Natural selection yes, but for what?

Groups across the political spectrum don’t like the idea that natural selection operates on us. The left because of the monstrosities produced by social Darwinism and eugenics. The devout because we have supposedly been formed by the creator in his image and further perfection is blasphemous.

Like it or not, there is excellent evidence for natural selection occurring in humans. One of the best is natural selection for the lactase gene.

People with lactose intolerance have nothing wrong with the gene for lactase which breaks down the sugar lactose found in milk.  Babies have no problem with breast milk.  The enzyme (lactase)  produced from the gene is quite normal in all of us; no mutations are found in the lactose protein.  However 10,000 years ago and earlier, cattle were not domesticated, so there was no dietary reason for a human weaned from the breast to make the enzyme.  In fact continuing to use energy to make the enzyme something it would never get to act on is wasteful. The genomes of our ancient ancestors had figured this out.   The control region (lactase enhancer) for the lactase gene is 14,000 nucleotides upstream from the gene itself, and back then it shut off after age 8.  After domestication of cattle 10,000 or so years ago, so that people could digest milk their entire lives a mutation arose changing cytosine to thymine in the enhancer. It spread like wildfire because back then our ancestors were in a semi-starved state most of the time, and carriers of the mutation had better nutrition.

Well that was the explanation until a recent paper [ Cell vol. 183 pp. 684 – 701 ’20 ]. It was thought that lacking the mutation you couldn’t use milk past age 8 or so. However sequencing of sites of the herdsmen of the steppes showed that they were using milk a lot (making cheese and yogurt) 8,000 years ago. Our best guess is that the mutation arose 4,000 years ago.

So possibly, the reason it spread wasn’t milk digestion, but something else. Nothing has changed the million nucleotide segment of our genome since the mutation arose — this implies that it was under strong positive natural selection. But for what?

Well, a million nucleotides codes for a lot of stuff, not just the lactase enzyme. Also there is evidence that people with the mutation is linked to metabolic abnormalities and diseases associated with decreased energy expenditure, such as obesity and type II diabetes, as well as abnormal blood metabolites and lipids.

The region codes for a microRNA (miR-128-1). Knocking it out in mice results in increases energy expenditure and improvement in high fat diet obesity. Glucose tolerance is also improved.

So it is quite possible that what was being selected for was the ‘thrifty gene’ miR-128-1 which would our semi-starved ancestors expend less energy and store whatever calories they met as fat.

In cattle a similar (syntenic) genomic region near miR-128-1 has also been under positive selection (by breeders) for feed efficiency and intramuscular fat.

So a mutation producing a selective advantage in one situation is harmful in another.

Another example — https://luysii.wordpress.com/2012/06/10/have-tibetans-illuminated-a-path-to-the-dark-matter-of-the-genome/

The mutation which allows Tibetans to adapt to high altitude causes a hereditary form of blindness (Leber’s optic atroxpy) in people living at sea level. 25% of Tibetans have the mutation. Another example of natural selection operating on man.

Lactose intolerance and the proteins of the synaptic cleft

What does lactose intolerance have to do with the zillions of proteins happily infesting the synaptic cleft?  Only someone whose mind was warped into very abstract thinking by rooming with philosophy majors in college would see a connection.

The synaptic cleft is of immense theoretical interest to neuroscientists, drug chemists and pharmacologists, and of great practical interest to people affected by neurologic and psychiatric disease either in themselves or someone they know (e.g. just about everyone).

Almost exactly a year ago I wrote a post about a great paper on the proteins of the synaptic cleft by Thomas Sudhof.  You may read the post after the *****

Well Dr. Sudhof is back with another huge review of just how synapses are formed [ Neuron vol. 100 pp. 276 – 293 ’18 ], which covers very similar ground.

It is clear that he’s depressed by the state of the field.  Here are a few quotes

“I believe that we may need to pay more attention to technical details than customary because the pressures on investigators have increased the tendency to publish preliminary results, especially results obtained with new methods whose limitations are not yet clear.”

Translation: a lot of the stuff coming out is junk.

“Given the abundance of papers reporting non-validated protein interactions that cannot possibly be all correct, it seems that confidence in a possible protein-protein interaction requires either isolation of a stable complex or biophysical measurements of interactions using recombinant purified proteins.”

Translation:  Oy vey !

