Friday Random Ten (27 May 2005)

As with most trends, I don't exactly ride the crest -- more like the wave after the wave. I'm kinda like the guy behind the guy behind the guy. I usually listen to entire albums, but I decided to break ranks, throw all my digital music into Winamp, hit random, and see what came out. It started out pop-punk, got kinda crunchy, turned a bit third-wave, and finished off with some Chrissie Hynde. I'm still not sure if this will be a regular feature.

1. Green Day - Jesus of Suburbia
2. Less Than Jake - Portrait Of A Cigarette Smoker At 19
3. Coheed & Cambria - The Camper Velourium III: Al The Killer
4. Turbonegro - Get It On
5. Long Beach Dub Allstars - It Ain't Easy
6. Phish - Bouncing Around the Room
7. Mad Caddies - Big Brother
8. Lagwagon - Mama Said Knock You Out
9. Pietasters - Stone Feeling
10. Pretenders - Talk of the Town

What about distance based methods?

DNA and protein sequence data from multiple species allow us to reconstruct the evolutionary relationships between those sequences -- a field known as phylogenetics. One of the earliest methods for constructed phylogenetic trees was borrowed from morphologists. This algorithm (known as the unweighted pair group method with arithmetic mean, or UPGMA) relies on a distance matrix to determine the relationships between sequences.

	A	B	C	D	E
B	2
C	4	4
D	6	6	6
E	6	6	6	4
F	8	8	8	8	8

The UPGMA algorithm assumes that all lineages are evolving at the same rate (oftentimes unrealistic), and it produces what is known as a "rooted tree." This algorithm is rarely used with molecular data due to its limitations. UPGMA has been replaced by the neighbor joining algorithm as the most favored distance based method (i.e., a method using a distance matrix). The neighbor joining algorithm allows for unequal rates of evolution between sequences and is designed specifically for molecular data.

Distance based methods produce one tree based on their algorithm. This is in contrast to maximum parsimony methods which explore all possible trees for the one with the fewest amount of evolutionary steps. (NOTE: With large data sets it becomes unfeasible to explore every tree, so search algorithms have been developed to expedite the process.) It is unclear whether or not the most parsimonious tree is the most probable, so some people question the biological meaning of parsimony methods.

Recently, with the advances in computing, it has become possible to construct phylogenies using maximum likelihood methods. Tree building using maximum likelihood requires one to choose a model of molecular evolution, and an entire field of research has developed concerning which models are appropriate for different scenarios.

A paper by Kolaczkowski and Thornton in Nature last October on the performance of parsimony and likelihood methods has inspired some discussion in the most recent edition of Trends in Genetics. Previous research showed that parsimony methods were subject to inaccurate results with certain branch length combinations. Kolaczkowsi and Thornton, however, found that likelihood methods perform much poorer than parsimony when evolutionary rates vary substantially over time. Interestingly, this paper does not include a comparison with any distance based methods.

Mike Steel has written a review of the Kolaczkowsi and Thornton paper for Trends in Genetics. In his review, Steel points out that the accuracy of likelihood approaches depend on choosing the appropriate model of molecular evolution, and Kolaczkowsi and Thornton's scenario must be considered as a plausible model. More importantly, he questions over-parameterizing one's models. Real life is extremely complex and can be described by an infinite amount of parameters; in order to model this complexity, however, one must determine which parameters are the most important and only include those that are necessary in one's model. Steel concludes in his review,

"In summary, ‘better, more realistic models’ should not mean ‘more parameter-rich models’ – these might ‘capture’ more of reality, but only when the numerous parameters that are required are close to their correct values. However, the power of a given amount of data to estimate several parameters accurately is generally low. Modest parameter models that capture the main features of the sequence data are more useful – learning how DNA evolves is crucial to this task and a challenge for the future."

If one is concerned with simplifying one's models, one should shy away from likelihood and rely on simple distance methods. I am not advocating UPGMA, but neighbor joining should always be considered a viable option. It is a shame that these papers and reviews only consider parsimony and likelihood methods without even acknowledging the existence of distance based approaches.

I am not arguing that one should only use distance based approaches, only that they should still be considered a viable method. Distance methods do rely on models of nucleotide or amino acid substitution to construct the distance matrices, but they are nowhere near as parameter dependent as likelihood approaches. It has always been explained me (and I try to echo this whenever necessary) that if your data is robust, you should recover the same tree topology regardless of which approach you use. Therefore, you should try multiple methods (distance based, maximum parsimony, maximum likelihood) and determine the similarities between the different phylogenies. Regions of the tree that disagree using different methods should not be regarded with high confidence. Ignoring a well established approach only weakens your conclusions. Are distance methods dead in the eyes of tree builders or just in the minds of modelers and parsimony and likelihood advocates?

