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Noncircular pupils explained

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Several years ago, I reviewed the book Evolution’s Witness: How Eyes Evolved, by Ivan Schwab. The book is downright encyclopedic, and I could not praise it highly enough. But in my review I wondered about elongated pupils, such as those of a cat, which are barely discussed the book. I remember reading somewhere that the elongated pupil could be stopped down farther than a circular pupil, but that explanation does not account for the problem that horizontal structures will be more clearly resolved than vertical structures (presuming that the pupil is elongated vertically and the eye is nearly diffraction limited).

A team from Berkeley and Durham University now proposes a better explanation. Without going into detail, they find that predators that ambush their prey, like cats, typically have vertically elongated pupils. From the abstract:

Vertically elongated pupils create astigmatic depth of field such that images of vertical contours nearer or farther than the distance to which the eye is focused are sharp, whereas images of horizontal contours at different distances are blurred. This is advantageous for ambush predators to use stereopsis to estimate distances of vertical contours and defocus blur to estimate distances of horizontal contours.

One way to put it: All the blur due to defocus is in the vertical direction, so horizontal contours are blurred when defocused, whereas vertical contours are not, because the blur is parallel to the contour; see their Figure 2(A). I do not want to go into detail, but they demonstrate that ambush predators, like the cat, that prowl close to the ground benefit from having good stereo vision for vertical contours. Prey animals, like the goat, often have horizontal pupils, which supposedly facilitate wide-angle views. Curiously, their pupils remain horizontal regardless of the orientation of their heads.

This paper goes a long way toward explaining why different animals have differently oriented pupils. You may see a video and a short article here and an NPR report here.

The paper does not explain how, when I was an elongating pupil in fourth grade, my teacher, an ambush predator if ever there was one, managed to see through 360°.

Why are giant pandas so lazy?

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Professor Steve Steve informs us of an article Why are pandas so lazy? in Science Now. Professor Steve Steve takes exception to the claim that he is lazy. Yes, it is true that the giant panda’s daily energy expenditure is about 5 MJ: roughly one-third that of a dog and about the same as a three-toed sloth. It is also true that Professor Steve Steve moves slowly and basks a lot in the sun. Why? Because the giant panda is a carnivore that survives on a low-energy plant diet, which his body is ill-equipped to digest. To conserve energy, he maintains a low body temperature, and his organs, including his brain, are small.

Professor Steve Steve demurs. He claims that he is not lazy; he is simply ruminating.

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.

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.

I am sure we all read it in the papers several weeks ago: Two-thirds of all cancers are caused by bad luck. The New York Times said so. Science magazine, which published the original article said so too.

Only problem, the original article did not say that, and to her credit, Jennifer Couzin-Frankel, the Science reporter who “said so too,” corrected the record in a sort of meditation on the difficulty of getting difficult scientific concepts correct while working on deadline.

In fact, the authors did not say that “[r]andom mutations may account for two-thirds of the risk of getting many types of cancer, leaving the usual suspects—heredity and environmental factors—to account for only one-third, …” as the Times put it. What they said was more subtle, that two-thirds of the difference in cancer rates between different tissues could be explained by random bad luck. That is, “[s]ome tissues are overtaken by cancer more readily than others, and mutations accumulating in stem cells explained two-thirds of that variability,” in Couzin-Frankel’s words.

It is good to know that Science is self-correcting.

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.

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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.

The Hebrew Bible says that God made humans from dust,* but maybe it was a slurry of clay and water. That is a tentative conclusion you might draw from an experiment that used a (very) high-powered laser beam to zap a suspension of clay in an aqueous solution of formamide, a very simple organic compound. The result has been reported in the press, but there is a somewhat more-precise article in Science magazine. (You may find the abstract of the original article here and the supporting information here. I did not get access to the full article.)

