March 2007 Archives

Dr. Michael Egnor is creationist neurosurgeon at SUNY Stony Brook—an embarrassment to that fine institution, I’d imagine—and the most recent addition to the Discovery Institutes’s roster. He is well known in the blogsphere for his ability to make the most illogical and obviously factually incorrect claims in an effort to discredit “Darwinism”. (Okay that is not actually a novel phenotype among the creationists and intelligent design activists.) For example, he actually argued that evolution had nothing to do antibiotic resistance, a Hovindesque argument. (Hopefully, Egnor pays his taxes and is not a complete Hovind imitation.)

Fact checking doesn’t matter when you are as arrogant as Egnor. In a memorable exchange, he argued that evolution was not important to medicine because not a single medical school had any classes or professors dealing with evolution. When it was shown that there was an entire evolution graduate program in his own medical school, he then argued that the existence of such programs doesn’t prove that evolution is important to medicine, ignoring completely what his original argument was. What rational man can make both these claims while completely ignoring the connection? I dubbed such an egotistical combination of ignorance and arroganceegnorance”.

But Egnor is simply unable to control his egnorance. He continues to write for the Discovery Institute, each time justifying the gift of his name to “egnorance”.—He is like a junky, except his addiction isn’t crack but making a total jackass out of himself.—In his latest pair of posts he is on roll, inventing fictions about history to illogically argue that because at some point in history someone didn’t use evolution in medicine or genetics, then evolution is not important to how those things are studied today. It is like arguing that, because Hippocrates didn’t practice neurosurgery, neurosurgery is dispensable to medicine.

Now Pat and PZ have handled this inept pair of posts; however, I want to one additional point in regards to the most recent one. According to Egnor,

… Darwin’s assertion that random variation was the raw material for biological complexity was of no help in decoding the genetic language of DNA.

Egnor is completely and utterly wrong. This is a total distortion of the actual research that went into determining the genetic code. The research program of Crick, Brenner, Benzer, and colleagues relied heavily on applying Darwinian principles (random mutation and selection) to model organisms. Specifically, they isolated mutations in bacterial viruses (phages), and then used selection to find revertants under controlled experimental conditions. With such data, Crick et al. (1961) were able to demonstrate that each residue in a protein was encoded by a non-overlapping triplet of nucleic-acid residues. In another example, with the same system Benner et al. (1967) used selection experiments on mutations to argue that UGA did not code for an amino acid and specifically argued that it must have an important function “because otherwise natural selection would have certainly allocated it to an amino acid.”

So in spite of Egnor’s egnorance, Darwin’s ideas were not only a help but very essential “in decoding the genetic language of DNA.”

Now the biotech industry is founded on the application of Darwin’s theory of natural selection. Selection is an essential part of the process that creates transgenic organisms, like bacteria that produce human insulin. Humans are unable to create transgenic organisms directly, instead they use recombination DNA technology, which randomly creates transgenic organisms from building blocks provided by the researcher. The result is a population of organisms, in which a small minority contains the desired transgenic trait. The researcher then uses Darwin’s mechanism, selection, to evolve a population that is enriched for the desired trait. And voila, with what to someone like Dr. Egnor must seem like wizardry, a population of bacteria can now produce human insulin, enriching and saving the lives of millions, all thanks to Charles Darwin.

References

  • Benner et al. (1967) UGA: A Third Nonsense Triplet in the Genetic Code. Nature 213:449-450 [link]
  • Crick et al. (1961) General nature of the genetic code for proteins. Nature 192:1227-1232 [link]

Playing a bit with The Scientists website, I found out that the story for which I was interviewed a while back will be about me. The title is “Scooped by a Blog” (make that “scooped by this blog”) and it will appear in volume 21, issue 4 (April) on page 21. This is information that I can gleam from an early table of contents. This could probably change. It also looks like I can buy reprints of the article, assuming that I can afford them. I need to remember to add that to my next grant or fellowship.

Ngila Advance Access

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Bioinformatics has published my latest paper via advance access. The copy which I link to below is my final submission to the Journal. The final published version will be slightly different because it will have been edited by the journals for publication in the actual journal.

