Recently in Evolution Category

Eudyptula Minor

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Eudyptula Minor – little penguin, Kangaroo Island, Australia. These penguins are nocturnal, but are apparently blind to the red light. Unfortunately, according to Kangaroo Island Penguin Center, “Our nocturnal Penguin Tours ceased in November 2013 due to the very low numbers of Penguins in the Kingscote colony. Predation by the increasing numbers of New Zealand Fur Seals from 2010 onwards has decimated the Penguin Colony, because the seals kill the adult penguins as they swim ashore at night to feed their chicks and therefore the chicks also die. We apologise for this, but the situation has been beyond our control.”

This post is by Joe Felsenstein and Tom English

Back in October, one of us (JF) commented at Panda’s Thumb on William Dembski’s seminar presentation at the University of Chicago, Conservation of Information in Evolutionary Search. In his reply at the Discovery Institute’s Evolution News and Views blog, Dembski pointed out that he had referred to three of his own papers, and that Joe had mentioned only two. He generously characterized Joe’s post as an “argument by misdirection”, the sort of thing magicians do when they are deliberately trying to fool you. (Thanks, how kind).

Dembski is right that Joe did not cite his most recent paper, and that he should have. The paper, “A General Theory of Information Cost Incurred by Successful Search”, by Dembski, Winston Ewert, and Robert J. Marks II (henceforth DEM), defines search differently than do the other papers. However, it does not jibe with the “Seven Components of Search” slide of the presentation (details here). One of us (TE) asked Dembski for technical clarification. He responded only that he simplified for the talk, and stands by the approach of DEM.

Whatever our skills at prestidigitation, we will not try to untangle the differences between the talk and the DEM paper. Rather than guess how Dembski simplified, we will regard the DEM paper as his authoritative source. Studying that paper, we found that:

  1. They address “search” in a space of points. To make this less abstract, and to have an example for discussing evolution, we assume a space of possible genotypes. For example, we may have a stretch of 1000 bases of DNA in a haploid organism, so that the points in the space are all 41000 possible sequences.

  2. A “search” generates a sequence of genotypes, and then chooses one of them as the final result. The process is random to some degree, so each genotype has a probability of being the outcome. DEM ultimately describe the search in terms of its results, as a probability distribution on the space of genotypes.

  3. A set of genotypes is designated the “target”. A “search” is said to succeed when its outcome is in the target. Because the outcome is random, the search has some probability of success.

  4. DEM assume that there is a baseline “search” that does not favor any particular “target”. For our space of genotypes, the baseline search generates all outcomes with equal probability. DEM in fact note that on average over all possible searches, the probability of success is the same as if we simply drew randomly (uniformly) from the space of genotypes.

  5. They calculate the “active information” of a “search” by taking the ratio of its probability of success to that of the baseline search, and then taking the logarithm of the ratio. The logarithm is not essential to their argument.

  6. Contrary to what Joe said in his previous post, DEM do not explicitly consider all possible fitness surfaces. He was certainly wrong about that. But as we will show, the situation is even worse than he thought. There are “searches” that go downhill on the fitness surface, ones that go sideways, and ones that pay no attention at all to fitnesses.

  7. If we make a simplified model of a “greedy” uphill-climbing algorithm that looks at the neighboring genotypes in the space, and which prefers to move to a nearby genotype if that genotype has higher fitness than the current one, its search will do a lot better than the baseline search, and thus a lot better than the average over all possible searches. Such processes will be in an extremely small fraction of all of DEM’s possible searches, the small fraction that does a lot better than picking a genotype at random.

  8. So just by having genotypes that have different fitnesses, evolutionary processes will do considerably better than random choice, and will be considered by DEM to use substantial values of Active Information. That is simply a result of having fitnesses, and does not require that a Designer choose the fitness surface. This shows that even a search which is evolution on a white-noise fitness surface is very special by DEM’s standards.

  9. Searches that are like real evolutionary processes do have fitness surfaces. Furthermore, these fitness surfaces are smoother than white-noise surfaces “because physics”. That too increases the probability of success, and by a large amount.

  10. Arguing whether a Designer has acted by setting up the laws of physics themselves is an argument one should have with cosmologists, not with biologists. Evolutionary biologists are concerned with how an evolving system will behave in our present universe, with the laws of physics that we have now. These predispose to fitness surfaces substantially smoother than white-noise surfaces.

