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.

Entropy and evolution

Blogging on Peer-Reviewed Research

One of the oldest canards in the creationists’ book is the claim that evolution must be false because it violates the second law of thermodynamics, or the principle that, as they put it, everything must go from order to disorder. One of the more persistent perpetrators of this kind of sloppy thinking is Henry Morris, and few creationists today seem able to get beyond this error.

Remember this tendency from order to disorder applies to all real processes. Real processes include, of course, biological and geological processes, as well as chemical and physical processes. The interesting question is: “How does a real biological process, which goes from order to disorder, result in evolution. which goes from disorder to order?” Perhaps the evolutionist can ultimately find an answer to this question, but he at least should not ignore it, as most evolutionists do.

Especially is such a question vital, when we are thinking of evolution as a growth process on the grand scale from atom to Adam and from particle to people. This represents in absolutely gigantic increase in order and complexity, and is clearly out of place altogether in the context of the Second Law.

As most biologists get a fair amount of training in chemistry, I’m afraid he’s wrong on one bit of slander there: we do not ignore entropy, and are in fact better informed on it than most creationists, as is clearly shown by their continued use of this bad argument. I usually rebut this claim about the second law in a qualitative way, and by example — it’s obvious that the second law does not state that nothing can ever increase in order, but only that an decrease in one part must be accompanied by a greater increase in entropy in another. Two gametes, for instance, can fuse and begin a complicated process in development that represents a long-term local decrease in entropy, but at the same time that embryo is pumping heat out into its environment and increasing the entropy of the surrounding bit of the world.

It’s a very bad argument they are making, but let’s consider just the last sentence of the quote above.

This represents in absolutely gigantic increase in order and complexity, and is clearly out of place altogether in the context of the Second Law.

A “gigantic increase in order and complexity” … how interesting. How much of an increase? Can we get some numbers for that?

Daniel Styer has published an eminently useful article on “Entropy and Evolution” that does exactly that — he makes some quantitative estimates of how much entropy might be decreased by the process of evolution. I knew we kept physicists around for something; they are so useful for filling in the tricky details.

The article nicely summarizes the general problems with the creationist claim. They confuse the metaphor of ‘disorder’ for the actual phenomenon of entropy; they seem to have an absolutist notion that the second law prohibits all decreases in entropy; and they generally lack any quantitative notion of how entropy actually works. The cool part of this particular article, though, is that he makes an estimate of exactly how much entropy is decreased by the process of evolution.

First he estimates, very generously, how much entropy is decreased per individual. If we assume each individual is 1000 times “more improbable” than its ancestor one century ago, that is, that we are specified a thousand times more precisely than our great-grandparents (obviously a ludicrously high over-estimate, but he’s trying to give every advantage to the creationists here), then we can describe the reduction in the number of microstates in the modern organism as:

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Now I’m strolling into dangerous ground for us poor biologists, since this is a mathematical argument, but really, this is simple enough for me to understand. We know the statistical definition of entropy:

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In the formula above, kB is the Boltzmann constant. We can just plug in our estimated (grossly overestimated!) value for Ω, have fun with a little algebra, and presto, a measure of the change in entropy per individual per century emerges.

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Centuries are awkward units, so Styer converts that to something more conventional: the entropy change per second is -3.02 x 10-30 J/K. There are, of course, a lot of individual organisms on the planet, so that number needs to be multiplied by the total number of evolving organism, which, again, we charitably overestimate at 1032, most of which are prokaryotes, of course. The final result is a number that tells us the total change in entropy of the planet caused by evolution each second:

-302 J/K

What does that number mean? We need a context. Styer also estimates the Earth’s total entropy throughput per second, that is, the total flux involved from absorption of the sun’s energy and re-radiation of heat out into space. It’s a slightly bigger number:

420 x 1012 J/K

To spell it out, there’s about a trillion times more entropy flux available than is required for evolution. The degree by which earth’s entropy is reduced by the action of evolutionary processes is miniscule relative to the amount that the entropy of the cosmic microwave background is increased.

