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.

---

[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].

---

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.

---

Theme: Nobel Laureates

 
NOBEL LAUREATES

November 13, 2006
Physiology or Medicine 1922
Otto Fritz Meyerhof
"for his discovery of the fixed relationship between the consumption of oxygen and the metabolism of lactic acid in the muscle"

November 22, 2006
Physiology or Medicine 1964
Jacques Monod
"for their discoveries concerning genetic control of enzyme and virus synthesis"

November 29, 2006
Chemistry 1964
Dorothy Crowfoot Hodgkin
"for her determinations by X-ray techniques of the structures of important biochemical substances"

December 6, 2006
Chemistry 1930
Hans Fischer
"for his researches into the constitution of haemin and chlorophyll and especially for his synthesis of haemin"

December 13, 2006
Chemistry 1902
Hermann Emil Fischer
"in recognition of the extraordinary services he has rendered by his work on sugar and purine syntheses"

December 20, 2006
Physiology or Medicine 1953
Hans Adolf Krebs
"for his discovery of the citric acid cycle"

January 3, 2007
Physiology or Medicine 1982
Sune K. Bergström, Bengt I. Samuelsson, and John R. Vane
"for their discoveries concerning prostaglandins and related biologically active substances"

January 10, 2007
Physiology or Medicine 2004
Richard Axel and Linda B. Buck
"for their discoveries of odorant receptors and the organization of the olfactory system"

Theme

A Sense of Smell
Nobel Laureates: Richard Axel, Linda Buck
January 17, 2007
Physiology or Medicine 1998
Robert F. Furchgott, Louis J. Ignarro, and Ferid Murad
"for their discoveries concerning nitric oxide as a signalling molecule in the cardiovascular system"

January 24, 2007
Chemistry 1978
Peter D. Mitchell
"for his contribution to the understanding of biological energy transfer through the formulation of the chemiosmotic theory"


January 31, 2007
Chemistry 1988
Johann Deisenhofer, Robert Huber, and Hartmut Michel
"for the determination of the three-dimensional structure of a photosynthetic reaction centre"

February 7, 2007
Physiology or Medicine 1978
Werner Arber, Daniel Nathans, and Hamilton O. Smith
"for the discovery of restriction enzymes and their application to problems of molecular genetics"

February 14, 2007
Chemistry 1972
Christian B. Anfinsen
"for his work on ribonuclease, especially concerning the connection between the amino acid sequence and the biologically active conformation"

February 21, 2007
Physiology or Medicine 1930
Karl Landsteiner
"for his discovery of human blood groups"

February 28, 2007
Chemistry 1937
Walter Norman Haworth
"for his investigations on carbohydrates and vitamin C"

March 7, 2007
Physiology or Medicine 1948
Paul Hermann Müller
"for his discovery of the high efficiency of DDT as a contact poison against several arthropods"

March 14, 2007
Chemistry 1980
Paul Berg
"for his fundamental studies of the biochemistry of nucleic acids, with particular regard to recombinant-DNA"

Theme

Transcription
Nobel Laureate: Roger Kornberg
March 21, 2007
Chemistry 2006
Roger D. Kornberg
"for his studies of the molecular basis of eukaryotic transcription"

March 28, 2007
Physiology or Medicine 1943
Henrik Carl Peter Dam
"for his discovery of vitamin K"
Edward Adelbert Doisy "for his discovery of the chemical nature of vitamin K"

Theme

Blood Clotting
Nobel Laureates: Henrik Dam, Edward Doisy
April 4, 2007
Chemistry 1948
Arne Wilhelm Kaurin Tiselius
"for his research on electrophoresis and adsorption analysis, especially for his discoveries concerning the complex nature of the serum proteins"





April 11, 2007
Physiology or Medicine 1953
Fritz Albert Lipmann
"for his discovery of co-enzyme A and its importance for intermediary metabolism"

Theme

Pyruvate Dehydrogenase
Nobel Laureate: Aaron Klug
April 18, 2007
Chemistry 1982
Aaron Klug
"for his development of crystallographic electron microscopy and his structural elucidation of biologically important nucleic acid-protein complexes"

April 25, 2007
Chemistry 1920
Walther Hermann Nernst
"in recognition of his work in thermochemistry"

May 2, 2007
Physiology or Medicine 1929
Christiaan Eijkman
"for his discovery of the antineuritic vitamin"


May 9, 2007
Physiology or Medicine 1947
Carl Ferdinand Cori and Gerty Theresa Cori, née Radnitz
"for their discovery of the course of the catalytic conversion of glycogen"

May 16, 2007
Chemistry 1907
Eduard Buchner
"for his biochemical researches and his discovery of cell-free fermentation"
[cell free synthesis of alcohol in yeast extracts: vitalism]

May 23, 2007
Physiology or Medicine 1994
Alfred G. Gilman and Martin Rodbell
"for their discovery of G-proteins and the role of these proteins in signal transduction in cells"


May 30, 2007
Physiology or Medicine 1968
Robert W. Holley, Har Gobind Khorana, and Marshall W. Nirenberg
"for their interpretation of the genetic code and its function in protein synthesis"

