Why Evolution is True is a blog written by Jerry Coyne, centered on evolution and biology but also dealing with diverse topics like politics, culture, and cats.
I’ll announce the three winners of the kitteh contest today: the first two runners-up this morning (they’re in no particular order), and then the grand prize winner this afternoon. Winners: be sure to contact me via email to claim your prizes.
As I said, the celebrity judges had a hard time. There were about 85 entries, many of them awesome. Thanks to Miranda Hale, Russell Blackford, and Ophelia Benson for making the difficult choices. I’ll be highlighting many of the other entries over the next few months.
The first runner-up (and by “first,” I mean “presented first”) is the combination of Doc Bill (human) and Kink (cat). Remember that each entry comprised both a picture and a story. Here’s Doc Bill’s:
My Best Friend
On the day I brought Kink home we stopped at the veterinarian’s office. Poor little Kink, barely 4-months old, had been poked and prodded all morning long and now had to suffer one more indignity before going home.
Doc Geoff pronounced Kink a paragon of fitness.
Putting Kink back into his travel container I commented idly that I needed to swing by the grocery store to get a box.
Geoff looked at me over the tops of his bifocals and asked, “Why?”
“Well,” I replied somewhat uncomfortably, “don’t kittens live in boxes until they can, uh, get around?”
Geoff regarding me as if a Bocydium globulare had landed on his knee said, “I suppose.”
We made our farewells and, shortly, Kink and I were home. Doc Geoff’s voice, however, was lodged in my skull, “I suppose.” Over and over.
That afternoon Kink made himself quite at home eating cat food until he could hardly walk, running up and down the stairs and playing with all the cat toys. He took a couple of cat naps but was ready for bedtime when we all turned in.
I walked into the bedroom with Kink and said, “You know, I think he’d feel more comfortable if he slept with us for a few nights.” I placed Kink behind my knees where he purred himself to the Land of Nod.
Four years later he’s still there and I can’t imagine it being any other way with my best friend. Thanks, Doc Geoff.
This is a picture of Kink on his first day in his new home:
The Guardian‘s “This week in wildlife” site has put up a new photo of the world’s rarest fly, the terrible hairy fly from Kenya. Here the wingless beast looks a bit like a spider mimic (predators might not be able to count legs), or maybe the legs are elongated simply to help it maneuver about in its rock-cleft, bat-guano environment.
Mormotomyia hirsuta (photo from Nairobi’s International Centre of Insect Physiology and Ecology (ICIPE).
And what creature do you think this is? (Answer: check the Guardian site.)
Finally, this is sweet (and should be on Pharyngula). The Guardian caption: “An octopus is released by a group of Buddhists into Victoria harbour in Hong Kong on 4 December 2010. The group gather regularly to release fish left unsold from Hong Kong’s thriving local markets back into the harbour, while offering prayers of long life and freedom from future captors.”
The Dec. 13 issue of The New Yorker has a provocative article about scientific “truth” by Jonah Lehrer, “The truth wears off: is there something wrong with the scientific method?” (You’ll need a subscription to read the whole thing.) It’s about what Lehrer calls the “decline effect”: the fact that an initial demonstration of something in science tends to be weakened or even disappear when later workers try to replicate it.
Lehrer gives lots of examples—including the bogus demonstrations of ESP by J.B. Rhine at Duke—but concentrates on more recent studies. One is from evolutionary biology: the work of Anders Møller on fluctuating asymmetry (FA) in barn swallows. FA is the phenomenon in which a trait of an individual is asymmetrical in random ways (e.g. the right side may be larger or smaller than the left). In the case of barn swallows, FA estimates the difference in length of the long feathers in their forked tails. In 1991, Møller showed that females prefer to mate with males having more symmetrical tails (less FA), presumably because FA was an index of the genetic quality of a male (more FA, worse genes).
Initial studies of other species showed a similar negative relationship between FA and fitness, but then the effect began to decline: by 1998, fewer studies of FA showed positive effects, and the effects that were demonstrated became smaller.