  11. Although moving uphill on a fitness surface is helpful to the organism, evolution is not actually a search for a particular small set of target genotypes; it is not only successful when it finds the absolutely most-fit genotypes in the space. We almost certainly do not reach optimal genotypes or phenotypes, and that’s OK. Evolution may not have made us optimal, but it has at least made us fit enough to survive and flourish, and smart enough to be capable of evaluating DEM’s arguments, and seeing that they do not make a case that evolution is a search actively chosen by a Designer.

This is the essence of our argument. It is a lot to consider, so let’s explain this in more detail below:

As usual I will pa-troll the comments, and send off-topic stuff by our usual trolls and replies to their off-topic stuff to the Bathroom Wall

Origin-of-life puzzle cracked?

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A pair of recent articles on the Science website seems to think so. Staff writer Robert Service says Researchers may have solved origin-of-life conundrum and writes,

Chemists report today that a pair of simple compounds [HCN and H2S], which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start. Although the new work does not prove that this is how life started, it may eventually help explain one of the deepest mysteries in modern science.

Well, yes, but that is a far cry from saying the puzzle is solved. Indeed, a comment to an “in-depth” article, Origin-of-life puzzle cracked, in Science magazine notes,

The title is certainly misleading, since the origin of life puzzle is still very far from “cracked.” Showing that biomolecules, even complex biomolecules, can be synthesized under plausible primordial conditions is very different from showing how those molecules could have assembled to produce the first cell. Only then can one claim to have cracked the puzzle.

That seems to me to be essentially correct, but then the author, Walter Steiner, adds, somewhat mysteriously, “Solving that puzzle will require the discovery of some currently unknown natural phenomenon.” Another commenter suggests some kind of broken symmetry.

The creationists, intelligent-design and otherwise, have moved in on the “conundrum” article, which is now about 1 week old and boasts almost 1000 comments, some of which actually make sense.

Ice stalagmite

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Photograph by James Rice.

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While we are still thinking of icicles, here is another ice stalagmite that James Rice sent us. We showed his picture of a natural ice stalagmite here, as well as another anthropogenic ice stalagmite here.

Teachers first, scientists second

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That is one of the disquieting results of a new survey, Enablers of doubt, by Michael Berkman and Eric Plutzer. The two Penn State professors interviewed a total of 35 students on 4 Pennsylvania campuses in 2013. All the students were training to be biology teachers; many were not comfortable with the theory of evolution, and many were “concerned about their ability to navigate controversy initiated by a student, parent, administrator, or other members of the community.” Indeed, instead of relying on their knowledge of biology, they intended to fall back on classroom-management techniques to deal with creationist students. Notably, these were not education students, but rather biology students who “take a set of required courses in educational psychology, classroom management, and methods of instruction.” Their lack of expertise in science seems not to concern them; to the contrary, they thought they would use their skills at avoiding controversy to avoid any controversies.

PT readers may remember Professors Berkman and Plutzer for their book, Evolution, Creationism, and the Battle to Control America’s Classrooms, which we reviewed here a few years ago. The disquieting conclusion of that book was that only about 28 % of biology teachers actually teach evolution according to recognized standards. The present study may help explain why.

The students, who attended a large research university, an institution that granted degrees at the master’s level, a Catholic college, or a historically Black university (all unnamed), were interviewed in focus groups. The interviews lasted 50-65 min and were conducted by the authors. The focus groups do not provide a statistical sample, but the authors attempted to include several different kinds of educational institution, and they consider the findings “suggestive.” Below the fold, some representative comments.

Icicle ripples

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An Icicle showing ripples due to impurities in the water. How the impurities cause the ripples is unknown.

Physics trumps biology

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Or, perhaps more precisely, Did dark matter kill the dinosaurs?, which is the way that an article in ScienceNOW put it.

Readers of PT doubtless know that there have been a half-dozen or so mass extinctions in the history of the earth, and they appear with a periodicity on the order of 30 million years. You can see an early graph here. The vertical arrows are separated by approximately 30 million years. Not every vertical arrow points to a mass extinction, so it might be better to say that the first harmonic of the data set is 30 million years; that is, if the periodicity is real, it sometimes skips a beat.