-----------------
NOTE: I may be biased in my opinion due to spending too much time around Masatoshi Nei's group. For those unfamiliar with the field, Nei developed the neighbor joining algorithm and has been a staunch advocate of distance based methods. He has always argued, "Why use a complex method when a much simpler one works just as well?" In other words, keep it simple, stupid.

Just another theory.

You can call it laziness (or patting myself on the back), but I've posted a comment I made on Pharyngula a few months ago. Mostly, I'm doing it so that I have a copy of this clever retort (ok, that's definitely self-back-patting) on my own site.

The comment was in response to this Wing Nut Daily article by Joseph Farah. He tried to explain why he doesn't believe in evolution, so I came up with why I don't believe in gravity. It's just as timely now as it was in December given the persistent nagging of the ID community. Enjoy.

Why I believe in unaided human flight

I was stunned the other day when I asked gravity-believing listeners to my nationally syndicated radio show to call in and tell me why they believed.

"Just give me one reason why you accept the theory," I said. "Just give me the strongest argument. You don't have to give me mountains of evidence. Just tell me why I should accept it."

Not one physicist called in.

Meanwhile, the phone banks lit up with dozens of gravity skeptics.

Go figure. For more than 100 years, gravity has been taught as fact in government schools to generations of children, yet there is still widespread skepticism, if not cynicism, about the theory across the country.

But, because of political correctness and the fear of ostracism, most people are afraid to admit what they believe about our inability to fly without the aid of airplanes or other man-made devices. That's why I wrote my last column – "I believe in unaided human flight."

The reaction to it has been unprecedented. While I expected mostly negative fallout, most letters have been quite positive.

So, I decided to take this issue a step further. Since the physicists don't want to tell me why they believe in their theory, I figured I would explain why I believe in mine.

The primary reason I believe, of course, is because Comic Books tell me so. That's good enough for me, because I haven't found Comic Books to be wrong about anything else.

But what about the worldly evidence?

The physicists insist that unaided human flight is impossible due to the gravitation pull of the earth.

I don't believe that for a minute. I don't believe there is a shred of scientific evidence to suggest it. I am 100 percent certain that humans have been flying since the God created the earth 6000 years ago. In fact, I'm not at all sure that people still don’t fly today!

Think of all the world's legends about superheroes. Look at those images. What were those folks seeing? They were clearly seeing people flying. You can see them etched in cave drawings. You can see them in ancient literature. You can see them described in Comic Books. You can see them in virtually every culture in every corner of the world.

Did the human race have a collective common nightmare? Or did these people actually see unaided human flight? I believe they saw people flying – what we now call superheroes.

Furthermore, many of the flying people in various parts of the world lived right along every other human. How did that happen?

And what about the not-so-unusual sightings of contemporary unaided human flight? Some of them have actually been captured on film.

There are also countless contemporary sightings of what appear to be flying humans in Asia and Africa.

You know what I think? I think we've been sold a bill of goods about gravity. I don't believe that it grounds us to the earth. In fact, I’m not at all sure I couldn’t fly today if I wanted to.

Physicists have put the cart before the horse. They start out with a theory, then ignore all the facts that contradict the theory. Any observation that might call into question their assumptions is discounted, ridiculed and covered up. That's not science.

How could all the thousands of historical records of superheroes and other flying humans throughout mankind's time on earth be ignored? Let's admit it. At least some of these observations and records indicate humans could fly fairly recently – if not still fly today.

If I'm right about that – which I am – then the whole gravity house of cards comes tumbling down.

This is the evidence about which the physicists dare not speak.

Worst. Comic strip. Ever.

This may be, hands down, the single worst comic strip ever written (in a good way):




Read the whole thing if you don't get the "jokes."

On this date in history . . .

On this day date (May 25) 80 years ago:

"John T. Scopes, young Dayton (Tenn.) high school teacher, tonight stands indicted for having taught the theory of evolution to students attending his science classes in violation of a law passed by the Tennessee Legislature and signed by the Governor on March 21, 1925."

This is not the date of the famous Scopes Monkey Trial that inspired the film Inherit the Wind; Scopes was merely indicted by a grand jury on this day in history. The trial did not begin until July 10.

