Sharon Begley, how could you?

Usually, Begley is reasonably good on science, but her latest piece is one big collection of misconceptions. It reflects a poor understanding of the science and of history, in that it confuses long-standing recognition of the importance of environmental factors in gene expression with a sudden reinstatement of Lamarckian inheritance, and it simply isn’t — she’s missed the point of the science and she has caricatured Lamarck.

Some water fleas sport a spiny helmet that deters predators; others, with identical DNA sequences, have bare heads. What differs between the two is not their genes but their mothers’ experiences. If mom had a run-in with predators, her offspring have helmets, an effect one wag called “bite the mother, fight the daughter.” If mom lived her life unthreatened, her offspring have no helmets. Same DNA, different traits. Somehow, the experience of the mother, not only her DNA sequences, has been transmitted to her offspring.

That gives strict Darwinians heart palpitations, for it reeks of the discredited theory of Jean-Baptiste Lamarck (1744-1829). The French naturalist argued that the reason giraffes have long necks, for instance, is that their parents stretched their (shorter) necks to reach the treetops. Offspring, Lamarck said, inherit traits their parents acquired. With the success of Darwin’s theory of random variation and natural selection, Lamarck was left on the ash heap of history. But new discoveries of what looks like the inheritance of traits acquired by parents–lab animals as well as people–are forcing biologists to reconsider Lamarckism.

She’s describing real and interesting phenomena, but it isn’t new and it isn’t revolutionary. These are results of plasticity and epigenetics, and we aren’t having heart palpitations over them (you’re also going to have a difficult time finding any “strict Darwinians” in the science community who are even surprised by this stuff). We load up pregnant women with folate and maternal vitamins and recommendations to eat well, and we tell them not to get drunk or smoke crack for a few months, because it is common sense and common knowledge that extra-genetic factors influence the health and development of the next generation. Genes don’t execute rigid, predetermined programs of development — they are responsive to the environment and can express radically different patterns in different contexts. The same genes build a caterpillar and a butterfly, the difference is in the hormonal environment that selects which genes will be active.

It’s the same story with the water fleas. Stressed and unstressed mothers switch on different genes in their offspring epigenetically, which lead to the expression of different morphology. It’s very cool stuff, but evolutionary biologists are about as shocked by this as they are by the idea that malnourished mothers have underweight babies. That environmental influences can have multi-generational effects, and that developmental programs can cue off of the history of the germ line, is not a new idea, especially among developmental biologists.

This is just wrong on evolution:

Water fleas pop out helmets immediately if mom lived in a world of predators; by Darwin’s lights, a population of helmeted fleas would take many generations to emerge through random variation and natural selection.

It misses the whole point. The population of water fleas have a genetic attribute that allows the formation of spines under one set of conditions, and suppresses them under others. This gene regulatory network did not pop into existence in a single generation! If it did, then Begley would have a big story, evolution would have experienced a serious blow, and we’d all be looking a little more carefully into this ‘intelligent design’ stuff. The pattern of gene regulation was the product of many generations of variation and selection; only the way it was expressed in a phenotype experienced a shift within a single generation.

It’s also not Lamarckism. It’s another of those short and simple-minded myths perpetuated by high-school textbooks that Lamarck and Darwin had competing explanations for the same phenomena. They did not. This story of giraffes stretching their necks is an example of the purported inheritance of acquired characteristics … and here’s some headline news, Darwin proposed exactly the same thing! Darwin did not have a solid theory of heredity, and he himself proposed a mechanism of pangenesis which permitted the inheritance of characters by use and disuse and by injury or malformation. The key difference is that Darwin proposed that these variations could lead to the formation of new species; Lamarck believed in the fixity of species, and thought that a species would merely express a constrained range of forms in differing environments.

Both were wrong. A concept called the Weismann barrier emerged in the late 19th century, which suggested that the only influences that can be transmitted across generations are those that affect the germ line, the cells that give rise to sperm and egg, and that modification of the somatic tissues alone would not propagate. This is correct, and it’s still true: nothing in these reports suggest anything but that when perturbed by environmental stressors, gametes can switch on different genetic programs.

I think epigenetics and plasticity are important and play a role in evolution, certainly, but these kinds of elaborations on how cells interact do not imply in any way that there is a revolution in evolution, or that evolutionary biology has had it all wrong, or that this is heresy in progress. It’s also annoying to see all the vague handwaving about discrediting a “Darwinian model” — what Darwinian model? These discoveries are about mechanisms of genetic inheritance, and Darwin didn’t have a valid mechanism in the first place. In that sense, the only real heresy that counted was Mendel’s.