“Pre- or postsynaptic specializations are surprisingly easy to induce by diverse signals. This was first shown in pioneering studies demonstrating that polylysine beads induce formation of presynaptic nerve terminals in cultured neurons and in brain in vivo.” Obviously this means that you have to be very careful when you claim that a given protein or two causes a synapse to form, which researchers have not been.”

Translation not needed.

Then on to the meat of the review.  “An impressive number of candidate synaptic Cell Adhesion Molecules (CAMs) has been described (9 classes are given each with multiple members). For some of these CAMs, compelling data demonstrate their presence in synapses and suggest a functional role in synapses. Others, however, are less well documented. If one looks at the results in total, the overall impression is puzzlement: how do so many CAMs contribute to shaping a synapse?”

Then from 281 – 286 he goes into the various CAMs, showing the extent and variety of proteins found in the synaptic cleft.  Which ones are necessary and what are they doing?  Can they all be important.  There must be some redundancy as knockout of some doesn’t do much.

Here is where lactose tolerance/intolerance comes in to offer succor to the harried investigator.

Bluntly, they must be doing something, and something important,  or they wouldn’t be there.

People with lactose intolerance have nothing wrong with the gene which breaks down lactose.  Babies have no problem with breast milk.  The enzyme (lactase)  produced from the gene is quite normal in all of us.  However 10,000 years ago and earlier, cattle were not domesticated, so there was no dietary reason for a human weaned from the breast to make the enzyme.  Something turned off lactase production — from my reading, it’s not clear what.   The control region (lactase enhancer) for the lactase gene is 14,000 nucleotides upstream from the gene itself.  After domestication of cattle, so that people could digest milk their entire lives a mutation arose changing cytosine to thymine in the enhancer.  The farthest back the mutation has been found is 6.500 years. 3 other mutations are known, which keep the lactase gene expressed past weaning.  They arose independently.  All 4 spread in the population, because back then our ancestors were in a semi-starved state most of the time, and carriers had better nutrition.

How does this offer succor to Dr. Sudhof?  Simply this, here is a mechanism to turn off production of an enzyme our ancestors didn’t need past weaning.  Don’t you think this would be the case for all the proteins found in and around the synapse.  They must be doing something or they wouldn’t be there.  I realize that this is teleology writ large, but evolutionary adaptations make you think this way.

*****

The bouillabaisse of the synaptic cleft

The synaptic cleft is so small ( under 400 Angstroms — 40 nanoMeters ) that it can’t be seen with the light microscope ( the smallest wavelength of visible light 3,900 Angstroms — 390 nanoMeters).  This led to a bruising battle between Cajal and Golgi a just over a century ago over whether the brain was actually made of cells.  Even though Golgi’s work led to the delineation of single neurons he thought the brain was a continuous network.  They both won the Nobel in 1906.

Semifast forward to the mid 60s when I was in medical school.  We finally had the electron microscope, so we could see synapses. They showed up as a small CLEAR spaces (e.g. electrons passed through it easily leaving it white) between neurons.  Neurotransmitters were being discovered at the same time and the synapse was to be the analogy to vacuum tubes, which could pass electricity in just one direction (yes, the transistor although invented hadn’t been used to make anything resembling a computer — the Intel 4004 wasn’t until the 70s).  Of course now we know that information flows back and forth across the synapse, with endocannabinoids (e. g. natural marihuana) being the major retrograde neurotransmitter.

Since there didn’t seem to be anything in the synaptic cleft, neurotransmitters were thought to freely diffuse across it to being to receptors on the other (postsynaptic) side e.g. a free fly zone.

Fast forward to the present to a marvelous (and grueling to read because of the complexity of the subject not the way it’s written) review of just what is in the synaptic cleft [ Cell vol. 171 pp. 745 – 769 ’17 ] http://www.cell.com/cell/fulltext/S0092-8674(17)31246-1 (It is likely behind a paywall).  There are over 120 references, and rather than being just a catalogue, the single author Thomas Sudhof extensively discusseswhich experimental work is to be believed (not that Sudhof  is saying the work is fraudulent, but that it can’t be used to extrapolate to the living human brain).  The review is a staggering piece of work for one individual.

