Amylase and human evolution

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I made a mistake that was quickly corrected by a correspondent. Yesterday, in writing about copy number variants in human genes, I used the example of the amylase gene on chromosome 1, which exists in variable numbers of copies in human populations, and my offhand remark was that the effect is “nothing that we can detect”, but that maybe people with extra copies would be “especially good at breaking down french fries”. Well, it turns out that we can detect this, that there was even a very cool study of this enzyme published last year, and that the ability to break down complex starches rapidly may have been a significant factor in human evolution.

So of course I have to tell you all about this now.

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Copy Number Variants are not evidence of design

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The Institute for Creation Research has a charming little magazine called “Acts & Facts” that prints examples of their “research” — which usually means misreading some scientific paper and distorting it to make a fallacious case for a literal interpretation of the bible. Here’s a classic example: Chimps and People Show ‘Architectural’ Genetic Design, by Brian Thomas, M.S. (Note: this is not the peer-reviewed research paper implied by the logo to the left — that comes later.) The paper is a weird gloss on recent work on CNVs, or copy number variants. Mr Thomas makes a standard creationist inference that I have to hold up for public ridicule.

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Evolving the Mona Lisa

Here’s an interesting example of genetic programming: use a program that slightly alters colored polygons, compares the results to a target, and selects variants that most resemble the Mona Lisa. After less than a million generations, a black square turned into this:

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Not bad. The description of the algorithm is a bit thin, but he promises to release the source code soon. It sounds like a million generations is an overestimate, since his population size in each generation was 1, and it also sounds like his selection was far more stringent than you’d find in nature, but it’s an interesting if oversimplified example of the power of chance and selection.

A Natural History of Seeing: The Art and Science of Vision

Simon Ings has written a wonderful survey of the eye, called A Natural History of Seeing: The Art and Science of Vision(amzn/b&n/abe/pwll), and it’s another of those books you ought to be sticking on your Christmas lists right now. The title give you an idea of its content. It’s a “natural history”, so don’t expect some dry exposition on deep details, but instead look forward to a light and readable exploration of the many facets of vision.

There is a discussion of the evolution of eyes, of course, but the topics are wide-ranging — Ings covers optics, chemistry, physiology, optical illusions, decapitated heads, Edgar Rice Burroughs’ many-legged, compound-eyed apts, pointillisme, cephalopods (how could he not?), scurvy, phacopids, Purkinje shifts…you get the idea. It’s a hodge-podge, a little bit of everything, a fascinating cabinet of curiousities where every door opened reveals some peculiar variant of an eye.

Don’t think it’s lacking in science, though, or is entirely superficial. This is a book that asks the good questions: how do we know what we know? Each topic is addressed by digging deep to see how scientists came to their conclusion, and often that means we get an entertaining story from history or philosophy or the lab. Explaining the evolution of our theories of vision, for example, leads to the story of Abu’Ali al-Hasan ibn al-Hasan ibn al-Haythem, who pretended to be mad to avoid the cruelty of a despotic Caliph, and who spent 12 years in a darkened house doing experiments in optics (perhaps calling him “mad” really wasn’t much of a stretch), and emerged at the death of the tyrant with an understanding of refraction and a good theory of optics that involved light, instead of mysterious vision rays emerging from an eye. Ings is also a novelist, and it shows — these are stories that inform and lead to a deeper understanding.

If the book has any shortcoming, though, it is that some subjects are barely touched upon. Signal transduction and molecular evolution are given short shrift, for example, but then, if every sub-discipline were given the depth given to basic optics, this book would be unmanageably immense. Enjoy it for what it is: a literate exploration of the major questions people have asked about eyes and vision for the last few thousand years.

The radiation of deep sea octopuses

Last week’s Friday Cephalopod actually has an interesting story behind it. It was taken from a paper that describes the evolutionary radiation of deep-sea cephalopods.

First, a little background in geological history. Antarctica is a special case, in which a major shift in its climate occurred in the last 50 million years. If you look at a map, you’ll notice that Antarctica comes very close to the southern tip of South America; 50 million years ago, they were fully connected, and they only separated relatively recently due to continental drift.

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What did Asa Gray think?

The Atlantic has republished Asa Gray’s review of Darwin’s Origin from 1860. It’s a fascinating read: Asa Gray was a general supporter of Darwin, and the two of them corresponded regularly, and the review is generally positive, pointing out the power of the evidence and the idea. However, Gray is also quite plain about the way the implications of the theory make him very uncomfortable, and you can see him casting about, looking for loopholes.

The prospect of the future, accordingly, is on the whole pleasant and encouraging. It is only the backward glance, the gaze up the long vista of the past, that reveals anything alarming. Here the lines converge as they recede into the geological ages, and point to conclusions which, upon the theory, are inevitable, but by no means welcome. The very first step backwards makes the Negro and the Hottentot our blood-relations; — not that reason or Scripture objects to that, though pride may. The next suggests a closer association of our ancestors of the olden time with “our poor relations” of the quadrumanous family than we like to acknowledge. Fortunately, however,— even if we must account for him scientifically,-man with his two feet stands upon a foundation of his own. Intermediate links between the Bimana and the Quadrumana are lacking altogether; so that, put the genealogy of the brutes upon what footing you will, the four-handed races will not serve for our forerunners;— at least, not until some monkey, live or fossil, is producible with great-toes, instead of thumbs, upon his nether extremities; or until some lucky ‘geologist turns up the bones of his ancestor and prototype in France or England, who was so busy “napping the chuckie-stanes” and chipping out flint knives and arrow-beads in the time of the drift, very many ages ago,-before the British Channel existed, says Lyell,— and until these men of the olden time are shown to have worn their great-toes in a divergent and thumblike fashion. That would be evidence indeed: but until some testimony of the sort is produced, we must needs believe in the separate and special creation of man, however it may have been with the lower animals and with plants.