Religion as the ultimate Big Mac

First, a warning: this is a link to a good science article, but it’s hosted on the Suicide Girls site, which contains many pictures of young ladies with attitude and tattoos in a state of deshabille. You may discover you are blocked at work. But do persevere! It will be worth it even if you have no interest in naked women!

Anyway, one of the broad points of dissension in the discussion of the evolution of religion can be split along one general question: was religion directly adaptive in the evolution of humans, or was it more of a side-effect of other useful cognitive and social properties? I’m on the side of the side-effect gang, and so this article on the evolution of religion jibes nicely with my position. And I really like this simple analogy:

The reason religion is so successful is that it taps into our primal-brains in much the same way that a Big Mac does — only more so. Religion gained its foothold by hijacking the need to give purpose at a time when humans had only their imagination — as opposed to the evidence and reason that we have today — to fathom their world. Spirits and demons were the explanation for illnesses that we now know are caused by bacterial diseases and genetic disorders. The whims of the gods were why earthquakes, volcanos, floods and droughts occurred. Our ancestors were driven to sacrifice everything from goats to one another to satisfy those gods.

Greasy, fatty, substanceless, and not at all good for you…but it tastes so good, and it’s cheap and readily available everywhere. That’s religion and fast food.

So read the whole thing, even if you do have to wait until you get home tonight.

Chemical replicators

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We’re one step closer to self-sustaining chemical replicators, similar to what would have existed a few billion years ago, before true cells evolved. Lincoln and Joyce have created a couple of relatively simple molecules that assemble themselves from even simpler precursors in a test tube.

It’s not as straightforward as the simplest scheme one might imagine. The simplest model would be for a single enzyme, E, to catalyze its own assembly from two smaller precursors, A and B. This formula would lead to a test tube full of A and B to be quickly converted to a test tube full of nearly nothing but E with the introduction of a single copy of E. The actual solution is a little more difficult to explain.

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Ancient spiders

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Spiders are amazingly sophisticated animals, and probably the premiere complex adaptation of modern spiders is the ability to spin silk. They have multiple internal glands that can produce multiple kinds of silk — webs contain different kinds, from structural strands to adhesive strands, and other kinds are used for spinning egg cases and for wrapping prey — and they are sprayed out through small spigots mounted on swiveling spinnerets, which are modified opisthosomal (abdominal) limbs. Obviously, these detailed features did not spontaneously appear all at once, but had to have evolved progressively. A couple of fossils have recently been described that reveal a) silk spinning is ancient, from at least the Permian, but that b) these early spiders did not have the full array of modern adaptations.

Here is a pair of fossils: Permarachne novokshonovi, from the Permian in Russia, and a more recent specimen, and Palaeothele montceauensis, from the Carboniferous in France. Both are eight-legged arthropods, and if you saw one scuttling about now you wouldn’t hesitate to call them spiders. There are some differences, though: Permarachne in particular shows a little less tagmosis, or fusion and specialization of segments, than we usually see in spiders, and it also has that prominent flagellum (which is completely different from a bacterial flagellum!), a long segmented ‘tail’ covered with sensory hairs that was probably a sense organ; it has no sign of a web-spinning function.

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(Click for larger image)
Paleozoic Araneae and Uraraneida. (A-C) Permarachne novokshonovi, Permian of Russia, PIN 4909/12. (A) Holotype part in rock matrix. (B) Explanatory drawing of A. (C) Close-up of flagellum showing whorls of setae. ch, chelicera; cx, coxa; fe, femur; mt, metatarsus; pa, patella; pl, ventral
plate; st, sternum; ta, tarsus; ti, tibia. (D) Palaeothele montceauensis, Carboniferous of France, In 62050a, X-ray CT scan showing appendages buried in the rock matrix; note, anal tubercle (arrowed)
is not a flagellum. (Scale bars: B, 1 mm; C and D, 0.1 mm.)