June 6, 2007
Chemistry 2004
Aaron Ciechanover, Avram Hershko, and Irwin Rose
"for the discovery of ubiquitin-mediated protein degradation"

June 13, 2007
Physiology or Medicine 1945
Sir Alexander Fleming, Ernst Boris Chain, Sir Howard Walter Florey
"for the discovery of penicillin and its curative effect in various infectious diseases"

June 20, 2007
Physiology or Medicine 1993
Richard J. Roberts and Phillip A. Sharp
"for their discoveries of split genes"

June 27, 2007
Physiology or Medicine 1937
Albert von Szent-Györgyi Nagyrapolt
"for his discoveries in connection with the biological combustion processes, with special reference to vitamin C and the catalysis of fumaric acid"

July 4, 2007
Chemistry 1928
Adolf Otto Reinhold Windaus
"for the services rendered through his research into the constitution of the sterols and their connection with the vitamins"

July 11, 2007
Chemistry 1961
Melvin Calvin
"for his research on the carbon dioxide assimilation in plants"

THEME

Deoxyribonucleic Acid (DNA)
Nobel Laureates: Crick, Watson, Wilkins
July 18, 2007
Physiology or Medicine 1962
Francis Harry Compton Crick, James Dewey Watson and Maurice Hugh Frederick Wilkins
"for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material"




July 25, 2007
Physiology or Medicine 1902
Ronald Ross
"for his work on malaria, by which he has shown how it enters the organism and thereby has laid the foundation for successful research on this disease and methods of combating it"

and

Physiology or Medicine 1907
Charles Louis Alphonse Laveran
"in recognition of his work on the role played by protozoa in causing diseases"

August 1, 2007
Chemistry 1962
Max Ferdinand Perutz and John Cowdery Kendrew
"for their studies of the structures of globular proteins"

August 8, 2007
Chemistry 1903
Svante August Arrhenius
"in recognition of the extraordinary services he has rendered to the advancement of chemistry by his electrolytic theory of dissociation"

August 22, 2007
Physiology or Medicine 1971
Earl W. Sutherland, Jr.
"for his discoveries concerning the mechanisms of the action of hormones"

August 29, 2007
Chemistry 1937
Paul Karrer
"for his investigations on carotenoids, flavins and vitamins A and B2"

September 5, 2007
Chemistry 1938
Richard Kuhn
"for his work on carotenoids and vitamins"

September 12, 2007
Physiology or Medicine 1969
Max Delbrück, Alfred D. Hershey, and Salvador E. Luria
"for their discoveries concerning the replication mechanism and the genetic structure of viruses"

September 19, 2007
Physiology or Medicine 1933
Thomas Hunt Morgan
"for his discoveries concerning the role played by the chromosome in heredity"

September 26, 2007
Physiology or Medicine 1999
Günter Blobel
"for the discovery that proteins have intrinsic signals that govern their transport and localization in the cell"


October 3, 2007
Physiology or Medicine 1983
Barbara McClintock
"for her discovery of mobile genetic elements"

October 10,2007
Chemistry 1909
Wilhelm Ostwald
"in recognition of his work on catalysis and for his investigations into the fundamental principles governing chemical equilibria and rates of reaction"

October 17, 2007
Chemistry 1926
The (Theodor) Svedberg
"for his work on disperse systems"

October 24, 2007
Chemistry 1946
James Batcheller Sumner
"for his discovery that enzymes can be crystallized"
[crystallization of urease from jack bean]

October 31, 2007
Physiology or Medicine 1959
Arthur Kornberg
"for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid"

November 7, 2007
Physiology or Medicine 1909
Emil Theodor Kocher
"for his work on the physiology, pathology and surgery of the thyroid gland"

November 14, 2007
Chemistry 1975
John Warcup Cornforth
"for his work on the stereochemistry of enzyme-catalyzed reactions"

November 21, 2007
Physiology or Medicine 1964
Konrad Bloch and Feodor Lynen
"for their discoveries concerning the mechanism and regulation of the cholesterol and fatty acid metabolism"

November 28, 2007
Physiology or Medicine 1992
Edmond Fischer and Edwin Krebs
"for their discoveries concerning reversible protein phosphorylation as a biological regulatory mechanism"

December 5, 2007
Physiology or Medicine 1955
Hugo Theorell
"for his discoveries concerning the nature and mode of action of oxidation enzymes"

December 12, 2007
Chemistry 1947
Sir Robert Robinson
"for his investigations on plant products of biological importance, especially the alkaloids"

December 19, 2007
Chemistry 1997
Paul Boyer and John Walker
"for their elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP)"

January 9, 2008
Chemistry 1915
Richard Willstätter
"for his researches on plant pigments, especially chlorophyll"

January 16, 2008
Chemistry 1989
Sidney Altman
"for their discovery of catalytic properties of RNA"

January 23, 2008
Chemistry 1989
Thomas R. Cech
"for their discovery of catalytic properties of RNA"

January 30, 2008
Chemistry 1984
Bruce Merrifield
"for his development of methodology for chemical synthesis on a solid matrix"

February 6, 2008
Physiology or Medicine 1965
"for their discoveries concerning genetic control of enzyme and virus synthesis"
François Jacob

