Monday's Molecule #53

 
This is a simple one. All you have to do is give the correct name of the residue in the middle of the picture.

There's a direct connection between this molecule and Wednesday's Nobel Laureate(s). Your task is to figure out the significance of today's molecule and identify the Nobel Laureate(s) who are responsible for that significance. (Hint: There's also a connection to last week's lecture in biochemisty.)

The reward goes to the person who correctly identifies the molecule and the Nobel Laureate(s). Previous winners are ineligible for one month from the time they first collected the prize. There are three ineligible candidates for this week's reward. The prize is a free lunch at the Faculty Club.

Send your guess to Sandwalk (sandwalk(at)bioinfo.med.utoronto.ca) and I'll pick the first email message that correctly identifies the molecule and the Nobel Laureate(s). Correct responses will be posted tomorrow along with the time that the message was received on my server. I may select multiple winners if several people get it right.

Comments will be blocked for 24 hours. Comments are now open.

UPDATE: There is no winner this week. Nobody got the residue and nobody guessed the name of the Nobel Laureate(s).

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Creationists as Victims

 
There's a new movie coming out in January. It's called Expelled and the star, Ben Stein^*, is going to reveal the secret evilutionist conspiracy. Apparently, the evilutionists have been persecuting creationists but not because they're idiots. No, apparently it's only because they dare to question the authority of Darwinism.

I'm sure you can't wait to see the movie. Here's a lengthy preview [expelledthemovie.com].

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^*I'm not sure why Ben Stein is an authority on this subject. Perhaps it's because he was a speech writer for Richard Nixon?

By Jove, I Think She's Got it!!!

 
Denyse O'Leary muses about the lecture I attended last Tuesday where Kirk Durston presented the case for Intelligent Design Creationism [Kirk Durston's Proof of God].

Here's what she says on her blog Uncommon Descent [We have the hat, but where’s that rabbit? High levels of information in “simple” life forms]. I'll go through it slowly but the bottom line is that Denyse O'Leary is finally beginning to understand mechanistic naturalism and what science is all about. It's only taken her, what ... ten years? Sheesh.

In Tuesday night, a guest speaker spoke to my adult night school class in why there is an intelligent design controversy. He talked about the central problem of evolution: The fact that high levels of information are present in life forms that are supposed to be early and simple.

We've discussed this on other posting. Kirk Durston did, indeed, say that ancient bacteria were complex and modern ones have become more simple. But his most important point was that the existence of protein folds cannot be explained by evolution, therefore they must have been intelligently designed (i.e., God did it).

Some guests attended the talk, and one of them announced that if intelligent design is correct, scientists would not see the need to do any research because Goddunit. Or something like that.

Actually, it wasn't one of the "guests"—it was one of the regular students. It happened to be the one who invited me as a "guest."

The question referred to the fact that "God did it" is a science-stopper. As soon as Kirk Durston concludes that protein folds are designed by God, that's the end of doing science. What else can be done? Does he plan to design experiments to prove that God did it? Does he plan to investigate how God might have done it, or when? Of course not. It's a science-stopper.

The more I thought about what he was saying, the more it puzzled me. Finally, I realized:

For the materialist, the PURPOSE of science is to show that high levels of information can be created without intelligence.

Therefore, in looking for causes of events, the materialist accepts ONLY a solution that shows that high levels of information can come from random assembly (= without intelligence).

I'm delighted to hear that Denyse O'Leary is capable of serious thought. (Who knew?) She's pretty much got it right.

In science you cannot invoke the supernatural. You are committed to finding naturalistic explanations of the natural world. The procedure is called methodological naturalism or methodological materialism [see Theistic Evolution: The Fallacy of the Middle Ground].

The debate over the conflict between science and religion has been going on for hundreds of years. In the past 50 years the debate has focused on the methodology of science and how it must exclude the supernatural if it's supposed to work properly. I'm shocked (not really) that Denyse has never heard of this before. It's one of the main themes in the writings of Phillip Johnson [see Are You as Smart as a Second Year University Student? Q1 and comments].

He has not shown that high levels of information can be created without intelligence. He assumes that his assertion is true and looks for evidence to support it.

