March 4, 2007 - March 10, 2007 Archives

RNA Designed to Evolve?

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On Uncommon Descent, JohnnyB states that

I’m currently working through Robustness and Evolvability in Living Systems, and came across the following information which seems to be right in line with Denton’s evolution by natural law ideas:

A final, especially counterintuitive feature of RNA sequence space is that all frequent structures are near each other in sequence space. Consider a randomly chosen sequence that folds into a frequent structure and ask how far one has to step away from the original sequence to find a sequence that folds into this second structure…For instance, for RNAs of length n = 100 nucleotides, a sphere of r = 15 mutational steps contains with probability one a sequence for any common structure. This implies that one has to search a vanishingly small fraction of sequence space…to find all common structures.

Yes, laws of nature have indeed led to RNA space being extremely suitable for ‘evolution’ due to its scale free nature. Of course, scale free networks have been shown to be able to arise from the simple process of duplication and preferential attachment. And that’s exactly what we observe in for instance gene duplication. In other words, johnnyb has once again observed how the designer is quite natural, reducing even further ID’s standing and underlining ID’s scientific vacuity as it provides NO explanations as to why, how etc. Unlike science.

I have discussed these fascinating properties of RNA space and the topic of evolvability in many postings at PandasThumb. It’s good to come to realize that some IDers are actually reading scientific research, even though accepting scientific explanations completely undermines ID’s attempt to hide in ignorance. JohnnyB also gives me some hope that IDers, properly exposed to real science, will quickly reject Intelligent Design as scientifically vacuous.

The Cincinnati Post has a story about the possibility that AiG’s creation science museum will encourage religious groups to hold conventions in the Cincinnati area. No word yet on whether it will discourage the realty base community from coming to Cincinnati as well.

But I guess that, with Kent Hovind in jail, AiG is going to have to pick up the slack in the mis-education of America.

Those who haven’t had the experience of reading Dr. Egnor’s contributions to the creation/evolution conflict will not know that he is a neurosurgeon at Stony Brook who has trumpeted his support for intelligent design and against evolution. Dr. Egnor has recently written an essay at the Ministry of Media Complaints of the Discovery Institute. Ever on-message, Dr. Egnor seems to think that doctors don’t need to know evolution because he objects to the Alliance for Science’s essay challenge. (Alliance for Science asked high schoolers to write an essay entitled and organized around the thesis, “Why would I want my doctor to have studied evolution.”)

Dr. Egnor has been the subject of multiple fiskings recently and this is a curiosity itself. I’m personally acquainted with at least four attending-level physicians who were creationists at the University of Kansas School of Medicine. Up at Minnesota, a chief resident in the department of surgery was a creationist. And now at Penn State, there’s at least one creationist. The Discovery Institute, fresh off their defeat from Dover, put a lot of effort into developing a five-page list of physicians who think evolution isn’t such a big deal - so why is Egnor getting all the infamy for his incredulity? I don’t have a good answer for that: maybe he’s just the DI “Flavor of the Month” or the only physician willing to write essays. What I can answer are Dr. Egnor’s claims that evolution is not needed in medical school.

And I’ll do it on the flipside.

God Creates a Kitten.

kittens500.jpg

Happy Half Century, PZ.

I find it interesting that despite several articles on the confluence of science and blogs in science magazines and journals and the establishment of blogs by many mainstream science news outlets, the AAAS’s EurekAlert! refuses to grant embargo credentials to bloggers. As Dr. Hsien Hsien Lei of Genetics and Health was recently told:

I appreciate your email, Hsien, but unfortunately, the decision must stand. Our eligibility criterion does not include writing blogs of any kind. Feel free to re-register in the future, should your writing outlets expand.

Did you get that? Blogging is a narrow outlet. I guess AAAS doesn’t think that thousands of daily readers is a broad enough audience to promote their articles. I guess such an derision of Web 2.0 might explain why PLoS has been successfully cutting into Science’s market.

How about we show EurekAlert! that there is a market out there for blog-based science news? I suggest that all the science bloggers out there, who read this, go apply for journalist access to EurekAlert!. Just fill out this form and mention your position as a blogger. Don’t forget to leave a comment here about your experience.

Hat Tip: Coturnix

Update:

In the comments, Ginger Pinholster, AAAS’s director of public programs, has clarified their position. It looks like those of us with dual affiliations, e.g. scientist-bloggers, are out of luck.

Our local “Dissenter from Darwinism,” Fred Skiff, gave a talk last Friday. Prior to the talk, I predicted:

One, that Skiff will provide a strawman version of evolutionary theory (heck, and science itself) as he did last time I saw him speak… Two, that Skiff will assert or imply that evolution implies atheism, and that if one accepts methodological naturalism, one therefore must also accept philosophical naturalism, and choose between evolutionary theory and their religious beliefs. Three, that he will assert that “intelligent design” is the sensible alternative to “orthodox” science, but its study is being repressed by “Darwinists” or something of that nature.