February 13, 2008
Physiology or Medicine 1965
"for their discoveries concerning genetic control of enzyme and virus synthesis"
André Lwoff

March 5, 2008
Chemistry 1954
"for his research into the nature of the chemical bond and its application to the elucidation of the structure of complex substances"
Linus Pauling

March 12, 2008
Physics 1915
"for their services in the analysis of crystal structure by means of X-rays"
Sir William Henry Bragg and Lawrence Bragg

March 19, 2008
Chemistry 1974
"for his fundamental achievements, both theoretical and experimental, in the physical chemistry of the macromolecules"
Paul Flory

April 2, 2008
Chemistry 1918
"for the synthesis of ammonia from its elements"
Fritz Haber

April 9, 2008
Chemistry 2003
"for structural and mechanistic studies of ion channels"
Roderick MacKinnon

April 23, 2008
Chemistry 1957
"for his work on nucleotides and nucleotide co-enzymes"
Lord Alexander Todd

April 30, 2008
Physiology or Medicine 1947
"for his discovery of the part played by the hormone of the anterior pituitary lobe in the metabolism of sugar"
Bernardo Houssay

May 7, 2008
Physiology or Medicine 2000
"for their discoveries concerning signal transduction in the nervous system"
Arvid Carlsson and Paul Greengard

May 14, 2008
Physiology or Medicine 1958
"for their discovery that genes act by regulating definite chemical events"
George Beadle and Edward Tatum

May 21, 2008
Chemistry 1970
"for his discovery of sugar nucleotides and their role in the biosynthesis of carbohydrates"
Luis Leloir

May 28, 2008
"for their preparation of enzymes and virus proteins in a pure form"
Wendell Stanley

June 4, 2008
Physiology or Medicine 1950
"for their discoveries relating to the hormones of the adrenal cortex, their structure and biological effects"
Edward Kendall, Tadeus Reichstein and Philip Hench

June 11, 2008
Chemistry 1872
"for their contribution to the understanding of the connection between chemical structure and catalytic activity of the active centre of the ribonuclease molecule"
Stanford Moore and William Stein

June 18, 2008
Physiology or Medicine 1972
"for their discoveries concerning the chemical structure of antibodies"
Gerald M. Edelman and Rodney R. Porter

June 25, 2008
Physiology or Medicine 1987
"for his discovery of the genetic principle for generation of antibody diversity"
Susumu Tonegawa

July 2, 2008
Physiology or Medicine 1929
"for his discovery of the growth-stimulating vitamins"
Sir Frederick Gowland Hopkins

July 9, 2008
Chemistry 2003
"for the discovery of water channels"
Peter Agre

July 16, 2008
Physiology or Medicine 1974
"for their discoveries concerning the structural and functional organization of the cell"
George E. Palade

July 23, 2008
Chemistry 1943
"for his work on the use of isotopes as tracers in the study of chemical processes"
George de Hevesy

July 30, 2008
Physiology or Medicine 1958
"for his discoveries concerning genetic recombination and the organization of the genetic material of bacteria"
Joshua Lederberg

August 6, 2008
Physiology or Medicine 1973
"for their discoveries concerning organization and elicitation of individual and social behaviour patterns"
Karl von Frisch, Konrad Lorenz, Nikolaas Tinbergen

August 13, 2008
Physiology or Medicine 1922
"for his discovery relating to the production of heat in the muscle"
Archibald Hill

August 24, 2008
Physiology or Medicine 1977
"for the development of radioimmunoassays of peptide hormones"
Rosalyn Yalow

August 27, 2008
Chemistry 1929
"for their investigations on the fermentation of sugar and fermentative enzymes"
Arthur Harden

September 3, 2008
Chemistry 1929
"for their investigations on the fermentation of sugar and fermentative enzymes"
Hans Karl August Simon von Euler-Chelpin

September 10, 2008
Chemistry 2002
"for his development of nuclear magnetic resonance spectroscopy for determining the three-dimensional structure of biological macromolecules in solution"
Kurt Wüthrich

September 17, 2008
Physiology or Medicine 1931
"for his discovery of the nature and mode of action of the respiratory enzyme"
Otto Heinrich Warburg

September 25, 2008
Physiology or Medicine 2002
"for their discoveries concerning 'genetic regulation of organ development and programmed cell death'"
Sydney Brenner, H. Robert Horvitz, and John E. Sulston

October 1, 2008
Physiology or Medicine 1959
"for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid"
Severo Ochoa

October 8, 2008
"for his discovery of Prions - a new biological principle of infection"
Stanley Prusiner

October 16, 2008
"for their discoveries concerning the genetic control of early embryonic development"
Christiane Nüsslein-Volhard and Eric F. Wieschaus

October 21, 2008
"for the discovery of the production of mutations by means of X-ray irradiation"
Hermann Joseph Muller

October 29, 2008
"in recognition of the contributions to our knowledge of cell chemistry made through his work on proteins, including the nucleic substances"
Albrecht Kossel

November 5, 2008
"for their preparation of enzymes and virus proteins in a pure form"
John Howard Northrop

November 13, 2008
Physiology or Medicine 1995
"for their discoveries concerning the genetic control of early embryonic development"
Edward Lewis