The stuff in the synaptic cleft is so diverse, and so intimately involved with itself and the membranes on either side what what is needed for comprehension is not a chemist but a sociologist.  Probably most of the molecules to be discussed are present in such small numbers that the law of mass action doesn’t apply, nor do binding constants which rely on large numbers of ligands and receptors. Not only that, but the binding constants haven’t been been determined for many of the players.

Now for some anatomic detail and numbers.  It is remarkably hard to find just how far laterally the synaptic cleft extends.  Molecular Biology of the Cell ed. 5 p. 1149 has a fairly typical picture with a size marker and it looks to be about 2 microns (20,000 Angstroms, 2,000 nanoMeters) — that’s 314,159,265 square Angstroms (3.14 square microns).  So let’s assume each protein takes up a square 50 Angstroms on a side (2,500 square Angstroms).  That’s room for 125,600 proteins on each side assuming extremely dense packing.  However the density of acetyl choline receptors at the neuromuscular junction is 8,700/square micron, a packing also thought to be extremely dense which would give only 26,100 such proteins in a similarly distributed CNS synapse. So the numbers are at least in the right ball park (meaning they’re within an order of magnitude e.g. within a power of 10) of being correct.

What’s the point?

When you see how many different proteins and different varieties of the same protein reside in the cleft, the numbers for  each individual element is likely to be small, meaning that you can’t use statistical mechanics but must use sociology instead.

The review focuses on the neurExins (I capitalize the E  to help me remember that they are prEsynaptic).  Why?  Because they are the best studied of all the players.  What a piece of work they are.  Humans have 3 genes for them. One of the 3 contains 1,477 amino acids, spread over 1,112,187 basepairs (1.1 megaBases) along with 74 exons.  This means that just over 1/10 of a percent of the gene is actually coding for for the amino acids making it up.  I think it takes energy for RNA polymerase II to stitch the ribonucleotides into the 1.1 megabase pre-mRNA, but I couldn’t (quickly) find out how much per ribonucleotide.  It seems quite wasteful of energy, unless there is some other function to the process which we haven’t figured out yet.

Most of the molecule resides in the synaptic cleft.  There are 6 LNS domains with 3 interspersed EGFlike repeats, a cysteine loop domain, a transmembrane region and a cytoplasmic sequence of 55 amino acids. There are 6 sites for alternative splicing, and because there are two promoters for each of the 3 genes, there is a shorter form (beta neurexin) with less extracellular stuff than the long form (alpha-neurexin).  When all is said and done there are over 1,000 possible variants of the 3 genes.

Unlike olfactory neurons which only express one or two of the nearly 1,000 olfactory receptors, neurons express mutiple isoforms of each, increasing the complexity.

The LNS regions of the neurexins are like immunoglobulins and fill at 60 x 60 x 60 Angstrom box.  Since the synaptic cleft is at most 400 Angstroms long, the alpha -neurexins (if extended) reach all the way across.

Here the neurexins bind to the neuroligins which are always postsynaptic — sorry no mnemonic.  They are simpler in structure, but they are the product of 4 genes, and only about 40 isoforms (due to alternative splicing) are possible. Neuroligns 1, 3 and 4 are found at excitatory synapses, neuroligin 2 is found at inhibitory synapses.  The intracleft part of the neuroligins resembles an important enzyme (acetylcholinesterase) but which is catalytically inactive.  This is where the neurexins.

This is complex enough, but Sudhof notes that the neurexins are hubs interacting with multiple classes of post-synaptic molecules, in addition to the neuroligins — dystroglycan, GABA[A] receptors, calsystenins, latrophilins (of which there are 4).   There are at least 50 post-synaptic cell adhesion molecules — “Few are well understood, although many are described.”

The neurexins have 3 major sites where other things bind, and all sites may be occupied at once.  Just to give you a taste of he complexity involved (before I go on to  larger issues).

The second LNS domain (LNS2)is found only in the alpha-neurexins, and binds to neuroexophilin (of which there are 4) and dystroglycan .

The 6th LNS domain (LNS6) binds to neuroligins, LRRTMs, GABA[A] receptors, cerebellins and latrophilins (of which there are 4)_

The juxtamembrane sequence of the neurexins binds to CA10, CA11 and C1ql.

The cerebellins (of which there are 4) bind to all the neurexins (of a particular splice variety) and interestingly to some postsynaptic glutamic acid receptors.  So there is a direct chain across the synapse from neurexin to cerebellin to ion channel (GLuD1, GLuD2).

