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May 1, 2012
Category: Evolution • Science
The latest Carnival of Evolution is at Evolving Thoughts, hosted by that guy Wilkins who usually covers the philosophical beat…but we'll let him out of that cage this one time.
The Carnival of Evolution 48 will be held right here, on Pharyngula. You can submit entries via the carnival widget; get them in before 1 June, or I'll ignore them and they'll be passed on to the next carnival host, who doesn't exist. And therefore doesn't have a blog. Which means your carefully crafted science post will be shipped off to dev:null. So you might also consider volunteering for the hosting duties some time. The electrons you save might be your own.
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Posted by PZ Myers at 10:01 AM • 0 Comments
April 30, 2012
Category: Organisms
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Posted by PZ Myers at 8:16 PM • 4 Comments
Category: Cephalopods • Organisms
Some species of cephalopods are incapable of concealing their sexual history. The males produce packets of sperm called spermatangia that they grasp with a specialized arm that they then reach out and splat, poke into their mate. In Octopoteuthis deletron, a deep-sea squid, these spermatangia are large, pale, and distinctive, so every time a squid is mated it's left with a little white dangling flag marking it — so sex is like a combination of tag and paintball. The males are loaded with ammo — 1646 were counted in the reproductive tract of one male — and the spermatangia can be counted using a video camera.
So a ROV went down deep into the Monterey Submarine Canyon and documented the profligate promiscuity of these squid. The females had been busy: individuals had between 21 and 147 spermatangia dangling from them.
The surprise was that the males were equally likely to have been inseminated multiple times in their life, between 15 and 25 times. They're all manic bisexuals! They're also creative in their sexual behavior; as you can see below, spermatangia are implanted everywhere, mantle, arms, ventrally, dorsally. It's all one big gay orgy down there under the sea.
Most cephalopods, this species included, live short lives and the perpetuation of the species relies on rapid, successful mating. The authors explain this same-sex mating behavior as an adaptive response to a life-style in which discrimination is less important than simply getting the job done.
We have only observed them as solitary individuals. The combination of a solitary life, poor sex differentiation, the difficulty of locating a conspecific and the rapidity of the sexual encounter probably results in the observed high frequency of spermatangia-bearing males in this species. Apparently, the costs involved in losing sperm to another male are smaller than the costs of developing sex discrimination and courtship, or of not mating at all. This behaviour further exemplifies the 'live fast and die young' life strategy of many cephalopods.
I prefer to think of it as a brief happy life spent writhing constantly, passionately in the arms of love.
Hoving HJT, Bush SL, Robison BH (2011) A shot in the dark: same-sex sexual behaviour in a deep-sea squid. Biol. Lett. doi:10.1098/rsbl.2011.0680.
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Posted by PZ Myers at 8:01 PM • 3 Comments
Category: Bad science • Neurobiology
The story so far: Mario Beauregard published a very silly article in Salon, claiming that Near-Death Experiences (NDEs) were proof of life after death, a claim that he attempted to support with a couple of feeble anecdotes. I replied, pointing out that NDEs are delusions, and his anecdotal evidence was not evidence at all. Now Salon has given Beauregard another shot at it, and he has replied with a "rebuttal" to my refutation. You will not be surprised to learn that he has no evidence to add, and his response is simply a predictable rehashing of the same flawed reasoning he has exercised throughout.
In his previous sally, he cited the story of Maria's Shoe, a tall tale that has been circulating in the New Age community for decades, always growing in the telling. This story is the claim that a woman with a heart condition was hospitalized, and while unconscious with a heart attack, her spirit floated out of the coronary care unit to observe a shoe on a third-floor ledge. As has been shown, she described nothing that could not be learned by mundane observation, no supernatural events required, and further, that the story is peculiarly unverifiable: "Maria" cannot be found, not even in the hospital records, and no one has been found who even knew this woman. The entire story is hearsay with no independent evidence whatsoever.
Beauregard attempts to salvage the story by layering on more detail. The description of the shoe was very specific, he says, right down to the placement of the laces and the pattern of wear, and she could not possibly have learned this by overhearing staff talking about it because "it would have been difficult for Maria to understand the location of the shoe in the hospital and the details of its appearance because she spoke very little English." This is a curious observation; the claim is that she could not understand a description of the shoe, but she was able to describe the shoe herself to a woman, Kimberly Clark Sharp, who did not understand Spanish.
"When I got to the critical-care unit, Maria was lying slightly elevated in bed, eyes wild, arms flailing, and speaking Spanish excitedly," recounts Sharp. "I had no idea what she was saying, but I went to her and grabbed her by the shoulders. Our faces were inches apart, our eyes locked together, and I could see she had something important to tell me."