In a nutshell, a team at the J. Heyrovský Institute of Physical Chemistry in Prague used a laser that can produce up to 1 kJ in a 300 ps pulse,** irradiated the suspension, and produced adenine, cytosine, guanine, and uracil, which are the bases of the RNA molecule. And apparently not a drop of thymine, one of the bases of DNA. The experiment is supposed to simulate the bombardment of the early Earth by comets and presumably supports the hypothesis that an RNA world came first.

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* Actually, Job, Isaiah, Psalms, and I imagine elsewhere say clay, as in, “We are the clay, and you are our potter.” (Don’t get excited; I consider the fact to have no significance whatsoever.)

** I am a laser physicist and wrote my thesis on laser-produced plasmas, so you must forgive me for somewhat stressing the laser, which to this day gives me a certain amount of pulse envy.

You may get an idea how science really works from an article by Boston science writer Kate Becker in today’s Boulder Daily Camera. (I think the column is exclusive to the Daily Camera.)

Becker describes the Bicep2 experiment, which looked for evidence of cosmic inflation by examining the polarization of the cosmic background radiation. The authors of the paper announced its conclusion before the paper had been submitted for review; since then, others have criticized their method and thrown the conclusion of the paper into doubt. Specifically, some think that cosmic dust may polarize the radiation in such a way as to give a false positive, in this case a polarization that mimics that of the cosmic background. The researchers have considered cosmic dust and disagree. At any rate, their article has finally been published, and you may find the abstract here. I read the abstract, but as Casca said, it was Greek to me, and I have no opinion concerning the conclusion. We will, as Becker notes, wait until other telescopes weigh in or the Bicep2 data are further evaluated.

Expanding the genetic alphabet

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By Gert Korthof.

“It is a very, very hard problem. Getting all the pieces to work means re-engineering 3.5 billion years of evolution. It’s so ambitious.” These are the words of a scientist 14 years ago [1]. He was talking about the project of inventing new bases to include in DNA and let the new DNA function in a living cell. Now an important milestone has been reached towards that goal. Scientists have succeeded in adding a new base pair, d5SICS (call it X) and dNaM (call it Y), to the DNA of the bacterium E. coli and let it replicate its DNA [2]. Furthermore, the growth rate of the bacterium was not significantly slowed down, and the DNA-repair system did not remove the new bases. These results give us hope for realistic answers to the so far speculative questions as to why evolution settled on only two base pairs in DNA. Could there be superior bases and superior DNA?

Plasmid_modified_from_wiki.jpg

Plasmid, modified from Wikipedia. The yellow dot is the new base pair.

25 years ago, according to a recent article in Science magazine, Richard Lenski put samples of E. coli bacteria into a dozen flasks filled with a solution of glucose and other nutrients, incubated them, stirred them, and every day removed 1 % and repeated the process, day after day, for 25 years (except for a brief interruption when he moved from one university to another). The author of the article, Elizabeth Pennisi, notes that Lenski’s bacteria

Not stated is whether they manage to lose weight, nor whether they still get cavities or develop diabetes. But a recent article in Science shows that cockroaches evolved an aversion to glucose after glucose was used for a number of years as a poisoned bait. That is, the cockroaches developed an aversion to the bait rather than a resistance to the poison. The Science article is kind of written in Greek

In response to the anthropogenic assault of toxic baits, populations of the German cockroach have rapidly evolved an adaptive behavioral aversion to glucose (a phagostimulant component of baits).

but The New York Times has a nice summary and notes, almost as a throw-away, that the result might have application to diseases, such as malaria, that are spread by mosquitoes.

Memo to potential trolls: Yes, yes, we know—they are still cockroaches!!

Evolving a new function via gene duplication and divergence

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Syntax Error: Malformed UTF-8 character (fatal) at /usr/local/lib/perl5/5.20/Carp.pm line 306.

Carbon dating to 50,000 years

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An article in Friday’s Science magazine details how a team of scientists provided a calibration for carbon dating accurately to 50,000 years, or about 10 times the age of the earth according to many creationists.

