January 30, 2005 - February 5, 2005 Archives

Avida in Discover Magazine

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Our congratulations go out to Carl Zimmer. Discover magazine published one of Carl Zimmer’s articles as a cover article. The article was titled “Testing Darwin” (Published in Discover Magazine Feb 2005)

Zimmer explores the relevance of work on Avida to evolution

One thing the digital organisms do particularly well is evolve.” Avida is not a simulation of evolution; it is an instance of it,” Pennock says. “All the core parts of the Darwinian process are there. These things replicate, they mutate, they are competing with one another. The very process of natural selection is happening there. If that’s central to the definition of life, then these things count.”

The work based on Avida is not well received by creationists who argue that Darwinian theory cannot explain the complexity of life. Although others have already shown that complexity and information in the genome can increase under the processes of variation and selection., Avida has recently been used to address the concept of irreducible complexity. (Note: Mark Perakh has addressed some the ever changing definitions of irreducible complexity in ID’s irreducible inconsistency revisited)

Ernst Mayr

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Sad news:

Dr. Ernst Mayr, the leading evolutionary biologist of the 20th century, died on Thursday in Bedford, Mass. He was 100.

Dr. Mayr's death, in a retirement community where he had lived since 1997, was announced by his family and Harvard, where he was a faculty member for many years.

He was known as an architect of the evolutionary or modern synthesis, an intellectual watershed when modern evolutionary biology was born. The synthesis, which has been described by Dr. Stephen Jay Gould of Harvard as "one of the half-dozen major scientific achievements in our century," revived Darwin's theories of evolution and reconciled them with new findings in laboratory genetics and in field work on animal populations and diversity.

One of Dr. Mayr's most significant contributions was his persuasive argument for the role of geography in the origin of new species, an idea that has won virtually universal acceptance among evolutionary theorists. He also established a philosophy of biology and founded the field of the history of biology.

"He was the Darwin of the 20th century, the defender of the faith," said Dr. Vassiliki Betty Smocovitis, a historian of science at the University of Florida in Gainesville.

In a career spanning eight decades, Dr. Mayr, the Alexander Agassiz Professor Emeritus of Zoology at Harvard, exerted a broad and powerful influence over the field of evolutionary biology. Prolific, opinionated and dynamic, Dr. Mayr had been a major figure and intellectual leader since the 1940's. Setting much of the conceptual agenda for the field, he put the focus just where Charles Darwin first placed it, on the question of how new species originate.

Though Dr. Mayr will be best remembered for his role as a synthesizer and promoter of evolutionary ideas, he was also an accomplished ornithologist. In fact, it was with the sighting of a pair of very unusual birds that Dr. Mayr's long career in biology began in 1923 at 19.

I am gathering up transcripts of television segments that deal with evolution, and I need some help. I watch a truly ludicrous amount of television, and follow the cable news chat shows pretty closely, but I'm sure there are many segments out there that I have missed. I'd appreciate it greatly if people could provide links to television segments they might have seen in the last few months.

Truth in advertising: IDEAcenter

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FAQ: Why isn’t intelligent design found published in peer-reviewed science journals?

Before reading further, we recommend that if you are interested in seeing the scientific underpinnings of intelligent design, that you read our article, “The Science Behind Intelligent Design to become familiar with the scientific basis for intelligent design.


I have a request from Benjamin Temchine, a producer with the program Your Call on KALW in the bay area—it's a daily political affairs and cultural call-in show. He is looking for teachers who are facing increasing difficulties in teaching evolution in the way they feel is scientifically justified, and would like to interview you live on the program on Monday, 7 February, at 10-11 AM PT, 1-2 PM ET. If you are interested in being interviewed, call him at (415) 516-5971.

The rest of us can also call in and give our opinions during the show at (866) 798-TALK, and listen in via the KALW RealAudio stream. Except for me, darn it. That hour is right in the middle of my lecture, and I think I'll be talking about codominance and blood antigens at that time.

