Levinthal's Paradox

Back in 1969, Cyrus Levinthal was thinking about protein folding (Levinthal, 1969). He wondered how long it would take for a protein to fold correctly if it had to sample all possible conformations in three-dimensional space.

THEME:

More posts on
Protein Structure
Imagine that there was only a single bond between each amino acid in a protein of 101 amino acid residues. Imagine that there were only three possible configurations around each of those bonds. This means that the protein could adopt 3¹⁰⁰, or 5 × 10⁴⁷ different conformations.

If the protein is able to sample 10¹³ different bond configurations per second then it would take 10²⁷ years to sample all possible conformations of the protein (Zwanzig et al. 1992). This is quite a long time. Far longer, in fact, than the age of the universe.

Small proteins usually fold spontaneously within seconds and even the largest proteins fold within minutes. The difference between the theoretical calculation and the observed result is known as Levinthal's Paradox.

It isn't really a paradox. Levinthal knew full well that proteins did not fold by sampling all possible conformations. He knew that protein folding involved local cooperative interactions such as formation of α helices and that the formation of such secondary structure elements proceeded in parallel and not sequentially as his thought experiment proposed.

We now know that protein folding is largely driven by hydrophobic collapse as the regions of secondary structure come together to exclude water. This process is a global process involving simultaneous rearrangements of hundreds of bonds at the same time. That's why proteins fold so rapidly. Cyrus Levinthal knew this.

The point of Levinthal's paradox is to demonstrate that when a mathematical calculation shows that some routine process is impossible, then it's the calculation that's wrong, or the assumptions behind the calculation. This point is lost on most Intelligent Design Creationists. They are tremendously fond of complex calculations proving that some biological process is impossible. To them, this is not proof that their calculations are flawed—it's proof that a miracle occurred.

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Levinthal, C. (1969) How to Fold Graciously. Mossbauer Spectroscopy in Biological Systems: Proceedings of a meeting held at Allerton House, Monticello, Illinois. J.T.P. DeBrunner and E. Munck eds., University of Illinois Press Pages 22-24 [complete text]

Zwanzig, R., Szabo, A. and Bagchi, B. (1992) Levinthal's paradox. PNAS 89:20-22. [PNAS]

Michael Egnor Gets It Right

 
Michael Egnor has posted a number of quotations from me about how I would deal with people who don't understand the basic principles of science [Dr. Larry Moran and Censorship of Intelligent Design].

He get it mostly right. If they are undergraduates who don't understand that evolution is a scientific fact, the Earth is 4.5 billion years old, and humans share a common ancestor with chimpanzees, then they flunk the course. If they are graduate students in a science department, then they don't get a Ph.D. If they are untenured faculty members in a science department, then they don't get tenure.

Readers might be amused at Michael Egnor's comments regarding Kirk Durston. It's further proof that IDiots are irony deficient. (Note that Kirk has not accepted my invitation to give a seminar here in the Biochemistry Department. I guess his "courage" has limits.)

Why should Mr. Durston’s willingness to present his scientific evidence for intelligent design to other scientists require courage? Isn't the presentation of evidence a routine part of science? Why should presenting evidence for intelligent design put Mr. Durston’s "scientific reputation on the line"?

Are you listening Kirk? Michael Egnor M.D. wonders why you don't come here and defend your evidence that protein folding demonstrates the existence of God.

I gave you two dates last November: you can give a seminar on Tuesday April 22nd or Tuesday April 29th.

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Mike Huckabee Promotes "Expelled"

 
Were you wondering what Mike Huckabee was up to these days? No? Okay, then you probably won't be interested in this video ....


Why is there such a strong correlation between being stupid and believing in the Bible? How can a man like Mike Huckabee be seriously considered as a candidate for "leader of the free world?"

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[Hat Tip: friend fruit]

Buy This Book!!!

 
Carl Zimmer is among the very best—possibly the best—of the modern science writers. His new book Microcosm: E. coli and the New Science of Life is going to be on sale May 6, 2008. Buy it, now. I just did.

Here's a synopsis from Publishers Weekly.

