Monday, 12 June 2023
Fall of the three brains theory?
Reptilian Brain Myth Is Still Alive and Kicking
Do we have a three-part brain — reptilian, mammalian, and human? Curiously, psychology textbooks teach us that we do and neuroscience studies teach us that we don’t. Who to believe? And how did that happen anyway?
In the 1960s, Yale University physiologist and psychiatrist Paul D. MacLean (1913–2007) offered the triune brain theory. On that view, the reptilian brain (brain stem) controls things like movement and breathing; the mammalian brain controls emotion (limbic system); and the human cerebral cortex controls language and reasoning (neocortex). That might have been just another theory except that it was widely promoted by celebrity astronomer Carl Sagan (1934–1996) in his book The Dragons of Eden (Random House, 1977). Praised in The Atlantic as “a rational, elegant, and witty book,” Dragons won a Pulitzer Prize in 1978, for “a distinguished book of non-fiction by an American author that is not eligible for consideration in any other category.”
Chiming Beautifully
The theory chimed beautifully with materialist thought of the day. The cool people already assumed a long slow process of evolution from mud to mind, with stops along the way for reptile, mammal, and ape. And, as we were constantly reminded, many of us may have got stuck along the way.
But, as neuroscience advanced over the years, unwelcome facts began to surface. The human brain is just not organized as if the story happened in that way. As University of Oslo psychology professor Christian Krog Tamnes puts the matter in an interview at Science Norway, “Those of us who research brain development and brain evolution have known for quite some time that this isn’t true”:
Instead, the cells that are similar to each other were found scattered throughout the brains of both species.
Emotions, such as fear and sadness, are not made in one specific place in the brain. In fact, several parts of the brain are always involved.
Which parts of the brain are active vary from time to time, and from person to person.
For example, Tamnes points to a paper on the topic last year: Despite 320 million years of separate evolution, lizards and mice share a core set of neuron types that are found all over the brain, “including in the cerebral cortex, challenging the notion that certain brain regions are more ancient than others.”
Northeastern University neuroscientist Lisa Feldman Barrett offers, “So if we absolutely need to have a metaphor, it’s much better to think of the brain as an orchestra. Even playing a simple song requires a lot of pieces to talk together effectively and in a coordinated way.”
So we can still have lots of problems but our Inner Lizard is not one of them.
What Psychology Students Are Learning
Psychology lecture rooms and textbooks have been curiously slow to let go of the reptilian brain myth, however. Is that perhaps because it is socially reassuring to think that everyone who questions our sincerely held beliefs is, neurologically maybe, a rat or reptile throwback? In 2020, Joseph Cesario and colleagues reported on a study of what psychology students are told about such matters:
This belief, although widely shared and stated as fact in psychology textbooks, lacks any foundation in evolutionary biology.
“Our experience suggests that it may surprise many readers to learn that these ideas have long been discredited among people studying nervous-system evolution. Indeed, some variant of the above story is seen throughout introductory discussions of psychology and some subareas within the discipline…
“To investigate the scope of the problem, we sampled 20 introductory psychology textbooks published between 2009 and 2017. Of the 14 that mention brain evolution, 86% contained at least one inaccuracy along the lines described above. Said differently, only 2 of the field’s current introductory textbooks describe brain evolution in a way that represents the consensus shared among comparative neurobiologists.”
CESARIO, J., JOHNSON, D. J., & EISTHEN, H. L. (2020). YOUR BRAIN IS NOT AN ONION WITH A TINY REPTILE INSIDE. CURRENT DIRECTIONS IN PSYCHOLOGICAL SCIENCE, 29(3), 255–260.
More information on the textbooks is offered here.
Puzzled by Sagan’s Role
Science writer and editor Ross Pomeroy seems genuinely puzzled by the role Sagan played in helping to popularize triune brain theory: “Carl Sagan was, and to this day is, generally regarded as an honest and skeptical broker of scientific information. That he presented such a disputed theory essentially as fact to the lay public is a bit surprising. What’s more, Carl Sagan continued to push the theory three years later in his far more widely read book, Cosmos.”
It’s not really so surprising if we look at the big picture. First, Sagan was a one-way skeptic. There were many things he was not skeptical about at all because they suited the popular worldview he shared and helped shape.