Until now, carbon dating was accurate only to about 13,000 years, or the ages of the oldest trees. The Science article is fairly dense, but Science has provided a helpful Perspective, and Popular Science has a nice article as well.

It turns out that the concentration of 14C in the atmosphere varies from year to year, so calculations of the age of a specimen need to be corrected for this yearly variation; uncorrected calculations are not wrong, but they may be in error by hundreds of years. Until now, we have had no detailed record of the 14C concentration beyond the age of the oldest trees. Now, however, a team led by Christopher Bronk Ramsey of the University of Oxford has examined sediments in a Japanese lake and extended carbon dating to approximately 50,000 years. The lake was chosen because the bed of the lake is anoxic and its sediments are thought to have been stable and untouched by ice-age glaciers. The new calibration will be significant to archeology and studies of climate change. Read the 2 articles I have cited for more detail.

Not an earthshaking discovery, to be sure, but it shows how science progresses, step-by-step, while creationism merely stagnates.

Acknowledgment. Thanks to Rolf Manne of the University of Bergen, Norway, for alerting me to the importance of Bronk Ramsey’s article.

Sequencing the Denisovan genome

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Syntax Error: not well-formed (invalid token) at line 1, column 243, byte 243 at /usr/local/lib/perl5/site_perl/mach/5.20/XML/Parser.pm line 187.

At Evolution2012 in spirit

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Evolution 2012 is starting tomorrow! This time it’s in Ottawa, representing the First Joint Congress on Evolutionary Biology – a meeting of the American Society of Naturalists (ASN), the Canadian Society for Ecology and Evolution (CSEE), the European Society for Evolutionary Biology (ESEB), the Society for the Study of Evolution (SSE), and the Society of Systematic Biologists (SSB).

Sadly, though, I can’t go this year. A good friend of mine is having her wedding right in the middle of the meeting. There’s only one wedding in someone’s life (well, hopefully!) and there are a lot of meetings, so I picked the wedding. I guess the wedding won’t be entirely evolution-free, seeing as the bride studies extinct giant sloths.

But at the moment I’m looking over the program for Evolution 2012 and experiencing a few missing-the-conference blues.

Ah, but here’s something to cheer me up. After you’ve been in science for awhile, you discover that you don’t even have to be at a meeting for your name to get into the program, due to the collaborations you are involved with! Here are the papers I’m a coauthor on:

cover_nature.jpgWell, I just got interviewed about this, so I suppose I should blog it! Today a review paper is coming out in Nature entitled “Approaching a state shift in Earth’s biosphere” (Nature, UC Berkeley press release) It is getting a huge amount of press, in part because of the message, and in part because of the upcoming United Nations Rio+20 Earth Summit in Rio de Janeiro.

The message of the paper is that, while much is uncertain, we think that the biosphere – the global community of species and ecosystems – is heading for a “state shift”, or “tipping point”, due to human activity. More on what exactly this means in a moment.

Male fruit flies, when prevented from mating, prefer an alcoholic beverage to a soft drink. See here, here, and here.

So, apparently, do some robots. Well, simulated robots, anyway.

The TalkOrigins Archive has two articles (here and here) on observed instances of speciation. Now a recent PNAS paper describes speciation in Aspidoscelis, a genus of whiptail lizards. The paper is titled “Laboratory synthesis of an independently reproducing vertebrate species.” From the abstract:

Here we report the generation of four self-sustaining clonal lineages of a tetraploid species resulting from fertilization of triploid oocytes from a parthenogenetic Aspidoscelis exsanguis with haploid sperm from Aspidoscelis inornata. Molecular and cytological analysis confirmed the genetic identity of the hybrids and revealed that the females retain the capability of parthenogenetic reproduction characteristic of their triploid mothers. The tetraploid females have established self-perpetuating clonal lineages which are now in the third generation.

Read more at Nobel Intent, to which we tip our hat.

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