Todd's Blog

At long last, the real story about science journalism: This is a news website article about a scientific paper Hey, I read it in The Guardian . It must be true. For added hilarity, be sure to click on the related link marked "The Journal (not the actual paper, we don't link to papers)." Feedback? Email me at toddcharleswood [at] gmail [dot] com.

Over at UD, a poster called niwrad thinks he's demonstrated that the human and chimp genomes are not really as similar as they really are. I briefly contemplated getting his code and showing how he was wrong, but I don't think that's a profitable use of my time, given my current schedule. So I'll just say that from his description, he never indicates that he actually aligned the chromosomes that he's testing (maybe he did, but I didn't see it in the description), which will inevitably lead to rubbish results. Further, the distance metric he uses doesn't appear to model indels, so that will also lead to further degradation of the similarity. If he actually used a real sequence alignment algorithm (like Smith-Waterman), he'd find the same thing the rest of us have found: the chimp and human genomes are >97% identical. But what about that paper by Britten ? The one where he showed that the 99% identity figure had ignored important indel data and...

Last week, when I wrote briefly about Jason Lisle's new paper in ARJ on starlight and time , I suggested that his explanation of other appearances of age was ad hoc . Here's what he wrote: We note that the ASC model only accounts for distant starlight and other earthward-directed phenomena that move at nearly the speed of light (such as neutrinos). It has been suggested that other celestial phenomena require billions of years: collisions of galaxies, jets of material from active galactic nuclei (AGNs), etc. However, I do not believe this is so. It seems to me that the mature creation argument works quite well on distributions of matter. Unlike light, the supernatural creation of matter in a specific configuration does not undermine any precondition of intelligibility; nor do we have biblical information that would be contrary to the idea that God may have created the matter in the universe very close to its present location. So, we should consider the possibility that galaxi...

I've heard from a few folks on Lisle's latest ARJ paper on the starlight travel time.  Some were guarded in their assessment, and others thought it was rubbish.  Folk over at sensuouscurmudgeon raise some interesting questions, like how a nonconstant speed of light relates to permittivity and permeability. I would be interested in Lisle's response to that.  As for myself, I'm still trying to wrap my brain around the whole thing. Then there was the really interesting revelation to me that his idea is not actually new.  It was originally published in an issue of TJ nine years ago, under Lisle's pseudonym at the time, "Robert Newton." Newton.  2001.  Distant starlight and Genesis: conventions of time measurement. TJ 15(1):80-85. [ PDF ] That was followed by considerable discussion ( PDF , PDF , PDF ), but it should be noted that though Hartnett was initially hostile to the idea, he later seems to have adopted it in his own cosmogony ( PDF ). As I...

In the latest paper from ARJ , Jason Lisle suggests that there is a "solution to the distant starlight problem." Here's the abstract: We here explore a way in which light from distant galaxies can reach earth within the biblical timescale. Though the universe is created mature, we will find that this by itself appears to be insufficient to explain our ability to see distant events, prompting the need for a solution to the “distant starlight problem.” The concept of synchrony conventions in physics is examined. The fact that relativistic physics precludes an absolute, invariant synchrony space is reviewed. We then explore the consequences and motivation for the use of the standard Einstein synchrony convention, followed by an investigation of alternative synchrony conventions. In particular, we find that an observer-centric anisotropic synchrony convention eliminates the distant starlight problem by reducing radially inward-directed light travel-time in the ...

This new paper from PNAS should be interesting to you irreducible complexity aficionados. Lynch. 2010. Scaling expectations for the time to establishment of complex adaptations . PNAS 107:16577-16582. Abstract Although the vast majority of research in evolutionary biology is focused on adaption, a general theory for the population-genetic mechanisms by which complex adaptations are acquired remains to be developed. The issue explored here is the procurement of novel traits that specifically require multiple mutations to achieve a fitness advantage. By highlighting the roles played by the forces of mutation, recombination, and random genetic drift, and drawing from observations on the joint constraints on these factors, the ways in which rates of acquisition of specific types of adaptations scale with population size are explored. These general results provide insight into a number of ongoing controversies regarding the molecular basis of adaptation, including the adaptive utility of...

Good grief, Phil, slow down will you? First, it was a clever paper on the intermediacy of Australopithecus afarensis ("Lucy") in American Biology Teacher , which I commented on here . Then it was his baraminology paper in Journal of Evolutionary Biology that showed that dinosaurs and birds should be considered members of the same baramin (I intend to formally respond to very soon, but in the meantime, you can read my initial impressions here ). Now, he's got a new paper in the latest Reports of the NCSE called "Vestigial structures exist even within the creationist paradigm." He's becoming quite the creationism scholar, cranking out three significant papers in the last year. He makes me look lazy in comparison! The basic message of the new paper is that vestigial organs are not "useless" but merely reduced. He ably refutes creationists' (mostly Bergman's) arguments against vestigial organs, but then he points out that even within c...

A few recent papers caught my attention. In the first, Chen et al. looked at an array of tandem repeats in DNA mismatch repair genes called MMR genes. These genes make proteins that allow bacteria (in this case Salmonella ) to fix DNA mutations. Without functional MMR genes, bacterial populations become more variable because they can't repair their mutations. The weird thing is that tandem repeats can lead to mutations, which could inactivate the MMR genes. So the genes that repair DNA mutations are themselves liable to inactivation by mutation. What's the big deal? Well, we know that having a high mutability allows bacteria to adapt to new environmental conditions, and since MMR genes repair mutations, it makes sense that a population would want to shut off some MMR genes if they need to adapt. But you need the genes around generally, since a having a lot of mutations is harmful. Sure enough, Chen et al. found similar repeat sequences in the MMR genes of >100 bact...