For example, as Justin Gregg recounted in 2013, in 1961, he joined a semi-secret society called the Order of the Dolphin, which sought a way to communicate with intelligent extraterrestrials. He bought into the idea that dolphins had a sort of super-intelligence and a language like ours. The theory was that if we could decipher that language, we could decipher any extraterrestrial one. The Order was certainly dedicated. Gregg recounts, “As the Princeton historian D. Graham Burnett has noted, members wore insignia shaped like bottlenose dolphins and sent each other coded messages to hone their dolphinese and alien-language-decoding skills.”
Were They Nuts?
It might seem so at this distance. But club members back then included evolutionary biologist J. B. S. Haldane (1892–1964) and chemistry Nobelist Melvin Calvin — alongside SETI founder Frank Drake (1930–2022).
The lesson here is that science functions better when we follow the evidence, as the neuroscientists are doing, than when we form fan clubs for cozy ideas championed by science celebs, as the psychologists appear to be doing — at least in this area.
Accurate timekeeping is always by design?
Compasses, Clocks — Intelligent Design in Time
One can look at a piece of art or engineering and use the design filter to rule out chance or natural law. How much more is the design inference valid when seeing a sequence of events that work together for a purpose? If a sculpture appears designed, how much more a pendulum clock, or a symphony? Life is filled with dynamically changing, yet carefully regulated processes.
Hippos and Hedgehogs
Take the protein Sonic Hedgehog (SHH), whimsically named after a Japanese videogame character able to run at supersonic speeds, curl into a ball and attack enemies. Well known for its role in regulating embryonic development, SHH doesn’t just sit in the cell; it signals other proteins with the precision of a conductor. Patterns in the embryo, such as left-right symmetry and dorsal-ventral axis, are regulated by this important protein, coded for by the sonic hedgehog gene. Kim and Blackshaw, writing in Science, tell about a new function for this dynamic regulator that carries on throughout life.
Virtually all mammalian physiological functions fall under the control of an internal circadian rhythm, or body clock. This circadian rhythm is governed by master neural networks in the hypothalamus that synchronize the activity of peripheral clocks in cells throughout the body. Environmental perturbations that are a regular part of modern life, such as artificial light and international travel, can disrupt circadian rhythms, leading to adverse consequences for mental and physical health. On page 972 of this issue, Tu et al. report that primary cilia–mediated Sonic Hedgehog (SHH) signaling allows cells in the master circadian clock to maintain synchronization and control circadian rhythmicity in mice, identifying an unexpected functional role for this developmental regulator.
How can a tiny protein within a cell have dramatic effects on the hypothalamus, and by extension on the entire body?
The master circadian pacemaker responsible for regulating our daily rhythms is located in the suprachiasmatic nucleus (SCN) in the anterior hypothalamus. The cells that make up this pacemaker maintain intercellular coupling of molecular circadian rhythms, ensuring synchrony of SCN neurons. Robust clocks keep time using redundant mechanisms, and the SCN is no exception. Signals that promote cellular synchrony include paracrine signaling by fast neurotransmitters and multiple neuropeptides as well as gap junction–dependent electrical coupling. This cellular synchrony ensures the robust output of the central clock and renders it resistant to signals that reset peripheral clocks.
At this point in the story, one of the superheroes of irreducible complexity enters: the cilium, described by Michael Behe in his books. Neurons in the SCN synchronize their clocks via SHH signals sent and received through their primary cilia. Those non-motile cilia then transmit the timing signals inside via the molecular trucks inside the cilia: the intraflagellar transport (IFT) trains.
The master circadian pacemaker in the suprachiasmatic nucleus (SCN) contains neuromedin S–expressing (NMS+) neurons that have primary cilia. The number and length of these cilia change throughout the day, which alters Sonic Hedgehog (SHH) signaling through Smoothened (SMO) co-receptors expressed on the cilia. When this signaling is disrupted, the cellular oscillators in the SCN become uncoupled, which affects circadian rhythmicity in mice.
Kim and Blackshaw call the discovery “surprising” for a protein that had been almost exclusively studied for its role in development. The new study by Tu et al. shows that adult organisms rely on SHH every day to keep the body clock running on time. That’s why they call it a “Super sonic circadian synchronizer.”
