Todd's Blog

Remember that Denisova mtDNA sequence from Siberia? The one published earlier this year that was more different from modern humans than Neandertals? In this week's Nature , the same research team has published the full nuclear genome of Denisova . It answers some of my questions and raises new ones. Some thoughts: 1. The genome is more similar to the Neandertals than to modern humans, which is different from the mitochondrial genome analysis , which placed Neandertals and humans together as sisters, with Denisova as the outgroup. The authors (Reich et al.) hypothesize that this represents incomplete lineage sorting, which is a phenomenon that occurs in the early stages of speciation when different genes have different phylogenetic histories. 2. They sequenced a second Denisovan mtDNA genome from a tooth found at the same site. This mtDNA genome differed from the first Denisovan mtDNA genome by only two nucleotide positions. This second mtDNA genome gives independent confirmati...

There's an interesting paper in PNAS from Zanno & Makovicky arguing that many coelurosaurs were herbivorous. From the abstract: Our findings detect 21 morphological features that exhibit statistically significant correlations with extrinsic fossil evidence of coelurosaurian herbivory, such as stomach contents and a gastric mill. ... The distribution of these features suggests that herbivory was widespread among coelurosaurians, with six major subclades displaying morphological evidence of the diet, and that contrary to previous thought, hypercarnivory was relatively rare and potentially secondarily derived. It's not exactly a "vegetarian T. rex ," but it's interesting nonetheless. Zanno & Makovicky. 2010. Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution . PNAS DOI 10.1073/pnas.1011924108. Feedback? Email me at toddcharleswood [at] gmail [dot] com.

From the secretary of the BSG: We would like to remind you of our upcoming "special edition" of our summer conference  "Origins 2011" which will be held in Rapid City, SD on July 27-29, 2011.  We will be observing the 50 th anniversary of the publication of the Genesis Flood. We will once again be joining with the Creation Geology Society for this special event/conference. You'll probably want to reserve some days around that date (say the 26th to the 31st), since we're also planning field trips and a special conference for the general public. Please reserve these dates now and plan on attending!! We would also want to announce our first call for abstracts. The abstract deadline will be April 1 st Look for updates to our website in the new year which will include abstract guidelines. Feedback? Email me at toddcharleswood [at] gmail [dot] com.

This week's Nature has some interesting stuff. There's a very blunt editorial on the recent arsenic-using proteobacterium and criticisms published on blogs. The authors of the original study (so far) refuse to respond to the blog criticisms, instead insisting that critics must go through the normal peer reviewed channels. Says Nature : Purists who hold peer review as the casting vote in such debates will read her words with approval. But the problem is that Wolfe-Simon's reticence is the polar opposite of the fanfare with which NASA trailed her discovery to the public. As a peer review purist, I admit that I am sympathetic to the desire to hash this out in the peer review press, but I agree that NASA started the whole mess with their overhyped press conference. Doesn't seem fair to dodge criticism now. Also from the editorial: Bloggers and online commentators have an important part to play in the assessment of research findings, and many researchers' blogs, i...

My latest essay at CFSI is pretty redundant if you've read this blog or followed my work for any length of time. The next batch will be more original. I promise. Creationism, evolution, and the origin of species Feedback? Email me at toddcharleswood [at] gmail [dot] com.

There were some interesting articles published this week. PNAS has a paper from Smith et al. on Neandertal development. Seems they matured faster than modern Homo sapiens . Yet more evidence that we're not the same species . Smith et al. 2010. Dental evidence for ontogenetic differences between modern humans and Neanderthals . PNAS 107:20923-20928. Over in Nature , there are two papers relevant to the old "phylotypic stage" argument. Though creationists generally conflate anything related to embryology and evolution as simply "recapitulation," historically there have been a number of distinct arguments that were used to relate evolution and embryology. A good number of them pre-date Origin . One such argument (or observation, if you will) was based on von Baer's observation that vertebrates at a particular stage of development were very similar. This stage was dubbed the "phylotypic stage" by German evolutionist (and lover of neolog...