No doubt, the full development and symmetry of Darwin’s hypothesis strongly suggest the evolution of the human no less than the lower animal races out of some simple primordial animal,— that all are equally “lineal descendants of some few beings which lived long be­fore the first bed of the Silurian system was deposited.”

Alas for Gray, his loopholes have been steadily closed.

I do like his conclusion, though — “uncanny” and “mischievous” are great virtues in a theory, I should think.

So the Darwinian theory, once getting a foothold, marches boldly on, follows the supposed near ancestors of our present species farther and yet farther back into the dim past, and ends with an analogical inference which “makes the whole world kin.” As we said at the beginning, this upshot discomposes us. Several features of the theory have an uncanny look. They may prove to be innocent: but their first aspect is suspicious, and high authorities pronounce the whole thing to be positively mischievous.

Odontochelys, a transitional turtle

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Now this is an interesting beast. It’s a 220 million year old fossil from China of an animal that is distinctly turtle-like. Here’s a look at its dorsal side:

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a, Skeleton in dorsal view. b, Skull in dorsal view. c, Skull in ventral view. d, Body in dorsal view. Teeth on the upper jaw and palatal elements were scratched out during excavation. Abbreviations: ar, articular; as, astragalus; ca, calcaneum; d, dentary; dep, dorsal process of epiplastron; dsc, dorsal process of scapula; ep, epiplastron; fe, femur; fi, fibula; gpep, gular projection of epiplastron; hu, humerus; hyo, hyoplastron; hyp, hypoplastron; il, ilium; ipt, interpterygoid vacuity; j, jugal; ldv, last dorsal vertebra; m, maxilla; n, nasal; na, naris; op, opisthotic; p, parietal; phyis, posterolateral process of hypoischium; pm, premaxilla; po, postorbital; prf, prefrontal; q, quadrate; sq, squamosal; st, supratemporal; sv1, 1st sacral vertebra; ti, tibia; ul, ulna; vot, vomerine teeth; I, V, 1st and 5th metatarsals.

Notice in the skull: it’s got teeth, not just a beak like modern turtles. The back is also odd, for a turtle. The ribs are flattened and broadened, but…no shell! It’s a turtle without a shell!

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Prediction: self-promoting hype meets interdisciplinary ignorance

There is a maddeningly vague press release floating around, and I think everybody has sent me a link to it now. It contains a claim by some chemists that they have discovered a new organizing principle in evolution.

A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.

The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said.

The researchers — Raj Chakrabarti, Herschel Rabitz, Stacey Springs and George McLendon — made the discovery while carrying out experiments on proteins constituting the electron transport chain (ETC), a biochemical network essential for metabolism. A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.

If true, this would be an extremely remarkable claim. An amazing claim. Something that would make all biologists sit up and take notice. Unfortunately, the puff piece writer and the scientists involved seem incapable of actually explaining what they found, which makes me extremely suspicious. This is just empty noise:

The research, published in a recent edition of Physical Review Letters, provides corroborating data, Rabitz said, for Wallace’s idea. “What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,” said Rabitz, the Charles Phelps Smyth ’16 Professor of Chemistry. “The data just jumps off the page and implies we all have this wonderful piece of machinery inside that’s responding optimally to evolutionary pressure.”

How? What is the mechanism? What kind of data suggests this peculiar notion? I’m unimpressed, so far, and unfortunately, Physical Review Letters hasn’t yet put the paper online. I’ll also point out that the history of statistical claims for exceptional mechanisms that extend evolution is littered with “never mind” moments — some clever dick comes along and points out the ways in which the result is an epiphenomenon, a product of the same old rules all along.

The other problem that often occurs is that one of the investigators opens his mouth and reveals that he is completely out of his depth, and that the team has absolutely no conception of how evolution actually works. This time, there is no exception.

“The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a ‘blind watchmaker’?” said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. “Our new theory extends Darwin’s model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness.”

Dear gob. Is this an indictment of Princeton, of chemists, or is Chakrabarti just a weird, isolated crank? That first sentence is not even wrong. Darwin answered the question of how complexity can arise, so no, we haven’t been puzzled by that general question; evolution is not completely random, so that part is a complete non sequitur; randomness easily generates lots of complexity, so even if we accept his premise, it invalidates his question; and how does he reconcile his assertion of “completely random” with his use of the simple metaphor of the “blind watchmaker”, which implies non-randomness? That’s a sentence that contradicts itself multiple times in paradoxical ways.

Anyway, I’ll be looking for the paper. My bet would be that it says nothing like the claims made for it by the press release, or that it will be an embarrassing error of interpretation by the authors.