Recently in Research News Category

Physics trumps biology


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


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?


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.

* 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


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 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


Bj�rn �stman at Pleiotropy describes new research in Science that shows how duplicated genes can evolve to perform new functions. It presents

… a new model/mechanism by which duplicated genes can retain the selection pressure to not succumb to deleterious mutations. They call it the innovation-amplification-divergene model (IAD).


IAD works like this: A gene initially has one function only (A). Then some genetic changes makes it also have a new function, b, which at first is not of too great importance. Then some environmental change favors the gene variants with the minor b-function (the innovation stage). This is then followed by duplication of the gene, such that there are now more than one copy that carries out A and b (the amplification stage). At this stage there is selection for more b, and at some point genetic changes in one of the copies results in a gene that is better at the new function, B. At this point, selection for the genes that do both A and b is relaxed, because the new gene (blue) carries out the new function. The original gene then loses the b function, and we are left with two distinct genes.

Michael Behe, of course, scoffs. Because the researchers did some manipulations that created conditions favorable to the evolution of the new function, Behe claims that

Needless to say, this ain’t how unaided nature works – unless nature is guiding events toward a goal.

Shucks. I guess every experimental manipulation ever performed has been an invalid method of studying some process. But as a PT crew member pointed out on the back channel, “this kind of shit happens all the time in nature.” See, for example, Gene duplication and the adaptive evolution of a classic genetic switch or Escape from adaptive conflict after duplication in an anthocyanin pathway gene.

Carbon dating to 50,000 years


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


There has been a good deal of publicity recently about the sequencing of the Denisovan genome by Svante P��bo’s group at the Max Plank Institute (see here and here for examples). Using brand new technology for sequencing single strands of DNA (single strands as opposed to the normal double-strand), the group was able to achieve a sequencing rate of 30x–every position in the genome was sequenced 30 times. That’s comparable to sequencing modern genomes.

While some of the coverage has focused on what can be inferred about the individual from whom the DNA was recovered (female, dark skin, brown eyes and hair) what is much more interesting are the relationships of the Denisovans to various modern human populations and to Neandertals. Also interesting is the identification of genetic changes that have occurred in modern humans, a number of the changes having to do with genes associated with brain function and nervous system development,

Since John Hawks has discussed the paper in some detail, I won’t, but will direct you to Hawks’ review of the research. One quotation from that piece–the final sentence–is worth repeating:

Evolution really is the fundamental principle of biology, but using evolution to learn about biology sometimes requires traveling through time. Ancient DNA gives us a time machine bringing new insights into reach.

I can hear the echo of Ken Ham’s minions mindlessly shouting “Were you there???” No, but this is the next best thing.

At Evolution2012 in spirit


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.

250 years of Bayes!


The Reverend Thomas Bayes died 250 years ago this month, in 1761. His famous “Essay Towards Solving a Problem in the Doctrine of Chances”, from which stems “Bayes’ Rule”, was published posthumously 247 years ago in 1764 by the Royal Society. A detailed review of the argument in modern notation is Edwards (1978) in the Scandanavian Journal of Statistics. Any of us scientists working today would be beyond lucky to have our work cited 250 later!

The R Revolutions blog highlights the anniversary and is posting videos explaining the significance of Bayesian thinking. Check it out!

Barnosky_etal_2011_Nature_Fig1.jpgThis isn’t exactly about creationism/evolution, but it’s still pretty cool. And I will find a way to tie it in, since I haven’t blogged on PT in, I think, months.

Contrary to what creationists believe, evolutionary biologists don’t sit around in biology departments plotting to overthrow God and morality. We spend our time doing things like statistics and programming and specimen preparation and experimental manipulation and DNA sequencing and field observation, and then give and hear talks and discussions about this research. The main thing we are interested in is not “proving evolution”, it is discovering cool facts and devising hypotheses to explain them, and then devising tests of those hypotheses (typically, statistical tests, something which creationists almost always ignore). In short, it’s like any other science.

This paper is a case in point:


Barnosky, Anthony D.; Matzke, Nicholas; Tomiya, Susumu; Wogan, Guinevere O. U.; Swartz, Brian; Quental, Tiago B.; Marshall, Charles; McGuire, Jenny L.; Lindsey, Emily L.; Maguire, Kaitlin C.; Mersey, Ben; Ferrer, Elizabeth A. (2011). “Has the Earth’s sixth mass extinction already arrived?” Nature 471(7336), 51-57. (DOI - Link)

Gene duplication enables a novel function to evolve

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The Sensuous Curmudgeon calls our attention to a new study by researchers at the University of Illnois and the Chinese Academy of Sciences that traces the evolution of a new function via gene duplication. Since I’m not a molecular guy, I’ll very briefly describe it and refer you to the news release and published paper (behind the PNAS paywall). Very briefly, the Antarctic eelpout has a gene that codes for an antifreeze protein, a member of a protein family called AFP III, that enables the eelpout to survive the freezing temperatures in Antarctic waters. It has been hypothesized on genetic homology grounds that the antifreeze gene evolved via duplication of a gene that codes for sialic acid synthase, a cellular enzyme, and subsequent selection for the antifreeze function in one of the duplicates via an escape from adaptive conflict process. From the linked news release:

“This is the first clear demonstration - with strong supporting molecular and functional evidence - of escape from adaptive conflict as the underlying process of gene duplication and the creation of a completely new function in one of the daughter copies,” Cheng said. “This has not been documented before in the field of molecular evolution.”

And from the Abstract:

We report here clear experimental evidence for EAC-driven evolution of type III antifreeze protein gene from an old sialic acid synthase (SAS) gene in an Antarctic zoarcid fish. We found that an SAS gene, having both sialic acid synthase and rudimentary ice-binding activities, became duplicated. In one duplicate, the N-terminal SAS domain was deleted and replaced with a nascent signal peptide, removing pleiotropic structural conflict between SAS and ice-binding functions and allowing rapid optimization of the C-terminal domain to become a secreted protein capable of noncolligative freezing-point depression. This study reveals how minor functionalities in an old gene can be transformed into a distinct survival protein and provides insights into how gene duplicates facing presumed identical selection and mutation pressures at birth could take divergent evolutionary paths.

As the Curmudgeon points out, this is precisely the kind of evidence that Disco ‘Tute attack mouse Casey Luskin asked for a year ago:

Many scientific papers purporting to show the evolution of “new genetic information” do little more than identify molecular similarities and differences between existing genes and then tell evolutionary just-so stories of duplication, rearrangement, and subsequent divergence based upon vague appeals to “positive selection” that purport to explain how the gene arose. But exactly how the gene arose is never explained. In particular, whether chance mutations and unguided natural selection are sufficient to produce the relevant genetic changes is almost never assessed.

There it is, Casey.

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