This is a cautionary tale about the dangers of leaping to grand conclusions on the basis of hearsay. It started back with the publication of Stephen Meyer's article in the August 2004 issue of the Proceedings of the Biological Society of Washington, which we took note of in the post Meyer's Hopeless Monster. In that post, we considered the political ramifications of that publication, leading us to say then:

The important issue is whether or not the paper makes any scientific contribution: does it propose a positive explanatory model? If the paper is primarily negative critique, does it accurately review the science it purports to criticize? The fact that a paper is shaky on these grounds is much more important than the personalities involved. Intemperate responses will only play into the hands of creationists, who might use these as an excuse to say that the "dogmatic Darwinian thought police" are unfairly giving Meyer and PBSW a hard time. Nor should Sternberg be given the chance to become a "martyr for the cause." Any communication with PBSW should focus upon the features that make this paper a poor choice for publication: its many errors of fact, its glaring omissions of relevant material, and its misrepresentations of the views that it does consider.

But martyrdom of Sternberg has been a topic of discussion for the past week... and the person accused of martyring him, Jonathan Coddington, has spoken out in a comment posted to a thread here on Panda's Thumb.

Doing Things With Words quotes a beautiful example from Carl Sagan:

Most curious is [Kepler's] view of the origin of the lunar craters, which make the moon, he says, "not dissimilar to the face of a boy disfigured by smallpox." He argued correctly that the craters are depressions rather than mounds. From his own observations he noted the ramparts surrounding many craters and the existence of central peaks. But he thought that their regular circular shape implied such a degree of order that only intelligent life could explain them. He did not realize that great rocks falling out of the sky would produce a local explosion, perfectly symmetric in all directions, that would carve out a circular cavity--the origin of the bulk of the craters on the moon and the other terrestrial planets. He deduced instead "the existence of some race rationally capable of constructing those hollows on the surface of the moon. This race must have many individuals, so that one group puts one hollow to use while another group constructs another hollow."

At least the Discovery Institute can take solace from the fact that they've now actually been compared to a scientist. It's far more flattering than they deserve, even though it was a scientist who was wrong

Robert Crowther from the Discovery Institute’s Media Complaints Division seems to be quite content to reference an ID friendly blogsite by Denyse O’Leary

If misreporting were a concern to Robert, he would certainly have pointed out the various problems with Denyse’s arguments. But like ‘teach the controversy’, it seems that correcting errors in reporting is mostly one sided.

Some of you may be wondering why none of us Thumbites have commented on David Klinghoffer’s op-ed about Richard Sternberg filing a complaint with U.S. Office of Special Counsel claiming discrimination at the Smithsonian. We have discussed it at length, but there is too little information to form an opinion about the complaint.

Is it possible that the Smithsonian over reacted to Sternberg’s abuse of his editorial power at PBSW? Sure. It is also possible that they didn’t. Although, Klinghoffer makes clear his opinion, he has failed to provide enough information in his op-ed to objectively determine and judge what has happened.

Because of the way the law typically works, it will probably be impossible to get the Smithsonian’s side of the story. Sternberg and his supporters can say virtually whatever they want to the media, and Smithsonian will have little ability to set the record straight. (The Discovery Institute’s Media Complaints Division will be of little help.)

However, it is interesting to note that Sternberg is a staff scientist for NCBI/NIH and is not employed by the Smithsonian. He is a research associate, which is an unpaid, “formal scholarly affiliation” with the Smithsonian. Since he is not an employee, he might not even be protected by the OSC.

Who can be protected by the OSC from prohibited personnel practices?

[u]General[/u]. OSC has jurisdiction over prohibited personnel practices committed against most employees or applicants for employment in Executive Branch agencies and the Government Printing Office.

Sponge relationships

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Sponges have been in the news lately, so how could I resist writing about a recent paper on sponge relationships? Sponges (phylum Porifera) are found in three classes: the Demospongia, the Calcarea, and the Hexactinellida, all of which are quite ancient with forms identified from the Cambrian. Fossil sponges can be identified by the arrangement of their skeletons, which consist of collections of spicules with characteristic shapes and chemical constitutions. Spicules of various sizes are organized into an interlocking meshwork that generates the supporting framework of the animal. Two characteristics of the spicules that are used to classify them are 1) shape, in particular the angle that the rays diverge from one another, and 2) the chemical structure, whether they are based on calcium or on silicon.

