Posted by John S. Wilkins on October 22, 2004 | Comments (42) | TrackBack (0)

A recent blog by Matt Young has more than a few folk upset. I am not upset, exactly, but I do not agree with the way he characterised the political spectrum, or the general features of the parochial duopoly he has drawn from American party politics. Most of all, though, I object to the notion that biology, in particular evolution, has any warrant in such debates at all.

Continue reading  “Politics and evolution”

Posted by Timothy Sandefur on October 22, 2004 | Comments (13) | TrackBack (3)

A while back I posted about the school district in York, Pennyslvania, which decided to add the creationist book From Pandas To People to their classrooms. The school board chose not to require it as part of the curriculum, but did place it in classes for teachers to use, which I said was inappropriate.

It turns out the school district has decided to go farther.

Continue reading  “Oh yeah? I dare you to sue us!”

Posted by PZ Myers on October 22, 2004 | Comments (2) | TrackBack (2)

The fugu is a famous fish, at least as a Japanese sushi dish containing a potentially lethal neurotoxin that was featured on an episode of The Simpsons. Fugu is a member of the pufferfish group, which have another claim to fame: an extremely small genome, roughly a tenth the size of that of other vertebrates. The genome of several species of pufferfish is being sequenced, and the latest issue of Nature announces the completion of a draft sequence for the green spotted pufferfish, Tetraodon nigroviridis, a small freshwater species.

Tetraodon has about the same number of genes as we do, 20,000-25,000, but they are contained in a total genome length of 340Mb vs. our huge 3.1Gb. One major difference is that in Tetraodon, transposable elements are rare: they have 73 types, present in less than 4000 copies, but humans have about 20 different types present in millions of copies. Transposable elements may be reverse transcriptases that blindly copy RNA sequences back into the DNA (called LINES) or shorter sequences that are processed by LINES, called SINES. These really are parasitic bits of selfish DNA, and somehow, pufferfish seem to be largely free of them.

One of the interesting things one can do with a pair of genome sequences is to start mapping synteny. Synteny represents the preservation of small regions of order within a chromosome; while the overall organization may have been scrambled by millions of years of chromosome breaks and fusions and duplications and deletions, we can still identify smaller blocks that maintain the same series of genes within them. For example, if we look on a chromosome of one organism and we see the series of genes A-B-C-D-E-F, and we look in another organism and find a chromosome with the genes W-X-C-D-E-Y-Z, we can see that the C-D-E chunk can be mapped directly to one region of that second organism's chromosome.

Continue reading "Pufferfish and ancestral genomes" (on Pharyngula)

Posted by Richard B. Hoppe on October 22, 2004 | Comments (3) | TrackBack (0)

Peter and Helen Evans, identified as real estate agents who “teach a philosophical approach to conservatism,” published a response to Evan Ratliff’s Wired article about the ID Movement.  The column was published on Mullenax News, a far-right wing Web site that advertises itself as “Always Tough” and “Always Honest.”  Pity the same can’t be said about its columnists.

Continue reading  “Real Estate Agents Against Evolution”

Posted by Ed Brayton on October 22, 2004 | Comments (13) | TrackBack (0)

Yes, folks, today is the Earth’s 6000th birthday, according to the famous Bishop Ussher. In 1650, he famously calculated the age of the Earth using the biblical timeline based upon the ages at which various people were begat and came up with October 22nd, 4004 BC. At around 6 pm. Technically, the 6000th birthday was actually in 1997, owing to odd lineups in various calenders, but such pedantry would just ruin a good party.

She looks pretty good for 6000, don’t you think? A little bigger around the equator, perhaps. The smog has made her a little more gray around the temples, and global warming a little thinner on top. But all in all, not a bad planet to call home. So raise a glass and sing “For she’s a jolly good planet”, something nobody can deny, and bust out the cake. What do you get for the planet that has everything?