SHH is essential for the development and specification of many brain structures during embryogenesis, including the SCN, and it also regulates axonal targeting, dendrite formation, and synaptogenesis. An ongoing role for SHH signaling in the adult SCN raises several important questions. It is unclear what cells are the relevant source of SHH or how its synthesis and release are regulated. Primary cilia regulate many other classes of extracellular signaling—such as Notch, Wnt, Hippo, and mammalian target of rapamycin (mTOR) pathways—often through receptor-independent mechanisms. Thus, it is unclear whether other extrinsic factors might contribute to controlling SCN function.
The Hippo pathway, which regulates body size, also transmits its signals about body size through the cilium. Look at this diagram to get a taste of the dynamic signals going on in the cell for that symphony of signals. The cilium looks more irreducibly complex than ever!
Encompassing a Body Compass
Understanding how SHH interacts with day-night cycles can help solve the problem of jet lag. It takes a while to resynchronize our body clock to the time of day in another location when we zoom off to another time zone and find the sun angle at odds with expectations. Time for a reset!
Just as the body clock can be reset by external cues, our internal compass can be reset by an external cue: namely, head direction. Results of experiments at McGill University, also done on mice, shows how whole-body actions interact with signals inside of cells.
This ability to accurately decode the animal’s internal head direction allowed the researchers to explore how the Head-Direction cells, which make up the brain’s internal compass, support the brain’s ability to re-orient itself in changing surroundings. Specifically, the research team identified a phenomenon they term ‘network gain’ that allowed the brain’s internal compass to reorient after the mice were disoriented. “It’s as if the brain has a mechanism to implement a ‘reset button’ allowing for rapid reorientation of its internal compass in confusing situations,” says Ajabi.
Fast Clocks, Slow Clocks
Speaking of development, we know that different animals have different gestation times: humans take nine months, mice around 20 days. Yet all of us live under the same day-night cycle. How do these “heterochronies” regulate themselves? It comes down to the dynamic activities going on inside cells as well, says a Focus article in Science Advances. The author’s one mention of evolution contributes nothing to the science:
In evolutionary developmental biology, differences in genetically controlled temporal programs are well recognized and referred to as heterochronies. These include differences in the time of initiation, duration, or rate of a process in comparison with an organisms’ ancestors or other species. Whereas shifts in the time of initiation or duration have been linked to genetic variation of regulatory sequences or differential expression dynamics, other heterochronies that emerge from changes in the rate of a process are distinct and usually involve the same genetic program operating at different speeds. This has been termed allochrony and does not seem to be explained by variations in regulatory sequences (Fig. 1, A to C). However, less is known about the mechanisms driving allochronies.
Nothing in Figure 1 owes anything to Darwinian evolution. Audiences know intuitively that any delicate dance is the work of a choreographer.
Developmental processes need to operate in harmony to synchronize cells, tissues, organs, and the whole organism. It is increasingly clear that a central element of this delicate dance is achieved by each cell using its own clock…. Cells offer the most basic model to expose timing control processes and to investigate the intrinsic genetic mechanisms that control timing.
Teresa Rayon’s article goes on to discuss the harmony between biochemical reactions, motor neurons, mitochondrial activity, metabolic rate and epigenetic mechanisms. The differences in scale between these players working toward a common goal—homeostasis—is astonishing.
Clocks that Must Not Reset
The body adjusts for day and night cycles, but some body clocks dare not change outside of tight limits: heart rate and breathing. We have a “resting heart rate” during sleep that was thought to be under the sole control of the parasympathetic nervous system, the nerve network that relaxes us. Scientists at Manchester University found, however, that the “fight-or-flight” sympathetic nervous system (SNS) works in concert with it to keep the heart ticking within its acceptable range. Listen to this orchestra play:
Importantly, transcription factors in the sinus node lost rhythmicity following the sustained β-adrenergic blockade. Thus, the team proposed that day-night rhythms in the sinus node are orchestrated by rhythmic β-adrenergic input from the SNS to regulate ion channel gene expression. “It’s a way of thinking about the involvement of the autonomic nervous system, not as commonly accepted, which is these very short range, immediate acute modulations of ion channel function, but through long range modulation by affecting gene expression in the heart or in the sinus node,” said D’Souza.
Here again is a case of tight coordination between cell signals and a body composed of trillions of cells. Talk about the tail wagging the dog: the goings on in specific ion channels in a cell membrane can influence the brain and the heart that are orders of magnitude larger. Sleep tight; your body knows what parts have to slow down and what parts must keep going.
