January 23, 2005 - January 29, 2005 Archives

Howdy folks.

Here are links to some recent articles supporting KNME’s decision not to air the creationist ‘infomercial’, “Unlocking the Mystery of Life.” Cheers, Dave

KNME Put Lock on Infomercial (N.M. Academy of Science )

The reason ID supporters want “Unlocking” shown on public television instead of religious stations is that they want the implied “seal of approval” that comes with being aired on KNME. They want to ride the coattails of PBS programs such as “Nova” and “Nature.” They want the respect given modern science, but they have not earned that respect in the science community.

Albuquerque Tribune Editorial: KNME did right thing to pull ‘science’ show

Journalists recognize the techniques in the program as “spinning” - in this case enlisting peer-reviewed science in making the case for an idea that hasn’t been submitted to the intense rigor of that same peer-review process. Intelligent design so far has failed to meet the most basic of scientific standards.

KNME is a precious community, regional and national TV resource. In this decision, it affirmed worthy and cherished values of public broadcasting. In adhering to those values, it deserves the support of Albuquerque and other New Mexico citizens.

Crosswinds Weekly: “Posing as science” by Steve Lawrence (will be over-written after this week…)

New Mexico’s largest public television station, KNME (channel 5), remains under fire for refusing to air an ersatz documentary that pushes creationism as science.

It is apparently well known that Albuquerque’s Public School administrators have refused to fire a high school science teacher nicknamed “Six-thousand-year Phil” who teaches his science students that the earth is only 6,000 years old. His proof? The Bible says so.

Previously on The Thumb:

Albuquerque PBS Station Under Fire by Creationists

The Discovery Institute’s Strange Allies (Jan. 21, 2005)

Today, Representative Ben Bridges of the Georgia House, introduced a bill, HB 179, that would require evidence against evolution be taught in Georgia’s public schools whenever evidence for evolution is taught. (However, his fairness is a one-way street.)

Word has it that the Republican leadership will not support the bill, which ensures it will have a short life.

The news is fresh, but it should be covered by the evening news and tomorrows papers. The only story on it so far is a short one.

I’ve gotten a hold of the meat of the bill and addressed it on my blog, De Rerum Natura.

Read it atGA HB 179: Bridges’ Ding Bill.”

Promiscuity in Evolution

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No, this is not another post about the sexual habits of female apes. This is about enzymes, and their ability to catalyze different reactions with different substrates, even those that aren’t found in nature. It’s a property known as “promiscuity”, one that’s being increasingly recognized as important in enzymology and enzyme evolution.

The usefulness of enzymes derives in part from their specificity, in that they don’t just catalyze any old reaction with any old substrate. It would be hard for cells to maintain homeostasis if enzymes were highly nonspecific; helpful reactions would be coupled with harmful side reactions, regulation would be impossible, and things would get messy real quick. So it’s useful for enzymes to specialize in certain functions so that they can be applied for specific tasks at specific times. But because nature is a bit sloppy, enzymes are often able to catalyze many reactions weakly in addition to the “native” functions that they specialize in. These additional weak activities are referred to as promiscuous activities, and they’re potentially very important in enzyme evolution. Now a recent study (subscription required) published in Nature Genetics by Amir Aharoni and coworkers sheds some light on why enzymes are promiscuous, and what it means for their evolvability. (There is some good non-technical commentary on the paper here and here.) It also badly knocks down some bold claims made by leading ID proponents.

Modeling metazoan cell lineages


A while back, I criticized this poorly implemented idea from Paul Nelson of the Discovery Institute, a thing that he claimed was a measure of organismal complexity called Ontogenetic Depth. I was not impressed. The short summary of my complaints:

  • Unworkable idea: There was no explanation about how we could implement and test the idea, and despite promises at the time, Nelson still hasn't produced his methods.
  • False assertions and confusing examples: He claims that all changes in early lineages are destructive, for instance, which is false.
  • Bad metaphors: He uses a terribly flawed metaphor of a marching band to explain how development works; I'd say that it's a better example of how development doesn't occur.
  • No research: Which is really a major shortcoming for a research program, that no research is being done.

