Recently in Research News Category

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.

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!

This 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:

NATURE | REVIEW

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)

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.

In Ediacaran roots extend deeper in time? Joe Meert described enigmatic fossil impressions that could be interpreted as Ediacaran metazoa (multi-celled animals) from strata some 100 million years older than previously known. Now Chris Nedin, a palaeontologist who has worked with Ediacaran and early Cambrian material, has a comprehensive post on his blog Ediacaran titled “770Ma Ediacara (?) Fossils from Kazakhstan (sadly no)”:

Two questions to be asked then. Are these deposits c. 770 million years old? Are these specimens examples of Ediacaran fossils?

I think the answer to the first question is yes, and the answer to the second question is no. I’ll explain below.

Leave comments here or there; Joe has already commented there.

This week’s issue of Science has a news article and a podcast about a USGS researcher who bred bacteria to live in an arsenic environment. If you do not subscribe to Science, you may read only slightly breathless articles in the New York Times and the Los Angeles Times.

A news article in today’s issue of Science suggests that global warming may drive many lizards to extinction. I have not read the technical article, which you may find here. According to the news article, Barry Sinervo of the University of California, Santa Cruz, and his colleagues suggest that lizards, which generally can tolerate high temperatures, may nevertheless suffer if the periods of high temperature grow longer. Specifically, if the lizards have to spend more time protecting themselves from the heat, then they become less fit because they must spend less time foraging for food. Sinervo and colleagues note that Mexico has lost 12 % of its lizard species in the last 35 years, and they suggest that 40 % of lizard populations could disappear and 20 % of lizard species could become extinct by 2080. Additionally, Sinervo says here that lizards that can move to higher elevations may end up outcompeting other species and driving them to extinction, so the 20 % figure may be conservative.

The Sacramento Bee has good pictures of the Lianga Bua, Indonesia, site where Homo floriesiensis remains have been found. As you will notice, they’re not just scraping the floor of a nice shallow cave with trowels.

Hat tip to James Kidder.

A common bleat from creationists is “Where are the millions of transitional fossils Darwin said there should be?” Martin Brazeau has an excellent post on taphonomy at The Lancelet reporting a paper in which folks let poor innocent critters rot in order to ascertain which anatomical features are likely to be preserved and which are likely to be lost before fossilization, and the implications for interpreting fossils of ‘soft’ tissues for phylogenetics. Comment there, please.

Hello from Kearney Nebraska, where I am lucky to be a speaker along with a great number of actually famous people at the University of Nebraska’s Evolution2009 conference. I am mostly offline at the moment, but I have been told that the Darwin Correspondence Project in Cambridge has just announced that I have won the prize for one of their competitions – finding the true source of a famous, but bogus, quote of Darwin. The quote goes as follows (there are many varieties):

It is not the strongest of the species that survives, nor the most intelligent that survives. It is the one that is most adaptable to change.

David Hone, a British paleontologist working in China who blogs at Archosaur Musings, has a fascinating post on tracking the reporting of a paper he recently published. Among other things, he was able to follow the ‘Chinese whispers’ or ‘telephone game’ transmission of the news stories by tracking errors that crept into the story as it was published here and picked up there:

Thus science stories can really pick up and spread this way, so although 24 hours after my press release I had only one mention in one paper, after 48 hours this was more than five and another 24 hours later this was more than twenty. One week later it’s up to about fifty and I am still getting new e-mails about this.

This spreading though is especially interesting as between the original press release(s), the paper itself and the blog post (and later interviews) I know which quotes and which information came from where and thus which errors or changes have come in at which stage and which media have picked them up from which other. It is noticeable therefore that one can track errors from report to report as they originate in one and then are copied to others (I tracked a spelling mistake of Tyrannosaurus as Tyrannosaurs across three generations of articles, and each time it appeared in basically the same sentence in the second paragraph of the report, each, theoretically written by a different journalist).

Shades of pseudogene phylogenies! Go and read it and enjoy it there, and comment there if you feel moved to do so to encourage him to keep ‘em coming.

I’m back from field work, and have finally gotten enough time to get my photos web-ready after returning from Batholiths Onland. (see Blogging Batholiths: Part 1 for a summary of the 1^st 8 days of the adventure, and a description of the scientific goals of the project; the part 1 photo essay is here.)