All I gotta say is: damn, I’m good. In a bit of what I assume was unintended irony, Skiff was introduced with a comment noting that discussions about intelligent design frequently generated “heat” but not a lot of “light,” after which Skiff spent much of his time railing against “Darwinists” and “Darwinism,” creating a strawman presentation of evolutionary biology, misinforming about theRichard Sternberg case, claiming that supporters of evolution were out to make it “illegal to question Darwinism” and that the National Center for Science Education (NCSE) has said to “destroy intelligent design by ruining reputations.” Is it any wonder Skiff receives a lot of heat after inflammatory rhetoric such as that? A summary of the rest of the talk is over at Aetiology.

I know that SUNY Stony Brook has a great evolutionary biology program. That being said, the ignorant rantings of neurosurgery professor Dr. Michael Egnor have to be an embarrassment to Stony Brook. Orac, a surgery professor himself, gives Egnor another drubbing over the incredulous comments he made on a recent Discovery Institute pod cast.

Just when I thought I could put the paper bag away…

…That all around evolution-ignorant but nonetheless eager lapdog of the Discovery Institute, SUNY Stonybrook Professor of Neurosurgery Dr. Michael Egnor, is back.

Rats. I thought that the utter drubbing he took at the hands of myself and my fellow ScienceBloggers (in particular PZ Myers) might have given him the message that he needs to lay low for a while. Apparently not. I guess he must have the monumental ego that more than a few neurosurgeons are famous for. (After all, it takes supreme confidence in one’s own abilities to be able to cut into the human brain and believe that the patient will come out OK.) It’s not enough this time for him to show up in the comments of PZ’s blog to make a fool of himself and embarrass scientific surgeons everywhere. This time around, he’s appearing on the Discovery Institute podcast, to be interviewed by fellow DI lapdog and sometimes attack poodle Casey Luskin in a a truly nauseating lovefest entitled, One Doctor’s Journey to Becoming a Darwin Doubter:

Not surprisingly, basically all Dr. Egnor’s “critique” of “Darwinism” boils down to is his personal incredulity that biological complexity could ever possibly have evolved from more simple elements without the input of intelligence, his anthropomorphizing the genetic code, and his concluding that, because the genetic code functions like a human language and because human language is created only by the “intelligent design” of humans, then the genetic code must have been intelligently designed. That’s it. No data supporting his position, just his “doubts.” His propensity to equate “randomness” with “meaninglessness” also strongly suggests the religious, not scientific, roots of Egnor’s “skepticism” about “Darwinism.”

Read the Entire Piece

Over at The Loom, Carl Zimmer discusses some interesting research on the origin of crabs, not the tasty kind but the ichy-bitey kind.

Question of the Day: How Do You Get Crabs From A Gorilla?

The scientists set out to recover the evolutionary tree of pubic lice, just as they had done with head lice. They analyzed DNA from human head lice, human pubic lice, as well as other species from the same genera that live on chimpanzees and gorillas. They also analyzed DNA from lice that live on monkeys and on rodents so that they could get a better sense of how pubic lice had evolved from a common ancestor with other species. The scientists not only drew branches for each species, but also estimated when those branches split over the course of history.

Their conclusion, which they published today in BMC Biology, is just as striking as their earlier one about head lice. But it is hardly the same. We did not get pubic lice from other hominids. We got them from the ancestors of gorillas.

Make sure you don’t miss this YouTube video on a visit to the now-closed Dinosaur Adventure Land, home base of convicted felon Kent “Dr. Dino” Hovind. It’s not exactly film festival material, but there are a lot of interesting tidbits.

HT: Pharyngula

An interesting phenomenon I have observed lately is that now that many Kent Hovind videos are on YouTube, a whole new group of people is realizing just what a wacky dude he was, and just how wacky it is that he is probably the most-known and quoted authority among the creationist public. Check out the Hovind-alia on YouTube (if you have an afternoon to kill…the stuff is strangely addictive).

Here's an interesting opportunity: Lynn Margulis, the controversial scientist, is going on a 'blog tour' to promote her new imprint of science books called Sciencewriters Books. What does that mean? She's going to hang out for a little while on a few blogs and chat and answer questions. If you've wanted to have a conversation with the author of the endosymbiont theory and critic of neo-Darwinian theory, here's your chance.

The tour will kick off on Monday, 12 March, at Pharyngula. She'll be sending me a short article that I'll post that morning, and we'll collect comments and questions. Later that afternoon or evening, she'll browse through those comments and answer the ones she finds interesting.

In addition, she'll be available in the Pharyngula chat room (channel #pharyngula on irc.zirc.org; if you don't have an IRC client, that link will let you use your browser to join in) from 12:00-1:30pm ET.

So mark it on your calendars: an online conversation with Lynn Margulis, next Monday, 12 March, at Pharyngula.

William Grassie, founder of the Metanexus Institute and the man in charge of the grant program for the Templeton Foundation under which Dembski received the grant that ended up being for No Free Lunch, has responded to Dembski’s posting of the grant proposal he made to receive the money. And there are several statements in this response that are very interesting. Like this one:

Continue Reading at Dispatches from the Culture Wars. Comments may be left there.