Discoveries that disconfirm his initial belief are not treated as evidence.

Keep looking, he says, keep looking … that magic information mill has GOT to be somewhere!

"Disoveries" that claim to disconfirm the assumption of naturalism are tested against reality. If a hypothesis appears to conflict with a naturalistic explanation then it's back to the drawing board. Scientists will re-examine their assumptions to see where they went wrong. They will devise new approaches and do experiments to collect more data. In other words, the apparent conflict stimulates research, it does not shut it down.

Keep looking, keep looking. This is an approach that has been enormously successful in science over the past several thousand years. Without that attitude we would still believe that all of humanity was wiped out in a flood and that the sun went around the Earth.

Contrast this scientific approach with the typical Young Earth Creationist approach to learning. How many of them are looking for evidence of how God made the Universe 6000 years ago? Where did he get all the atoms, for example? Did he make any mistakes? Belief in the Bible is a science-stopper.

Here's another example. Kirk Durston stops doing science once he's decided that God made proteins. There's nothing else he can do. On the other hand, scientists look at his data and try to explain where he went wrong and why there could be naturalistic explanations. In this case, it's not too hard to discover where Kirk made most of his errors. This is what science is all about and this is why Intelligent Design Creationism isn't science. It's a science-stopper.

Look at bacterial flagella. Michael Behe pronounced that flagella were created by God when he published Darwin's Black Box in 1996. How much research into the origin of flagella did this stimulate among Intelligent Design Creationists? None at all. What's the point?

Scientists did not accept the conclusion that God did it. They continued to work on the problem and now we have a pretty good explanation for the origin of bacterial flagella. Pretty soon the creationists will have to abandon this example but it sure won't be because of any scientific work they did. No scientific advances come for assuming that God did it.

What if random assembly is not in fact the answer? Then either

1. No solution is found (because there never was any solution in the direction in which he is looking)

or

2. An inadequate solution is patched together and defended as the best available solution - usually that means that claims for the solution are overstated wildly to the public.

But it is the materialist scientist’s duty to keep looking for the magic mill even if the fact that random assembly did not occur is overwhelmingly obvious.

Actually the two scientific possibilities are:

1. We found a naturalistic explanation for the claims of religion. Historically, this is what happens most of the time and it's why the claims of religion have repeatedly been shown to be false.


2. We don't know the answer but we'll keep working on the problem. This is what's happening with the most recent claims of the creationists. It takes a few years to demonstrate their nonsense and during that time the correct scientific position is that the questions hasn't been decided. (Sometimes we can say we have a tentative solutions that needs refinement.)

So far, in several thousand years of testing creationist claims there isn't a single one that hasn't fallen to the onslaught of rationalism.

And he displays his virtue to his peers by never questioning the system and by showing hostility and contempt for anyone who does question it.

Given his initial convictions, the materialist cannot believe that a non-materialist is actually doing science. He cannot envision any approach to the fact base that does not have as its base an effort to show that the information was created randomly.

There are many religious scientists who do a pretty good job of being scientific most of the time. They know that methodolgical naturalism is a powerful assumption with a proven track record and that resort to the supernatural has never led to further understanding. As I said above, I'm shocked that Denyse is only now coming to the realization that her understanding of science was seriously flawed. Apparently, in spite of the fact that she has written two books, she never understood the scientific method.

As for "hostilty," yes, it's true. Some of us get very frustrated with so-called scientists who don't understand the fundamental concepts of the scientific methd and what it means to be a scientist.

As a matter of fact, the fact base could easily be approached otherwise, and often more fruitfully, too. If we assume that an object in nature is designed, we do not waste time trying to imagine how it could have come about randomly. We study its characteristics and make predictions about its behaviour, function, and so forth.

That's just a bunch of bull manure. Part of the statement is true—creationists stop trying to find an evolutionary explanation as soon as they conclude that God did it. But the second part is completely false. Creationists stop all investigations once they've concluded that supernatural beings are involved. They don't try to figure out how God's mind worked.