  • Demospongia. Spicules are siliceous, with a triradiate symmetry—the spicule rays typically diverge at 60° or 120°. Individual spicules may look like a caltrop, with points to the corners of an imaginary tetrahedron.
  • Calcarea. Spicules are made of calcite, with a triradiate or tuning fork shape.
  • Hexactinellida. Spicules are siliceous, with a hexactine or tetraradiate symmetry—the spicule rays diverge at 90° angles. Picture a child's set of jacks clustered together.

Our understanding of the relationships between these three, however, has been getting juggled about. My copy of Clarkson's Invertebrate Palaeontology and Evolution, for instance, groups the Demospongia with the Calcarea in the subphylum Gelatinosa on the basis of the organization of the soft tissues and spicule shape, and sets the Hexactinellida apart in the subphylum Nuda, while admitting that there are complications that make the groupings prone to radical revision. One alternative is to group them by whether their spicules are made of calcareous or silicaceous, which would mean that the Hexactinellida and Demospongia are sister lineages, with the Calcarea the odd man out.

Bitting and Butterfield are attempting to resolve these relationships by examining a Cambrian sponge, Eiffelia globosa. Eiffelia is a member of a somewhat problematic group of sponges called the heteractinids which have been classified in the Calcarea because they have spicules made of calcium carbonate, and hexaradiate spicules that are at least close in shape to those of calcareans. What the authors suggest, though, is that Eiffelia is actually a good transitional form that also has tetraradiate spicules and two mineralogically distinct layers to their spicules that may represent both a calcareous core and a silicaceous outer rind.

Continue reading "Sponge relationships" (on Pharyngula)

Check out Darwinsucks.com:

Welcome to Darwin Sucks Where we fish for the truth on the theory of evolution

Before you visit, make sure you:

  • Turn up your speakers
  • Read a bit about the bacterial flagellum
  • Remember, the theory of relativity is just a theory
  • Ponder the fact that the earth-sun distance varies about 3.4% within a single year. How many million miles this represents will be left as an exercise for the reader

An important story on the front page of Tuesday’s New York Times Science section documents the widespread phenomenon of teacher self-censorship – teachers avoid the “E-word” because of pressure from parents or administrators. The story is by Cornelia Dean. Here is the story: “Evolution Takes a Back Seat in U.S. Classes.” See discussion/commentary at NCSE News, Jason Rosenhouse’s EvolutionBlog, Pharyngula, and Chris Mooney’s blog.

But, the most entertaining comments were over at the Discovery Institute’s Media Complaints Division. See especially the bit about “the local amateur hour”:

Irony of the Month

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From the Thomas More Law Center, which is defending Dover, PA’s inclusion of intelligent design in biology class:

According to Richard Thompson, President and Chief Counsel for the Law Center, “It’s a common tactic for the ACLU to pile-on plaintiffs to give the impression that more people support their position than actually do. In this case, a recent poll of Dover residents shows that a majority support the school district.”

Christian Wire Service: Court Asked to Dismiss Several Plaintiffs From Evolution Lawsuit

Francis Beckwith has an article about the Cobb County disclaimer case in Legal Times which is misleading and alarmist. According to Professor Beckwith, the decision is a threat to religious tolerance. Nothing, however, could be further from the truth.

Nazis, Nazis all …

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Former chemist and professional creationist Jonathan Sarfati of Answers in Genesis Ministry continued today in the decades old creationist tradition of trying to directly equate evolutionary biology with the Nazis. In an article for The Conservative Voice, called “The Holocaust and Evolution”, Sarfati accuses biologists and science educators of complicity with, if not out and out responsibility for, the Nazi Holocaust, and the Columbine High School killings.

I normally do not read posts on Access Research Network (ARN). Sometimes, though, some of my colleagues point to certain curious posts there and in such rare cases I briefly look them up. Such was the occasion a few days ago when a contributor to ARN advised about a funny exchange of posts on ARN with the participation of William Dembski.