Good news from Idaho

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This good news comes from Idaho’s Science Teachers Association who have approved an official position against teaching intelligent design in Idaho’s public schools.

Ironically, Idaho’s Science Teachers Association has a website at the address “idscienceteachers.org” :-)

The Christian Post reports

In Idaho this past weekend, science teachers officially noted that they will not allow the instruction of intelligent design in their school systems.

The Idaho Science Teachers Association supported their position by saying that intelligent design, an opposing conjecture to evolution theory, is not approved by the scientific community, so it has no place being taught as a science.

“It basically would be unethical to teach creation science or intelligent design because it is not science, and it does not belong in a science classroom,” said Rick Alm, president of the ISTA’s board, in the Idaho Statesman.

I have another observation in pop culture’s war on ignorance. (Okay, that is an oxymoron.)

On tonight’s Family Guy, “Airpot ‘07“, Peter attends “The Redneck Comedy Tour” and decides that he wants to become a redneck. So he buys a pick-up truck, puts the couch on the front lawn, and hits on his daughter. Then he sits down with Brian to watch Carl Sagan’s Cosmos.

Scene: Brian and Peter are on the couch watching TV. Peter is wearing cowboy boots, jeans, large brass belt buckle, flannel shirt, and a green John Deere cap.

TV Announcer: We now return to Carl Sagan’s Cosmos … edited for rednecks.

Sagan on TV (occasionally dubbed over by a redneck voice): I’m Carl Sagan. Just how old is our planet. Scientists believe its four b—hundreds and hundreds of years old—Scientists have determined that the universe was created by a—Goooooooood—Big Bang. If you look at the bones of a—Jesus–asaurus rex, it is clear by the use of carbon dating that—Mountain Dew is the best soda ever made.

Brian: Peter, do we have to watch this?

Peter: This is what rednecks watch, Brian.

Peter takes a can of chewing tobacco from his shirt pocket and begins to dip.

Of course, carbon dating cannot be used on the fossils of a “Jesusasaurus rex”; other forms of radiometric dating with longer half-lifes have to be used.

Update: Below the fold, I’ve posted the scene from YouTube. Thanks Chris Hyland.

Hi all,

Last weekend I meet a few friends for lunch in Raleigh’s Cameron Village. We had a great time sitting out side drinking coffee and eating sandwiches. I really want to do it again, both in Raleigh and other great towns. On that note, I’ll be tagging along with Evolgen’s RPM to the Fly Conference in Philadelphia next week. If any of my fans will be at the conference or just in the area, go drop RPM a line and see if we can meet up for cheese steaks and bamboo beer.

Now for some pictures of the Raleigh meetup. [Note: You can find many of my pictures in my gallery, including ones from the Science Blogging Conference, where many people were begging me for photos.]

nic_george.jpg

Nic George, a postdoc at NCSU, is agreeing here to be my vassal. I made him a offer he couldn’t refuse.

I wrote back in December about Prof. Steven Gey, one of the great advocates for evolution and quality science education in the nation, being diagnosed with ALS. A group of his colleagues and students have decided to run a triathlon to raise money for ALS research. You can help them reach their goal of raising $10,000 in the event by going to this page and clicking on “donate now” on the right hand side. Prof. Gey was one of the attorneys who represented the winning side in the landmark 1987 Supreme Court case Edwards v Aguillard. He has been a tireless worker on behalf of protecting science education ever since. This is a small way we can help repay all that he has done in helping us reach our goals.

Briant Trent, professional essayist, screenwriter and novelist, reports in the American Chronicle on a question he asked Intelligent Design proponent Jonathan Wells during the Cato Insitute sponsored debate between Shermer and Wells.

His simple question, and Wells’ answer shows the scientific vacuity of Intelligent Design. So what was the question? Brian asked Wells what his alternative to the evidence for natural selection was

“I don’t think I’m obligated to propose an alternate theory,” Wells publicly stated. “I don’t pretend to have an alternate theory that explains the history of life.”

It would come as no surprise to us here at the Thumb that our readers would accept a physician not giving antibiotics for an ailment unless that physician felt that the infection was bacterial, that the therapy was warranted, and that the selection of antibiotics was appropriate for the suspected organism. Doctors restrict their antibiotic use because of evolution: indiscriminate use of antibiotics leads to the evolution of resistance to those antibiotics in those bacteria that survive the infection. I suspect many of our readers also know that antibiotics are given to livestock routinely to help them grow bigger, faster. Our friends at ScienceBlogs are all over this topic and the problems it presents. By way of summary, if you give animals an antibiotic that looks and acts like one you give humans, resistance will also evolve there, just as surely as it will from a doctor who reaches for his prescription pad before he’s taken an adequate history or completed an adequate exam.

This morning’s Washington Post has a disturbing article on the approval of cefquinome for use in cattle. It’s disturbing for a number of reasons, and we’ll discuss them on the flipside.

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