I hope Denyse does some reading in order to catch up. She should look at Philip Johnson's proposal for a God-based (non-materialistic) science. It ain't gonna happen. Why in the world would scientists shop using a method that has bee so successful?

The idea that invoking the supernatural could be a more "fruitful" approach to science, as Denyse says above, is outlandish to the point of idiocy. There are no scientific advances that have come from assuming God did it. That's always a science-stopper.

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Taking Science on Faith

 
Paul Davies is a Professor of Physics at Arizona State University. In 1995 he received the Templeton Prize, which is awarded "for Progress Toward Research or Discoveries about Spiritual Realities." As you might have guessed, this prize goes to people who make up stories about the compatibility of science and religion.

Davies has written a number of books about science and religion, including Cosmic Jackpot.

His latest foray into the world of Christian apologetics is an op-ed piece in yesterday's New York Times [Taking Science on Faith]. Quite a few bloggers have pointed out the major (and I do mean major) logical flaws in this piece. Here's PZ Myers' take on it [Faith is not a prerequisite for science]. PZ has links to the other sites.

Paul Davies is a scientist. I don't understand where he gets such stupid ideas about science. Maybe it's in church.

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Another Proof of God

 

You should probably watch this video to get some idea about how the creationist mind works.

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[Hat Tip: Effect Measure]

Bacterial Genomes and Evolution

 
I recently became aware of the fact that Intelligent Design creationists are promoting a strange idea. They bacteria were very complex when life first formed and their genomes have been degrading over time. Kirk Durston, a graduate student at the university of Guelph, pushed this idea in a course on intelligent design. Durston used a number of scientific references to prove his point. The main one was a paper by Miraa et al (200) from Nancy Moran's lab [Bacteria Genomes Are Degrading].

Ryan Gregory is one of the world's leading experts on genomes and their evolution. He's also a Professor at the University of Guelph. Ryan has published an excellent description of what the Mira et al. (2000) paper shows and what it does not show. You should all read it [Bacterial genomes and evolution].

For Kirk Durston's sake, I hope Ryan Gregory isn't on his Ph.D. oral committee.

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148 Years Ago Today

 
John Wilkins tells us what happened 148 years ago today. Unfortunately, he doesn't tell us what happened today in Australia.

Check out The Corpus Callosum to see how much the historical event cost back then [Happy Birthday].

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Frightened YEC's

 
Shaliniat at Scientia Natura: Evolution and Rationality found this cartoon [It must be hard living in fear of science]. It's cute so I'm stealing it from her. It's originally from cectic.

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Excellence at the

 
Monado at Science Notes points us to a Visual Library set up by Access Excellence at the National Health Museum [Graphics Library resources online]. Here's a description of Access Excellence.

Access Excellence, launched in 1993, is a national educational program that provides health, biology and life science teachers access to their colleagues, scientists, and critical sources of new scientific information via the World Wide Web. The program was originally developed and launched by Genentech Inc., and in 1999 joined the National Health Museum, a non-profit organization founded by former U.S. Surgeon General C. Everett Koop as a national center for health education. Access Excellence will form the core of the educational component of the National Health Museum Website that is currently under development.

This is an admirable goal. The web is full of garbage and it would be nice to collect all the good stuff in one site so that teachers and students could use it. I thought I'd check it out to see how "excellent" it is.

Of course they get The Central Dogma of Molecular Biology wrong but I can't really blame them for that since lots of scientists get it wrong as well [see Basic Concepts: The Central Dogma of Molecular Biology].

One of the next images I checked was the one shown below. It's labeled RNA Ribonucleic Acid - A More Detailed Description. Now, it seems to me that one of the major distinguishing features of RNA is missing. Can you tell what it is?


The graphic shown below is called Nucleotide - A More Detailed Description. It claims to show the structure of a nucleotide in more detail. The boxed region of the DNA molecule does depict a nucleotide but the structures on the right (i.e., more detail) do not. Instead, these are the bases that make up a nucleotide. It may seem nitpicky but why can't they get it right?


Here's a suggestion to the people who run the Access Excellence website: why not ask a few biochemists to check out the science before you post information on the site? Would that be asking too much?