There is far more to the review. But here is something I didn’t see there.  People have talked about proton wires — sites on proteins that allow protons to jump from one site to another, and move much faster than they would if they had to bump into everything in solution.  Remember that molecules are moving quite rapidly — water is moving at 590 meters a second at room temperature. Since the synaptic cleft is 40 nanoMeters (40 x 10^-9 meters, it should take only 40 * 10^-9 meters/ 590 meters/second   60 trillionths of a second (60 picoSeconds) to cross, assuming the synapse is a free fly zone — but it isn’t as the review exhaustively shows.

It it possible that the various neurotransmitters at the synapse (glutamic acid, gamma amino butyric acid, etc) bind to the various proteins crossing the cleft to get their target in the postsynaptic membrane (e.g. neurotransmitter wires).  I didn’t see any mention of neurotransmitter binding to  the various proteins in the review.  This may actually be an original idea.

I’d like to put more numbers on many of these things, but they are devilishly hard to find.  Both the neuroligins and neurexins are said to have stalks pushing them out from the membrane, but I can’t find how many amino acids they contain.  It can’t find how much energy it takes to copy the 1.1 megabase neurexin gene in to mRNA (or even how much energy it takes to add one ribonucleotide to an existing mRNA chain).

Another point– proteins have a finite lifetime.  How are they replenished?  We know that there is some synaptic protein synthesis — does the cell body send packages of mRNAs to the synapse to be translated there.  There are at least 50 different proteins mentioned in the review, and don’t forget the thousands of possible isoforms, each of which requires a separate mRNA.

Old Chinese saying — the mountains are high and the emperor is far away. Protein synthesis at the synaptic cleft is probably local.  How what gets made and when is an entirely different problem.

A large part of the review concerns mutations in all these proteins associated with neurologic disease (particularly autism).  This whole area has a long and checkered history.  A high degree of cynicism is needed before believing that any of these mutations are causative.  As a neurologist dealing with epilepsy I saw the whole idea of ion channel mutations causing epilepsy crash and burn — here’s a link — https://luysii.wordpress.com/2011/07/17/we’ve-found-the-mutation-causing-your-disease-not-so-fast-says-this-paper/

Once again, hats off to Dr. Sudhof for what must have been a tremendous amount of work

A Troublesome Inheritance – IV — Chapter 3

Chapter III of “A Troublesome Inheritance” contains a lot of very solid molecular genetics, and a lot of unfounded speculation. I can see why the book has driven some otherwise rational people bonkers. Just because Wade knows what he’s talking about in one field, doesn’t imply he’s competent in another.

Several examples: p. 41 “”Nonethless, it is reasonable to assume that if traits like skin color have evolved in a population, the same may be true of its social behavior.” Consider yes, assume no.

p. 42 “The society of living chimps can thus with reasonable accuracy stand as a surrogate for the joint ancester” (of humans and chimps — thought to be about 7 megaYears ago) and hence describe the baseline from which human social behavior evolved.” I doubt this.

The chapter contains many just so stories about the evolution of chimp and human societies (post hoc propter hoc). Plausible, but not testable.

Then follows some very solid stuff about the effects of the hormone oxytocin (which causes lactation in nursing women) on human social interaction. Then some speculation on the ways natural selection could work on the oxytocin system to make people more or less trusting. He lists several potential mechanisms for this (1) changes in the amount of oxytocin made (2) increasing the number of protein receptors for oxytocin (3) making each receptor bind oxytocin more tightly. This shows that Wade has solid molecular biological (and biological) chops.

He quotes a Dutch psychologist on his results with oxytocin and sociality — unfortunately, there have been too many scandals involving Dutch psychologists and sociologists to believe what he says until its replicated (Google Diederik Stapel, Don Poldermans, Jens Forster, Markus Denzler if you don’t believe me). It’s sad that this probably honest individual is tarred with that brush but he is.

p. 59 — He notes that the idea that human behavior is solely the result of social conditions with no genetic influence is appealing to Marxists, who hoped to make humanity behave better by designing better social conditions. Certainly, much of the vitriol heaped on the book has come from the left. A communist uncle would always say ‘it’s the system’ to which my father would reply ‘people will corrupt any system’.