The updated photo tour includes reactions to the activist who tried to sabotage the project, finally getting some data, splendid photos from team members, and more. Part 2 starts off with a hike up to the gorgeous falls in Hagensborg, BC, and can be found here.

Comments may be left here or there, but nowhere in between.

Update: a piece about the failed attempt to sabotage the project, “Eco-warrior trashes seismic experiment” by Rex Dalton, appears in the 23 July 2009 issue of Nature.

Update, Aug. 5^th, 2009: Forest fires have come to the region. More below the fold.

I am currently in British Columbia, Canada, participating in the Batholiths Onland experiment.

Nominally, this large group effort involving over 50 scientists and grad students is for “a seismic refraction and wide-angle reflection survey across the Coast Mountains batholith of British Columbia, Canada.”

This rather terse description does not really do justice to the project, which has the purpose of discovering why continental mountain ranges are often made of granite instead of basalt.

Relevance to the Panda’s Thumb? (1) Real science involves real work; when is the last time you saw a creationist actually measure something, or use a shovel? (2) Real scientists think the earth is billions of years old. You just can’t scientifically reconcile these batholiths with a 10,000-year old earth without being more than a little schizophrenic.

The latest issue (July/August, 2009) of Discover Magazine had a handful of splendid articles, but what really caught my eye was a remarkably detailed image of a 100-million-year-old wasp that had been fossilized inside an opaque piece of amber (p. 39). I could not find the picture on the Discover website, but I easily tracked it to here, where you may see it along with a number of other images.

According to the Discover article, Paul Tafforeau and colleagues at the European Synchrotron Radiation Facility used a beam of x-rays to probe the interiors of bits of amber that are opaque to visible light. They found hundreds of fossilized beetles, ants, wasps, flies, and bits of plants, and made tomograms (or 3-dimensional reconstructions) of some of them. None of the trapped insects was bigger than a few millimeters, presumably because larger insects were not so easily trapped by the resin.

Discover notes that the team found more than 600 insects, none of which appears to be a modern species. It is not clear how many different species those insects represent, but Tafforeau says, “Each scan is a new discovery,” so I infer that they have discovered a great many new, ancient species - and that is among small insects only.

If you believe, with Lucretius and certain of our creationist colleagues, that species are not born but only die out, then all I can say is there must have been at one time one helluva lot of species.

I’ve been thinking about comets a lot lately, trying to image C/2009 G1, reading “The Hunt for Planet X”, wondering why Galileo was so wrong about them and recently reading a Young Earth creationist blog post on them. The latter referred to a very interesting pre-publication article. And I’d like to discuss this article, as this illuminates not only the origins of comets but also how science is done.

Image Credit ESO (click to embiggen).

The Gliese 581 system delivers again. Giese 581 is a red dwarf star 20.4 light years away that until recently boasted the lightest extrasolar planet ever found. At 5 Earth masses, Gliese 581c was not exactly a second Earth, but it and 7 Earth mass Gliese 581d captured the worlds imagination as they seemed to be in the habitable zone of their parent star, where liquid water can exist.

Now the smallest mass planet ever has been discovered around Gliese 581, a 1.9 mass planet Gliese 581e, presumably rocky, that screams around Gliese 581 in a little over three days. At a mere 0.03 Astronomical Units from its star, Gliese 581e is a Mercury-like world, baking in the close embrace of the Red Dwarf.

(The following is a slight adaptation of this essay. Readers may post questions and/or comments there as well as here.) As this series of essays has explained, the polyadenylation of messenger RNAs is a vital aspect of gene expression in eukaryotic cells (and a not-so-unimportant facet of RNA metabolism in other contexts). Polyadenylation is mediated by a sizeable complex that includes various RNA-binding proteins, nucleases, and other interesting activities. Genetic studies in yeast indicate that virtually every subunit of the core complex is essential - for viability and for pre-mRNA processing and polyadenylation in vitro and in vivo. (This review is freely available and serves as a good starting point for readers who wish to explore the subject further.) Biochemical and/or immunological depletion studies reveal a similar scenario in mammals, and a less-expansive set of studies suggests that a similar rule of thumb will apply in plants. The bottom line of all of this is that almost all of the subunits of the polyadenylation complex seem to be essential - remove one, and the complex cannot function. In the vernacular of a proponent of intelligent design, the polyadenylation complex would seem to be irreducibly complex.

