Hagfish, hagfish, hagfish!

November 21, 2011 • 10:24 pm

by Greg Mayer

I’m teaching vertebrate zoology this semester, and one of my favorite topics in the course is the hagfish. Hagfish are jawless, eel-like fish, whose closest relatives are lampreys. (They were once though to be more primitive than lampreys, but molecular data show the two to form a holophyletic group.)  I was thus quite pleased to find that Vincent Zintzen from the Museum of New Zealand and colleagues have a recent paper in Scientific Reports on hagfish defensive and predatory behavior, with accompanying videos.  There’s more at the website of Te Papa Tongarewa (which is the name of the museum in Maori).

Hagfish are well known for producing copious amounts of viscous slime to discourage predators. In the following video, what’s most remarkable to me is how rapidly the hagfish produces sufficient slime to almost instantaneously deter the predators.

Here’s a closeup of slime production from the Vancouver Aquarium:

And here’s a hagfish preying on a burrowing fish. Zintzen et al. suspect the fish has been killed or disabled by choking with slime while in the burrow.

Hagfish are usually thought of as scavengers (notice the cages of dead meat used as bait in the video).  Here’s a more usual feeding episode: large numbers of hagfish gathering on a whale carcass. That sounds like David Attenborough doing the narration.

Finally, here’s an abridged, combined version of the Te Papa videos (if you want to get the under 4 minute version of the whole story):

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Zintzen V., Roberts, C.D., Anderson M.J., Stewart A.L., Struthers C.D. & Harvey E.S. 2011. Hagfish predatory behaviour and slime defence mechanism. Scientific Reports 1: 131, 6 pp. pdf (Scientific Reports is put out online-only by Nature Publishing Group; papers are given at least some peer review, but are not evaluated for how important or interesting they are.)

David Berlinski makes an ass of himself defending intelligent design

November 21, 2011 • 9:30 am

I know of no critic of evolution—perhaps save the late William F. Buckley, Jr.—who is at once so eloquent and so ignorant as David Berlinski.  The man has spent years attacking evolutionary biology and defending intelligent design (ID), and is, to my knowledge, the only living creationist who is not religious. (He claims to be an agnostic, though I have trouble believing that.) He’s also a Senior Fellow of the Discovery Institute, a position reserved for only the Highest Poo-Bahs of Ignorance.

Yesterday, at the Discovery Institute’s News and Views site, Berlinski wrote “Majestic Ascent: Berlinski on Darwin on Trial,” a post apparently designed to fête the twentieth anniversary of Phillip Johnson’s execrable Darwin on Trial: the book that launched the ID movement.  Johnson’s book is full of inaccuracies and lies (I use the word deliberately, because no honest scholar could make the claims that he did).  And, sure enough, Berlinksi’s post is full of lies as well.  I’m not going to analyze it in detail, but here are a few blatant misrepresentations.

First, a specimen of how incredibly pompous and awkward Berlinski’s writing is. Do not write like this!  I think he’s trying to ape Gould’s style, possessed with a big vocabulary but lacking Gould’s wit and erudition.

Comments such as these [Michael Ghiselin’s withering criticism of Darwin on Trial] had the effect of raw meat dropped carelessly among carnivores. A scramble ensued to get the first bite. No one bothered to attack the preposterous Ghiselin. It was Richard Dawkins who had waggled his tempting rear end, and behind Dawkins, fesse à fesse [buttock to buttock] Charles Darwin. With the publication in 1991 of Darwin on Trial Phil Johnson did what carnivores so often do: He took a bite.

This metaphor is neither apposite nor appetizing.  At any rate, here’s what Berlinski says. The first thing he gets dead wrong is the fossil record:

Every paleontologist writing since Darwin published his masterpiece in 1859, has known that the fossil record does not support Darwin’s theory. The theory predicted a continuum of biological forms, so much so that from the right perspective, species would themselves be seen as taxonomic artifacts, like the classification of certain sizes in men’s suiting as husky. Questions about the origin of species were resolved in the best possible way: There are no species and so there is no problem. Inasmuch as the historical record suggested a discrete progression of fixed biological forms, it was fatal to Darwin’s project. All the more reason, Darwin argued, to discount the evidence in favor of the theory. “I do not pretend,” he wrote, “that I should ever have suspected how poor a record of the mutations of life, the best preserved geological section presented, had not the difficulty of our not discovering innumerable transitional links between the species which appeared at the commencement and close of each formation, pressed so hardly on my theory.”

This is, as Johnson noted, self-serving gibberish.

Self-serving gibberish my butt! Darwin recognized full well that he didn’t have enough fossils to confirm his theory, and at least he admitted it.  Would that the idiots at the Discovery Institute were intellectually courageous enough to write a chapter on “difficulties on theory,” as did Darwin! Since when has an IDer admitted any problem with that theory?