No Real Hope for Evolution
One study on biological clocks attempted to “Darwinize” them, but only for the very simplest case: the KaiA/B/C oscillator in cyanobacteria (see this video for a quick presentation of this clock). “The central role of circadian rhythms in many biological processes, controlled by the day and night cycle on Earth, makes their evolution a fascinating topic,” say eight evolutionists in an open-access paper in Nature. They attempt to show a stepwise evolution “From primordial clocks to circadian oscillators.” Good luck.
Circadian rhythms play an essential part in many biological processes, and only three prokaryotic proteins are required to constitute a true post-translational circadian oscillator. The evolutionary history of the three Kai proteins indicates that KaiC is the oldest member and a central component of the clock. Subsequent additionsof KaiB and KaiA regulate the phosphorylation state of KaiC for time synchronization. The canonical KaiABC system in cyanobacteria is well understood, but little is known about more ancient systems that only possess KaiBC…. Here we investigate the primordial circadian clock in Rhodobacter sphaeroides, which contains only KaiBC, to elucidate its inner workings despite missing KaiA. Using a combination of X-ray crystallography and cryogenic electron microscopy, we find a new dodecameric fold for KaiC, in which two hexamers are held together by a coiled-coil bundle of 12 helices. This interaction is formed by the carboxy-terminal extension of KaiC and serves as an ancient regulatory moiety that is later superseded by KaiA. A coiled-coil register shift between daytime and night-time conformations is connected to phosphorylation sites through a long-range allosteric network that spans over 140 Å. Our kinetic data identify the difference in the ATP-to-ADP ratio between day and night as the environmental cue that drives the clock. They also unravel mechanistic details that shed light on the evolution of self-sustained oscillators.
The authors build phylogenetic trees to argue that KaiC is more ancient than KaiA and KaiB. While admittedly rigorous, their work does not explain the origin of KaiBC itself, the gene that codes it, or its functional connection to diurnal cycle. KaiC, as shown in the video, is the largest and most complex protein in the clock with 518 amino acids arranged in a geometrically-elegant pair of hexamers that can undergo conformational changes essential for its operation. Its function is intimately tied to specific serine and threonine residues at precise locations.
At best, their evolutionary hypothesis shows a division of labor when KaiA is present. Oddly, the authors say that the KaiBC clock in R. sphaeroides “can perform both autophosphorylation and nucleotide exchange on its own and does so faster than its more recently evolved counterparts.” The paper leaves many unasked and unanswered questions. They offer no stepwise evolution from the simple prokaryotic clock to the “complex and highly sophisticated” circadian clocks in eukaryotes. There is no mention of mutations or natural selection. And a chicken-and-egg conundrum arises when asking which came first: the gene or the protein. Why would a gene sequence 518 aa long emerge by mistake without a function being known for it? That’s too improbable. If the protein came first and ticked like a clock, how did the code for it become embedded in the genome, which has a different alphabet? In the concluding discussion, the authors give an essentially magical explanation, calling the simplest of clocks “an example of convergent evolution.” If one did not already believe in the creative power of natural selection, this paper would prove little and make less sense.
In the arts, design is evident in both static and dynamic works. If paintings and sculptures evince design, much more do finely crafted instruments performing in harmony in real time. That’s ID in the 4th dimension.
The fall of the selfish gene?
Cognitive Cells? A Newer Challenge to Neo-Darwinism
In September 1957, Nobel Prize-winning biophysicist Francis Crick (1916–2004) announced the “Central Dogma” in biology, at a symposium at Oxford University. The dogma is currently given in the Biology Dictionary thus: “genetic information flows primarily from nucleic acids in the form of DNA and RNA to functional proteins during the process of gene expression.” This view that genes rule underpins mainstream assumptions about how traits are inherited; from there, it governs accepted assumptions about evolution. So the ground on which Darwin’s modern defenders stand, propounding the only true history of life, is narrow but it is firm.
Sir Francis Crick is perhaps better known to laypeople for his 1994 book, The Astonishing Hypothesis: The Scientific Search for Soul, which he opened by announcing
The Astonishing Hypothesis is that “You”, your joys and your sorrows, your memories and your ambitions, your sense of identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules. As Lewis Carroll’s Alice might have phrased it: “You’re nothing but a pack of neurons.”
And the pack of mindless neurons that you think is you was created by those genes.