------------

Edited: Scopes was not endicted on the "day" 80 years ago; he was indicted on this "date" 80 years ago. How could I allow myself to commit such an egregious semantical mistake!?

National Academy Elections

The National Academy of Sciences has published their election procedures in the current issue of PNAS. The article is accompanied by this figure summarizing the procedure:




Yeah, I find it extremely confusing too.

Clone me a pony.

By now you have heard about the Korean group who successfully cloned lines of embryonic stem cells with nuclei from individuals with injuries or diseases. There is plenty of debate on the subject (John Rennie provides a nice review of some opinions), and President Bush has stood fast on his anti-cloning position:

"I worry about a world in which cloning becomes acceptable. Secondly, I made my position very clear on embryonic stem cells. I'm a strong supporter of adult stem cell research, of course. But I made it very clear to the Congress that the use of federal money, taxpayers' money to promote science which destroys life in order to save life is -- I'm against that. And therefore, if the bill does that, I will veto it."

There have also been new developments in equine cloning. The Jockey Club, which regulates thoroughbred racing in North America, will not allow artificial insemination, let alone cloning. You can read all of the rules here. The Jockey Club is against cloning for different reasons that the Bush administration, but none of it is based in solid science. Dan Rosenberg, president of the farm that breeds Kentucky Derby and Preakness winner Smarty Jones said:

"Part of the intrigue, part of what makes horse racing so appealing is the challenge and the art of breeding a better animal. It will become less appealing if it comes down to which owners and breeders can hire the best scientists. Do we really want races that pit 10 Secretariats against each other?"

His argument assumes:

1. Geneticists will be able to identify alleles that make horses win races;
2. Geneticists will be able to engineer horses that have winning genotypes;
3. And a horse's racing success is mostly due to genetic factors (as opposed to environment, the jockey, or dumb luck).

Until there is concrete evidence that breeders that use cloning or genetic manipulation have an unfair advantage over traditional breeders, there is no reason to disallow cloning. Besides, breeding by selecting for winning horses is a form of genetic engineering (albeit primitive) that may or may not lead to success (I don't have the statistics and I'm too lazy to look them up). This is an issue of an old guard establishment protecting its traditional methods from modern scientific advances. Much like Bush's position on stem cell research and cloning is based on faith and religious doctrine, the horse racing community is adhering to its traditions without understanding the science behind racing performance.

Don't fear the end of equine cloning just because the Jockey Club does not allow it -- Olympic jumping horses can still compete even if they are clones.

Michael Lynch Chimes In.

Michael Lynch has written a must read Nature letter on the ID article. Here are some of his best points:

"Two factors have facilitated the promotion of ID. First, IDers like to portray evolution as being built entirely on an edifice of darwinian natural selection. This caricature of evolutionary biology is not too surprising. Most molecular, cell and developmental biologists subscribe to the same creed, as do many popular science writers. However, it has long been known that purely selective arguments are inadequate to explain many aspects of biological diversity . . . But features of the genome, such as genomic parasites or non-coding introns, which aren't so evolutionarily favourable (nor obviously 'intelligent' innovations), can be more readily explained by models that include random genetic drift and mutation as substantial evolutionary forces.

. . .

"Less widely appreciated is that evolution has long been the most quantitative field of biology, well grounded in the general principles of transmission genetics. Yet few students at university, and almost none at high school, are exposed to the mathematical underpinnings of evolutionary theory. The teaching of evolution purely as history, with little consideration given to the underlying mechanisms, reinforces the false view that evolution is one of the softer areas of science.

"Here is a missed opportunity. Our failure to provide students with the mathematical skills necessary to compete in a technical world is a major concern in the United States. Mathematics becomes more digestible, and even attractive, when students see its immediate application. What better place to start than with the population-genetic theory of evolution, much of which is couched in algebraic terms accessible to school students?"

I don't know if I'd go much beyond simple transmission genetics (i.e., Punnett squares) and the Hardy Wienberg equation in a high school biology class. I've taught senior biology majors that had a hard time grasping these simple concepts. Even though the mathematics are simple -- nothing more than basic algebra -- many of the concepts are abstract and difficult to grasp for some students. Students oftentimes have a difficult time understanding what the Hardy-Weinberg theorum is testing and how to interpret the results.

Lynch's point, however, is extremely important: it should be made clear that evolutionary biology (specifically evolutionary genetics) is one of the most quantitative fields in biology, and evolutionary biology is not a "soft science."