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Harper Blocks Greenhouse Gas Emission Targets

 
Prime Minister Harper is attending the Commonwealth Summit in Kampala, Uganda. For those of you who aren't familiar with the Commonwealth of Nations, it represents 53 nations that were formerly part of the British Empire [Commonwealth of Nations].

These nations have just voted to suspend Pakistan from the Commonwealth until it holds free elections [Pakistan suspended from Commonwealth]. Stephen Harper lead the way here by calling for Pakistan's suspension.

The current debate is over establishing binding targets for greenhouse gas emissions as part of a strategy to reduce global warming. Canada and Australia are the only nations who oppose this resolution. Ironically, with the change in government in Australia today, it's likely that Canada is now the only nation to oppose binding targets.

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[Hat Tip: Brian Larnder at Primordial Blog (Stephen Harper Embarrasses Canada Again)]

[Photo Credit: cbcnews]

Goodbye John Howard

 
The latest results from today's election in Australia point to a defeat for the current Prime Minister, John Howard [Labor sweeps to victory in Australia election]. Not only will the Liberal-National Party coalition lose the election but it looks like Howard will lose his own seat in Parliament.

I don't know enough about Australian politics to know what this means. Howard is a staunch ally of the United States and he sent Australian troops to Iraq. I believe that Australia is one of the few industrialized countries, other than the USA, to refuse to sign the Kyoto agreements.

Does this mean that Australia will withdraw its remaining troops from Iraq and sign on to Kyoto now that Kevin Rudd and the Australian Labor party are in power?

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[Photo Credit: Australian flag - Job Search: John Howard - Wikipedia]

Kirk Durston Interview

 
Here's an online interview with Kirk Durston on canadianchristianity.com for those who want to know more about his views on Intelligent Design Creationism [Evolution under fire? -- Part 1]. By all accounts Kirk seems to be a Young Earth Creationist in the sense that he prefers the literal interpretation of the Bible until it has been proven wrong.

Here's a part of the interview that seems unblievable.

I have been doing a great deal of work in ID over the past few years -- and have given presentations of my work in universities, both in Canada and the USA, that are well attended by both students and faculty. I have been very surprised by the fact that no significant objections to the evidence I present are being raised in these venues. I never bash Darwinism, I simply show them the positive evidence for ID -- and it goes over very well indeed.

I am currently working on a paper dealing with functional information, under the guidance of a professor in bioinformatics who wants to see my work published. It will be very low-key, mentioning nothing about ID, yet laying the groundwork for some major advances in this field -- if it is, by some miracle, accepted for publication.

I'm surprised that he has never heard any significant objections to the evidence he presents in his talk. I didn't have any trouble recognizing several lies and distortions and I wasn't the only one on Tuesday night.

Maybe he gives a different talk in other venues? In any case, we'll see whether the experts on protein folding hear at the University of Toronto will be as gullible when they hear the "positive evidence for ID" next Spring [A Scientific Test for the Intelligent Designer].

Oh, I almost forgot, in his Tuesday evening presentation he did bash "Darwinism." I guess that's one more difference between what I heard and his normal talks to students and faculty. Either that or .....

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A Scientific Test for the Intelligent Designer

 
Kirk Durston has been participating in the discussion on the thread Kirk Durston's Proof of God. He's been having a bit of difficulty keeping up with the scientific criticisms of his proposed proof of the existence of God an Intelligent Designer. I can understand the problem. In an online debate everyone is on a level playing field. When a paper is mentioned, we can all check it out before replying.

So, Kirk proposes another way of handling the discussion.

I thank Larry for extending the opportunity to post a method to test for whether ID is highly probable or not (the way I phrased it in my lecture). I've been mulling this over even before Larry posted the invite. I have reservations about doing it in this particular forum, primarily because the numbers that would be involved are too few to justify the time and, secondly, I would prefer a live lecture where the back and forth dialogue would be greatly enhanced. I've thought that, perhaps, this could be done at the U of T over a 2 hour period. Larry could book a room and chair the event. I could present my proposal (as I repeatedly referred to it in my lecture) of a method to test for ID. I would sincerely hope that Larry et al would be able to set aside the usual hostility and personal attacks and, instead, run a collegial, honest event. As I repeatedly stressed in my lecture this past week, I am NOT claiming to have a 'proof' for ID. Rather, I am proposing a scientific method to test for it that is a work in progress. When this could take place is another question. Certainly not this semester. I am currently swamped with getting the next phase of my research up and running, and a couple of papers in progress. I cannot even afford the time o respond to these posts and will likely have to bow out today. My suggestion would be sometime in 2008, preferably after the winter semester, say, late April or May.