What is interesting is that some of the extinctions appear to have been caused by collisions with an asteroid, whereas others may be the result of long periods of extreme volcanism – yet all the extinctions occur with the same period of 30 million years.

Pygoscelis papua

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Photograph by Dan Phelps.

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Pygoscelis papua – gentoo penguin, Danco Island, Antarctica.

Imagine that you want to analyze the 3.2 billion bases of the human genome. If you recruited every undergraduate student at ASU, all 70,000 of us, to type those data into a spreadsheet, it would still take about 13 hours. So you develop a computer program that analyzes the data for you. But then you find out that your huge data set amplified small errors in your algorithm and gave you the wrong answer. This is the issue facing evolutionary biologists using genomic data, a practice that is becoming standard to construct reliable phylogenies (see our previous posts about the new bird and insect phylogenies). Our lab, working under Dr. Reed Cartwright, has developed a novel method to quickly analyze genomic data and produce an accurate phylogeny that improves upon previous techniques.

The giant panda genome was assembled using de novo techniques in 2010, but better methods of phylogeny construction are in development. Image: Wikipedia

Historically, scientists have compensated for potential inaccuracies in genomic-size data in two ways: by using better statistical tools to analyze the data after they have been acquired or by acquiring fewer, more informative data.

In the first method, you start with sequenced genomes in the form of short fragments (about 100 base pairs) and develop computational algorithms to compare those sequences to a reference genome for reassembly, like Liu et al. did in their 2003 analysis of primate genomes. The reference genome is one that we know with a high level of confidence; for example, the human genome is reliably known and often used as a reference. If, however, a reference is unavailable or unreliable, you could use a computer program to assemble the sequences with a process known as de novo assembly, which Li et al. used to construct the giant panda genome in 2010. These programs, called assemblers, use graphical techniques (for example, De Brujin graphs) to remove errors in phylogenetic trees and resolve repeated data that are harder to determine in short sequences than longer ones. Algorithms like this can greatly improve the accuracy of conclusions made from genomic data, but de novo assembly without a reference genome requires high quality annotation of the sequences and, once the genome is reconstructed, time-consuming alignments of similar sequences to produce a phylogenetic tree.

Alternatively, you could acquire fewer data in the first place. You would need to determine which markers in a genome are informative and necessary to draw certain conclusions and then only obtain those data. By reducing the size of the data set and eliminating unnecessary information, we improve the accuracy without having to implement sophisticated analytical techniques. McCormack et al. used this principle in 2012 to determine the tree of placental mammals from certain markers. However, the major drawback of this method is that markers appropriate for a particular project or species most likely cannot be reused for other projects. The ability to recycle genomic data reduces the cost and time of phylogenomic studies.

Our lab is working on a program that constructs phylogenetic trees more quickly and easily than either of these methods. The program, called SISRS, combines genome assembly with identification of homologous genes to rapidly reconstruct phylogenies without the need of a reference genome or annotation. In the next post, we’ll go into detail about how SISRS works and what makes it a better way to analyze genomic data.

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

Chelepteryx collesi

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Photograph by Jim Foley.

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Chelepteryx collesi – white-stemmed gum moth, Canberra, Australia. Mr. Foley writes, “The caterpillar is about 12 cm long! Yet another member of the Australian fauna you don’t want to mess with. … We seem to have more venomous stuff than most places: lots of snakes, stonefish, spiders, jellyfish, blue-ringed octopus, etc., not to mention the crocodiles and sharks.”

The tenth annual Evolution Weekend, February 13-15, is almost upon us. To check out what’s going on in your neighborhood, click here. This year’s theme is Science and Religion in Dialogue: Past, Present, and Future. The Evolution Weekend website notes,

Evolution Weekend is an opportunity for serious discussion and reflection on the relationship between religion and science. An ongoing goal has been to elevate the quality of the discussion on this critical topic, and to show that religion and science are not adversaries. Rather, they look at the natural world from quite different perspectives and ask, and answer, different questions.

Religious people from many diverse faith traditions and locations around the world understand that evolution is quite simply sound science; and for them, it does not in any way threaten, demean, or diminish their faith in God. In fact, for many, the wonders of science often enhance and deepen their awe and gratitude towards God.