Cartwright RA (2007) Ngila: Global Pairwise Alignments with Logarithmic and Affine Gap Costs. Bioinformatics. advance access 3/25/07; doi: 10.1093/bioinformatics/btm095 [link]

Abstract:

Summary: Ngila is an application that will find the best alignment of a pair of sequences using log-affine gap costs, which are the most biologically realistic gap costs.

Availability: Portable source code for Ngila can be downloaded from its development website, http://scit.us/projects/ngila/. It compiles on most operating systems.

Supplementary Information: Appendices

Terrapin at 518 West

I went out the dinner last night with a couple of professors and an invited speaker. We ate Italian at 518 West. I checked out their menu online before I went, and discovered that 518 West serves Terrapin Beer.

Woohoo!

That is the first restaurant since I left Athens—other than a Doc Chey’s in Greenville, SC—that had Terrapin. I of course did not let the occasion go to waste and ordered a Rye Pale Ale. It was fun. Too bad everyone else wanted to drink red wine, so I couldn’t convince them to try a Terrapin.

Watch this amazing end to the Division II Basketball Championship game. Winona State is the defending national champion and hasn’t lost a game in two years, winning a record 57 straight games. With 45 seconds to go, Winona State is up 74-67 to Barton College, then Anthony Atkinson takes over:

 

CNN has a story on developments at the National Association of Evangelicals’s meeting. It appears that ultra-conservative, partisan Republican lapdogs are no longer able to dictate politics to evangelicals. The association rejected a push by prominent, Fox-News evangelicals like Dobson and Bauer to reject global warming, affirming its support of Washington policy director Cizik’s message that on global warming is offensive to God.

But they didn’t stop there. The association went further in distancing itself from partisan Republican politics by condemning the acts of torture that the US has done in the war on terror. That’s not a watered-down, general condemnation, but a specific condemnation of the White House’s policies. I’m wondering how long until the hardcore Republican pundits denounce the NAE as a bunch of terrorist loving, traitorous Democrats.

And finally am I the only one who finds this ironic?

But Dobson and the other signatories of the letter to the National Association of Evangelicals board said evidence supporting global warming was not conclusive and that the organization “lacks the expertise to settle the controversy.”

“The issue should be addressed scientifically and not theologically,” they said, calling on the group’s board to either rein in Cizik or encourage him to resign.

When was the last time Dobson or other Fox-News evangelicals thought that they shouldn’t speak on something because it was out of their expertise? From creationism to Terri Schaivo the religious right is always butting in on topics that they not only lack the expertise for but also completely reject the opinion of experts. They’ve had much success in dumbing down our politics for the last thirty years. I wonder if the happenings of the NAE is a sign that Christian progressives are beginning to make inroads into the religious right.

The Scientist is “the magazine for life science professionals”. There will be a story (maybe more than one) about science blogs in next month’s issue. It appears to have been inspired by January’s NC Science Blogging Conference. I was interviewed for the story last month about the my accomplishment of writing a blog post, unrelated to my research, that lead to a surprising coauthorship on a scientific paper. (See Blog About Hothead and Get an Easy Paper.)

I have not seen the article yet, but it appears that I may be playing a central part in it because The Scientist asked me yesterday for a 4x6 photo. Apparently it is not going to be a simple head shot. Tiffany and I went out to the JC Raulston Arboretum yesterday and took some photos with my new digital camera; I wanted to send The Scientist a high quality photo (and my desk is not photogenic). It was actually quite annoying to be in front of the camera for once. I like to take photos, not be in them. We also had some creative disagreements. Tiffany wanted photos with flowering trees. I preferred the look of greenery in the background.

After I got home, and looked at the photos, I chose to send them one of me in the Japanese garden.

reed-garden.jpg

This is not the first time that the origin of Comai and Cartwright (2005) has been mentioned in an article. Last year in Science Elizabeth Pennisi mentioned me in passing, but without actually mentioning me or this blog.