Lehrer cites another study of many results in ecology and evolution:
In 2001, Michael Jennions, a biologist at the Australian National University, set out to analyze “temporal trends” across a wide range of subjects in ecology and evoutionary biology [see reference below]. He looked at hundreds of papers and forty-four meta-analyses (that is, statistical synthesis of related studies), and discovered a consistent decline effect over time as many of the theories seemed to fade into irrelevance. . . . Jennions admits that his findings are troubling, but expresses a reluctance to talk about them publicly. “This is a very sensitive issue for scientists,” he says. “You know, we’re supposed to be dealing with hard facts, the stuff that’s supposed to stand the test of time. But when you see these trends you become a little more skeptical of things.”
What causes these “declines”? Lehrer suggests that it’s a combination of two things. The first is publication bias: an initial enthusiasm for publishing only positive results. (I’d add that this bias could swing toward publishing negative results after an initial discovery becomes something of a dogma: researchers are then motivated to disprove it.) The second is “selective reporting”: not overt fraud, but what Lehrer characterizes as “one of subtle omissions and unconscious misperceptions, as researchers struggle to make sense of their results. Steven Jay Gould referred to this as the ‘shoehorning’ process.'”
This, then, is not (as Lehrer’s title implies) an indictment of the scientific method of testing and replication per se, but of scientists and the culture of science. Lehrer winds up criticizing the “slipperiness of empiricism,” suggesting that much of what we “know”—even about things like the strength of gravity and the weak coupling ratio of neutrons—may simply be wrong. His ending is provocative:
The decline effect is troubling because it reminds us how difficult it is to prove anything. We like to pretend that our experiments define the truth for us. But that’s often not the case. Just because an idea is true doesn’t mean it can be proved. And just because an idea can be proved doesn’t mean it’s true. When the experiments are done, we still have to choose what to believe.
I tend to agree with Lehrer about studies in my own field of evolutionary biology. Almost no findings are replicated, there’s a premium on publishing positive results, and, unlike some other areas, findings in evolutionary biology don’t necessarily build on each other: workers usually don’t have to repeat other people’s work as a basis for their own. (I’m speaking here mostly of experimental work, not things like studies of transitional fossils.) Ditto for ecology. Yet that doesn’t mean that everything is arbitrary. I’m pretty sure, for instance, that the reason why male interspecific hybrids in Drosophila are sterile while females aren’t (“Haldane’s rule”) reflects genes whose effects on hybrid sterility are recessive. That’s been demonstrated by several workers. And I’m even more sure that humans are more closely related to chimps than to orangutans. Nevertheless, when a single new finding appears, I often find myself wondering if it would stand up if somebody repeated the study, or did it in another species.
But let’s not throw out the baby with the bathwater. In many fields, especially physics, chemistry, and molecular biology, workers regularly repeat the results of others, since progress in their own work demands it. The material basis of heredity, for example, is DNA, a double helix whose sequence of nucleotide bases codes (in a triplet code) for proteins. We’re beginning to learn the intricate ways that genes are regulated in organisms. The material basis of heredity and development is not something we “choose” to believe: it’s something that’s been forced on us by repeated findings of many scientists. This is true for physics and chemistry as well, despite Lehrer’s suggestion that “the law of gravity hasn’t always been perfect at predicting real-world phenomena.”
Lehrer, like Gould in his book The Mismeasure of Man, has done a service by pointing out that scientists are humans after all, and that their drive for reputation—and other nonscientific issues—can affect what they produce or perceive as “truth.” But it’s a mistake to imply that all scientific truth is simply a choice among explanations that aren’t very well supported. We must remember that scientific “truth” means “the best provisional explanation, but one so compelling that you’d have to be a fool not to accept it.” Truth, then, while always provisional, is not necessarily evanescent. To the degree that Lehrer implies otherwise, his article is deeply damaging to science.
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UPDATES: Over at Wired, Lehrer explains his thesis a bit more and responds to readers’ questions.
