqueductal gray, Ob olfactory bulb, S.ot olfactory tubercle, S.d dorsal striatum.

Subthalamic nucleus and exploration

If we now treat exploration as a distinct action system, then it needs its own control system and column in the proto-striatum. The within-system choice for exploration is the left and right turns for a random walk, and the between-system choices are between the exploration system and the odor-seeking system.

As a possible neural correlate of exploration, consider the sub thalamic nucleus (H.stn). The sub thalamic nucleus is derived from the hypothalamus, specifically from the same area as the retromammilary area (H.rm aka supramammilary), which is highly correlated with hippocamptal theta, locomotion and exploration.

[Watson et al. 2021] finds a locomotive function of H.stn, where specific stimulation by the parafascicular thalamus (T.pf) produces locomotion via the midbrain locomotive region (MLR). T.pf includes efference copies of motor actions from the MLR as well as other midbrain action efference copies. In the proto-striatum model, the feedback from MLR to striatum uses T.pf.

Exploration locomotive path through H.stn. H.stn sub thalamic nucleus, MLR midbrain locomotive region, T.pf parafascicular thalamus.

Seek and explore with dual striatal columns

Suppose the striatum manages both odor seeking (chemotaxis) and default exploration (Lévy walk). The two actions are conflicting with a complex priority system. When a food odor first appears, the animal should seek toward it (priority to seek), but if no food exists the animal should resume exploration (priority to explore). To resolve the between-system conflict, the two strategies need to columns with lateral inhibition to ensure that only one is selected.

Dual striatum columns for seek and explore strategies. B.rs reticulospinal motor command, H.stn sub thalamic nucleus, Ob olfactory bulb, P.ge globus pallidus external, S.d1 direct striatum projection, S.d2 indirect striatum projection, Snc substantia nigra pars compacta, Snr substantia nigra pars reticulata.

Selecting the seek column enables the odor sense to MLR path, seeking the potential food odor. Selecting the explore column enables the H.stn to MLR path, randomly searching for food.

Note: the double inversion in both paths is to reduce neuron noise [Cohen et al. 2009]. Removing inhibition reduces noise, where adding excitation would add noise. In the essay stimulation, this double negation isn’t necessary.

Striatum with dopamine/habenula control

The previous dual column circuit isn’t sufficient for the problem, because it lacks a control signal to switch between exploit (seek) and explore. The striatum dopamine circuit might help this problem by bringing in the foraging implementation from essay 17.

A major problem in essay 17 was the tradeoff between persistence and perseverance in seeking an odor. Persistence ensures that seeking an odor will continue even when the intermittent. Perseverance is a failure mode where the animal never gives up, like a moth to a flame. As a model, consider using dopamine in the striatum as persistence or effort [Salamone et al. 2007], and control of dopamine by the habenula as solving perseverance with a give-up circuit.

Explore and exploit (seek) columns controlled by dopamine. H.l lateral hypothalamus, Hb.l lateral habenula, H.stn sub thalamic nucleus, MLR midbrain locomotive region, Ob olfactory bulb, P.em pre thalamic eminence, P.ge globus pallidus external, S.d1 striatum direct projection, S.d2 striatum indirect projection, Snc substantia nigra pars compacta, Snr substantia nigra pars reticulata.

The striatum uses two opposing dopamine receptors named D1 and D2. D1 is a stimulating modulator though a G.s protein path, and D2 is an inhibiting modulator through a G.i protein path. In the above diagram, high dopamine will activate the seek column via D1 and inhibiting the explore column via D2. Low dopamine inhibits the seek column and enables the explore column. So dopamine becomes an exploit vs explore controller.

In many primitive animals, dopamine is a food signal. In c.elegans the dopamine neuron is a food-detecting sensory neuron. In vertebrates, the hunger and food-seeking areas like the lateral hypothalamus (H.l) strongly influence midbrain dopamine neurons both directly and indirectly. Indirectly, H.l to lateral habenula (Hb.l) causes non-reward aversion [Lazaridis et al. 2019].

For the essay, I’m taking H.l as multiple roles (H.l is a composite area with at least nine sub-areas [Diaz et al. 2023]), both calculating potential reward (odor) via the H.l to Vta/Snc connection, and cost (exhaustion of seek task without success) via the H.l to Hb.l to Vta/Snc connection.

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