November 19, 2008
Literature 1930
"for his vigorous and graphic art of description and his ability to create, with wit and humour, new types of characters"
Sinclair Lewis

November 27, 2008
Physiology or Medicine 1988
"for their discoveries of important principles for drug treatment"
George Hitchings and Gertrude Elion

December 3, 2008
Physiology or Medicine 2000
"for their discoveries concerning signal transduction in the nervous system"
Eric Kandel


December 10, 2008
Chemistry 1980
"for their contributions concerning the determination of base sequences in nucleic acids"
Walter Gilbert


December 17, 2008
Chemistry 1980
"for their contributions concerning the determination of base sequences in nucleic acids"
Fred Sanger


December 17, 2008
Chemistry 1990
"for his development of the theory and methodology of organic synthesis"
Elias Corey


January 14, 2009
Physiology and Medicince 1936
"for their discoveries relating to chemical transmission of nerve impulses"
Sir Henry Hallett Dale and Otto Loewi


January 21, 2009
Physiology or Medicince 1936
"for their discoveries concerning the humoral transmittors in the nerve terminals and the mechanism for their storage, release and inactivation"
Ulf von Euler and Julius Axelrod


January 29, 2009
Chemistry 2008
"for the discovery and development of the green fluorescent protein, GFP"
Osamu Shimomura


February 5, 2009
Chemistry 2002
"for their development of soft desorption ionisation methods for mass spectrometric analyses of biological macromolecules"
John B. Fenn and Koichi Tanaka


February 11, 2009
Physiology or Medicine 1974
"for their discoveries concerning the structural and functional organization of the cell"
Christian de Duve


February 20, 2009
Chemistry 1993
"for contributions to the developments of methods within DNA-based chemistry: for his fundamental contributions to the establishment of oligonucleotide-based, site-directed mutagenesis and its development for protein studies"
Michael Smith


February 26, 2009
Chemistry 1993
"for contributions to the developments of methods within DNA-based chemistry: for his fundamental contributions to the establishment of oligonucleotide-based, site-directed mutagenesis and its development for protein studies"
Kary Mullis


March 4, 2009
Physiology or Medicine 1923
"for the discovery of insulin"
Frederick Banting and J.J.R. Macleod


March 11, 2009
Chemistry 1958
"for his work on the structure of proteins, especially that of insulin"
Fred Sanger


March 19, 2009
Chemistry 1960
"for his method to use carbon-14 for age determination in archaeology, geology, geophysics, and other branches of science"
Willard Libby

March 25, 2009
Physiology or Medicine 1952
"for his discovery of streptomycin, the first antibiotic effective against tuberculosis"
Selman Waksman

April 1, 2009
Nobel Prize in Chemistry 1905
"in recognition of his services in the advancement of organic chemistry and the chemical industry, through his work on organic dyes and hydroaromatic compounds"
Adolf von Baeyer

April 8, 2009
Nobel Prize in Physiology or Medicine 2007
"for their discoveries of principles for introducing specific gene modifications in mice by the use of embryonic stem cells"
Mario Capecchi, Martin Evans, and Oliver Smithies


April 16, 2009
Physiology or Medicine 1951
"for his discoveries concerning yellow fever and how to combat it"
Max Theiler


April 23, 2009
Physiology or Medicine 2001
"for their discoveries of key regulators of the cell cycle"
Sir Paul Nurse

May 1, 2009
Physiology or Medicine 1908
"in recognition of their work on immunity"
Paul Ehrlich

---

OK. Everyone take a deep breath ....

 
It's just another small step towards understanding development and regulation. We've been expecting it for months [Reprogramming Somatic Cells].

It's not that big a deal. Frogs were cloned from somatic cells over 40 years ago. Sheep and lots of other animals have also been cloned from somatic cells. We know that somatic cells can be reprogrammed. Now we know a little bit more about how to do it.

This is not the end of an "ethical" dilemma. Lots of countries were already allowing work with human embryos to create embryonic stem cell lines. We've got lots of them. Sure, it means that the USA will have a better excuse to continue to block embryonic stem cell research but given the political climate that was probably going to happen anyway.

We're not helping science by turning this into a circus and creating false expectations of medical cures just around the corner. A little perspective is in order here.

---

Tangled Bank #93

 
The latest version of the Tangled Bank has been posted on from Archaea to Zeaxanthol [Tangled Bank #93].

Ahoy me mateys and welcome to the 93rd edition of the Tangled Bank, humbly hosted by yours truly. For those of you returning to from Archaea to Zeaxanthol, welcome back. For those new to my blog, let me give you a quick introduction.

---

Bacteria Genomes Are Degrading

 
At one point in his talk last night Kirk Durston mentioned the bacterial flagella. He acknowledged that the "Darwinists" have proposed an evolutionary pathway from a Type III secretory structure to flagella.

This pathway is improbable, according to Durston, because flagella are more complicated than secretory pores so flagella have to evolve first.

What? Yes, that's right. Scientists have now shown that the most primitive bacteria were very complex and evolution has been all downhill from then on. Modern bacteria are less complex. Thus the type III secretory apparatus had to evolve from the more complex bacterial flagella. (The actual situation is complicated [Evolution in (Brownian) space: a model for the origin of the bacterial flagellum]. What I'm addressing here is the claim of general loss of information in bacterial evolution.)