An Interesting New Paper
But what about the evidence that neurons self-organize? An interesting new paper in Progress in Biophysics and Molecular Biology calls for a different Central Dogma, recognizing forces other than genes:
Accumulating scientific discoveries support the need for a revised Central Dogma to buttress evolutionary biology’s still-fledgling migration from a Neodarwinian canon. A reformulated Central Dogma to meet contemporary biology is proposed: all biology is cognitive information processing.
The word “cognitive” is worth examining. According to Merriam–Webster, it means
of, relating to, being, or involving conscious intellectual activity (such as thinking, reasoning, or remembering)
or
based on or capable of being reduced to empirical factual knowledge.
Which definition do the authors, William B. Miller Jr. (UCLA), František Baluška (University of Bonn), and Arthur S. Reber (University of British Columbia), mean when they tell us that “As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology.” Do they mean that cells, in some sense, think?
Thoughtful Cells
They don’t quite say but the hints are intriguing. Darwin-shaped biology lags behind the times, they say, despite the accumulating contrary evidence that “non-random genetic mutations are common, linked to structural factors, epigenetic impacts, and biased DNA repair mechanisms,” among other things.
More directly, they write: “The crux of that difference separating Crick’s Central Dogma from a modern idiom is the contemporary recognition that cellular cognition governs the flow of biological information.”
So cells are smarter than we thought… ? They offer a brief look at the many bewilderingly complex feedback loops in typical cells. In their view, how should biology change? Here are some snippets from their Conclusion:
When biology is framed as an informational interactome, all forms of biological expression interact productively in a continuous, seamless feedback loop. In that reciprocating living cycle, there is no privileged level of causation since all aspects of the cell as an organized whole participate in cellular problem-solving
So the cell acts on itself (self-organization) instead of merely being acted upon by the neo-Darwinian genes. But also, they write,
The origin of self-referential cognition is unknown. Indeed, it can now be declared biology’s most profound enigma. Yet, that instantiation can be properly accredited as equating with the origin of life.
“Self-Referential Cognition”
In short, we have no idea how cells, which have been around for billions of years, could become so complex that they can be compared to intelligent beings (“self-referential cognition”) without any design in nature at all. Well, maybe they couldn’t have. Maybe the main thing to take away here, whether the authors intend it or not, is this: If biologists don’t want intelligent design, they will surely need to come up with something more convincing than Crick’s materialism.
Two other things are worth noting: Dogmas in science often do not age well because challenges are mounted by brilliant investigators but the dogma is defended by tenured mediocrities and — in the case of any type of Darwinism — pop science writers and education pressure groups. Even when the dogma is mouldy and rotten, it can be hard to overturn once it is embedded in the institutional culture on which their careers all depend.
Second, conundrums like this help us understand why panpsychism (all life forms/cells are conscious) is beginning to replace materialism in science.
Here’s the Problem
In a nutshell: The only really satisfactory form of materialism is eliminative materialism, meaning that minds are merely what brains do and human consciousness is simply an evolved illusion. You are indeed nothing but a pack of neurons. But if so, that very theory is an illusion like all the others.
In a world of awe-inspiringly complex life forms, it probably makes more sense for the materialist to adopt panpsychism. Thus words like “cognitive” and “self-referential” can be attached to cells without risk. I am not claiming that the authors are panpsychists, of course. My point is that their approach should be welcome to panpsychists.
Anyway, there is a definite nudge in that direction. University of Chicago biochemist James Shapiro titled a 2021 journal paper “All living cells are cognitive.” The same year, prominent neuroscientist Antonio Damasio, said in a book excerpt at The Scientist, that we cannot deny viruses “some fraction” of intelligence, based on the way their strategies resemble those of insects. Scientific American has run a number of pieces sympathetic to panpsychism over the years. New Scientist also offered a sympathetic long form discussion last year.
From a panpsychist perspective, human consciousness is not a mere illusion generated by a pack of neurons. It is the most highly developed known form of consciousness among life forms, all of which are conscious to some extent. That is, it is real in the same way that cell cognition and self-organization are real. So humans can learn about cells and propound theories about them that are not necessarily illusions but rather a meta level of consciousness.
Of course, panpsychism doesn’t do much to resolve the “profound enigma” of how such a world of life could come to exist without any intelligent intention or design. But that’s not what the materialist most needs right now anyway. He most needs to believe that his own findings are not just a user illusion. He can admit the profound enigma and leave the matter there.
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