But Darwin didn’t need evidence from fossils to support his theory: he had enough evidence from biogeography, from vestigial organs, from embryology, from the hierarchical arrangement of life, from evidence of heritable variation and from the efficacy of artificial selection—to convince people of evolution even if there had been no fossils.  And convince thinking people he did.

Of course, since Darwin’s time the “missing” fossil evidence has appeared—in spades.  It’s all detailed in my book, and you can find it online, too. We have intermediates between early fish and amphibians, early amphibians and reptiles, reptiles and birds, and reptiles and early mammals. We have lineages, especially of marine microfossils, but also of larger animals like horses, showing gradual change that accumulates into what can only be seen as macroevolution.

We have the once-missing intermediates between terrestrial artiodactyls and whales: a fine fossil series.  And, of course, we have all those fossils in the hominin family tree, from early australopithecines with apelike skulls and more modern human-like postcranial skeletons to more modern forms that closely resemble modern humans in nearly every feature. None of these were known in Darwin’s time.

For Berlinski to pretend that the fossil evidence doesn’t support Darwin, when every bloody fossilized tooth, bone, leaf, and integument cries out “evolution”, is the height of stupidity. Or, since I don’t think Berlinski is stupid, let’s say the height of intellectual dishonesty.  Berlinkski knows of the fossil record, and pretends it doesn’t exist. He’s a liar.

He also lies about whether Darwin (or modern biologists) think there are species. Berlinski implies that Darwin denied the existence of species. He didn’t, though he was at times confused about what they represented. Modern biologists, of course (at least most of them, with the exception of a few botanist or systematist miscreants), also realize that species are real units of nature, and most of us understand that they are reproductive units, separated from other such units by genetic barriers to interbreeding.

After handily disposing of evolution, Berlinski takes out after natural selection:

Few serious biologists are today willing to defend the position that Dawkins expressed in The Blind Watchmaker. The metaphor remains stunning and so the watchmaker remains blind, but he is now deaf and dumb as well. With a few more impediments, he may as well be dead. The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief.

What Berlinski is saying here is twofold.  First, that there is no evidence for natural selection, either on genes or organisms. That’s palpable nonsense.  We have by now accumulated hundreds of cases of natural selection acting in real time on traits, not to mention evidence for a). the efficacy of artificial selection and b). the presence of pervasive genetic variation in natural populations, both of which indicate that fitness differentials in nature will lead perforce to evolutionary change.

Second, Berlinski implies that Kimura’s neutral theory nullifies natural selection.  It doesn’t. Kimura’s theory was a big advance in the field, suggesting and working out the consequences of genetic variants that don’t affect fitness.  And, indeed, much of molecular evolution (and an unknown amount of phenotypic evolution) may have been affected by drift. But even Kimura didn’t deny that natural selection was an important evolutionary force, and the only known evolutionary force that can produce adaptations. To say that the neutral theory left the emergence of complex biological features “an emigma” is simply a misrepresentation of what the neutral theory was about.

Further, population geneticists are starting to realize that evolution on the molecular level is NOT “entirely stochastic”.  First, we have the obviously adaptive and maladaptive molecular substitutions in coding positions in DNA: both the good ones, like mutations for insecticide resistance in insects, and the deleterious ones, like the molecular mutation in the beta chain of hemoglobin that causes sickle-cell anemia.

Further, recent sequencing work is beginning to show that many substitutions in DNA that were once thought to be “entirely stochastic”—due to the substitution of nucleotides that made no difference in fitness—actually do have effects on fitness, and so are not neutral.  These include many substitutions in the “third” or noncoding positons of DNA. Substitutions there, while they may not affect the sequence of the protein ultimately produced by that stretch of DNA, can have a fitness effect by drawing on pools of “transfer” RNA or nucleotide bases that are more or less abundant.

The “stochasticity” of molecular evolution is an unsettled issue, but it’s already clear that much of DNA evolution does not adhere strictly to Kimura’s neutral theory.  Berlinski belies his ignorance here; he’s obviously not kept in touch with the literature.  Or perhaps he has, but is lying again.

Those are the two main factual claims in Berlinski’s piece (three if you count the “nonexistence” of species), and he’s wrong on both counts. The rest is his usual pompous lucubrations about Gould, theistic evolution, the materialism of science, and so on. And a slur slung our way as well:

That much is at stake explains a good deal about the rhetoric of discussion in the United States, its vile tone. Biologists such as Jerry Coyne, Donald Prothero, Larry Moran or P.Z. Myers are of the opinion that if they cannot win the argument, they had better not lose it, and what better way not to lose an argument than to abuse one’s antagonist? If necessary, the biological establishment has been quite willing to demand of the Federal Courts that they do what it has been unable to do in the court of public opinion.