I suggested that this was bull not correct and Durston responded with a slide showing the scientific papers that proved it. The most important paper was

Mira, A., Ochman, H. and Moran N.A. (2000) Deletional bias and the evolution of bacterial genomes. Trends Genet. 17:589-96. [PubMed]

I asked Durston what would happen if I called Nancy Moran (no relation, that's her above) and asked her whether she agreed that primitive bacteria were complex and all modern bacterial lineages are losing information. He affirmed that she would and that's what modern evolutionary biologists are saying. There are other papers that say the same thing. He accused me of not being aware of them.

This is the abstract of the Mira et al. (2000) paper.

Although bacteria increase their DNA content through horizontal transfer and gene duplication, their genomes remain small and, in particular, lack nonfunctional sequences. This pattern is most readily explained by a pervasive bias towards higher numbers of deletions than insertions. When selection is not strong enough to maintain them, genes are lost in large deletions or inactivated and subsequently eroded. Gene inactivation and loss are particularly apparent in obligate parasites and symbionts, in which dramatic reductions in genome size can result not from selection to lose DNA, but from decreased selection to maintain gene functionality. Here we discuss the evidence showing that deletional bias is a major force that shapes bacterial genomes.

I think it's pretty obvious from the abstract that they're discussing a particular problem in bacterial evolution; namely selection for small compact genomes. This point is clear in the paper as well.

At no point in the paper do the authors suggest anything close to what Durston says. There's no mention of primitive bacteria having the full complexity of all modern species including the myxobacteria and photosynthetic bacteria etc. Why in the world do the Intelligent Design Creationists have to lie about things like this? (I assume it's a lie because the only other possibility is ignorance and a Ph.D. student in biophysics can't be stupid enough to misunderstand such a key principle of evolution, right?)

Naturally in a forum like this Durston had me at a disadvantage. He was displaying the scientific papers and I had to admit that I had not read them recently enough to comment. The point was not lost on some members of the audience. The atheist scientist was trumped by the religious graduate student who was more aware of the scientific literature.

"Frustrating," doesn't begin to cover it ...

---

Kirk Durston's Proof of God

 
I went to the lecture in Denyse O'Leary's course last night [I'm Going to a Lecture on Intelligent Design]. As promised, the guest speaker was Kirk Durston, a graduate student in biophysics at the University of Guelph.

It was a very frustrating experience. Like most Intelligent Design Creationists, Durston was all over the map in terms of spreading lies and misconceptions about science. This scattergun approach seems to be very successful for them. I assume it's because no one person can address all of the problems with their presentation. Most people will catch one or two flaws but they'll assume that everything else has to be correct.

I'll come back to some of these lies in another posting but right now I'd like to explain his main argument.

Kirk Durston has a background in computer science and his project has to do with analyzing the sequences of conserved gene families.

The Intelligent Design Creationist part of his study relies heavily on the work of Douglas Axe (Axe, 2000; Axe, 2004). Axe is head of Biologic Institute a "research" company in Redmond, WA (USA) with ties to the Discovery Institute [We're in Trouble Now].

The papers Axe published in the prestigious Journal of Molecular Biology represent work he did as a post-doc in Cambridge UK. The goal was to show that the probability of a protein adopting a particular three-dimensional fold is very, very low.

Durston is pursuing this line of work and he described it in his talk last night with plenty of equations and diagrams. There were about 15 people in the room and it's almost certain that nobody other than me had any idea what was going on. But it all sounded very sophisticated.

As it turns out, not understanding the science shouldn't have been such a big deal since the form of his argument was obviously silly. At least I thought it was obvious. Here's the way it went ...

1. By making assumptions A, B, C, and D and constructing equations E and F he is able to predict that no protein will have more than X amount of information.


2. By making a few assumptions about protein families it is possible to measure the amount of information in a folded domain by plugging the data into his equations. It turns out that most proteins have more than X information.


3. Therefore God exists (i.e., the protein must have been intelligently designed).

This are (at least) two major flaws in this argument and it doesn't take an expert in computer science or biochemistry to detect them.

First, when you formulate a scientific hypothesis you test it against scientific reality. If the predictions of your hypothesis are not fulfilled then your hypothesis is falsified. At that point it's back to the drawing board. You need to reconsider your assumptions or your equations because they were not successful. That's how science is done but that's not how Intelligent Design Creationism is done.

Second, the sudden appearance of God in the conclusion is illogical. There's no mention of God intelligent design in the premise. It just pops out of the argument without any warning. This is not how logic works and it's certainly not how science works.

I tried to point this out last night but nobody in the audience was paying attention and Durston was in no mood to discuss logic after having spent close to two hours practicing something else.

We have a word to describe people who can't construct a simple logical argument. It seems to have slipped my mind .... what is it ..... oh, yeah, now I remember ... IDiot.

---

Axe, D. (2000) Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors. J. Mol. Biol. 310:585-595.

axe, D. (2004) Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds. J. Mol. Biol. 341:1295-1315.

Nobel Laureates: Konrad Bloch and Feodor Lynen

 

The Nobel Prize in Physiology or Medicine 1964.