It is in this context that the recently-completed genome of the parasitic organism Giardia lamblia enters the fray. Last year, the complete sequence of G. lamblia, some 12 million base pairs, was determined and analyzed. The authors of the study published in Science noted a number of interesting things - a preponderance of genes encoding protein kinases, evidence for substantial horizontal gene flow from bacteria and archaebacteria, and a streamlined core gene expression machinery (transcription and RNA processing). This streamlining is especially notable in the case of the polyadenylation machinery. Remarkably, of all the subunits in the yeast complex, genes for only three* can be found in G. lamblia (see the figure that follows this paragraph - adapted from Fig. 1 of Morrison et al.).

An interesting new paper is just out today in PLoS ONE. You recall the announcement a few years back that soft tissue that resembled organic tissue had been isolated from a Tyrannosaurus femur. This started off a huge controversy in the field (and beyond)–researchers disagreeing with each other whether the structures seen were indeed blood cells and vessels; creationists crowing about how this finding represented “proof” that the earth was indeed young and dinosaurs had existed just a few thousand years ago; and of course, talk of cloning and DNA analysis. On the side of “soft tissue = dino blood” were findings that reported identification of the iron-containing protein heme (potentially from the red blood cells) and morphology of cells and vessels similar to that seen in modern-day ostriches and emu. However, the new paper by Kaye et al. provides an alternative explanation: that the structures aren’t actual vessels and cells, but are instead iron-rich bacterial biofilms. Read the rest over at Aetiology…

The Rockefeller University presents a two day symposium on “From RNA to Humans”

With videos of all the lectures

Session 1: Archaean Chemistry and Earliest Fossils

• The RNA World and the Molecular Origins of Life Gerald F. Joyce, The Scripps Research Institute
• The Origins of Cellular Life Jack W. Szostak, Harvard Medical School
• Can the Distribution of Protein Domains Shed Light on the Tree of Life Russell F. Doolittle, University of California, San Diego
• The Earliest Life on Earth Roger Buick, University of Washington
• Proterozoic Life and Environments Andrew H. Knoll, Harvard University

Session 2: Cells, Cellular Evolution and Protein History

• The Tree of Life and Major Transitions in Cell Evolution Thomas Cavalier-Smith, University of Oxford
• The Origin of Eukaryotes Eugene V. Koonin, National Center for Biotechnology Information, National Institutes of Health
• Barking up the Wrong Tree: The Dangers of Reification in Molecular Phylogenetics and Systematics W. Ford Doolittle, Dalhousie University
• RNA Interference May Provide a Window on the RNA-to-DNA World Transition Phillip A. Sharp, Massachusetts Institute of Technology

Evening Lecture, 6 – 7 p.m.

Feeding and Gloating for More: The Challenge of the New Creationism Jerry A. Coyne, The University of Chicago

Session 3: Development of Eukaryotic Genetic Capacity and Multicellularity

• The Deep Evolutionary History of Eukaryotes Andrew Roger, Dalhousie University
• Demonstrating the Sufficiency of Microevolutionary Processes David Penny, Massey University
• Genes and Development: A Comparison of Human and Amphioxus Genomes Peter W.H. Holland, University of Oxford
• Cnidaria and the Evolution of the Bilaterian Body Plans: Insights from an Outgroup Ulrich Technau, University of Vienna

Session 4: Human Evolution through the Lens of DNA Sequences

• Evolution of Human Populations L. Luca Cavalli-Sforza, Stanford University School of Medicine
• Accelerated Evolution in the Human Genome Katherine S. Pollard, University of California, Davis
• Probing Human Brain Evolution at the Genetic Level Bruce T. Lahn, The University of Chicago
• A Neanderthal Perspective on Human Origins Fairfield Osborn Memorial Lecture , Svante Pääbo, Max Planck Institute for Evolutionary Anthropology