While I do not entirely agree with the sentiment expressed in the first paragraph, it is better than some of the alternatives.

Finally, NCSE reminds us that the anniversary of Darwin’s birth is February 12, and House Resolution 67 would recognize

Charles Darwin as a worthy symbol on which to focus and around which to build a global celebration of science and humanity intended to promote a common bond among all of Earth’s peoples.

Rep. Jim Himes introduced the bill on February 2, and, according to a press release from the American Humanist Association, it is the latest in a series of such resolutions, the previous four having been introduced by Rep. Rush Holt and Rep. Pete Stark. Although the PR is not explicit, I think we may infer that none has so far passed the House.

At Jerry Coyne’s bl*g Why Evolution Is True he has a new post calling attention to a web site on The Third Way of Evolution. It was apparently put up last year by James Shapiro, Denis Noble, and Raju Pookottil. It presents statements by 43 people expressing their view that a new Way of Evolution is needed. It has apparently been up for over 8 months, but only recently was mentioned by Denyse O’Leary at Uncommon Descent.

None of these people are, as far as I can tell, creationists. Many are working, or retired scientists or engineers. Jerry gives telling analyses of the views of some of the more prominent critics among them, citing his own past demolitions of their views. An interesting point is that all of these people are said to have agreed to being listed on the TWOE website.

A unified statement by 43 people, mostly scientists of some reputation, laying out a new evolutionary synthesis, should attract a lot of attention. However, the Third Way site does not do that. The difficulty is that each of these people seems to march to a different drummer, and in a different direction. They go off over the horizon in different directions, each convinced that theirs is the promising new direction. The common theme is that “The Modern Synthesis is dead, and I have a replacement for it!” But there is no agreement on what the replacement should be.

It is fun reading. Let’s have a thread there. Calling these folks creationists is not helpful; overwhelmingly they simply aren’t creationists. (The Second Way is, Shapiro et al. point out, creationism. To me it is a bit strange to hear creationism cited as a Way of Evolution, when what it actually says is “no way”.)

A very useful activity would be to characterize the views of some of the 43. Are they:

  • Lamarckians?
  • Mutational teleologists?
  • Saltationists?
  • (etc.)

Let’s discuss. I will, as usual, try to vigorously pa-troll the comments and send off-topic comments to the Bathroom Wall. Interventions by our usual creationist trolls and replies to those will go to the BW.

What comes to mind when you think about insects? For a lot of people, the word sends a shiver up their spine as they imagine the tiny, creeping legs, buzzing wings, stinging tails, and biting fangs. But what those people may not know is that insects comprise one of the most important classes of animal; there are more species of insect than any other animal group, and they can claim being the first animals to achieve many things, including flight and social societies.

Insect evolution is historically poorly understood, and the lack of a well-resolved and supported tree of insects has left researchers with many questions about their evolutionary relationships. For example, how are grasshoppers, crickets, cockroaches, and termites related? Which species are the closest living relatives to Holometabola, the group containing beetles, moths, butterflies, wasps, bees, and ants? What is the timeline of insect evolution? Answering these questions could help us understand how different insect traits evolved, which could reveal insights into the mechanism of evolution itself.

Silverfish (left) evolved to lose their wings and other appendages independently from other insects like jumping bristletails (right), and they make up their own branch on the new phylogenetic tree of insects. Images: Wikipedia

Scientists with the international 1KITE project set out to answer these questions and more by using phylogenomics to compare 1478 genes among 103 species of insect. First, they sequenced the DNA to find genes that were present in all the species, most of which coded for proteins involved in translation, protein transport, neurogenesis, and other basic cellular functions. Similar to the study of birds that we talked about last time, Misof et al. used improved methods of analysis to reduce errors from such a large dataset. Before analyzing the data, the researchers accounted for possible sources of bias by removing confounding factors; for example, they removed any data that violated the assumption that evolution is a time-reversible process. They then discarded any sequences that were misaligned and generated their tree with maximum likelihood models as well as a partitioning scheme to improve the accuracy of the assumed model of evolution. Using data from two sources, nucleotides and amino acid sequences, the researchers generated two matching phylogenetic trees.

