Hox genesis


One of the hallmark characters of animals is the presence of a specific cluster of genes that are responsible for staking out the spatial domains of the body plan along the longitudinal axis. These are the Hox genes; they are recognizable by virtue of the presence of a 60 amino acid long DNA binding region called the homeodomain, by similarities in sequence, by their role as regulatory genes expressed early in development, by the restriction of their expression to bands of tissue, by their clustering in the genome to a single location, and by the remarkable collinearity of their organization on the chromosome to their pattern of expression: the order of the gene’s position in the cluster is related to their region of expression along the length of the animal. That order has been retained in most animals (there are interesting exceptions), and has been conserved for about a billion years.

Think about that. While gene sequences have steadily changed, while chromosomes have been fractured and fused repeatedly, while differences accumulated to create forms as different as people and fruit flies and squid and sea urchins, while continents have ping-ponged about the globe and meteors have smashed into the earth and glaciers have advanced and retreated, these properties of this set of genes have remained constant. They are fundamental and crucial to basic elements of our body plan, so basic that we take them completely for granted. They determine that we can have different regions of our bodies with different organs and organization. Where did they come from and what forces constrain them to maintain their specific organization on the chromosome? Are there other genes that are comparably central to our organization?

[Read more…]

Bilateral symmetry in a sea anemone



There are quite a few genes that are known to be highly conserved in both sequence and function in animals. Among these are the various Hox genes, which are expressed in an ordered pattern along the length of the organism and which define positional information along the anterior-posterior axis; and another is decapentaplegic (dpp) which is one of several conserved genes that define the dorsal-ventral axis. Together, these sets of genes establish the front-back and top-bottom axes of the animal, which in turn establishes bilaterality—this specifically laid out three-dimensional organization is a hallmark of the lineage Bilateria, to which we and 99% of all the other modern animal species belong.

There are some animals that don’t belong to the Bilateria, though: members of the phylum Cnidaria, the jellyfish, hydra, sea anemones, and corals, which are typically radially symmetric. A few cnidarian species exhibit bilateral symmetry, though, and Finnerty et al. (2004) ask a simple question: have those few species secondarily reinvented a mechanism for generating bilateral symmetry (so that this would be an example of convergent evolution), or do they use homologous mechanisms, that is, the combination of Hox genes for A-P patterning and dpp for D-V patterning? The answer is that this is almost certainly an example of homology—the same genes are being used.

[Read more…]

Cancel those Florida vacation plans!

Weep for poor persecuted Kent Hovind. They’ve shut down Dinosaur Adventure Land.

County commissioners showed no sympathy to members of the Creation Science Evangelism ministry who spoke out Thursday night at a commission meeting about the county’s actions.

“Scripture also says ‘Render unto Caesar what Caesar demands.’ And right now, Caesar demands a building permit,” County Commission Chairman Mike Whitehead said.

On the other hand, these guys are criminal con-artists and scum, so hold back those tears.

Legal questions are nothing new for Dinosaur Adventure Land and the leaders of the church group that operates it:

  • In 2004, The Internal Revenue Service raided Hovind’s home and businesses. Agents said Hovind had failed to pay taxes. That case is pending, and federal attorneys declined to comment about it.
  • While the building permit case was in court, the ownership of the theme park was transferred to Stoll, who resides in Washington State, according to court papers. Stoll has been investigated at least twice by federal authorities, court records show.

Last year, the U.S. attorney in Seattle filed a lawsuit against Stoll, charging him with promoting a scheme encouraging people to avoid paying taxes by claiming to be religious entities, according to news reports.

A federal judge ruled against Stoll, ordering him to stop the practices. Stoll said Thursday that he doesn’t recognize the ruling because he was never properly served with court papers.

(via God is for Suckers)


The Cambrian vendobiont S. psygmoglena, gen.sp.nov., composite photo of part and counterpart to show both upper and lower surfaces.

From the pre-Cambrian and early Cambrian, we have a collection of enigmatic fossils: the small shellies appear to be bits and pieces of partially shelled animals; there are trace fossils, the tracks of small, soft-bodied wormlike animals; and there are the very peculiar Edicaran vendobionts, which look like fronds and fans and pleated or quilted sheets. In the Cambrian, of course, we find somewhat more familiar creatures—sure, they’re weird and different, but we can at least tentatively see them as precursors to the modern members of their respective phyla. It’s not surprising, though, that the farther back in time we go, the stranger animals appear, and the more difficult it is to place them in our phylogenies.

So here’s something cool and helpful—it looks like a vendobiont, but it’s been found in the Lower Cambrian fossil beds of Chengjiang. It’s also very well preserved, and has features that suggest affinities to the ctenophores.