The question isn't whether a seriously ill woman with poor command of English could see the shoe; it's whether a healthy, ambulatory, English-speaking woman who has made a career out of the myth of NDEs could see the shoe. Beauregard's additions to the anecdote do not increase its credibility at all.
Beauregard adds another anecdote to the litany, the story of another cardiac patient who was resuscitated and later recounted seeing a particular nurse while his brain was not functional. Seriously — more anecdotes don't help his case. He threatens to have even more of these stories in a book he's in the process of publishing, but there's no point. He could recite a thousand vague rumors and poorly documented examples with ambiguous interpretations, and it wouldn't salvage his thesis.
This new anecdote is more of the same. The patient is comatose and with no heart rhythm when brought into the hospital; over a week later, he claims to recognize a particular nurse as having been present during his crisis, and mentions that she put his dentures in a drawer.
I am underwhelmed. I must introduce Beauregard to two very common terms that are well understood in the neuroscience community.
The first is confabulation. This is an extremely common psychological process in which we fill in gaps in our memory with fabrications. I described this in my previous response, but Beauregard chose to disregard it. The patient above has a large gap in his memory, but he knows that he existed in that period, and something must have happened; he knows that he was resuscitated in a hospital, so can imagine a scene in which he was surrounded by doctors and nurses; he knows that his dentures are missing, so he suspects that someone put them somewhere, likely one of the people surrounding him during the emergency. So his brain fills in the gap with a plausible narrative. This whole process is routine and unsurprising, and far more likely than that his mind went wandering away from his brain.
The second term is confirmation bias. Only positive responses that confirm Beauregard's expectations are noted. The patient guessed that a nurse he met during his routine care was also present during his episode of unconsciousness, and he was correct. What if he'd guessed wrongly? That event would be unexceptional, nobody would have made note of it, and Beauregard would not now be trotting out this incident as a vindication of his hypothesis. This is one of the problems of building a case on anecdotes; without knowledge of the range and likelihood of various results, one can't distinguish the selective presentation of chance events from a measurable phenomenon.
While unaware of basic concepts in science, Beauregard seems to readily adopt the most woo-ish buzzwords. His explanation for this purported power of the mind to exist independently of any physical substrate is, unfortunately and predictably, quantum mechanics. Every charlatan in the world seems to believe that attaching "quantum" to a word makes it magical and powerful and unquestionable. I have to accept Terry Pratchett's rebuttal: "'Let's call it Quantum!' is not an explanation." And neither is Beauregard's feeble insistence that the universe possesses quantum consciousness, that psychic powers represent quantum phenomena, or that there is an infinitely loving Cosmic Intelligence.
Beauregard then accuses me of having an ideological bias, and that I'm a fanatical fundamentalist. He, of course, is the dispassionate, objective observer with no axe to grind, only interested in reporting the scientific facts. Unfortunately, his book The Spiritual Brain reveals to the contrary that he has some very, very strange beliefs.
"Individual minds and selves arise from and are linked together by a divine Ground of Being (or primordial matrix). That is the spaceless, timeless, and infinite Spirit, which is the ever-present source of cosmic order, the matrix of the whole universe, including both physics (material nature) and psyche (spiritual nature). Mind and consciousness represent a fundamental and irreducible property of the Ground of Being. Not only does the subjective experience of the phenomenal world exist within mind and consciousness, but mind, consciousness, and self profoundly affect the physical world...it is this fundamental unity and interconnectedness that allows the human mind to causally affect physical reality and permits psi interaction between humans and with physical or biological systems. With regard to this issue, it is interesting to note that quantum physicists increasingly recognize the mental nature of the universe."
If I am an ideologue, it's only in that I demand that if you call something science, it bear some resemblance in method and approach to science, not mysticism. Beauregard insists on trying to endorse the babbling piffle above as science by reciting the number of publications he has made, and how much grant money he's got, when I'm looking for verifiable, reproducible, measurable evidence.
I would also remind him that Isaac Newton, who was probably an even greater scientist than the inestimable Beauregard, wasted much of his later years on mysticism, too: from alchemy and the quest for the Philosopher's Stone, to arcane Biblical hermeneutics, extracting prophecies of the end of the world from numerological analyses of Revelation. While his mechanics and optics have stood the test of time, that nonsense has not. That his mathematics and physics are useful and powerful does not imply that he was correct in his calculation that the world will end before 2060 AD; similarly, Beauregard's success in publishing in psychiatry journals does not imply that his unsupportable fantasies of minds flitting about unfettered by brains is reasonable.