I'm happy to oblige and I've booked a room for either Tuesday April 22nd or Tuesday April 28th. I invite Kirk Durston to come and present his evidence that protein folding studies indicate the presence of an intelligent designer.

This will be an informal scientific debate attended by scientists who are familiar with protein folding. We have a lot of them here at the University of Toronto. Here's a list of the active labs working in this area in our Department [Protein Folding]. Here are the labs in the Dept. of Medical Biophysics [Molecular and Structural Biology]. And here are the labs in the Dept. of Molecular Genetics [Structural Biology].

I'm pretty sure we could get 20-30 graduate students, postdocs, and faculty members to come out and hear the protein folding evidence for intelligent design. They are experts in the same field as Kirk and I'm sure they will be able to show him where he's going wrong. It will be good for them to get exposure to the quality of work on protein folding that's being done at the University of Guelph.

I think it's safe to say that most of my colleagues have no idea of the importance of their work in the Intelligent Design Creationism field of scientific research. This is an opportunity for them to learn from Kirk Durston. Hopefully, after listening to Kirk my colleagues will be more open to the idea of intelligent design when it comes to reviewing research grants, scientific papers, or even sitting on Ph.D. oral exams—provided Kirk makes a convincing case.

I admire Kirk for his willingness to subject his scientific evidence for intelligent design to a group of experts on protein folding. It's very courageous of him since he's putting his scientific reputation on the line.

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[Photo Credit: The Figure is from my textbook, Horton et al. (2006) p. 110. It's taken from the work of my departmental colleague Hue Sun Chan, one of the world's leading experts on the theoretical aspects of protein folding.]

ROM Finds Skeleton in it's Closet

 
Monado at Science Notes has the story [ROM finds skeleton in its closet].

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What She Said

 
Monado of Science Notes has pointed out, once again, the major flaw in Intelligent Design Creationism [ The Masked Man speaks]. In spite of all the blustering and rhetoric, Intelligent Design Creationism boils down to just one thing—arguments against evolution. Here's what Monado says ...

I throw in my two cents' worth:

There is indeed a huge, huge logical fallacy at the base of Dembski's argument. It's the assumption that if you pick enough holes in evolution to let the air out, "God did it" is the only remaining conclusion. That's known as a false dichotomy.

In reality, there are a lot more than two choices. If the received explanation of evolution were not true, it would be back to the drawing board for everyone. If it isn't random mutation plus natural selection plus sexual selection plus genetic drift, then perhaps it's inheritance of acquired characteristics plus natural selection plus sexual selection plus genetic drift. There's no reason to jump to the conclusion that unnatural causes are needed.

The result of pushing the false dichotomy is that ID proponents are ready to use every rhetorical trick in the book, misrepresent evolution, continue to quote falsified "facts," and invent mathematical proofs based on strained assumptions that evolution can't occur without angels pushing the molecules. Dembski's arguments have been falsified again and again. Mutation produces new information. Mutation can produce improvements. Mutation can double the genetic material and then modify it (in spite of the "if I copied this paper I haven't doubled my knowledge" rhetoric). Natural selection is neither directed by God nor random at a particular time and place. It is probabilistic, however. When Dembski claims that something is impossible and actual researchers explain step by step how that could happen, his argument is demolished. The fact that our evidence is always "pathetic" and his evidence is non-existent tells you who has the logic on their side and who is blowing smoke.

Many people have said this before but we need to keep hammering away at this point [see Kirk Durston's Proof of God]. There's no logic to Intelligent Design Creationism other than discrediting evolution on the assumption that God is the only other option.

This is why we call them IDiots.

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