The new phylogenetic tree was able to answer many questions about insects with a higher statistical confidence than previous studies:

  • Earwigs, ground lice, stoneflies, crickets, gladiators, ice crawlers, webspinners, stick and leaf insects, praying mantids, and termites comprise a branch on the tree (a monophyly) called Polyneoptera, a hypothesis proposed in previous studies.
  • The study proposed the new conclusion that lice are the closest living relatives to beetles, moths, butterflies, wasps, bees, and ants.
  • Insects originated around 479 million years ago, a finding that contradicts previous estimates of about 400 million years ago.
  • Insects inhabited land at about the same time as plants (around 450 million years ago) and developed flight after they had established colonies, corroborating a 2013 study.
  • Remipedia, a class of blind crustaceans found in caves, is the closest living species to insects, confirming prior studies.
  • Silverfish comprise their own branch on the tree, as other recent studies have proposed, implying that they evolved to lose their head endoskeleton, leg-like structures called styli, and the sacs on their legs (coxal vesicles) in parallel to but separately from winged insects.

While many of the conclusions drawn by the new study are not completely new findings, the history of insect evolution is controversial and relationships previously proposed lacked certainty. The ability of the 1KITE researchers to confirm and deny these relationships with such high confidence shows the power of genomic analysis. But as with the recent bird phylogeny paper, the methods of analysis had to change to accommodate a larger dataset; specifically, confounding factors that could lead to biased conclusions were a larger concern than for previous studies. Jarvis et al. chose with their bird analysis to modify their programs to create a better phylogenetic tree, while Misof et al. removed data with these confounding factors during analysis. It remains to be seen which genomic data analyses produce the best results, but what we do know is that genome sequencing will play a major role in future phylogenetic studies of all species.

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

Maroon Bells

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Maroon Bells, Aspen, Colorado.

A new PBS series, Earth: A new wild, will highlight China’s breeding of giant pandas with the intention of introducing them into the wild. One goal of the series is to demonstrate that humans and nature are interdependent, according to its producer, M. Sanjayan. The 5-part series will begin on February 4. You may see a 1.5-min clip from the show at the link above. You may also see photographs of newborn panda triplets here.

There is no truth to the rumor that our colleague Professor Steve Steve sired any of the baby pandas.
———
Acknowledgment. Thanks to Debbie Bloom Garelick for the initial link.

What do flamingoes and pigeons have in common? You might say very little—after all, flamingoes are long–legged, vibrantly–colored water–dwellers and the pigeons we often see inhabiting our cities appear to be completely the opposite. But according to a study published last month in Science magazine, flamingoes and pigeons are more closely related than previously thought.

The groundbreaking new study used phylogenomics to compare the genes of 48 bird species. It is the first study of its kind to use whole genomes to construct the tree of birds, thousands of genes altogether. Prior studies attempting to resolve some of the more controversial bird relationships only examined 10–20 genes, meaning that the researchers in the new study had much more data to analyze and could be more confident in their results.

Flamingoes and pigeons are more closely related than you might think, according to a new study. Images: Wikipedia

Scientists have been revising our understanding of the tree of birds using phylogenetics over the past decade. In 2006, when the cost to sequence a single genome was $10 million, Ericson et. al. published one of the earliest phylogenetic bird papers, using 5 genes from 87 species for their analysis. Hackett et. al. conducted another phylogenetic study of birds in 2008, when sequencing a genome had fallen to $1 million, this time using 19 genes from 169 species for comparison. While these studies were able to divide modern birds into their larger classifications, some of the deeper relationships remained unresolved and the researchers were still unable to establish with certainty the timing of the bird “big bang”—the rapid and successive divergence of birds into many species. Scientists agree that this divergence occurred around the time of the mass extinction of non-avian dinosaurs about 65 million years ago, but they debate whether birds diversified before or after the mass extinction.

Jarvis et. al. (2014) found that the bird big bang happened immediately after the extinction, taking a relatively short 10–15 million years. Using thousands of genes, they could draw this and other conclusions with more certainty. But with so much data, the researchers could not use standard phylogenetic analysis tools; they needed to develop new ones.