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Posted by PZ Myers at 11:50 AM • 51 Comments
April 27, 2012
Category: Cephalopods • Organisms
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Posted by PZ Myers at 12:05 PM • 1 Comments
Category: Creationism
It's always amusing to see creationists try to explain why Charles Darwin was wrong, especially when they make up lists of reasons "Darwin's theory of evolution does not hold up to scientific scrutiny." These are always people who wouldn't know what scientific scrutiny was if it knocked them immobile with a carefully measured dose of Conus snail toxin, strapped them to an operating table, and pumped high-intensity Science directly into their brains with a laser. As I often wish I could do.
Anyway, some ignorant jebus-lover hacked together a list of 10 "mistakes" that Darwin made. Strangely, they completely miss his actual errors (probably because they've never read anything by Darwin and don't have enough knowledge of biology to recognize where he has been superceded) and babble on about what are actually creationist errors.
1. "Warm little pond" theory: There is no solid evidence of life arising spontaneously from a chemical soup.
Actually, there is. We know that organic chemicals arise spontaneously all the time in nature — they're even detectable floating about in space. We also know that biology is chemistry, and that every process driving biological phenomena is ultimately physical and chemical. We also know that life arose in a geologically brief period early in the history of the earth. It's certainly a better explanation than that some invisible guy said some magic words and poof, life appeared spontaneously with all the complexity of extant forms.
By the way, the "warm little pond" wasn't part of Darwin's theory. It was a brief speculation made in an 1871 letter to Hooker.
"It is often said that all the conditions for the first production of a living organism are now present, which could ever have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sorts of ammonia and phosphoric salts, - light, heat, electricity &c.; present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed."
That's actually still an entirely reasonable hypothesis, and not a mistake at all, especially when you recognize that he was suitably cautious in his publications. Here's what he said in The Variation of Animals and Plants under Domestication, for instance.
"As the first origin of life on this earth, as well as the continued life of each individual, is at present quite beyond the scope of science, I do not wish to lay much stress on the greater simplicity of the view of a few forms, or of only one form, having been originally created, instead of innumerable miraculous creations having been necessary at innumerable periods; though this more simple view accords well with Maupertuis's philosophical axiom 'of least action.'"
2. Simplicity of the cell theory: Scientists have discovered that cells are tremendously complex, not simple.
Total fiction, but an oft-repeated lie by creationists. Scientists in Darwin's day had access to light microscopes with resolution as good as ours today; they were actively studying the structure of the cells, identifying and naming organelles, teasing apart the choreography of cell division. They were entirely aware of the mysteries and complexities of the cell's contents.
And again, there was nothing in any of Darwin's writings that presupposed that cells had to be simple.
3. Theory about the cell's simple information: It turns out cells have a digital code more complex and lengthy than any computer language made by man.
Wait, isn't this the same as #2? I'm seeing some padding going on already.
But no, the genome is not a computer program written in a complex computer language. The words "digital code" are not magic, nor do they imply any supernatural origin.
4. Theory of intermediate fossils: Where are the supposed billions of missing links in the evolutionary chain?
Oh, really? This is the most absurd creationist claim: we keep digging up transitional fossils and waving them in front of their noses, and they just close their eyes and chant "lalalalala".
5. Theory of the variation of species: Genetic adaptation and mutation have proven to have fixed limits.
They do? Where is this "proof"? When I can see from the molecular evidence that a fruit fly, a squid, and a human all share a common core of related genes, I have to say that if there are such limits, they are very wide — wide enough to encompass the entirety of life on earth.
If he means that there are limits such that a mouse will not give birth to an orangutan or a cabbage, I'd agree…but no biologist proposes any such ridiculously saltational view of evolutionary change. It's always the creationists who demand that a cat give birth to a monkey before they'll believe in evolution.
6. Theory of the Cambrian Explosion: This sudden appearance of most major complex animal groups at the same low level of the fossil record is still an embarrassment to evolutionists.
They are so embarrassed about it that they keep writing about it and studying it!
Remember, though, "sudden appearance" means over tens of millions of years…and it's a creationist who believes the whole of the earth's history is about a thousandth of the length of just this one geological period who is claiming that 20 million years is untenably sudden. It's also not true that that animals abruptly appeared: we have evidence of precursors, and even within the Cambrian we see patterns of change from beginning to end.
7. Theory of homology: Similarity of structures does not mean the evolution of structures.
This is the one case where this creationist has dimly caught a glimpse of a real argument within biology. We've been wrestling with the concept of homology for a long, long time — with problems of definition and implementation. These arguments, however, do not cast doubt on the evidence for evolution, so I'm not about to get into them here (this is where a philosopher of science would be much more useful!)