That consistency is not William Dembski’s forte is not news. However, once in a while this inordinately prolific propagandist for intelligent design offers notions that are so obviously contrary to others of his own notions that one wonders whether Dembski is serious or his opuses are spoofs designed mainly to attract attention to his voluminous output. Also, it is funny that there is a bunch of Dembski’s admirers (such as, for example, Salvador Cordova) always ready to spin his notions in a positive light, often doing that in a truly acrobatic manner.

A group of eight ID/creationists on the Kansas state science standards committee recently submitted a proposal for revisions to the first draft of the standards that are a mishmash of typical claims: science needs to not be limited to natural explanations, “origins science” is different because we can’t really observe the past, common descent and macroevolution are unproven and in doubt, and so on. (The proposal can be found here)

Fortunately, at the science standards meeting last Thursday all but one of the ID proposals were rejected by committee vote (and the one was a reasonable suggestion.) Reporters from all over the state (and from the London Times) were at the meeting: you can read newspaper reports here at the Salina paper, here in Topeka, here from the AP, and here this morning in the London Times.

However, one interesting part of the story has gone unpublicized: committee chairperson Steve Case received responses to the ID proposal from a number of quite respectable and reputable scientists, all of whom gave the committee permission to make their responses public.

Consequently, Kansas Citizens for Science is putting these papers on our website: visit KCFS: Standards 2005 to see reviews by * Joe Heppert, University of Kansas * Kenneth Miller, Brown University * Robert Dennison, Texas biology teacher * E.O. Wiley, University of Kansas * Taner Edis, Truman State University * Gary Hurd, Ph.D. * Douglas L. Theobald, University of Colorado at Boulder * Scott Brand, University of Alabama at Birmingham * Patricia Princehouse, Case Western Reserve University

I don’t have time to summarize the results here, but this all makes pretty interesting reading - there are some pretty scathing and on-target remarks here. The IDnet’s proposal is quite a bit more thorough and extensive than any of the disclaimers or policies that have been in the news elsewhere recently, and so it provides more specific issues to respond to. Enjoy.

Icons of ID: Apples and Oranges

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On ARN Mike Gene is arguing, amongst others, that there is a similarity between the publication of Meyer’s paper in PBSW and Pennock’s paper in Annual Review of Genomics and Human Genetics. Mike is wrong.

When the Meyer paper came out, the critics began to complain the Meyer paper was a drastic departure from the traditional focus of the journal. Now that we can see how the Pennock paper undercuts this complaint, we finally get some ad hoc rationalizations. I am utterly unswayed by Myrmecos’ attempt to argue one is a drastic departure from the traditional focus, while the other is not.

The hugely successful Media Complaints Division at the Discovery Institute Center for [the Renewal of] Science and Culture already covers the major land masses of three medium sized planets and is the only part of the Institute to have shown a consistent growth in recent years.* Just last week, Time magazine reviewed the various recent attempts by creationists and “intelligent design” advocates to force public schools to misinform students about the scientific status of modern evolutionary theory (see previous PT post). The DI Media Complaints Division, working overtime this week, put extra effort into complaining about the Time article (DI #1, DI #2).

For good measure they have been complaining about the “Legacy Media” in general. (I think that somebody at the Media Complaints Division flipped a switch and activated a microchip telling all employees to insert “Legacy Media” wherever a normal person would say “the media.”) Strangely, all this talk about the “Legacy Media” temporarily disappeared on Friday, when a pro-ID opinion piece (probably wildly inaccurate – we’ll see what the other side says) appeared in the Wall Street Journal with the apparent purpose of attempting to incite a witch hunt against the rabid pack of herpetologists, acarologists and cephalopodologists (especially those crazy cephalopodologists) at the Smithsonian. So I guess the media is only “legacy” when they aren’t trumpetting your cause. But really, who cares about self-consistency and favoring honesty over spin when you are trying to get good coverage from the media? (Except maybe the media, which has a tough time with complex science but which can sniff spin from 100 feet away – but remember, they’re just the “Legacy Media.”)

But you haven’t seen anything yet. With the publication of a longish story on the various ID battles in the February 7 issue of Newsweek, the DI Media Complaints Division might have to expand onto a fourth medium-sized planet.

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