I've seen this on a couple of humor blogs, but I haven't noticed it on any of the creation/evolution sites. So I figured I'd alert the community. There's going to be a "First Annual Catholic Conference on Geocentrism." The title: "Galileo was wrong: the Church was right." At least they're not going for sheer sensationalism. Speakers and talks include: Dr. Robert Sungenis: Geocentrism: They Know It But They’re Hiding It Mr. Mark Wyatt: Introduction to the Mechanics of Geocentrism Dr. Robert Bennett: Scientific Experiments Showing Earth Motionless in Space Msr. Rick/Wyn Delano: Scientific Evidence: Earth in the Center of the Universe Mr. Martin Selbrede: Answering Common Objections to Geocentrism Dr. Gerry Bouw: The Biblical Firmament: Outer Space is Not Empty Dr. Robert Sungenis: Galileo and the Church: What Really Happened? Mr. John Salza, Esq.: The Fathers and Exegesis of Scripture on Geocentrism Dr. E. Michael Jones: English Ideology, Newton...

So it's been a while. I've been meaning to post something , but I'm revising two courses this semester, which is like having to write four blog posts a week. That takes up a lot of my time. Plus I've got several manuscripts in revision, and I'm working on an exciting new student project. Blah, blah, excuses, excuses. I'm busy. So is everyone else. I did think the paper on adaptive radiation in elephant fish Paramormyrops was extremely interesting. These fish look very similar, but there is a closely-related "species flock" in Africa. Why are there so many species living in such close proximity (as many as 20 species in one location)? It seems they have different signaling methods using their electric organs. Arnegard et al. (the authors of the study) think that sexual selection accounts for the adaptive radiation of these fish, since the electric signaling is used for mate selection. So it's an example of adaptive radiation where the sp...

Abstracts from the 2010 meeting of the Creation Geology Society are now available online. Check them out at the CGS website . They also have a brief announcement about the upcoming BSG/CGS conference, "Origins 2011," to be held in Rapid City, SD on July 27-30 next year. Be sure to start thinking about your contributions now. Feedback? Email me at toddcharleswood [at] gmail [dot] com.

Poor devil: Famed Tasmanian devil euthanized after tumor found Feedback? Email me at toddcharleswood [at] gmail [dot] com.

Then again... maybe not. Check out this post at Paul Garner's blog: Fossils that rewrite evolutionary history...or not, as the case may be He's talking about this paper: Tarver et al. 2010. Is evolutionary history repeatedly rewritten in light of new fossil discoveries? Proc R Soc B doi: 10.1098/rspb.2010.0663. Long story short: You can say it legitimately about dinosaurs, since discoveries there really do tend to upset previous evolutionary scenarios, but not about catarrhine primates (the Old World monkeys and apes, which includes Homo sapiens ). Funny thing is that I tend to hear people saying their new hominid fossil rewrites evolutionary history more often than I hear the same thing about some new dinosaur fossil. Paul points to Ida as a prime example. The paper's free, so check it out. Feedback? Email me at toddcharleswood [at] gmail [dot] com.

That didn't take long: James J. Lee, Hostage-taker and Darwinist Writes Klinghoffer: My purpose here, of course, isn't to suggest that Darwinism drives people mad or anything like that, but merely to point out, as I've done in the past, the strange attraction Darwinian theory exerts on some people who are crazy, or wicked, or both. Uh huh. Why is it that I can think offhand of far more wacko Christians than I can wacko "Darwinists?" Seriously, you should read some of the crazy emails I get. Then again, I'll bet Klinghoffer doesn't care what I think: I've written about this many times before and received much abuse for it Guess I'm just one of the abusers, eh? Whatever. I stand by what I wrote this morning . Feedback? Email me at toddcharleswood [at] gmail [dot] com.

The hostage crisis at Discovery Communications yesterday put me in mind of how words influence actions. Did you happen to read the alleged hostage taker's statement (at this point, he has been unofficially identified as James J. Lee)? It's like the very worst possible environmentalist stereotype come to life. He demanded that the Discovery Channel do something to curb human population growth and encourage sterility. He claimed that humans were "filth" that destroy the planet. And of course, he demanded that the Discovery Channel should teach about evolution, or in his words, "Talk about Malthus and Darwin until it sinks into the stupid people's brains until they get it!!" It was a terrible tragedy that ended in the hostage taker's death, but before anyone gets too smug about how Darwinism leads to violence, let's remember two words: James Kopp. You know, the guy who bought a sniper rifle and assassinated abortionist Barnett Slepian? The ...

There's an interesting paper in this week's nature on antibiotic resistance in bacteria: Bacterial charity works leads to population-wide resistance Bacteria show remarkable adaptability in the face of antibiotic therapeutics. Resistance alleles in drug target-specific sites and general stress responses have been identified in individual end-point isolates. Less is known, however, about the population dynamics during the development of antibiotic-resistant strains. Here we follow a continuous culture of Escherichia coli facing increasing levels of antibiotic and show that the vast majority of isolates are less resistant than the population as a whole. We find that the few highly resistant mutants improve the survival of the population’s less resistant constituents, in part by producing indole, a signalling molecule generated by actively growing, unstressed cells. We show, through transcriptional profiling, that indole serves to turn on drug efflux pumps and oxidat...