What about the production of silk and webs in these old spiders? Here’s another specimen, Attercopus fimbriunguis, a 376 million year old fossil. It’s a little less dramatic because these are fragments of cuticle that have been carefully extracted by dissolving the rocky matrix with acid; it means, unfortunately, that it is more fragmented, but the advantage is that now we can zoom in microscopically and see far more detail in the structure. What we can now see in pieces of the ventral plates of the opisthosoma are small spigots, and in a few cases, there are even strands of spider silk still extended from these pores. In F, there’s also a nice shot of a chelicera (fang) from the spider — it’s wicked sharp, but the small holes seem to be preservation artifacts, and there’s no sign that venom secretion, another important spider adaptation, has evolved yet.

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Attercopus fimbriunguis, Devonian of New York (localities: G, Gilboa; SM, South Mountain), macerated from matrix with HF and slide-mounted. (A) First-described “spinneret,” G 334.1b.34; darkness of cuticle reflects number of layers, so this fragment is folded over
twice. (B) Palpal femur, SM 1.11.12; arrow indicates patch of distinctive spinules. (C) Piece of cuticle from corner of opisthosomal ventral plate showing setae, spigots, and possible silk strand, SM 1.11.4.
(D) Close-up of E showing possible silk strand emerging from spigot shaft, SM 1.11.4. (E) Flagellar structure with 12 segments (including possible distalmost) from original Gilboa locality; segments show distal
collars and setae, G 334.1a.4. (F) Close-up of cheliceral fang showing a number of holes (arrowed), the most distal of which had been interpreted as a venom-gland
opening, G 329.22.9. (Scale bars: 0.5 mm, except F, 0.25 mm.)

One of the critical observations here is very simple: no spinnerets. These spiders did not have the modified limbs with sets of spigots that we see nowadays, but instead, had a series of spigots arrayed across the bottom of the abdomen. They almost certainly were not able to make webs: what they could have done was produce sheets of silk, of the kind that could be used to make egg cases or wrap around prey. These are another example of a transitional fossil, forms that have only some of the capabilities of a later organism.

(via Cheshire, who promises to have his own post on this paper soon.)

Selden PA, Shear WA, Sutton MD (2008) Fossil evidence for the origin of spider spinnerets, and a proposed arachnid order. Proc Nat Acad Sci USA 105(52):20781-20785.

Evolutionary gems

This week, Nature magazine published a short list of recent important developments in evolutionary biology that support the theory of evolution, as a tool to help explain that evolution is definitely a dynamic and useful theory in our field and to demonstrate that the evidence is still growing. Here’s a short summary of the 15 stories the editors picked out, but you should also read the freely available article, 15 Evolutionary Gems. Teachers, put this in your classroom!

  1. The discovery of Indohyus, an ancestor to whales.

  2. The discovery of Tiktaalik, an ancestor to tetrapods.

  3. The origin of feathers revealed in creatures like Epidexipteryx.

  4. The evolution of patterning mechanisms in teeth.

  5. The developmental and evolutionary origin of the vertebrate skeleton.

  6. Speciation driven indirectly by selection in sticklebacks.

  7. Selection for longer-legged lizards in Caribbean island populations.

  8. A co-evolutionary arms race between Daphnia and its parasites.

  9. Non-random dispersal and gene flow in populations of great tits.

  10. Maintenance of polymorphisms in populations of guppies.

  11. Contingency in the evolution of pharyngeal jaws in the moray.

  12. Developmental genes that regulate the shape of beaks in Darwin’s finches.

  13. Evolution of regulatory genes that specify wing spots in Drosophila.

  14. Evolution of toxin resistance.

  15. The concept of evolutionary capacitance: the idea that environmental stress can expose hidden variations that are then subject to selection.

Machines of aggressively loving grace

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Squid don’t just make sperm: they package it up into fairly elaborate little torpedoes called spermatophores, which are either handed to the female with a specially modified arm called the hectocotyl arm, or squirted onto her with a penis. Once on the female (or a male, it really doesn’t matter), the spermatophore everts, forming a structure called the spermatangia, in which all the packed sperm uncoil, ready to do their job, and the whole mass is anchored to the target with a cement body. These structures do show species-specific differences, but here is one example from Heteroteuthis dispar.

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Heteroteuthis dispar. Spermatophore (a) and spermatangium (b)

Now the curious observation: squid are often captured festooned with spermatophores and spermatangia, and in many cases, the spermatangia may be imbedded deeply into the musculature of the animal — so it’s not simply as if the spermatophores are lovingly placed in an appropriate orifice, they are piercing the female (or the male, again, they don’t care that much), tearing deep into the interior. The question is, how do they get in there?

