This isn't math, but I felt like commenting anyway. That shining example of
an Intelligent Design advocate, Dr. Michael Egnor, is back once again. And this time,
his point, such as it is, is to basically fling insults at PZ Myers. What did PZ do to bring on his ire?
Well, PZ was annoyed with Time magazine, because for their "Time 100" list, they
had Michael Behe write the entry about Richard Dawkins. The passage which Engor took such offense at was the following:
The incompetence is stunning. Richard Dawkins makes the Time 100 list, and who do they commission to write up his profile?
Michael F**king Behe.
That's not just stupid, it's a slap in the face. It would have been no problem to find a smart biologist, even one who might be critical of Dawkins' message, to write something that expressed some measure of respect from the editorial staff. But to dig up a pseudoscientific fraud whose sole claim to fame is that he has led the charge to corrupt American science education for over a decade is shameful.
Now, what's wrong with PZ's reaction, according to Egnor?
Yes. PZ used the word "Fucking" to refer to Behe.
I added the asterisks. Both Behe and Myers are college biology professors who teach young biologists and biochemists the methods of scientific inquiry and, by example, teach students the appropriate standards of scientific discourse.
Which professor is shamefully corrupting American science education?
Yup. That's it. It's the one word. In the mind of Michael Egnor, throwing off a nasty word in the heat of the moment is a grave offense, far worse than spending more than a decade as a professional liar, far worse an offense for a scientist than, say, pretending to know the content of several dozen papers that you've never read.
Now, I'm not exactly PZs biggest fan. I think he's abrasive and arrogant. But I also know, from the experience of reading his writings, that he's an intelligent, passionate advocate for science; he's a teacher who works hard at teaching his students real science, critical thinking, and the scientific method.
And I agree with him about the incredible stupidity of asking Behe to write the piece on Dawkins. Behe is not a legitimate scientist. Behe is a dreadful hack who's spent most of the last two decades hard at work on a program to deliberately and dishonestly misrepresent science as part of a political agenda. He's been caught lying repeatedly; his ideas, such as they are, have been discredited. He even made an ass of himself in the Kitmiller trial, by handwaving away a stack of papers that he'd never seen before, because even without reading them, he just knew that they contained
nothing of any relevance. Choosing him to write a profile of Richard Dawkins is just plain offensive. It's sort of like asking PZ to write a profile about the Pope's influence as a theologist.
So, Dr. Egnor. Which professor is shamefully corrupting American science education? The professor who is a passionate (if arrogant) teacher of real science? Or the dishonest (and arrogant) professor who is an advocate of introducing misrepresentations into the science curriculum in order to discredit scientific theories that disagree with his religious beliefs?
Let's try looking at one other little quote, which I think is pretty illustrative of the difference between the two as educators. PZ is a tireless advocate for the teaching of real science to all science students. Behe, on the other hand, at the end of his interview with the director of the movie "Flock of Dodos", said "Why should I care what gets taught in public school? My kids don't go to public schools."
Who's the teacher who really cares about science education? And who's the one corrupting it? Look at the facts, and it's pretty obvious.
Of course, Dr. Egnor won't do that. Because as he's demonstrated in the past, he
doesn't need to waste his time looking at petty little things like facts, because he already knows the truth. Just like Professor Behe.
Now, I'm not exactly PZs biggest fan. I think he's abrasive and arrogant.
What's not to like?
Behe has kids? Michael Fucking Behe. I guess you could also say Michael Fucked Behe, if he's no longer getting any. That's none of our business. A third option is Michael Cuckold Behe; maybe that's what Egnor was hinting at... Oh, my!
"Now, I'm not exactly PZs biggest fan. I think he's abrasive and arrogant."
Being abrasive and arrogant is an integral part of the blogging ethos, especially when you're as great as someone like me or PZ.
Once again, we have an IDiot going around claiming style is more important than substance.
Mustafa, Tyler, et al.:
I've often found that "abrasive" writing has that character because it is made of tiny diamonds.
(Lots of people have said that in person, PZ Myers is astonishingly mild-mannered. From my own experience, I'd tend to agree, with some reservations. I think he sees a pretty bleak picture of the current and future state of critical thought in this country. I'm often a bad judge of character, so take whatever I say with the appropriate skepticism!)
As for relevant matters:
How frequently do you find that people who complain about obscenity (a) have no logical arguments to articulate and (b) exhibit characteristics of superstitious thinking? The idea that I can cause problems by using a one-syllable word for the natural process which made us all happen, that there is a moral weight to the sound, seems strikingly similar to the notion that there are some Names You Don't Say Out Loud. . . .
I'm one of those who doesn't care for excessive use of obscenities. I just find them ugly and unnecessary most of the time.
That said, P.Z.'s reaction was eminently appropriate. I can't think of a more concise way of expressing the complete idiocy of having Behe write a bio for Dawkins.
As I understand it, Prof. Behe has 10 children who are all home schooled (apparently Mr. Behe, a Roman Catholic, is also down on the Catholic schools which have the temerity to teach evolution). I certainly hope that the administration at Lehigh Un. carefully monitors the courses taught by Prof. Behe to insure that his crap does not enter the curriculum.