Posted by PZ Myers on October 20, 2004 | Comments (20) | TrackBack (0)

The human genome project has reached another landmark, the effective completion of the euchromatic sequence. It's still not 100% done, but the remaining small bits are going to require some new tricks to ferret out. You may recall announcements all over the place back in 2001 that the genome had been sequenced, but that was the draft sequence; 90% of the euchromatic genome was done, but there were still about 150,000 gaps scattered through it. You have to think of this project as something like assembling a colossal jigsaw puzzle—when the draft was done, we had a pretty good idea of the structure of the picture, and maybe had the borders done, but there were still these broad patches of solid colors that hadn't been pieced together yet. At this point, though, most of those have been filled in and the gaps are smaller and sparser.

Some numbers: the completed sequence so far consists of 2,851,330,913 nucleotides. There are only 341 gaps left in the sequence. and 33 of those are in the heterochromatin (the mildly boring, repetitive chunks of the genome, which correspond to those regions of solid color in a jigsaw puzzle), representing 198 megabytes of stuff that still has to be sequenced. In the euchromatin (the more interesting and complex stuff) there are more gaps, 308, but they are much smaller, so only 28 Mb of mystery remains. The total length of the genome is 3.08 Gb, with 2.88 Gb of it in the form of euchromatin.

The new, better defined sequence allows for a more accurate count of total gene number, and that number has dropped once again. We're down to 20-25,000 protein-coding genes. Some may think that knocks us off our pedestal a bit more, but that sounds like plenty to me.

One thing that leaps out at anyone reading the announcement is the importance of evolution in analyzing and understanding the genome. They used alignment with the chimpanzee draft sequence, for instance, to search for deletions. They are identifying recent duplications by their degree of divergence from neighboring genes, and have found 1,183 new genes that have arisen since the human and rodent lineages split. They're tracking the death of genes by identifying sequences with small numbers of disabling mutations (we seem to be losing olfactory genes at a rapid clip, relative to rodents).

The bottom line is that the HGP has provided us with a better tool for all kinds of research.

Nonetheless, the euchromatic human genome can now be regarded as effectively known. The accuracy and completeness of the current near-complete human genome sequence has important consequences for biomedical research. It allows systematic searches for the causes of disease—for example, to find all key heritable factors predisposing to diabetes or somatic mutations underlying breast cancer—with confidence that little can escape detection. It facilitates experimental tools to recognize cellular components—for example, detectors for mRNAs based on specific oligonucleotide probes or mass-spectrometric identification of proteins based on specific peptide sequences—with confidence that these features provide a unique signature. It allows sophisticated computational analyses—for example, to study genome structure and evolution—with confidence that subtle results will not be swamped or swayed by noisy data. At a practical level, it eliminates tedious confirmatory work by researchers, who can now rely on highly accurate information. At a conceptual level, the near-complete picture makes it reasonable for the first time to contemplate systems approaches to cellular circuitry, without fear that major components are missing.

International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431:931-945.

Posted by PZ Myers on October 20, 2004 | Comments (0) | TrackBack (0)

We have another Tangled Bank—#14 is online at Prashant Mullick's Weblog. He had me worried for a while that darn few submissions were coming in, but as usual, there was a last-minute flurry and we have an entertaining and diverse assemblage of biology posts.

There will be more to come at The Sixth International in two weeks, so send us those links. Also, I'm still looking for more hosts, so if you're willing to collect and organize a few web links, volunteer!

Posted by PZ Myers on October 19, 2004 | Comments (3) | TrackBack (0)

Here's a story that Darwin got completely wrong. He had observed that certain species had profoundly reduced or rudimentary organs, and he explained them not as a consequence of natural selection, but as evidence of the inheritance of acquired characters.

But we learn from the study of our domestic productions that the disuse of parts leads to their reduced size; and that the result is inherited.
It appears probable that disuse has been the main agent in rendering organs rudimentary. It would at first lead by slow steps to the more and more complete reduction of a part, until at last it became rudimentary,- as in the case of the eyes of animals inhabiting dark caverns, and of the wings of birds inhabiting oceanic islands, which have seldom been forced by beasts of prey to take flight, and have ultimately lost the power of flying.