8. Theory of ape evolution : Chimpanzees have not evolved into anything else. Neither has man.
But a proto-chimp/human — our last common ancestor — evolved into both humans and chimps.
This is a very silly argument. It's like claiming that because none of my children have yet reproduced, it is impossible that my wife and I produced them.
9. Theory of the tree of life: Rather than all life branching from a single organism, evidence has revealed a forest of life from the very beginning.
Goddamn you, New Scientist! Ever since they ran their stupid, misbegotten cover, the creationists have been crowing about Darwin being proven wrong. The tree model is still largely accurate for multicellular life, but we have to add a component of horizontal gene transfer, and we recognize that at the root of the tree of life, in all those single-celled organisms, the profligate exchange of genes across species is much, much more common.
But this is still evolution! It's also an entirely natural mechanism; there aren't angels or gods mediating bacterial conjugation or viral transduction.
10. Rejection of an intelligent designer: This opened the door for many to reject God, the Bible and Christianity.
That's no mistake. You should reject gods, holy books, and various cults, because they're all bullshit.
That was a pathetic effort, so typical of creationists. I've seen many such lists of Darwin's errors, and there's a lot of overlap…but there's one thing I've never seen appear on any of them. Why don't they ever mention Darwin's biggest mistake, his theory of blending inheritance, pangenesis? It was completely wrong, it was even incompatible with natural selection, yet the creationists never seem to latch onto it as a tool for defaming Darwin. Is it because then they'd also have to understand that another natural mechanism, one that is intrinsically about chance and statistics, so thoroughly replaced Darwin's mechanism? Is it because they neither understand the theories Darwin proposed, nor Mendelian genetics?
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Posted by PZ Myers at 11:24 AM • 40 Comments
April 25, 2012
Category: Development • Evolution • Fossils • Genetics • Molecular Biology • Organisms • Science
A while back, I told you all about this small piece of the biochemistry of the fly eye — the pathways that make the brown and red pigments that color the eye.
I left it with a question: if even my abbreviated summary revealed considerable complexity, how could this pathway evolve? Changing anything produces a failure or change in the result. Before I answer, let's make the problem even harder, because I love a challenge (although actually, I'm cheating — it's going to turn out that complexity is not a barrier, but an opportunity).
The pigment pathways above are far downstream: they operate in the differentiated compound eye of the fly. Long before that, there are a set of genes that have to be activated first to trigger formation of the head and eye in the larva. And this is that pathway:
At the top of the hierarchy are two genes in Drosophila, eyeless (ey) and twin of eyeless (toy). Remember, genes are named for their mutant effect, so the normal function of eyeless is to initiate eye development. These genes switch on sine oculis and eyes absent (notice the effort to find synonyms to describe genes that cause missing eyes when broken) that activate each other and feed back on eyeless to generate a robust response. Another gene, dachshund (this one named for another part of its phenotype: it makes flies with very short legs) also feeds back on eyeless.
This circuit has multiple outputs: so, dac, optix and eyg. All of these have effects further downstream, in that catch-all category labeled "eye development" here. In that broad label lie multiple processes: the pigment pathways above, but also all kinds of elaborate interactions that recruit cells to specific photoreceptor functions, that organize supporting cells, like hair cells and lenses, and that induce the neural tissue of the retina and deeper parts of the nervous system. The genes ey and toy initiate a whole deep, branching network of genes that cascade together to build the many bits and pieces of the eye.
These two master control genes, eyeless and twin of eyeless, also have a synonym. To everyone's surprise, versions of this circuit are found in all animals with eyes, and the common name for this universal regulator of eye formation is Pax6, and that's what I'll call it in the rest of this article.
And look at this! Isn't it cool? All these eyes use this same Pax6 gene regulatory network to initiate development.
General scheme of eye evolution. The first step in eye evolution is the evolution of a light receptor molecule which in all metazoans is rhodopsin. In the most ancestral metazoa, the sponges, a single Pax gene, but no opsin gene has been found. In the cubozoan jellyfish Tripedalia, a unicellular photoreceptor has been described in the larva. The adult jellyfish has complex lens eyes that form under the control of PaxB, whereas the eyes of a hydrozoan jellyfish (Cladonema) are controlled by PaxA. We propose that from the unicellular photoreceptor cell, the prototypic eye postulated by Darwin originated by a first step of cellular differentiation into a photoreceptor cell and a pigment cell, controlled by Pax6 and MITF, respectively. From this prototype, all the more complex eye types arose monophyletically. As a mechanism, we propose intercalary evolution of progressively more genes such as lens genes into the eye developmental pathway (after Gehring and Seimiya 2010). Starting from the common prototype, the various eye types evolved by divergent, parallel, and convergent evolution, generating a magnificent biodiversity.