First of all, the team developed a custom algorithm for filtering out gene sequences that were unaligned or incorrectly aligned. Once the data from the aligned genes were gathered, the researchers used a new and more efficient program (implementing a maximum likelihood model) to construct the phylogenetic relationships from the raw data. Finally, the researchers used a method called data binning to reduce errors that arise from the mathematical assumption that species divergence occurred instantaneously (when it more likely occurred gradually). Using these new methods and the added information from so many genes, the researchers were able to confirm and reject with more conviction some of the branches proposed by the previous studies, like the flamingo-pigeon relationship.

The red-billed tropicbird is a member of the Tropicbird family, which is excluded from Pelecaniformes in the new phylogenetic tree of birds. Image: Wikipedia

Along with this relationship and resolving the timing of the bird divergence, the researchers discovered several other important findings about birds. From some of the traits of the bird tree, they could conclude that the common ancestor of land birds was an apex predator, or a predator at the top of the food chain with no predators of its own. Also, the new tree of birds contradicts previous trees by excluding eagles and New World vultures from Falconiformes, the group containing falcons, kestrels, and other birds of prey. Similarly, the group Pelecaniformes excluded tropicbirds, a family of seabirds. Finally, the study revealed some characteristics about the way songbirds gained their vocal abilities with a gene that is similar to the one giving humans the ability to learn speech. This finding has gained a lot of recognition because of its potential application to the study of human speech.

As we’ve talked about in previous posts, using a complete set of genomic data can give us a more accurate phylogenetic tree and more confidence in results like the ones we just mentioned, as long as the analytical methods are appropriate for big data sets. Because the researchers in this new study improved their methods to reduce the error and noise that can be found in big data sets, their tree is probably the most accurate tree of birds produced so far. But all mathematical models of natural phenomena are at least somewhat incorrect, so it is likely that researchers will make further improvements to the methods and the tree.

Regardless, the field of phylogenetics is changing to realize the full potential of genome sequencing. As the tools to analyze these data improve, we’ll continue to gain new insights into species relationships and evolution with greater confidence than ever before. Who knows what other surprising relationships we’ll discover?

See the complete tree of birds here.

This series is supported by NSF Grant #DBI-1356548 to RA Cartwright.

Equus quagga burchellii

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Photograph by Alice Levine.

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Equus quagga burchellii – Burchell’s zebra, Namibia.

Proterozoic schists

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Photograph by Jim Kocher.

Photography contest, Honorable Mention.

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Painted Wall – Black Canyon of the Gunnison River, Montrose, Colorado, May, 1999; Kodachrome 64. Proterozoic schists intruded by pegmatite dikes (~1.25 Ga). Vertical relief is ~2,200 ft.

Color vision may be 300 Ma old

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According to a blurb in Science yesterday, researchers have discovered a fossilized fish whose eyes show traces of pigment and also fossilized rods and cones. The existence of the cones suggests that color vision developed at least 300 Ma ago. You may read the full article, which appears in Nature Communications, by following the link from the Science article; you can read it only on screen – a pdf will cost you $32.

_____

P.S. Yes, I learned about Nature‘s sharing policy by tracing the link from Science. If you follow the link to the Nature article itself, you get only the abstract.

Are men idiots?

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That is, are male members of the species Homo sapiens idiots? No, but according to a recent article, they are more likely to be idiots than women are.

The only thing surprising about this conclusion is that it is so unsurprising. For years now, whenever my daughter or I see a bicyclist dash madly across 4 lanes of traffic, we announce to each other, “Another male trying to improve the gene pool.” We are uncertain who said it first, but my daughter somewhat sheepishly thinks it was she. Which, of course, makes me think that we brought her up right.

The study that drew the unsurprising conclusion looked at the recipients of the Darwin Awards over the past 20 years. To qualify for a Darwin Award, you have to remove yourself from the gene pool, generally by killing yourself, but I suppose that castration would do about as well.

After the usual mutterings about selection bias and noting that the study was retrospective (double-blind would have been kind of tricky), the authors conclude that ~90 % of Darwin Award winners were male. They propose a Male Idiot Theory, which to my mind is at least as good as Molière’s diagnosis, she is mute because she has lost her speech.

NPR reported on the article here. Some of the comments are interesting, and some suggest a sociobiological explanation, which I will leave to your imagination – suffice it to say that among our early ancestors, only the men had to take the risk of hunting elephants. Or whatever.

The authors of the original article assure us that they plan an observational study and even now are scheduling holiday parties, both with and without alcohol.

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