When most readers hear the words E. coli, they think tainted hamburger or toxic spinach. Noted science writer Zimmer says there are in fact many different strains of E. coli, some coexisting quite happily with us in our digestive tracts. These rod-shaped bacteria were among the first organisms to have their genome mapped, and today they are the toolbox of the genetic engineering industry and even of high school scientists. Zimmer (Evolution: The Triumph of an Idea) explains that by scrutinizing the bacteria's genome, scientists have discovered that genes can jump from one species to another and how virus DNA has become tightly intertwined with the genes of living creatures all the way up the tree of life to humans. Studying starving E. coli has taught us about how our own cells age. Advocates of intelligent design often produce the E. coli flagellum as Exhibit A, but the author shows how new research has shed light on the possible evolutionary arc of the flagellum. Zimmer devotes a chapter to the ethical debates surrounding genetic engineering. Written in elegant, even poetic prose, Zimmer's well-crafted exploration should be required reading for all well-educated readers. (May 6)

Copyright © Reed Business Information, a division of Reed Elsevier Inc. All rights reserved.

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Having a Wife Creates More Housework for Men

 
A newly released study looks at the amount of house work done by men and women in different living situations. Like most of these surveys, the data is based on interviews and on diaries kept by men and women. The most remarkable results are reported in a press release from the University of Michigan [Exactly how much housework does a husband create?].

Here's how they describe the data collection process.

For the study, researchers analyzed data from time diaries, considered the most accurate way to assess how people spend their time. They supplemented the analysis with data from questionnaires asking both men and women to recall how much time they spent on basic housework in an average week, including time spent cooking, cleaning and doing other basic work around the house. Excluded from these "core" housework hours were tasks like gardening, home repairs, or washing the car.

Assuming that this is a reliable way of accessing workload, the study published a chart showing the amount of housework done by maried and single men and women.


The 2005 results show that when women get married they end up doing 7 hours more housework per week but when men get married they end up doing 8 hours more housework per week. The take-home message is clear. Women are a lot more costly than men. Women do more to mess up a house than men do.

Pay attention, men. It may not be worth the effort to get married.

The title of the press release is interesting: Exactly how much housework does a husband create?. Here are the opening paragraphs.

ANN ARBOR, Mich.---Having a husband creates an extra seven hours a week of housework for women, according to a University of Michigan study of a nationally representative sample of U.S. families.

For men, the picture is very different: A wife saves men from about an hour of housework a week.

The findings are part of a detailed study of housework trends, based on 2005 time-diary data from the federally-funded Panel Study of Income Dynamics, conducted since 1968 at the U-M Institute for Social Research (ISR).

Is it just me or does there seem to be a disconnect between the statements in the press release and the chart that's published on the same page?

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Toronto Diversity

 
According to the latest census results, visible minorities make up 46.9% of the population of Toronto and 42.9% of the greater Toronto area. Check out the story in The Toronto Star and watch a video showing the change in precentage of visible minorities fro 1951 to 2006 [Visible minorities gaining].

How does this compare with other cities around the world? My impression is that Toronto is one of the more diverse cities in the world.

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Ramachandran Plots

THEME:

More posts on
Protein Structure
The peptide bond has considerable double-bond character and this prevents rotation around that bond in the polypeptide chain. Adjacent amino acids can adopt different configurations by rotation around the two other bonds in the backbone. The angle of the bond between the nitrogen atom (blue) and the α-carbon atom (black) is &Phi (phi) and the angle of the bond between the α-carbon atom and the carbonyl carbon atom (grey) is Ψ (psi) [The Peptide Bond]. These angles are measured in degrees where 180° is the angle of the bonds when all of the atoms of both residues lie in the most extended conformation. Rotation in one direction is positive so the values go from 0° to 180° and in the other direction they go from 0° to -180°. (180° = -180° in this notation.)

Most of the amino acid residues in a given protein are found in some form of secondary structure such as α helix, β strands, or turns.

The Φ and Ψ bond angles for each residue in the α-helical structure are very similar as shown on the left. This is why the structure is so regular. Similarly, the Φ and Ψ bond angles for every residue in a β strand are similar. Since the residues in a β stand are in an extended form, the Φ and Ψ angles in this conformation are close to 180°.

For any given protein, you can plot all of the bond angles for every pair of residues. These can be plotted on a diagram called a Ramachandran plot, named after the biophysicist G.N. Ramachandran (1922 - 2001). Such a plot shows that most of the residues in β strands have similar bond angles that cluster in a region near the top left-hand corner of the diagram. Similarly, residues in a right-handed α helix have very similar bond angles around Ψ=-45°, Φ=+45°.

The residues in Type II turns also have very characteristic bond angles. Some regions of the Ramachandran plot will be empty because of steric clashes between the oxygen atoms [see The Peptide Bond]. These regions are mostly located in the lower right-hand corner of the plot.


Let's look at some specific examples. One of the proteins we saw in the slideshow was an all-α protein called human serum albumin [PDB 1BJ5]. Another was an all-β protein called Jack bean conconavalin A [PDB 1CON].