A few simple observations have revealed the answer. Spermatophores can be triggered by a gentle squeeze, at which time all of their fertilization machinery will fire. Here are some photos of some spermatophores going to work on a squid carcass.

i-cfa7b64f89849ec640df781a4b43dd43-implant.jpeg(A) Placement of spermatophores on a dead male specimen of Moroteuthis ingens (mantle length ~300
mm) and initiation of the spermatophoric reaction by pressing on the ejaculatory apparatus with a forceps. (B)
Same specimen, but submerged in seawater, showing the ejaculating spermatophores. (C) Exterior view of
implanted spermatangia in tissue of a female, showing the site of penetration and part of the amber ejaculatory
apparatus. (D) Interior view of same spermatangia, showing the sperm mass and the amber ejaculatory apparatus.

(Read the caption carefully. That’s a human triggering sperm to ejaculate into a dead male squid. It’s gay necrophiliac bestiality! You don’t see that in the papers every day.)

The answer is that spermatophores also release digestive enzymes and actively burrow into the target tissue. Squid sperm show an aggressive persistence and vigorously active assault on the female body that our own pathetic human emissions lack…I feel a little inadequate, but I’m sure women are a bit relieved.

Another interesting observation is the function of the squid penis. It seems to be less an intromittent organ than a kind of hose to direct the ejaculations onto the female. In natural situations, unlike the photographs above, it is responsible for initiating the spermatophore reaction. Each spermatophore has a threadlike extension of a surrounding membrane, and tugging on that triggers the reaction. It’s like a squad of paratroopers leaping out of a phallic airplane, each attached by a static line that yanks the rip cord as they emerge.

Hoving HJT, Laptikhovsky V (2007) Getting under the skin: autonomous implantation of squid spermatophores. Biological Bulletin 212: 177-179.

Soon, we’ll be reading your minds!

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No, not really, but this is still a cool result: investigators have used an MRI to read images off the visual cortex. They presented subjects with some simple symbols and letters, scanned their brains, and read off the image from the data — and it was even legible! Here are some examples of, first, the images presented to the subjects, then a set of individual patterns from the cortex read in single measurements, and then, finally, the average of the single scans. I think you can all read the word “neuron” in there.

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Reconstructed visual images. The reconstruction results of all trials for two subjects are shown with the presented images from the figure image session. The
reconstructed images are sorted in ascending order of the mean square error. For the purpose of illustration, each patch is depicted by a homogeneous square,
whose intensity represents the contrast of the checkerboard pattern. Each reconstructed image was produced from the data of a single trial, and no postprocessing was applied. The mean images of the reconstructed images are presented at the bottom row. The same images of the alphabet letter ”n” are displayed in
the rightmost and leftmost columns.

Before you get all panicky and worry that now the CIA will be able to extract all of those sexy librarian fantasies out of your brain by aiming a gadet at your head, relax. This is an interesting piece of work, but it has some serious limitations.

  • This only works because they are scanning the part of the visual cortex that exhibits retinotopy — a direct mapping of the spatial arrangement of the retina (and thus, of any images falling on it) onto a patch of the brain at the back of your head. This won’t work for just about any other modality, except probably touch, and I doubt it will work for visualization/cognition/memory, which are all much more derived and much more complexly stored. Although I’d really like to know if someone closes their eyes and merely imagines a letter “E”, for instance, whether there isn’t some activation of the visual cortex.

  • The process was time consuming. Subjects were first recorded while staring at random noise for 6 seconds in 22 trials. This was necessary to get an image of the background noise of the brain, wwhich was subtracted from subsequent image measurements. The brain is a noisy place, and the letter pattern is superimposed on a lot of background variation. Then, finally, the subject has to fixate on the test image for 12 seconds.

  • Lastly, a fair amount of math has to be flung at the scan to extract the contrast information. This is probably the least of the obstacles, since computational power seems to increase fairly rapidly.

Give this research some more time, though, and I can imagine some uses for being able to record specific aspects of brain states. I’d be more interested in a device that can read pre-motor cortex though — I’d like to get rid of this clumsy keyboard someday.

Miyawaki Y, Uchida H, Yamashita O, Sato M-a, Morito Y, Tanabe HC, Sadato N, Kamitani Y (2008) Visual Image Reconstruction from Human Brain Activity using a Combination of Multiscale Local Image Decoder. Neuron 60(5):915-929.

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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