The work, reported in the 25 March 2005 issue of Nature, stunned plant biologists, who have since offered several explanations for how the mutant gene could be corrected; one graduate student’s proposal on his blog even became part of a Plant Cell paper.

Oh well, hopefully I get more exposure in next month’s The Scientist. I’ll let y’all know what happens.

Openlab 2006

featured in openlab 2006

My copy of The Open Laboratory (2006) arrived today. I haven’t had much time to look at it, but Bora appears to have done an excellent job on it with such short notice. I hope that together we can make the 2007 even better.

Game Theory and Net Neutrality

A researcher at the University of Florida and his colleagues have used game theory, which is important to evolution and economics, to show that net neutrality encourages internet service providers (ISPs), companies that offer dial-up, cable modem, DSL, or similar access to the internet, to increase their bandwidth. The ISP industry is currently pressing congress to pass legislation ending net neutrality.

Under the current, net neutrality law, ISPs are required to partition their bandwidth based on the size of a site and how much their customers access a site. However, if net neutrality is ended then ISPs will be allowed to partition their bandwidth based not on their customers needs but on which websites can pay the most money. If net neutrality is ended, then ISPs will be able to extort money from content providers like Yahoo, Google, or even small fry like PT, by offering to increase (or threatening to decrease) the speed at which the customers of said ISP can access the content provider’s sites.

According to an article in ScienceDaily, the researchers showed that customers lose out if net neutrality is ended, for the simple fact that ending net neutrality encourages ISPs to decrease the bandwidth available to their customers.

More important, the researchers found that the incentive for broadband service providers to expand and upgrade their service actually declines if net neutrality ends. Improving the infrastructure reduces the need for online content providers to pay for preferential treatment, Bandyopadhyay said.

“The whole purpose of charging for preferential treatment to content providers is that one content provider gains some edge over the other,” he said. “But when the capacity is expanded, this advantage becomes negligible.”

He gave the analogy of the expansion of a two-lane highway where drivers willing to pay a toll to subsidize road improvements are rewarded with exclusive use of a faster lane.

“If the road is upgraded from two to four lanes, with one express lane, these drivers might say ‘Three lanes are good enough for me. I don’t want to have to pay a toll any longer,’” he said. “So the desire to pay a toll when the road is expanded gets lesser.”

The experience of other countries also suggests that better service – up to three times faster – results when there is greater competition, Cheng said.

“In Japan and Korea, where there is net neutrality and much greater competition among broadband providers than in the United States, there are also higher broadband speeds,” he said.”

Hat Tip: Cortunix.

Terrapin Beer

Terrapin is an award-winning microbrew from Athens, GA. It is the only beer that I drink, and Prof. Steve Steve’s favorite. The beer is very good, and there is a family-friend connection to the company.

I’ve been unable to find it in Raleigh since I moved here, but last week I called Total Wine in Cary and found out that they were starting to carry it later that week. I haven’t had time to go over there and get some, but I will next time I’m in the area.

I guess I’m not the only one who found out about this because, as I was putting the recycling out today, I saw that someone in one of my fellow townhouses drinks Terrapin as well. Sweet!

Now if only I can find out who they are and see if they are Georgia fans as well. Maybe I’ll have to put a bulldog on my front steps.

Update:

I went out and bought a six-pack of Terrapin’s Golden Ale. (They were out of the Rye Pale Ale.) Total Wine is supposed to be getting in a bunch of Terrapin beers “soon”, but they have no idea when “soon” will be. It looks like there is not enough supply for the demand up here. Hopefully, Terrapin will be able to make more when they open their new Athens brewery over the summer.

Egnorance

Egnorance (noun)—the egotistical combination of ignorance and arrogance.

(Note: In the post linked to above, Burt has publicized a definition of “egnorance” that I suggested to him in email.)

Literalism Joke Spotted

Check out the source code at the bottom of this page.

See anything funny?

When PZ Turns Fifty …

God Creates a Kitten.

kittens500.jpg

Happy Half Century, PZ.