According to the BBC news, scientists have rediscovered the bizarre Terrible Hairy Fly (Mormotomyia hirsuta), last seen in 1948 and thought to be extinct. It has the most restricted of habitats, apparently living only in a 20-meter cleft in one rock in Kenya, and breeding on the guano of bats inhabiting the cleft. It’s covered with large bristles and has vestigial wings (evidence for evolution, of course) and tiny eyes.
Mormotomyia hirsuta
This is on top of another “rediscovered” fly, Thyreophora cynophila, a bizarre orange-headed creature that breeds on decayed animal corpses. It hadn’t been seen for over 150 years, but in September was reported from two localities in Spain.
In yesterday’s Slate, Daniel Sarewitz has a remarkably snarky and unreflective piece, “Lab politics,” accusing scientists—who are mostly Democrats—of subordinating scientific truth to an explicitly political agenda. (Sarewitz, director of the Consortium for Science, Public Policy and Outcomes at Arizona State University, was trained as a scientist: he has a Ph.D. in geology from Cornell.)
Here’s his logic. A Pew survey last year showed that 55% of American scientists are Democrats, 32% are independent, and only 6% are Republicans (the rest “don’t know”). Further, the political parties diverge strongly in how they feel about issues like climate change. While 66% of Democrats say that the results of human activity on climate are being felt now, only 31% of Republicans agree. From this Sarewitz suggests darkly that scientists’ warnings about global warming reflect not the data, but our commitment to types of social change that are advanced by the controversy:
Or could it be that disagreements over climate change are essentially political—and that science is just carried along for the ride? For 20 years, evidence about global warming has been directly and explicitly linked to a set of policy responses demanding international governance regimes, large-scale social engineering, and the redistribution of wealth. These are the sort of things that most Democrats welcome, and most Republicans hate. No wonder the Republicans are suspicious of the science.
Think about it: The results of climate science, delivered by scientists who are overwhelmingly Democratic, are used over a period of decades to advance a political agenda that happens to align precisely with the ideological preferences of Democrats. Coincidence—or causation? Now this would be a good case for Mythbusters.
. . . The climate debacle is only the most conspicuous example of these debilitating tendencies, which play out in issues as diverse as nuclear waste disposal, protection of endangered species, and regulation of pharmaceuticals.
Sarewitz’s solution? More Republican scientists—and a call for us to investigate why there are so few of them:
Yet there is clearly something going on that is as yet barely acknowledged, let alone understood. As a first step, leaders of the scientific community should be willing to investigate and discuss the issue. They will, of course, be loath to do so because it threatens their most cherished myths of a pure science insulated from dirty partisanship. In lieu of any real effort to understand and grapple with the politics of science, we can expect calls for more “science literacy” as public confidence begins to wane. But the issue here is legitimacy, not literacy. A democratic society needs Republican scientists.
It is interesting that so many scientists are Democrats. It’s not clear whether those with Democratic leanings are more likely to go into science, or whether being in science reinforces views that align with Democratic politics. Likely both are involved. I suspect, for instance, that it has something to do with love of the truth, which feeds into both correlations. Regardless, though, it’s pure sophistry of Sarewitz to suggest that something like global warming is a scientific controversy manufactured purely to push a liberal agenda. The alternative view is that the facts have convinced scientists that global warming is real and has dire consequences, and that—since we’re not Republicans—we don’t care to hide these consequences to protect business and industry.
Curiously, Sarweitz also notes that despite the Democratic leanings of scientists, 90% of Americans trust the scientific community as a whole—more than any other institution including the Supreme Court. Why would that be, unless the public senses that scientists are more objective than members of other institutions, and less willing to corrupt their pronouncements in the service of politics or philosophy?
Christmas will be here before you know it, and I’ve thoughtfully compiled a short list of gifts that might appeal (for receiving or giving) to readers of this website.
Owl pellets from Mountain Home Biological. These are cheap: only $2.65 for an extra large pellet, which can contain up to 6 prey! Hours of fun for the young naturalist. Optional dissection kit just $2.25.