Coyne's Reply.

Jerry Coyne has replied to the Nature cover story on Intelligent Design. Coyne's letter is short, so I suggest you read the entire thing if you have a subscription to Nature. Here are some of his key points:

"[T]he science classroom is the wrong place to teach students how to reconcile science and religion. For one thing, many scientists deem such a reconciliation impossible because faith and science are two mutually exclusive ways of looking at the world . . . The real business of science teachers is to teach science, not to help students shore up worldviews that crumble when they learn science . . . [ID] has no more place in the biology classroom than geocentrism has in the astronomy curriculum . . .

"[S]tudents who cannot handle scientific challenges to their faith should seek guidance from a theologian, not a scientist. Scientists should never have to apologize for teaching science."

I'm glad someone (especially one of the leaders in his field) has called out Nature's absolute ineptitude in reporting the ID "debate."

Tangled Bank 28.

Better late than never:

Tangled Bank #28 is up at The Medical Madhouse. Go read about science . . . I order you!

More on Darwinists.

The ID camp loves calling mainstream evolutionary biologists "Darwinists" (see the Wedge Document). I've discussed my feelings on that word before so I won't go any further into it. It has been suggested that we should call the IDers "Dembskists" (scroll down to comment #6).

In the spirit of over splitting, I think we should divide biologists into multiple camps (just like during the selection/neutrality debates) named after the founder of their fields. For example, those interested in genetics and the neo-Darwinian synthesis can be referred to as "Dobzhanskyists." People interested in systematics and evolution can be called "Mayrists." We can call the "bean-bag" theoretical popgen folks "Wrightists," "Fisherists," or "Haldanists." And let's call people who ardently support neutral explanations despite evidence for selection "Kimuraists." Isn't this fun!?

Furthermore, we can divide the IDiots into groups depending on their beliefs. If they acknowledge evolution and common descent, but feel that God must have done something during the course of evolution, we can call them "Beheists." If they believe that common descent is a fallacy, we should call them "Wellsists." (See this post on Dispatches from the Culture Wars on the inconsistency of the ID movement.)

---------------
Edited to add:
How could I forget! The evo-devo folks can be called "Carrollists."

Split Up

DarkSyd at UTI has a great series on hominid evolution.

This got me to thinking (again) about how taxonomists overly split the hominid lineage. If we were talking about any other mammal, everything within the genus Homo would be one species (possibly broken into subspecies), and all apes would be classified as a single genus (or maybe just Homo, Pan and Gorilla). Of course, mammalian taxa are overly split relative to other vertebrate taxa, vertebrate taxa are overly split relative to other animal taxa, and (I'm assuming) animal taxa are overly split relative to plants, fungi, and prokaryotes.

Taxonomy is a combination of observation and classification (a fairly objective process) and hierarchical naming (more subjective). Some of the oversplitting of certain taxa could be due to the amount of knowledge we have regarding those taxa. For example, we know much more about primates because we are interested in our origins so paleontologists search for those fossils. This contrasts with, say, what we know about insects -- there has been much less study on these critters relative to the amount of species diversity within this group. This is the subjectivity involved in observation and classification.

The other reason for oversplitting of hominids, mammals, animals, etc is that we tend to oversplit things that are similar to us. We put chimpanzees in a separate genus (we even put other hominids in separate genera!) despite the fact that we diverged from them within the last 10 million years. Contrast this with another well characterized group: Drosophila. According to the most recent molecular dating, the last common ancestor of all Drosophila species existed approximately 60 million year ago, yet they are considered a single genus. Granted, this genus is split into subgenera, groups, subgroups, species complexes, species, and (sometimes) subspecies, but they are all still considered to be in the same genus.

I think I'm done beating this drum to a dead horse -- to mix my metaphors.

Piling on Saletan

Wow! I think I was the first to post on William Saletan's Slate article on the Kansas Kangaroo Court. Since then it seems like everyone has offered their two cents. Here's a list of bloggers that I could find that had something to say about Saletan's ignorance (in no particular order). Call it the "Carnival of the Saletan Haters."

1. evolgen - Saletan Fails the Test
2. Pharyngula - Saletan and Engbers…aw, heck. I never cared much for Slate, anyway.
3. Sci Am Perspectives - Wipe this slate clean
4. Evolutionblog - Despair
5. Evolving Thoughts - The ID Know Nothing Party
   

Please suggest any other blog entries in the comments section.