Recently, Nature published a paper by Azevedo et al. that superficially might resemble Nelson's proposal, in that it attempts to quantify the complexity of developing organisms by looking at the pattern within their early lineages. The differences are instructive, though: this paper clearly explains their methodology, presents many of the limitations, and draws mostly reasonable conclusions from the work. It is an interesting paper and contains some good ideas, but has a few flaws of its own, I think. My main objections are that its limitations are even greater than the authors mention, and there are some conclusions that are driven by a strongly adaptationist bias.

Continue reading "Modeling metazoan cell lineages" (on Pharyngula)

Morris on Dembski

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William Dembski's book, The Design Revolution, has attracted the notice of the Institute for Creation Research. Henry M. Morris has a brief review and critique in the February 2005 issue of Back to Genesis titled "The Design Revelation".

That makes a score of Tangled Banks!

The Tangled Bank

It's another Tangled Bank at Jasmine Cola—these things just seem to grow and grow, and there's a pile of stuff to read over there.

The next event will be hosted at About Town on 9 February. Send links for the next edition to me, to host@tangledbank.net, or to Xavier.

Another Tangled Bank is almost upon us

The Tangled Bank

Another Tangled Bank will be appearing at JasmineCola this Wednesday. Have you sent a link to your science writing to host@tangledbank.net, PZMyers, or using the contact form at JasmineCola yet? You're running out of time!

If you've never heard of this strange Tangled Bank thing, check out the description at the Tangled Bank homepage, where you'll also find many links to other science articles on the web.

Creationists often dismiss examples of evolutionary change as “that’s just a loss of information.” There are many problems with this claim (see also here and here), but here is a new one: it appears that in at least one case, humans evolved by “loss of information” (in this case, loss of a gene) from their apelike ancestors. Carl Zimmer mentions this in passing in a post on the cell-surface sugars, Neu5Ac and Neu5Gc:

A new article in Time Magazine just came across my bloglines account.

Stealth Attack On Evolution” was on the whole a decent article. I am sure the Discovery Institute will carp anyway, even though they get quoted and even get their list of 300+ scientists cited (translation: 300+ scientists signing on to an extremely vague statement not even supporting ID, and with only 4 Steves), because they will be annoyed that the the article points out the fact that this represents a miniscule proportion of the scientific community.

One passage in the Time article was particularly groanworthy:

They [evolutionary biologists] developed the theory of punctuated equilibriums, for example, to address the fact that species remain unchanged for long periods, then suddenly start evolving.

“Equilibriums”? Eh? And most everything else about the sentence is wrong, also. How hard would it be for a journalist to say,

By the 1940’s, biologists had synthesized Darwin’s natural selection and Mendel’s genetics into the discipline of population genetics, the mathematical theory describing how genes spread through populations under the influence of natural selection. A finding from population genetics was that small populations can evolve more rapidly than large populations, and this finding, along with extensive field observations, were combined to produce the theory of allopatric (geographically localized) speciation. In 1972, Gould and Eldredge applied these results about speciation to the fossil record, producing the model of “punctuated equilibria.” They argued that if speciation was typically allopatric, the fossil record would most commonly record only widespread species, and that these would typically evolve slowly. New species (closely related to the old species) would tend to evolve in small, isolated populations, and then spread. They would therefore appear “suddenly”, geologically speaking. Punctuated equilibria therefore predicts that species-species transitions involving whole populations would tend to be relatively rare in the fossil record. It specifically did not say that “transitional fossils” in general are absent. Gould, annoyed at creationist misrepresentations of his position, specifically said in rebuttal, “Transitional forms are generally lacking at the species level, but they are abundant between larger groups.” *

Sigh. Well, I can dream, can’t I?

Psychologists tell us that one of the primary manifestations of guilt is to accuse others of doing what one is guilty of themselves. This is why, for instance, a cheating husband will often exhibit jealous paranoia about his wife cheating on him, and vice versa. They know the lies that they've been telling, so they continually presume that they are being lied to as well. For a perfect illustration of this phenomenon, look no further than the recent obsession of ID apologists like Casey Luskin with Nazi comparisons in the ID/evolution dispute. While howling in feigned outrage at the terrible unfairness of such comparisons, they ignore the fact that such comparisons have been used by them and their colleagues for constantly for years. The latest example is John West's post on the DI blog, complaining about a comment made by Jeffrey Selman, the plaintiff in the Cobb County case. He writes:

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