Dear Chancellor Adolf Hitler,
Since you've been our Man of the Year, Henry Ford suggested that we ask if you'd like to review this new book by Albert Einstein, also one of our Men of the Year. We are working towards a "Time 100" list.
p.s. please don't use any inflammatory language.
It's Kitzmiller, not Kitmiller according to Wikipedia
So, Egnor doesn't think those young biologists and biochemists can figure out what the asterisks stand for?
Another story on the mechanism of evolution, with humans as "designer" but still using something more akin to natural selection than to ID:
Scientists Evolve New Proteins From Scratch
Source: Arizona State University
Date: May 23, 2007
Cell Biology, Molecular Biology, Genetics, Evolution, Biology, Biotechnology
Science Daily -- Nature, through the trial and error of evolution, has discovered a vast diversity of life from what can only presumed to have been a primordial pool of building blocks. Inspired by this success, a new Biodesign Institute research team, led by John Chaput, is now trying to mimic the process of Darwinian evolution in the laboratory by evolving new proteins from scratch. Using new tricks of molecular biology, Chaput and co-workers have evolved several new proteins in a fraction of the 3 billion years it took nature.
The 3-D structure (ribbon diagram) of protein DX (gray) superimposed with the parent sequence, protein 18-19 (gold). The zinc metal ion is shown in orange and the ATP ligand is colored by atom type. (Credit: John Chaput, Biodesign Institute at Arizona State University)
Their most recent results, published in the May 23rd edition of the journal PLoS ONE, have led to some surprisingly new lessons on how to optimize proteins which have never existed in nature before, in a process they call 'synthetic evolution.'
"The goal of our research is to understand certain fundamental questions regarding the origin and evolution of proteins," said Chaput, a researcher in the institute's Center for BioOptical Nanotechnology and assistant professor in Arizona State University's department of chemistry and biochemistry. "Would proteins that we evolve in the lab look like proteins we see today in nature or do they look totally different from the set of proteins nature ultimately chose" By gaining a better understanding of these questions, we hope to one day create new tailor-made catalysts that can be used as therapeutics in molecular medicine or biocatalysts in biotechnology."
The building blocks of proteins are 20 different amino acids that are strung together and folded to make the unique globular shape, stability and function of every protein. The mixing and matching of the amino acid chain like numbers in the lottery are what favor the odds in nature of finding just the right combinations to help generate biological diversity. Yet no one can predict how the string of amino acids sequence folds to make the 3-D functional structure of a protein.
To select the raw ingredients to create the proteins, Chaput's group (which includes Harvard collaborator Jack Szostak, and ASU colleagues Jim Allen, Meitian Wang, Matthew Rosenow and Matthew Smith) began their quest by further evolving a protein that had been previously selected from a pool of random sequences.
Jack Szostak and Anthony Keefe first made the parental protein in 2001. To achieve their feat, they stacked the odds of finding just one or two new proteins and generated a library of random amino acid sequences so vast -- 400 trillion -- that it dwarfs the number of items in the entire Library of Congress (134 million).
They started with a small protein stretch 80 amino acids long. This basic protein segment acts as a protein scaffold that can be selected for the ability to strongly clutch its target molecule, ATP.
There was only one problem, the parental protein could bind ATP, but it wasn't very stable without it.
"It turns out that protein stability is a major problem in biology," said Chaput. "As many as half of the 30,000 genes discovered from the human genome project contain proteins that we really don't know what their structure is or whether or not they would be stable. So for our goal, we wanted to learn more about the evolution of protein folding and stability."
Chaput's group decided to speed up protein evolution once again by randomly mutating the parental sequence with a selection specically designed to improve protein stability. The team upped the ante and added increasing amounts of a salt, guanidine hydrochloride, making it harder for the protein fragment to bind its target (only the top 10 percent of strongest ATP binders remained). After subjecting the protein fragments to several rounds of this selective environmental pressure, only the 'survival of the fittest' ATP binding protein fragments remained.
The remaining fragments were identified and amino acid sequences compared with one another. Surprisingly, Chaput had bested nature's designs, as the test tube derived protein was not only stable, but could bind ATP twice as tight as anything nature had come up with before.
To understand how this information is encoded in a protein sequence, Chaput and colleagues solved the 3-D crystal structures for their evolutionary optimized protein, termed DX, and the parent sequence.
In a surprising result, just two amino acids changes in the protein sequence were found to enhance the binding, solubility and heat stability. "We were shocked, because when we compared the crystal structures of the parent sequence to the DX sequence, we didn't see any significant changes," said Chaput. "Yet no one could have predicted that these two amino acids changes would improve the function of the DX protein compared to the parent.
The results have helped provide a new understanding of how subtle amino acid changes contribute to the protein folding and stability. Chaput's team has developed the technology potential to take any of nature's proteins and further improve its stability and function. "We have the distinct advantage over nature of being able to freeze the evolution of our lab-evolved proteins at different time points to begin to tease apart this random process and relate it to the final protein function," said Chaput.
Next, Chaput plans on further expanding his efforts to evolve proteins with new therapeutic features or catalytic functions.
Note: This story has been adapted from a news release issued by Arizona State University.
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