"for their discoveries concerning the mechanism and regulation of the cholesterol and fatty acid metabolism"

Konrad Bloch (1912-2000) and Feodor Lynen (1911-1979) received the Nobel Prize in Physiology or Medicine for their work in deciphering the cholesterol biosynthesis pathway.

Feodor Lynen is mainly responsible for working out the pathway from acetate (acetyl CoA) to mevalonate [How Lipitor® Works] while Konrad Bloch worked mostly on the rest of the pathway [How to Make Cholesterol][Making Squalene].

Last week's Nobel Laureate, John Cornforth, was rewarded for discovering the exact mechanisms that give rise to a stereospecific product [Nobel Laureate: John Cornforth].

The 1964 presentation speech was given by Professor S. Bergström, member of the Nobel Committee for Physiology or Medicine of the Royal Caroline Institute.

Your Majesties, Your Royal Highnesses, Ladies and Gentlemen.

Since the start of the Nobel Foundation the professorial staff of the Karolinska Institute has chosen the prizewinners in Physiology or Medicine. This year the Karolinska Institute has been reorganized into a medical university and the duties of the professorial staff have been taken over by the medical faculty of the enlarged Karolinska Institute. As the last item on its agenda the professorial staff was to decide this year's Nobel Prizewinners in Physiology or Medicine and on October 15 Professors Konrad Bloch and Feodor Lynen were awarded the prize for their discoveries concerning the mechanism and regulation of the cholesterol and fatty acid metabolism.

The word cholesterol means gallstone and the reason for this name is that cholesterol was isolated almost 200 years ago from human gallstones. Another connection between cholesterol and human diseases has been established more recently. During the last decade there has been a lively discussion, also in the newspapers, about the correlation between atherosclerosis and the amount of cholesterol and other fats in diet and in blood. This discussion has perhaps concealed from many the fact that cholesterol is a necessary constituent of all our cells and that it fulfills important functions. The elucidation of its chemical structure is one of the foremost achievements in organic chemistry during the 1910's and 1920's. In 1928 the German chemists Windaus and Wieland received Nobel Prizes in Chemistry for their work on the structure of cholesterol and the closely related bile acids. The four-ring carbon skeleton characteristic of cholesterol was later found not only in a number of sterols of plant and animal origin but also in the precursors of vitamin D, in the male and female sex hormones, in the hormones from the adrenal cortex, etc.

Nothing was known about the way they were formed or about their interrelationships. When this year's prizewinners started their scientific career, Professor Hevesy had done his discoveries concerning the use of isotopes as tracers in the living organism. When first the stable and later the radioactive isotopes of hydrogen and carbon became available, they were first extensively used by a group at Columbia University that was headed by the late Rudolph Schoenheimer and in which Bloch played an important role. The work of the group with isotopically labeled compounds has laid the foundation of our general knowledge of the dynamic state in the living cell.

One of the fundamental discoveries was the elucidation of the role of acetic acid as a building block for cholesterol as well as fatty acids. Lynen, working in Wieland's laboratory on the metabolism of acetic acid, succeeded in isolating the so-called activated acetic acid, which is the precursor of all lipids in our body and the common denominator of a number of metabolic processes. With all possible refinements in the utilization of isotope techniques, Bloch and collaborators were able to show in a series of brilliant investigations how the two carbon atoms of acetic acid are used for the synthesis of a long hydrocarbon with thirty carbon atoms, squalene, which in turn is cyclized in a novel type of reaction to a steroid with thirty carbon atoms, lanosterol. This lanosterol is then transformed in a complicated series of reactions into cholesterol, which has twenty-seven carbon atoms. Of special interest are the reactions leading to the formation of the hydrocarbon squalene, and the elucidation of these reactions, which are common for the biosynthesis of many other lipids and natural products, is due not only to Bloch and Lynen and collaborators but also to Popjak and Cornforth in England and Folkers and co-workers in the U.S.A. In connection with this work Lynen made two other discoveries of great importance to our understanding of the mechanisms of cellular metabolism: the elucidation of the mechanism of action of the vitamin biotin and the determination of the structure of cytohemin.

At an early stage Bloch made another discovery of fundamental importance in showing that cholesterol is the precursor of bile acids and of one of the female sex hormones. These discoveries opened up a new field of research that has engaged a great number of scientists in different disciplines. We know now that all substances of steroid nature in our body are formed from cholesterol.

Mainly through the basic biochemical work of this year's prizewinners do we know today in detail how cholesterol and fatty acids are synthesized and metabolized in the body. These processes comprise series of reactions with a great number of individual steps. For instance, the formation of cholesterol from acetic acid is a process involving some thirty different steps. Derangements of this complicated mechanism of formation and metabolism of lipids are in many cases responsible for the genesis of some of our most important diseases, especially in the cardiovascular field. A detailed knowledge of the mechanisms of lipid metabolism is necessary to deal with these medical problems in a rational manner.

The importance of the work of Bloch and Lynen lies in the fact that we now know the reactions which have to be studied in relation to inherited and other factors. We can now predict that we, through further research in this field in the near future, can expect to be able to do individual specific therapy against the diseases that in the developed countries are the most common cause of death.