This is interesting. There's a new piece by Carl Zimmer on Slate.com on those bacteria that supposedly can grow on arsenate instead of phosphate (see my post here ), and it's not a friendly piece. It's called "This paper should not have been published." That kind of gives away the punchline, doesn't it? They quote a lot of microbiologists who are extremely critical of the work. You can read a detailed critique at Rosie Redfield's blog: Arsenic-associated bacteria (NASA's claims) Rosie makes a lot of good points, leaving me quite skeptical of the original paper. In the Slate piece, Zimmer compares this overhyped NASA announcement to the overhyped NASA announcement about alleged bacterial fossils in Martian meteorite ALH 84001 . The big difference is that the evidence for life on Mars was entirely inferential and open to interpretation. This alleged arseno-DNA, however, can be tested. Rigorously. That means we won't have to wait long ...

A few days ago, I posted a note about Koonin and Wolf's paper responding to Theobald's Nature paper on test common ancestry. I wrote it in haste after quickly reading over the paper. Now that I've had time to think it over, I'd like to make some clarifications to my original post. First off, I noted that the paper was published in an online journal called Biology Direct . I think it's fair to note that the editor of Biology Direct is none other than Koonin himself. Why should that matter? Well, here's another point I made in my original post: The result, they say, is statistically significant sequences with no true phylogenetic signal. In principle, this sounds like it would work, but they don't actually show that their random sequences are significantly similar and without phylogenetic signal. So I have that reservation at least. But again, in principle, this method should indeed generate significantly similar protein sequences without phylogenet...

There's a fascinating new paper in Science online from Wolfe-Simon et al. reporting their discovery of a strain of Gammaproteobacteria (called GFAJ-1) that can grow on arsenate instead of phosphate. Isn't that fascinating!? I know what you're thinking: why do I care? Great question. You see, phosphate is biochemically really, really important. Phosphate makes up part of the backbone of DNA, so organisms need phosphate to keep their genes replicating properly. Phosphate is also found in RNA, which is involved in the expression of genes and the formation of proteins. Phosphate is also important for basic metabolism. The "energy unit of the cell" is ATP, adenosine tri phosphate . Many unfavorable metabolic reactions can be accomplished by going through a high-energy intermediate bonded to phosphate. Oh yeah, cell membranes? Phospho lipid bilayers with phosphate! Phosphate is one of the most important inorganic components of living things. It's kind...

Responding to my essay on antievolutionism at CFSI, a reader wrote: Although I think that you ... have a great point, I also believe that you may be missing a larger point. ... I believe that organizations like the Discovery Institute play a very valuable role. Although they may or may not contribute much scientifically to a better understanding of origins, they do provide great moral support to believers who feel overwhelmed by the secular scientific challenge to their faith. We are all part of the same body, after all (at least most of us are, lol). Perhaps each unique part of the body has its own unique role. Your thoughts? I think you're absolutely correct about different goals and perspectives, and that's a perspective I think we all need to keep in mind when thinking about AIG's new Ark Encounter project. Some readers yesterday thought I was being too smug or judgmental in my comments about the Ark Encounter, but I want to assure you that I was entirely sincer...

AIG's latest project is indeed the Ark Encounter theme park, with a life-sized model of Noah's Ark as the centerpiece. Announcement from the Governor of Kentucky Same press release at the AIG website Ark Encounter Youtube channel Official Ark Encounter website  (as of this writing at 4:10, the official site is still showing a countdown to 4 p.m. tomorrow ) What do I think? Personally, I don't really care. I can easily think of dozens hundreds thousands of more important projects to spend $150 million on, but it's not my money. What is curious though is why they think they ought to do this. Clearly the governor and the investors are excited about the economic impact. But what's in it for the rest of creationism? We still don't have a comprehensive model to understand Flood geology, a topic that creationists often bitterly and angrily debate. We're also deeply divided in our approach to biological problems (witness the tempest over hominid ba...