p. 61 — the effect of mutations of lactose tolerance on survival on society are noted — people herding cattle and drinking milk, survive better if their gene to digest lactose (the main sugar in milk) isn’t turned off after childhood. If your society doesn’t herd animals, there is no reason for anyone to digest milk after weaning from the breast. The mutations aren’t in the enzyme digesting lactose, but in the DNA that turns on expression of the gene for the enzyme (e.g. the promoter). Interestingly, 3 separate mutations in African herders have been found to do this, and different from the one that arose in the Funnel Beaker Culture of Scandinavia 6,000 yers ago. This is a classic example of natural selection producing the same phenotypic effect by separate mutations.

There is a much bigger biological fish to be fried here, which Wade doesn’t discuss. It takes energy to make any protein, and there is no reason to make a protein to help you digest milk if you aren’t nursing, and one very good reason not to — it wastes metabolic energy, something in short supply in humans as they lived until about 15,000 years ago. So humans evolved a way not to make the protein in adult life. The genetic change is in the DNA controlling protein production not the protein itself.

You may have heard it said that we are 98% Chimpanzee. This is true in the sense that our 20,000 or so proteins are that similar to the chimp. That’s far from the whole story. This is like saying Monticello and Independence Hall are just the same because they’re both made out of bricks. One could chemically identify Monticello bricks as coming from the Virginia piedmont, and Independence Hall bricks coming from the red clay of New Jersey, but the real difference between the buildings is the plan.

It’s not the proteins, but where and when and how much of them are made. The control for this (plan if you will) lies outside the genes for the proteins themselves, in the rest of the genome. The control elements have as much right to be called genes, as the parts of the genome coding for amino acids. Granted, it’s easier to study genes coding for proteins, because we’ve identified them and know so much about them. It’s like the drunk looking for his keys under the lamppost because that’s where the light is.

p. 62 — There follows some description of the changes of human society from hunter gathering, to agrarian, to the rise of city states, is chronicled. Whether adaptation to different social organizations produced genetic changes permitting social adaptation or were the cause of it isn’t clear. Wade says “changes in social behavior, has most probably been molded by evolution, through the underlying genetic changes have yet to be identified.” This assumes a lot, e.g. that genetic changes are involved. I’m far from sure, but the idea is not far fetched. Stating that genetic changes have never, and will never shape society, is without any scientific basis, and just as fanciful as many of Wade’s statements in this chapter. It’s an open question, which is really all Wade is saying.

In defense of Wade’s idea, think about animal breeding as Darwin did extensively. The Origin of Species (worth a read if you haven’t already read it) is full of interchanges with all sorts of breeders (pigeons, cattle). The best example we have presently are the breeds of dogs. They have very different personalities — and have been bred for them, sheep dogs mastifs etc. etc. Have a look at [ Science vol. 306 p. 2172 ’04, Proc. Natl. Acad. Sci. vol. 101 pp. 18058 – 18063 ’04 ] where the DNA of variety of dog breeds was studied to determine which changes determined the way they look. The length of a breed’s snout correlated directly with the number of repeats in a particular protein (Runx-2). The paper is a decade old and I’m sure that they’re starting to look at behavior.

More to the point about selection for behavioral characteristics, consider the domestication of the modern dog from the wolf. Contrast the dog with the chimp (which hasn’t been bred).

[ Science vol. 298 pp. 1634 – 1636 ’02 ] Chimps are terrible at picking up human cues as to where food is hidden. Cues would be something as obvious as looking at the containing, pointing at the container or even touching it. Even those who eventually perform well, take dozens of trials or more to learn it. When tested in more difficult tests requiring them to show flexible use of social cues they don’t

This paper shows that puppies (raised with no contact with humans) do much better at reading humans than chimps. However wolf cubs do not do better than the chimps. Even more impressively, wolf cubs raised by humans don’t show the same skills. This implies that during the process of domestication, dogs have been selected for a set of social cognitive abilities that allow them to communicate with humans in unique ways. Dogs and wolves do not perform differently in a non-social memory task, ruling out the possibility that dogs outperform wolves in all human guided tasks.

All in all, a fascinating book with lots to think about, argue with, propose counterarguments, propose other arguments in support (as I’ve just done), etc. etc. Definitely a book for those who like to think, whether you agree with it all or not.