Sorry, David, but I didn’t abuse my antagonists, but tried to correct them by writing a calm, non-strident book about the evidence for evolution, one that has done pretty well.  Yes, I’ll sometimes abuse morons like you, but only because you know that evidence and yet deliberately lie to the undereducated to keep them in the state of ignorance that religions prefer.

And yes, we do demand that Federal courts enforce the law, because we won’t have religious dogma insinuating itself into our children’s science classes. Or would you prefer to have science determined by the majority whim of the electorate? If so, then be prepared to have homeopathy and spiritual healing taught in medical schools, astrology in psychology classes, and alchemy in chemistry classes.

The reason why the “court of public opinion” doesn’t like evolution has nothing to do with its truth, and everything to do with its supposedly unsavory implications.  It tells us that we’re neither the products of a special design by God, nor imbued by a deity with some celestial purpose and meaning. People don’t like these implications and so they reject the theory. It has nothing to do with them having learned the evidence for evolution and found it insufficient.

I have news for you, David: you’re going to die in a few decades.  You probably don’t like that fact, either (I’m not comfortable with my own mortality, either), but it’s true. Deal with it.

Oh, and you can haz: Berlinski’s own video highlighting how awesome he is on his website. Note the trendy Frenchiness:

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Jim Watson: an anecdote

November 21, 2011 • 12:41 am

I found an old review on my computer today—one I’d written for the Times Literary Supplement in 2007.  The book under review was Avoid Boring People: And Other Lessons from a Life in Science, by J. D. Watson, and my title was, obviously, “Unlucky Jim”. (Watson had just been dismissed as director of the Cold Spring Harbor Laboratories for racist remarks.)

Alas, the piece is no longer online, and I won’t bore you with its contents (my review was mixed), but the end of the piece is an anecdote I’d like to relate.

Whenever I ponder Watson, my thoughts go back to a Saturday afternoon in the spring of 1992—Alumni Day at the University of Chicago.  As a colleague and I were chatting in the lab, we were accosted by a rumpled, elderly gentleman with wild wisps of white hair.  The man informed us that the room in which we were standing was a teaching lab when he was an undergraduate.  My colleague told him that it was now used for research—DNA research.  “What do you do with the DNA?” asked the man. Assuming that the visitor knew nothing about molecules, my colleague provided a patient and detailed explanation of how he was determining the sequence of a DNA fragment, using the analogy of coloured beads on a string. The man listened carefully and enthusiastically, sporadically nodding his grasp of the details.

The ageing alumnus finally introduced himself.  My friend, who turned a flaming crimson, had been explaining DNA, as if to a child, to Jim Watson, Mr. DNA himself!  But, far from being offended, Watson was so pleased that a scientist had taken such time and care to explain his work that he endowed our department with a generous lectureship.  That, too, is the real—and complex—Jim Watson.

And, nineteen years later, my department still has a yearly Watson lecture on molecular evolution.

Thought for the day

November 20, 2011 • 10:34 am

by Matthew Cobb

Maybe it’s a sign of my own advanced age, but I found this thought rather interesting. Life has been around on Earth for a bit over 3 billion years, maybe even 4 billion years. Physicists tell us that the Sun will eventually swell and turn into a red giant (it won’t explode in a supernova as it isn’t massive enough). But before it turns into that fat old sun in the sky and swallows up the Earth, it will have rendered life on Earth impossible by simply making the place too darn hot. That will happen in around 1 billion years. So if you reckon that the window of opportunity for life on Earth is around 4 or 5 billion years, that means life is around 75% or 80% of the way through our alloted span – on this planet at least. So, Life, looking back on things, what do you think the best bits were? What was your greatest achievement? And what do you hope to do in the years that remain? After all, you’re someway along the downhill slope now…

I have landed

November 20, 2011 • 6:05 am

After several fun-filled days in Valencia, marred somewhat by a pretty dreadful throat virus that forced me to croak rather than speak when I gave my scientific talk, I have arrived in Madrid for the Spanish evolution meetings.  These start tomorrow, and I give the first talk at 12:30. My voice is still weak but I’ll muddle through.

I have tales to tell and many pictures to show, but that must wait until I return to America (I didn’t bring my connector to upload pictures).  Rest assured, though, that you’ll see a picture of the best paella Valenciana in Valencia , and many other comestibles as well.

I took the fast train from Valencia to Madrid, which reaches speeds of 300 km per hour and goes halfway across Spain in just an hour and a half.  I am now installed in the Residencia de Estudiantes near the Natural History Museum and the site of the talks: the campus of the Spanish foundation that funds science (the equivalent of America’s NSF).