That's the power of a gene regulatory network. Switch on just one of the key genes, and it recruits all the downstream genes and triggers a whole series of actions to assemble a complex structure. That strange grey object to the right is a developing Drosophila wing — the dark fringe is the line of bristles that surround the leading and trailing edges of the fully-formed wing — which has had the Pax6 gene inappropriately expressed in a few cells at the base. Just switching on that one gene has led to the construction of an eye with its red pigment right there, where flies should not have eyes.
The ability to build elaborate organs with a simple switch is a reflection of the modular nature of developmental programs. It also simplifies evolution; small, simple changes can lead to dramatic novelties. Zap, one mutation can lead to an abrupt saltational change.
Now wait a moment, you will say. Suddenly plopping an eye onto a wing sounds disastrous: it really is a kind of hopeful monster, emphasis on "monster", and is almost always going to be grossly deleterious. This can't be a viable pathway for evolutionary change, can it? And you'd be right. But what about portions of a pathway? Look back up at the eye development pathway, the second figure in this article. What if you just switched on optix, one of the second-order transcription factors? Then you'd just activate some of the tools of eye construction.
It's been done. The hideous blob to the left is the nascent antenna of a fruit fly, and optix has been inappropriately switched on…and what do you get? It activates the pigment pathway (that biochemical sequence illustrated in the first image at the top of this page), and it creates a bright red spot on the antenna. This is non-trivial; it means the precursors and transporters are all at work, and all the enzymes in the xanthomattin and drosopterin pathways are doing their job. One switch, and you get a whole hierarchy of genes producing a complex output. This could be one way new traits appear, by redeploying genes from established pathways.
Saying they could isn't the same as saying they did, of course. But here are a few examples that suggest that eye network genes have been redeployed to create morphological novelties. In Heliconius butterflies, for instance, the red spots on their wings can be traced back to embryonic patterns of expression of optix in the developing wings.
Even more dramatically, here's an extinct biting midge preserved in amber, and look at that wing: what was I saying about switching on eye genes inappropriately in the wing would be deleterious? I was wrong. This is an insect with a compound eye growing in its wing.
It's extremely unlikely that that alar eye functioned as a visual organ: any photoreceptor signals coming from a platform flapping several times a second would be hopelessly confusing. Most likely what it was was a species-specific sexual signal, like the spots on many fly wings — this one is just more elaborately structured and expensive than most. Alternatively, one hypothesis for the formation of spots on insect wings is that they are intended to resemble eyes — large eyes, far apart, making the animal look much larger to predators — so Eohelea may have just been carrying the eyespot mimicry to an extreme. Either way, building these eyes is developmentally trivial.
It may also represent a transitional state: first the initiator of a genetic cascade is co-opted and expressed at a novel time or place, and then selection can hone it down over time, adding new control points that, for instance, suppress irrelevant ommatidium formation in the alar eye while allowing the functional pigment expression to continue.
One last example: this is the Cambrian worm, Microdictyon. Notice anything unusual?
There's a pair of eyes in the head, where you'd expect them…but all those other eyes along the sides are morphologically indistinguishable from the anteriormost pair. There is some argument about whether these structures actually are eyes, but they are definitely hexagonal arrays that closely resemble the hexagonally structured ommatidia of the compound eyes of insects. If they weren't functional eyes, it seems likely that they are at least produced by the redeployment of the structural genes of the compound eye.
And if they were functional eyes, well, that is just freakin' cool.
The bottom line, though, is that because complex developmental networks are functionally constrained — think of them as software modules that respond to molecular inputs and produce morphological outputs — their complexity is not a barrier to evolution at all, but instead provide opportunities for generating interesting evolutionary novelties.
Gehring WJ (2012) The animal body plan, the prototypic body segment, and eye evolution. Evolution & Development 14(1):34-36.
Monteiro A (2012) Gene regulatory networks reused to build novel traits. Bioessays 34:181-186.
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Posted by PZ Myers at 12:34 PM • 16 Comments
Category: Organisms
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Posted by PZ Myers at 10:05 AM • 1 Comments
April 23, 2012
Category: Organisms
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Posted by PZ Myers at 11:04 PM • 1 Comments
April 16, 2012
Category: Organisms
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Posted by PZ Myers at 9:00 AM • 3 Comments
…and this is a 