This is very cool and very clear. I’m folding up my copy of Styer’s paper and tucking it into my copy of The Counter-Creationism Handbook, where it will come in handy.

Styer DF (2008) Entropy and evolution. Am J Phys 76(11):1031-1033.

The Mason’s Apprentice

My latest Seed column slipped quietly onto the interwebs last week — it’s an overview of how the glues that hold multicellular organisms together first evolved in single celled creatures, represented today by the choanoflagellates.

Just as a teaser, the next print edition that should be coming out soon will continue the focus on enlightening organisms of remarkable simplicity with a description of the results of the Trichoplax genome. Get it! You will also be rewarded with a great issue focusing on science policy.

The dumbification of Spore

As anyone who has followed computer games at all lately knows, Spore is the recently released computer game from Maxis that was initially touted as a kind of partial simulation of evolution. Unfortunately, It wasn’t a very good simulation of much of anything, and as a game it has only been a partial success, with some parts being quite entertaining and others deserving a resounding “meh”. (Disclaimer: I have the game, but haven’t bothered to install it yet; I’ve let Skatje play it for me, and I’ve read the reviews, and suffered a noticeable loss of enthusiasm from that exposure.)

Now there is a revealing inside view of the Spore development process, with some tantalizing hints of some really great stuff that was implemented in early versions of the game, that never made it to release. Here’s the problem: the developers divided into two competing/complementary teams with radically different goals, a “cute team” and a “science team”. Guess who won?

This was Spore’s central problem: Could the game be both scientifically accurate and fun? The prototyping teams were becoming lost in their scientific interests. Chaim Gingold, a team member who started as an intern and went on to help design the game’s content creation tools, recalls a summer spent playing with pattern language and cellular automata: “It was just about being engaged with the universe as a set of systems, and being able to build toys that manifested our fascination with these systems and our love for them.” But from within this explosion of experimental enthusiasm came an unexpected warning voice. Spore’s resident uber-geek and artificial intelligence expert Chris Hecker was having strong misgivings about how appealing all this hard science would be to the wider world. “I was the founding member of the ‘cute’ team,” he says with pride. “Ocean [Quigley, Spore’s art director] and Will were really the founding members of the ‘science’ team. Ocean would make the cell game look exactly like a petri dish with all these to-scale animals and Will would say, ‘That’s the greatest thing I’ve ever seen!’ and some of us were thinking, ‘I’m not sure about that.'”

(That, by the way, is from the Seed magazine article on the game. You’ve probably already seen it since you all subscribe, right?)

This is the annoying mantra of far too many people, from Barbie to Chris Hecker: “science is hard”. Yes, it is…and that’s what makes it fun! Games are also hard, if they’re any good — you often have to master difficult moves, arcane strategy, work fast or plan far ahead, or solve tricky puzzles, and that’s why we choose to play them, that’s the appeal. What I was looking for in Spore was for someone to take a look with a gamer’s eyes at the process of science and extract from it the puzzle-solving essence and make it approachable and entertaining; instead, they seem to have given up on the science and instead created animated plush dolls for amusement’s sake.

It’s a real shame. There is a little hope in an unlikely suggestion:

I hope that Maxis announces that it intends to rectify this odd deviation from their plan through expansion packs, including a complete overhaul of the Cell Stage and Creature Stage, at minimum. The forced linear progression of the game and forced evolution should also be removed from the Cell and Creature Stages, as it is not faithful to the freedom of the advertised product. (Evolution to a better brain should be optional, at least in the Creature Stage, as it was in the earlier videos.) I do not believe that we have a right to demand it be free, as the development costs of this game are already astronomical. This may have not been as much of a problem if they hadn’t been spending the past few years removing content.

Somebody at Maxis should have encouraged everyone to embrace the science. It could have been great. I don’t know why they didn’t, but I suspect that a bean counter somewhere noted that it never hurts to underestimate the intelligence of the buying public…and decided to embrace the lowest common denominator instead of aspiring to greatness.