Our desktop Cat Seat gives cats a comfortable place to rest on the desk that’s out of the way, yet still only an arm’s length from a scratch on the belly. Designed for cat owners who work in a home or small office, this indispensable item maintains that all-important distance between paws and keyboard, while giving your cat a cozy nesting box that’s still within easy reach of affection. The soft cushion and high walls will appeal to your cats, while you’ll appreciate the solid pine construction in a choice of attractive finishes. It can be clamped firmly to either side of the desk, or simply placed flat on top–felt pads protect your furniture. Can support a 20-lb. cat, and even small dogs. Cushion cover is machine-washable. 16 1/4″ w x 11″ d x 5″ h.
Cats and humans look very different. Or do they? 32-day old embryos of the two species look pretty identical, as shown here (guess which is the cat! Answer at the end):
Why do they look so similar? This is one of the oddest riddles in biology, which has now been given a new answer following the publication of two articles in Nature today. To understand why this is so important, we need to go back nearly 200 years.
In 1828, Karl von Baer – the first man to observe the human egg – studied a number of embryos of different species and noted that the common features of large groupings of organisms, such as vertebrates, develop before the more specific characters. So, for example, human embryos have tails, and they also have folded structures around their neck that are similar to those seen in fish embryos, and which turn into gills in our water-dwelling relatives.
At the end of the 19th century, the German embryologist Ernst Haeckel turned this observation into an evolutionary “law”, in which he suggested that each organism, as it grows, goes through its evolutionary past. He put this in a fancy phrase: “Ontogeny recapitulates phylogeny”, and provided some neat drawings (these are from Wikipedia):
Ernst Haeckel's Embryological Illustrations from 1874. Taken from Wikipedia. From right to left: Human, dog, deer, pig, chicken, tortoise (note the shell), salamander and fish.
Although this might sound clever, it is not actually true (and it has been suggested that Haeckel’s drawings were not as accurate as they should have been!). Human embryos do not have gills – the embryonic structures become our jaws, not gills. Furthermore, Haeckel’s idea was based on a linear view of evolution that is plain wrong. Species do not evolve in a straight line, but a complex branched pattern. We share a common ancestor with a cat, but our lineages have been going their own way – and evolving differently – ever since.
But even if Haeckel was wrong, it doesn’t get away from the bizarre fact that human embryos have tails. What’s going on there? It turns out that the situation is more complex than Haeckel realised. At the earliest and latest stages of embryonic development, organisms within a given group look very different. But in a middle phase, they all tend to look pretty much the same. This effect is at its strongest in the different animal phyla – vertebrates, arthropods and so on – and is referred to as the “phylotypic” period, because each phylum has a typical common embryonic form which species in that phylum adopt, before turning into their final, species-specific shape.
This “hourglass” shape of embryonic development – specific/common/specific – has long intrigued biologists, but some people felt it might not be true, as it was based primarily on observations of physical similarity, not on the underlying genetic processes. Nature has just published two studies of very different model systems – the fruitfly Drosophila and the zebrafish – that cast a new light on the genetics of the “hourglass”, showing that the oldest genes are involved in the middle, “phylotypic” period.
The study on Drosophila – carried out by a team led by researchers from the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Duke University and the University of Manchester – looked at the genes that are expressed during the embryonic development of fruitfly eggs from six Drosophila species, some of which have been separate for 40 million years. Even within these apparently-identical species (one fruitfly looks pretty much like another, unless you are an entomologist – or a fly), there are big differences in the genes that are expressed early and late in development but, just as predicted by the hourglass model, each species tends to express the same genes during the middle, “phylotypic” period.
As you might expect, these middle genes are involved in important processes that are common to all the Drosophila species, such as synthesizing biomolecules, organizing chromosomes and above all controlling anatomical development. Genes that are not involved in development tended not to follow the “hourglass”.
In a partner article, researchers from the Max Planck Institute for Evolutionary Biology and Ruđer Bošković Institute looked at the genes that are activated in 60 different stages of the zebrafish, from the embryo on into the adult. As with Drosophila, they found that the oldest genes were expressed during the middle, “phylotypic” period of embryonic development. Younger, more specific, genes tended to be expressed in the earlier and later phases, with the intriguing exception of the oldest animals, which once again tended to express evolutionarily ancient genes.