I've also found an article Saletan published three years ago on Intelligen Design. He closes with:

That, in a nutshell, is ID. It offers no predictions, scope modifiers, or experimental methods of its own. It's a default answer, a shrug, consisting entirely of problems in Darwinism. Those problems should be taught in school, but there's no reason to call them intelligent design. Intelligent design, as defined by its advocates, means nothing. This is the way creationism ends. Not with a bang, but with a whimper.

Well, at least he knows that ID is a sham. Now, how does he explain his drivel yesterday?

Saletan Fails the Test

Slate's chief political correspondent and famed liberal mouthpiece (note: that's not intended as an insult) William Saletan has chimed in on the Kansas Intelligent Design "trial." He apparently thinks that we biologists aren't doing a good enough job defending evolution from the creationists.

Liberals, editorialists, and biologists wonder aloud how people can refuse to see evolution when it's staring them in the face. Maybe they should ask themselves. It's the creationists in Kansas who are evolving. And it's the evolutionists who can't see it.

Oh, we can see how they've "evolved." They've gone from dishonest biblical literalists, to dishonest pseudo-scientists -- quote mining and double-talking their way to international media coverage.

Saletan paints the picture of creationist evolution from "the early, authoritarian stage of creationism—the equivalent of Australopithecus " to the "Homo Sapiens" form which "abandons Biblical literalism, embraces open-minded inquiry, and accepts falsification, not authority, as the ultimate test." If that's not complete and utter bullshit, I don't know what is. None of the incarnations of creationism were/are falsifiable (there will always be "gaps" in evolution -- all of science is filled with gaps). Sure, they IDiots like to act like they're scientists, saying things like, "An ID proponent recognizes that ID theory may be disproved by new evidence." But what John Calvert and William Harris (the IDiots behind that quote) fail to mention is that every claim from their camp has been debunked (go read the TalkOrigins archives if this is new to you).

Saletan's cutesy metaphor may fool some people, but no one with a good understanding of biology should fall for that shit. He writes, "Creationists aren't threatening us. They're becoming us." No, they're trying to get religion into the classroom through back doors and underhanded maneuvers. It's the same shtick they've been trying for years now. It's like dressing an elephant in a pink tutu and having it dance the nutcracker suite. It's still a five ton quadruped with a trunk and big floppy ears, and ID is still creationism dressed up to look like science.

He closes with his greatest fallacy of all:

It's too bad liberals and scientists don't welcome this test. It's too bad they go around sneering, as censors of science often have, that the new theory is too radical, offensive, or embarrassing to be taken seriously. It's too bad they think good science consists of believing the right things. In the long view—the evolutionary view—good science consists of using evidence and experiment to find out whether what we thought was right is wrong.

It's too bad you didn't do any god damn research, William. The IDiots took our test and failed. Every single one of their tired old arguments has been disassembled, disproved, and dismissed. We don't have a problem with them because their ideas are too radical. Science is, by convention, extremely conservative, but we do accept new ideas if they have merit. Check out West-Eberhard's ideas on developmental plasticity (I blogged about it here). We have critically evaluated the ID movement, seen it for what it is, and then dismissed it accordingly. They have no evidence, no experiments, and, hence, no theory.

I'm greatly disappointed in William Saletan's failure to adequately research the topic before publishing his uninformed opinion. This is the kind of shitty journalism I'd expect from the Wingnut camp. I'm going to have to reevaluate some of his other pieces to see if this is a common trend or a one time mistake. Hopefully the IDiots easy to digest bullshit doesn't appeal to other liberal journalists the same way it appeals to Saletan.

Chimera

A recent article (subscription required) in the NY Times Science section discusses the role of interspecies chimeras in biomedical research. They point out the chimeric organisms are nothing new:

“Biologists have been generating chimeras for years, though until now of a generally bland variety. If you mix the embryonic cells of a black mouse and a white mouse, you get a patchwork mouse, in which the cells from the two donors contribute to the coat and to tissues throughout the body. Cells can also be added at a later stage to specific organs; people who carry pig heart valves are, at least technically, chimeric.”

Regardless of the minimal ethical controversy amongst biologists, new research using other animals (e.g., pigs) to harvest human organs derived from progenitor cells has the potential to "gross out" most Americans. In essence, it's analogous to watching a horror film with a mad scientist manipulating the natural order for some (often undefined) egomaniacal purpose. According to the article,

“From the biologists' point of view, animals made to grow human tissues do not really raise novel issues because they can be categorized as animals with added human parts. Biologists are more concerned about animals in which human cells have become seeded throughout the system.”