Professor Bloch, Professor Lynen. You have both started your research in Munich and you have proceeded the proud tradition of this town in a splendid way.

Feodor Lynen, you are now standing with dignity in the array of the earlier Munich Nobel Prizewinners, Adolf von Baeyer, Hans Fischer and Heinrich Wieland.

Konrad Bloch, you have like Emil Fischer and Richard Willstätter left Munich and continued your work in the New World.

I have made a very short summary of your successful research work in the field of lipids. You have provided us with detailed knowledge of many fundamental metabolic reactions. This knowledge forms the necessary basis for the study of the different medical problems in the field of lipid metabolism.

It can now be anticipated that in the near future we will learn how to deal with many of these diseases in a rational and successful way.

On behalf of the Caroline Institute I have the honour to congratulate you on your brilliant work and I now ask you to receive your prizes from the hands of His Majesty the King.

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[Photo Credits: Konrad Bloch plaque is from Wikipedia. Restricted photos of Feodor Lynen are available on ViewImages]

Best Lab Website

 
New Scientist is running a contest for the best laboratory website. The ten finalists are listed on the New Scientist website [Laboratory Website and Video Awards].

One of the finalists is the lab website of T. Ryan Gregory of Genomicron [Please vote for my lab website.].

Now, I'm not saying that you should hop on over to the New Scientist site and vote for Ryan Gregory just because he's such a nice guy and he's a blogger. And certainly not just because it's a Canadian lab. Of course you shouldn't do that. This is a legitimate scientific poll and heaven forbid that there would be any shenanigans in the voting. No siree, Bob.

You should carefully examine each and every one of the ten finalists and make an honest judgment about the best site. I choose Ryan Gregory's lab site as my #1 pick. If you don't want to waste time you can trust me and vote for him too. Pick the Emili lab site as your #2 choice 'cause Andrew Emili is a colleague of mine has the next best site.

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[Photo Credit: Gregory Lab: Genomic Diversity]

Two Cultures

Stephen Fry has posted a long description of a debate he had with an American aquaintance about global climate change [Getting Overheated]. You should read the whole thing but there's one part that caught my eye.

We must begin with a few round truths about myself: when I get into a debate I can get very, very hot under the collar, very impassioned, and I dare say, very maddening, for once the light of battle is in my eye I find it almost impossible to let go and calm down. I like to think I’m never vituperative or too ad hominem but I do know that I fall on ideas as hungry wolves fall on strayed lambs and the result isn’t always pretty. This is especially dangerous in America. I was warned many, many years ago by the great Jonathan Lynn, co-creator of Yes Minister and director of the comic masterpiece My Cousin Vinnie, that Americans are not raised in a tradition of debate and that the adversarial ferocity common around a dinner table in Britain is more or less unheard of in America. When Jonathan first went to live in LA he couldn’t understand the terrible silences that would fall when he trashed an statement he disagreed with and said something like “yes, but that’s just arrant nonsense, isn’t it? It doesn’t make sense. It’s self-contradictory.” To a Briton pointing out that something is nonsense, rubbish, tosh or logically impossible in its own terms is not an attack on the person saying it – it’s often no more than a salvo in what one hopes might become an enjoyable intellectual tussle. Jonathan soon found that most Americans responded with offence, hurt or anger to this order of cut and thrust. Yes, one hesitates ever to make generalizations, but let’s be honest the cultures are different, if they weren’t how much poorer the world would be and Americans really don’t seem to be very good at or very used to the idea of a good no-holds barred verbal scrap. I’m not talking about inter-family ‘discussions’ here, I don’t doubt that within American families and amongst close friends, all kinds of liveliness and hoo-hah is possible, I’m talking about what for good or ill one might as well call dinner-party conversation. Disagreement and energetic debate appears to leave a loud smell in the air.

I understand this difference. Here in Canada we're half way between Europe and America in terms of debate tactics. In some cases you can have lots of fun carrying on in a "British" tradition. But from time-to-time you encounter some people from the "American" cultural tradition and they take great offense at such behavior.

The problem is especially acute when dealing with creationists. They are very good at politely lying and spreading misinformation with a pleasant smile on their faces. They are ever so respectful of the "other side" while, at the same time, implying that all scientists are really stupid.

But when you try and call them on their lies you are immediately dismissed for being rude and uncivilized. The average "Christian" will only tolerate polite discourse and by that they mean non-confrontational. As long as you tells lies in a quiet polite voice it's okay.

We also see the problem when discussing militant atheists. People like Richard Dawkins and Christopher Hitchins are just behaving normally in the culture in which they were raised. It's Americans who see this as a particularly disrespectful way of behaving. That's why American atheists are so often opposed to the so-called militant atheists and think they're hurting the cause.

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[Hat Tip: RichardDawkins.net]

[Photo Credit: stephenfry.com]

How Lipitor® Works

 
In previous postings we learned how cholesterol is made from squalene and squalene is made from the six carbon compound mevalonate [How to Make Cholesterol] [Making Squalene].

Today we'll cover the synthesis of melavonate from three molecules of the 2-carbon compound acetate.