[Read more…]

Peter Singer in Salon

These darn philosophers—how dare they make you think, even when you disagree with much of what they say? Peter Singer is one of those infuriating people who sometimes sounds so silly, but still makes a strong case.

He has an interview in Salon—if you don’t want to fuss with their ads, I’ve put an interesting excerpt below the fold. Maybe it’s time for me to get back to vegetarianism…

[Read more…]


If you’ve been wondering where I am today, I’m dyin’ here, man. I’ve been grading freshman essays and quizzes all day long—my eyes are fiery red orbs and my brain is liquefying, but I’ve only gotten about halfway through the massive pile. This is going to be an agonizing week, I can tell…and it doesn’t help that I’m going to have to pack up in the middle and zoom down to Madison to bring my son home for the summer break (maybe I should make him grade some of these papers…).

It also doesn’t help that I put a trick question on the last quiz, one that was trivial to answer if the students had actually done the reading, but there was no way you’d guess it if you hadn’t, and 90% of the students missed it. Hey, gang, Aldo Leopold was writing about the compass plant—how many times did I tell you to read that chapter of A Sand County Almanac? There will be more questions like that from the readings on the final exam, I guarantee you that.

Now I’m all cranky as well as bleary eyed. I think it’s time for me to tune out until tomorrow, when I’ll hit these stacks of papers again.

Favorite corpses

You know you’ve got an interesting blog post when one of your sentences begins, “Two of my favourite corpses…” It’s got cute pictures of dead things, too.

My favorites were actually collections rather than individuals. One set was in a barn loft owned by my aunt and uncle; apparently, the previous owner of their ranch had gone nuts and slaughtered all of his chickens before committing suicide himself. The dead birds had just been left there (the dead rancher had been carted away; my cousins and I had grisly speculations about what he’d look like if he’d been left there, too), and their bodies had mummified in the dry Eastern Washington climate. You could track the course of the massacre by examining their sad little bodies.

Another was near an abandoned barn near our home in Western Washington. Every fall, hunters and skeet shooters would gather there, and we’d hear shotguns going off all the time. We wouldn’t go near the place in the fall—those guys were crazy, drunk, and reckless. In the spring, though, we’d walk the fields around the barn and survey the skeletal remains of the carnage. Among the broken skeet (and a lot of fully intact discs), we’d find the bones of seagulls and killdeer and sparrows and once even an owl—anything that flew by was a target.

Those experiences did leave me with a rather low impression of Men With Guns.

Bill O’Reilly: Pinhead in rose-colored glasses

Bill O’Reilly is upset that little kids are using profanity, and he has a ludicrously sentimental vision of small town America.

OK. That happens every day, all day in the public schools here in New York City. And I know it happens in Chicago and Los Angeles and Boston and Washington, D.C. In any major urban center. It doesn’t happen in the small towns; it happens in the cities. I live in New York. I’m not gonna have my 6-, 7-, 8-, 9-year-old go to a school where they’re saying that stuff in the hallway and the teacher doesn’t do anything about it. You know, private school, that does not happen.

Oh, brother. I grew up in a small town in the 60s and 70s—Kent, WA, population 14,152 (we lived on the edge of town, right near the city limits sign, and I caught the school bus every day right under that message)—and my fellow children were obscenely profane all the time. I now live in an even smaller place, population just a hair over 5,000, and if you want to hear some hair-raising language, walk by the elementary school playground. Heck, I’ve been startled a few times while walking past the Catholic school yard in town. I don’t have much experience with private schools, but I would be very surprised if human nature was much changed by the imposition of tuition (and, come to think of it, some of the most casually explicit chatterers I remember from the old school days were the most well-off kids).

Here’s what real small town America is like: petty, irrational hatreds, intolerance, and vicious smears of anyone who is the slightest bit different, leavened with far too few more charitable individuals. My daughter and several of her friends have been joining in the “Gay? Fine by me.” campaign—basically, they just express support for people with different sexual preferences in a very low key way. How do you think other fine, upstanding Middle American school kids react?

Today was the second Gay-Day. A bunch of us wore our “gay? fine by me.” T-shirts to school. Funny that the first time people didn’t react, but then they went boom this time. It was the standard moronic bashing. Flicking us off in the hall, calling us fags, asking if we were gay, asking why we liked gay people, saying that gay people should be shot, that they aren’t real people.

Bill O’Reilly, bigoted blowhard that he is, probably thinks that kind of thing is just fine, as long as they don’t use the “f”-word*. Personally, I’d rather see kids cussing like sailors as long as they were tolerant of each other’s differences. I’m afraid, though, that small towns aren’t exactly shining beacons of idealistic American values…those progressive values, no less, that are the antithesis of what O’Reilly promotes.