It's easy to feel mildly embarrassed for Darwin on reading this now; it was an honest error, though, and since he had no good model for inheritance, he fell back on an old idea, that the use or disuse of an organ in the parent would have an effect on its progeny. Blind fish lost their eyes because Mom and Dad fish lived in the dark and never used their eyes, so Junior inherited weaker eyes.

As it is difficult to imagine that eyes, though useless, could be in any way injurious to animals living in darkness, their loss may be attributed to disuse.

Well, actually, Charles…it's not difficult to imagine at all. Eyes are fragile, pulpy things that represent a significant investment in energy. I could imagine that there would be a slight selective advantage to jettisoning something an animal isn't using, that costs it effort to develop or is a weak or sensitive point of attack. Since we've long discarded the hypothesis of the inheritance of acquired characters, that's one of the primary explanations for the loss of eyes in cave animals—their absence was an advantage.

Another explanation is that eyes are effectively a neutral character in dark environments, and that there is therefore no selective advantage in maintaining them. Cave organisms acquired mutations that knocked out the eyes, and in the absence of selection to maintain sight, these mutations accumulated until the entire population was lacking eyes.

There is a third possibility, now supported by observations in blind cave fish of the genus Astyanax. Despite being wrong on the mechanisms of inheritance, Darwin was no dummy, and he almost figured this one out. If he'd had just a little more intuition about development, he might have suggested this idea. Here's the tantalizingly close passage:

By the time that an animal had reached, after numberless generations, the deepest recesses, disuse will on this view have more or less perfectly obliterated its eyes, and natural selection will often have effected other changes, such as an increase in the length of the antennae or palpi, as a compensation for blindness.

The third possibility requires that one recognize that development is not infinitely plastic, that characters are linked in development, and that maybe the only way to develop these compensatory structures is at the expense of the eyes—that is, that there is a selective advantage to developing long antennae or palpi or other organs, but that the simplest developmental process to do so involves cannibalizing eye tissue. This explanation is an example of the way knowledge of developmental biology can inform our understanding of evolutionary biology.

Continue reading "Development of cavefish eyes" (on Pharyngula)

Posted by Matt Young on October 18, 2004 | Comments (50) | TrackBack (3)

Dick Armey, the former House majority leader has famously (or infamously) remarked that liberals are not very bright (Johnson, 2004).  The claim is as arrogant as it is wrong: neither faction has a monopoly on intelligence.  The difference is in the gut.

Steven Johnson, in “The Political Brain,” notes that people become Republicans or Democrats before they learn what those parties stand for.  He argues that people with like outlooks congregate and that party affiliation initially results from whom you hang around with rather than from dispassionate consideration of the issues.

Johnson notes further that you cannot make a so-called rational decision without emotional involvement, and that is what I want to amplify on here.

Continue reading  “Social Darwinism and "The Political Brain"”

Posted by Jim Foley on October 18, 2004 | Comments (5) | TrackBack (0)

Alfred Russel Wallace, the co-discoverer of natural selection, published a book in 1903 called “Man’s Place in the Universe: a Study of the Results of Scientific Research in Relation to the Unity or Plurality of Worlds”. Stephen Jay Gould wrote about it in one of his Natural History columns, and later reprinted it as the essay “Mind and Supermind” in his book The Flamingo’s Smile. Gould summarizes Wallace’s argument thus:

…Wallace examined the physical structure of the earth, solar system, and universe and concluded that if any part had been built ever so slightly differently, conscious life could not have arisen. Therefore, intelligence must have designed the universe, at least in part that it might generate life.

Sound vaguely familiar?  Compare it to a synopsis of Privileged Planet, a book currently being hyped heavily by the Discovery Institute. (Gould, however, was writing his essay in response to proponents of the ‘anthropic principle’, especially Freeman Dyson.)

Continue reading  “Privileged Planet, Mk. 1”

Posted by PZ Myers on October 17, 2004 | Comments (0) | TrackBack (0)

Remember! The next edition of the Tangled Bank will be at Prashant Mullick on Wednesday. Send your submissions directly to Prashant, to host@tangledbank.net, or to me.