I am neither a developmental biologist, knowledgeable in biomedical ethics, nor too concerned with the entire stem cell debate (which I think falls into this debate somewhere). What I am interested is molecular biology, genetics, and evolution, where there is a great history of chimeric forms. I'll discuss some of the ones I find most interesting below.

Chimeric genes play an integral role in molecular biological research. One such example is the GAL4-UAS system. By combining the upstream activation site (UAS) for the yeast gene GAL4 with your gene of interest, you can cause your gene to be activated in the presence of GAL4. These chimera aren’t structurally different (i.e., it is still the same protein), but instead of the normal regulatory elements associated with the gene, it now has the yeast UAS. A researcher can control where the GAL4 gene is expressed by creating a chimera made up of the GAL4 gene and a regulatory element for a certain tissue. Wherever GAL4 is expressed, your gene of interest will be expressed because it has been fused to the UAS.

Researchers often use fusion proteins to study the location of a particular protein in an organism or cell. These fusion proteins are a chimera of the coding sequence of a gene of interest and some label (often times a fluorescent protein such as green fluorescent protein, a.k.a. GFP). Studies of this sort can be used to view where a gene is expressed, how an organ develops, or how some subcellular machinery functions. I won’t go any further into this topic as it’s beyond my area of expertise, but hopefully I’ve shown the utility of molecular chimeras in biological research.

What I find most interesting are naturally occurring chimeras. The NY Times article makes the point that chimera violate natural laws. We are quickly realizing that molecular chimeras, however, are common in nature. The easiest of these to comprehend is interspecies hybridization (whole genome chimeras). Hybridization has the potential to induce speciation, and these species can be thought of as a chimera of the two parent species (yes, I do realize that I’m stretching the concept of chimera a bit here).

Better examples of natural occurring chimera resemble fusion genes used in molecular biology laboratories. One such gene (jingwei) has been studied by Manyuan Long for over a decade. Long and his colleagues have shown that a transcript of the gene alcohol dehydrogenase (Adh) inserted into the middle of another gene (yellow emperor) in the Drosophila melanogaster genome. The insertion interrupted the normal functioning of yellow emperor – an event that would oftentimes be under strong negative selection. It is expected that the insertion event would be selected against, but in this instance there was strong positive selection for this chimeric gene. In case you are curious, the naming of these genes (jingwei and yellow emperor) comes from Chinese mythology.

Other naturally occurring chimeric genes resemble the GAL4-UAS system – a complete open reading frame (i.e., protein coding sequence) fused to a new regulatory region. This is usually what happens when a retrotransposed gene becomes a functional gene. As we begin to accumulate more genome sequences, comparative techniques should enable us to find more example of naturally occurring molecular chimeras. Another Adh fusion gene has recently been found, and many more Drosophila fusion genes may be identified with the wealth of genomic data. I have identified a couple of partially duplicate genes in the Drosophila genome that I study that may form functional transcripts with the genes they inserted next to. I hope to characterize these further in order to further understand the role of chimera in molecular evolution.

Here, fishy fishy.

Check out the newest thing from the fundy right:



Personally, I wouldn't buy one even if I

1. Supported Dubya;
2. Were a Christian (fundamentalist or not);
3. Wanted to insert my religious beliefs into the public sector.

I don't know if I should find it offensive, humorous, or indicative of the sad state of "mainstream" American politics. I do know that I prefer these fish much more:





Via Orac.

Comparative Genomics in Humans and Chimps.

A recent article by some folks at Cornell and Celera is generating some hype in the science blogosphere (for a brief synopsis, click here). You can read about it at the Loom, Pharyngula, and Mike the Mad Biologist. All three blogs provide good summaries and discussions of the results, so I won't add very much.

What makes this study better than your run-of-the-mill comparative analysis is the inclusion of polymorphism data. For example, they could infer selective sweeps in SCML1 based on the lack of intraspecific polymorphisms. Also, the interpretation of the results adds to the general appeal. If you wanna know why, read the article, synopsis, or blog entries for yourself.

Tangled Bank XXVII

Tangled Bank XXVII (that's 27, I think) is up at Buridan's Ass. Wow, that sounds a lot like, "Tangled Bank 27 is up Buridan's Ass." That sounds uncomfortable. Pretty soon there will be more Tangled Banks than Super Bowls.