Fascinating as these studies are, they only answer half the question. We now know how this “phylotypic” middle phase of the “hourglass” is produced – through the expression of ancient genes. But we do not know why.
The Drosophila group found evidence that natural selection in the form of selective constraint is acting on these patterns of gene expression, perhaps related to the fact that there is a best way of assembling the shared aspects of each body shape, constraining innovation and resulting in the conservation of ancient, highly effective genes involved in development.
The zebrafish group take a slightly different tack and refer to Darwin’s suggestion that environmental influences might be strongest at the earliest and latest phases of development, meaning that in the middle, phylotypic phase, the embryo is less “visible” to adaptation by natural selection, leading to a lack of evolutionary innovation. This would also explain the fact that very old fish express very ancient genes – once an organism is past reproductive age, it generally cannot be “seen” by natural selection.
These two papers shed a new light on one of the most bizarre questions in biology – why do so many embryos look alike? They show that although ontogeny does not recapitulate phylogeny, phylogeny is involved in ontogeny – the way we grow does shed light on our evolutionary past. The “hourglass” is real at the visible and molecular level, and the genes that specify the middle, more general, shape of an organism are some of the oldest in each species’ genome.
Now we need to know why, and above all why did you and I have a tail when we were only a few weeks old?
In commenting on an earlier draft of this post, Jerry responded to this final point this way:
“I think we know the answer to that question–at least sort of, but you imply that it’s a complete mystery. Clearly our development evolved from an ancestral developmental plan, that that ancestor had a tail, gills, etc. We retain that plan (yes, we’re not sure why, but probably because changing it would have screwed up everything downstream). Don’t you think you should give the readers at least a BIT of explanation about this stuff? It is, after all, the question with which you begin!”
Well sorry, folks, but Jerry’s pearls of wisdom are as much as you’re going to get on that point. Come up with your own tales about tails in the comments below!
Answer: The cat is on the left. Or maybe it’s the right.
[Edit: There’s a nice summary of these papers over at Discovery, together with some useful quotes from the authors.]
I didn’t post on the bacterium that supposedly evolved to incorporate arsenic into its DNA because I was ill, late to the party, and, frankly, not really equipped to judge that paper, which was published in Science. In yesterday’s Slate, however, Carl Zimmer wades into the fray, talking to a number of scientists who attacked the study, including Rosemary Redfield of the University of British Columbia, who published a withering takedown of the original paper. Zimmer’s piece is straightforwardly called “This paper should not have been published.”
Zimmer’s interviewees are pretty unanimous in claiming that the evidence that arsenic was really incorporated into the DNA—the paper’s major finding—is unconvincing. It might well have been a contaminant. Critics blame the paper’s appearance on shoddy science, credulous authors, and poor reviewers.
Zimmer asked two of the paper’s authors to respond to these criticisms, and they refused, claiming that they weren’t going to debate their results in the media. As Zimmer reports, others see this as evasion:
While Redfield considers Wolfe-Simon’s research “flim-flam,” she think it’s fine for the NASA scientists to hold off responding to their critics. She is working on a formal letter to Science detailing her objections. But Jonathan Eisen of UC-Davis doesn’t let the scientists off so easily. “If they say they will not address the responses except in journals, that is absurd,” he said. “They carried out science by press release and press conference. Whether they were right or not in their claims, they are now hypocritical if they say that the only response should be in the scientific literature.”
Eisen’s right. It’s incumbent on the authors, who flogged their paper via press conference, to at least give some sort of public response, if only to say that they’re looking into it and repeating their experiments. This is a new era of science, in which reaction to a paper by fellow scientists can be virtually instantaneous, and not always pretty. I, for one, welcome it. I’d rather know now rather than later if there are problems with this “new life form.” Further, these critiques and counter-critiques aren’t always easy to find when they’re in the scientific literature: many journals bury them somewhere in the online version.