Ngila Paper Accepted

Today I learned that Bioinformatics accepted my application note on Ngila, which is a global alignment program I wrote during my dissertation. If you are interested in checking out the program, you can download the source code from its website.

I’ll post a link to the paper when it becomes available.

I believe that my grandmother used to live in this house.

My mom has sent more pictures from tornado-devastated Americus.

Tornado Hits Home

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Sumter Country, Georgia, where my mother grew up and is now living—oh yeah, former President Jimmy Carter is from there as well—got hit by a tornado yesterday. My mother has sent me pictures of the damage that Americus (the county seat and her town) suffered. Three people lost their lives and the hospital is destroyed.

However, Habitat for Humanity is based in Americus, so my guess is that in two weeks 10,000 volunteers will have rebuilt the town. Please note that the tornado did not hit the west part of Americus, so my family is okay, only losing utilities and services.

My mother sent me pictures today, which I’m putting up below the fold. The man with the hurt head is my step-father, who slipped while playing on some wreckage and hit his head on a fallen log.

Openlab 2007

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Openlab 2007

We are now taking submissions for Openlab 2007, the science blogging anthology.—Bora has the story.—Bora was very successful in putting together Openlab 2006, and I have joined him in editing the 2007 edition. Together we will be putting together a list of worthy posts, and sending the list out for judging/review next December. Only this time we will get started in compiling the list in March instead of at the last minute in December.

With the help of Anton Zuiker, we have put together a submission form on Wufoo for the nomination of worthy blog posts. You can make as many nominations as you’d like, but don’t go crazy because we still have to review all submissions. Any original blog entry made between 12-20-06 and 12-20-07 is eligible.

If you want to spread the word, I have put together a badge that you can use to link to the submission form. Feel free to copy the below code into a sidebar on your blog. I am working with the Wufoo people to put together a Movable Type template that can automatically complete some of the information in the nomination form. So for instance, you can include it in all your entries and encourage your readers to nominate good posts of yours.

I have also put together a badge for all the 2006 winners to place on their blogs. I’m hoping that most 2006 winners will also place a 2007 badge on their blogs as well.

2007 200px:

Nominate Posts For: Openlab 2007

<strong>Nominate Posts For:</strong><br />
<a href="http://openlab.wufoo.com/forms/submission-form/" rel="external">
<img src="http://scit.us/openlab/openlab07-200.png" width="200" height="125"
alt="Openlab 2007" title="The Best Science Writing on Blogs 2007" /></a>

2007 150px:

Nominate Posts For: Openlab 2007

<strong>Nominate Posts For:</strong><br />
<a href="http://openlab.wufoo.com/forms/submission-form/" rel="external">
<img src="http://scit.us/openlab/openlab07-150.png" width="150" height="94"
alt="Openlab 2007" title="The Best Science Writing on Blogs 2007" /></a>

2007 100px:

Nominate Posts For: Openlab 2007

<strong>Nominate Posts For:</strong><br />
<a href="http://openlab.wufoo.com/forms/submission-form/" rel="external">
<img src="http://scit.us/openlab/openlab07-100.png" width="100" height="63"
alt="Openlab 2007" title="The Best Science Writing on Blogs 2007" /></a>

2006 150px:

featured in openlab 2006 View My Openlab Entry

<a href="http://www.lulu.com/content/631016/" rel="external">
<img src="http://scit.us/openlab/openlab06-150.png" width="150" height="93"
title="The Best Writing on Science Blogs 2006" alt="featured in openlab 2006" />
</a><br />
<a href="http://a.link.to.your.post.goes.here">View My Openlab Entry</a>

2007 75px:

featured in openlab 2006 View My Openlab Entry

<a href="http://www.lulu.com/content/631016/" rel="external">
<img src="http://scit.us/openlab/openlab06-75.png" width="75" height="47"
title="The Best Writing on Science Blogs 2006" alt="featured in openlab 2006" />
</a><br />
<a href="http://a.link.to.your.post.goes.here">View My Openlab Entry</a>

Let me know if you need other sizes or wish to offer alternative badges.

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