Below is a stock photo of the Residencia, a cultural center with a famous history. It’s been on this site since 1915. Here’s part of the Wikipedia entry:

The Residence’s influence was particularly strong from its foundation in 1910 until the outbreak of the Spanish Civil War in 1936. During this time, many Spanish artists and writers, members of the Generation of ’98 and Generation of ’27, visited, studied and lectured at the Residence, including Federico García Lorca, Luis Buñuel, Salvador Dalí, José Ortega y Gasset, Rafael Alberti, Dámaso Alonso, Luis Cernuda, Miguel de Unamuno, Antonio Machado and Ramón del Valle-Inclán, and other innovative thinkers such as Einstein, Howard Carter, Gilbert Keith Chesterton, Paul Valéry, Marie Curie, Igor Stravinski, Paul Claudel, Louis de Broglie, Herbert George Wells, Max Jacob, Le Corbusier, Keynes, etc. The biopic Little Ashes (2009) depicts the Residencia in the 1920s, and the relationship of Lorca, Dalí, and Buñuel who were there at the time. [JAC: note that Rotten Tomatoes gives this film a low rating, as it should since it stars Robert Pattinson as Salvador Dali.]

I wish I knew if any of these folks had stayed in my room.

Brother Blackford on “other ways of knowing”

November 19, 2011 • 11:38 pm

In a nice piece at Talking Philosophy called “Is science so limited?”, Russell Blackford takes up the perennial question of whether there are “other ways of knowing” beyond those involving science.

I’ve always maintained that there are no other reliable ways of knowing beyond science if one construes science broadly—as meaning “a combination of reason and empirical observation.” Some people don’t like definition, and prefer to take science as “the practices of working scientists.”  I don’t have any great objection to that, as it’s largely a semantic question.  The real question is whether there’s any way beyond empirical observation and reason to establish what is true about the world.  I don’t think so, and I believe Russell agrees with me.  And we both agree that religion, insofar as it doesn’t rely on empiricism and reason but on revelation and self-confirming dogma, doesn’t produce truth.

Russell sees, as do I, science not as something absolutely distinct from traditional empiricism, but simply as a new and more refined “way of knowing” that is not discontinuous with how people found out stuff before science came along:

Consider the rise of science in Europe in the sixteenth and seventeenth centuries, and beyond. This produced a new breed of empirical investigators – the breed who eventually came to be known as “scientists” – and they developed a range of techniques to high levels of precision and sophistication. These “scientists” used, for example, increasingly sophisticated mathematical models, rigorously controlled experimental design and apparatus, and new instruments that extended the human senses. They were able to engage in unprecedentedly precise and systematic study of various phenomena that had previously resisted human efforts, particularly very distant or vastly out-of-scale phenomena, very small phenomena, and phenomena from very deep in time – before human beings and written records. This enabled them to develop a radically new image of the cosmos and our place in it. By the end of the eighteenth century, it was starting to come together in a way that is still broadly recognisable, though far more has been discovered since, and it’s clear enough that far more remains to be discovered in the future.

What is often forgotten is that the distinctively scientific techniques that were refined and extended so much over the last four to five centuries were continuous with what had gone before and that, to the extent that they were new they added something. Nothing was subtracted from the tools of rational inquiry available to scholars (or to ordinary people).

We part company only in one respect: Russell seems to consider science itself unable to answer some questions that do have real answers. As he says:

It’s not a matter, then, of science being limited. Science enables some questions to be given reliable answers for the first time (the age of the Earth, for example, and composition of our solar system), but it in no way prevents answers to other questions, such as what is outside my window; how to translate Tasso into English; or what might be a “thick”, coherent, and convincing interpretation of Bleak House. Science did not render us helpless to answer these questions, though it certainly added to what we know about, say, very distant, small, or ancient phenomena.

What is outside his window can indeed be answered by empirical observation (especially if it’s verified by Jenny and others), but I’m not sure there is one definitive answer for “how to translate Tasso into English?”, or “what is the most convincing interpretation of Bleak House?” (Convincing to whom?)

Those questions, unlike factual questions about the world that can be answered by science or observation, have a multiplicity of answers that will never be agreed on by everyone. Therefore they are not questions that have a definitive empirical answer; their answers are not “facts.”

When I regard the issue of “ways of knowing,” then, I look at it as “ways of knowing that are agreed on by everyone who is not perverse” (that’s Gould’s definition of “fact”).  That’s a scientist’s definition of fact, of course.  If ways of knowing vary from person to person, as would the best translation of Tasso, then we elide into the realm of religion, where each faith swears that it knows what is true, but those ways differ among religions.

Russell and I also have some differences in what we regard as “facts”; see our exchange of comments here and here.  But for those of you who have accused me of dissing philosophy, let me affirm that I think Russell’s brand of philosophy is very useful in helping superstition and separating what we can know from what we can’t. And I also see much value in ethical philosophy, such as that of Peter Singer.