When acetate is involved in biosynthesis reactions it is "activated" by forming a thioester linkage to coenzyme A ("thio" means sulfur). Coenzyme A was discovered by Nobel Laureate: Fritz Lipmann.

The first step in the pathway is the joining of two molecules of acetyl CoA to make the 4-carbon compound acetoacetyl CoA. Note that this molecule is still joined to coenzyme A. In the second step, another acetyl group is transferred to acetoacetyl CoA to make the 6-carbon molecule 3-hydroxyl-3-methylglutaryl CoA (HMG CoA). HMG-CoA was Monday's Molecule.

The last step is cleavage of the thioester linkage between the 6-carbon compound and CoA releasing mevalonate.

This last step is catalyzed by an enzyme called HMG-CoA reductase. This is an oxidation-reduction reaction where the reduction of HMG-CoA is coupled to the oxidation of NADPH. This enzyme is regulated inside the cell and this controls the biosynthesis of cholesterol since mevalonate is an essential intermediate in the pathway.

Lipitor® and similar drugs control cholesterol synthesis by inhibiting the enzyme HMG-CoA reductase. If we draw the substrate in a way that shows its structure, you can see that Lipitor® and Mevacor® resemble the business end of the molecule—the part that's cleaved by the enzyme. These drugs are effective inhibitors because they bind to the active site of the enzyme.



The class of HMG-CoA reductase inhibitors is called statins. They are used to control serum cholesterol levels in the hopes of reducing the risks of coronary heart disease. There don't seem to be any serious side effects to inhibiting mevalonate production in spite of the fact that mevalonate is required for synthesis of some hormones and of the essential cofactor ubiquinone [Ubiquinone and the Proton Pump].

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Parental Guidance Suggested

 

This rating was determined based on the presence of the following words:

* dead (2x)
* sex (1x)

I wonder what kind of rating I would get if Sandwalk were rated in France? Do they have a "milquetoast" rating?

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Swift Boat Funder T. Boone Pickens Reneges On John Kerry Million Dollar Offer

 
Anyone who spoke out against the war in Viet Nam and who knew Jane Fonda would get my vote. Especially if the other choice was someone who didn't even like Jane Fonda.

Do you remember the Swift Boat campaign against John Kerry? You should. It's going to be important in the next year since we're very likely to see something similar in the next Presidential election campaign.

One of the founders of Swift Boat Veterans for Truth (sic) has just offered one million dollars if Kerry can prove that there was even one lie in the ads they placed on television. Kerry takes up the challenge but, it seems as though there's some fine print ... [ Swift Boat Funder T. Boone Pickens Reneges On John Kerry Million Dollar Offer]. Imagine that.

Pickens supports Rudy Giuliani so it's unlikely that Giuliani will be swiftboated. Hmmm, I wonder who the target will be ....

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[Hat Tip: Canadian Cynic]

I'm Going to a Lecture on Intelligent Design

 
Denyse O'Leary is teaching a course on Intelligent Design at the University of St. Michael's College, University of Toronto [Denyse O'Leary's University Course on Intelligent Design].

The outline of the course was posted on Post-Darwinist [ COURSE: By Design or by Chance? An introduction to the intelligent design controversy].

Students in the course are allowed to invite a guest for one lecture and one of my friends, who shall remain nameless for now, has urged me to come along. By all accounts the course is going well and Denyse is presenting both sides of the controversy.

Tonight's lecture is ...

Session 5. Intelligent design: What the ID proponents actually say (and don’t say) Tuesday November 20, 2007

Michael Behe, author of Edge of Evolution (2007), sees actual design where, for example, Richard Dawkins, author of The Blind Watchmaker, sees the illusion of design. Who’s right? Are they both wrong?

Guest: Kirk Durston, biophysics PhD candidate at the University of Guelph.

Kirk Durston (right) is the National Director of the New Scholars Society. According to his biography on their website,

KIRK DURSTON, B.Sc (Physics), B.Sc. (Mech. Eng.), M.A. (Philosophy), Ph.D. Candidate (Biophysics) at the University of Guelph.

Kirk Durston is the National Director of the New Scholars Society. He is currently a Ph.D. candidate in Biophysics at the University of Guelph, specializing in the application of information to biopolymers. His other interests include amateur astronomy, wilderness canoeing & camping, and landscape photography & art.

What is it about creationists that they always seem to have multiple redundant degrees? In this case he has two Bachelor's degrees. What's with that?

It's easy to find out what Kirk believes because there's a Statment of Faith on the website.

The sole basis of our beliefs is the Bible, God's infallible written Word, the 66 books of the Old and New Testaments. We believe that it was uniquely, verbally and fully inspired by the Holy Spirit, and that it was written without error (inerrant) in the original manuscripts. It is the supreme and final authority in all matters on which it speaks.We accept those large areas of doctrinal teaching on which, historically, there has been general agreement among all true Christians. Because of the specialized calling of our movement, we desire to allow for freedom of conviction on other doctrinal matters, provided that any interpretation is based upon the Bible alone, and that no such interpretation shall become an issue which hinders the ministry to which God has called us.

Jeffrey Shallit had a few things to say about Kirk Durston on Recursivity [Kirk Durston: Apologist for Genocide]. This is going to be an interesting lecture.

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