If you click on the PDB numbers of these proteins you will be directed to the Protein DataBase (PDB) entry for these proteins. Click on "Structural Analysis" then "Geometry" in the left-hand sidebar of these PDB entries to see the link to "Ramachandran plot." This will take you to the two diagrams shown below for Human serum albumin (left) and Jack bean conconavalin A (right).

The Ψ and Φ angles of every residue in the protein are plotted. Note that for the all-α protein (left) almost all the angles cluster around the region identified as α helix. Similarly, for the all-β proteins (right) the angles cluster in the upper left-hand corner of the plot where you expect to find residues in β strands.

Large regions of the plot are empty indicating that many conformations are disallowed for steric or thermodynamic reasons. The point is that the number of conformations of polypeptides in solution is not infinitely large. Most residues cluster in regions of secondary structure (α helix, β strands, turns). These are thermodynamically stable structures and polypeptides will spontaneously adopt these secondary structures very rapidly.

The overall conformation of a polypeptide then depends on the arrangement of secondary structure motifs relative to each other. Even at this level, there are preferred motifs such as β barrels and α helix bundles.

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Come to Our Birthday Party!!

 
Click on Birthday Party for sharper images.

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Get a Job!!

Position	Assistant Professor (2)
Location	Department of Biochemistry, University of Toronto
Position Description	The Department of Biochemistry, University of Toronto invites applications for two tenure-track positions at the rank of Assistant Professor commencing on July 1, 2008. The Department is interested in individuals who employ modern molecular approaches in studies of macromolecular complexes, membrane protein structure, lipid-protein interactions and dynamics, single molecule visualization and dynamics in living cells, non-coding RNA, or chromatin. Successful applicants will be expected to establish an independent research program, compete effectively for external funding, and contribute actively to the undergraduate and graduate teaching programs in the Department. Salary will be commensurate with qualifications and experience. Applicants should arrange to have three letters of reference sent directly to the mailing address below. In addition, applicants should send their curriculum vitae, copies of significant publications, and a 2-3 page description of their research plans either by e.mail to: chair.biochemistry@utoronto.ca or by mail to the address below. Closing date for applications is April 30, 2008, or until the positions are filled. The University of Toronto is strongly committed to diversity within its community and especially welcomes applications from visible minority group members, women, Aboriginal persons, persons with disabilities, members of sexual minority groups, and others who may contribute to the further diversification of ideas. All qualified candidates are encouraged to apply; however, Canadians and permanent residents will be given priority.
Eligibility	We seek candidates with a Ph.D. in biochemistry, biophysics, cell biology or a related discipline. Candidates must also have at least two years post-doctoral training and have an excellent publication record.
Contact	Interested candidates are encouraged to apply to: Chair, Department of Biochemistry Room 5205, Medical Sciences Building University of Toronto Toronto, Ontario, M5S 1A8, Canada.
Posted	March 13, 2008

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The Peptide Bond

THEME:

More posts on
Protein Structure
Proteins consist of one or more strings of amino acids joined end-to-end to produce a polypeptide. The characteristics of each protein are due to the different amino acids that are combined to make the polpeptide(s). Each of the 20 or so common amino acids has a different side chain but the basic structure is common to all amino acids.

Amino acids have a central α-carbon atom, a carboxylate group (—COO^⊖), and an amino group (—NH₃^⊕). The fourth group attached to the α-carbon is the side chain (The third group is —H). Side chains can be as simple as —H (= glycine), or —CH3 (= alanine). In the example shown on the right, the side chain is —CH₂OH (= serine).

Proteins are synthesized by the translation machinery consisting of ribosomes , aminoacyl-tRNAs, and various translation factors. The template for synthesis is messenger RNA (mRNA) copied from the gene. Amino acids are strung together in a particular order specified by the mRNA codons.

The biosynthesis reaction is complex. It is coupled to hydrolysis of at least three ATP equivalents because the joining of two amino acids is thermodynamically unfavorable. The actual chain elongation reaction is catalyzed by the peptidyl transferase activity of the ribosome. The new bond that is created is called a peptide bond.


In the reaction shown above, the carboxylate group of the amino acid alanine is joined to the amino group of the amino acid serine to create a dipeptide with a peptide bond. Water is eliminated in this reaction. During protein synthesis the reaction continues as the mRNA is translated and long strings of several hundred amino acid residues are made.

The peptide bond has some interesting properties that play an important role in determining the three-dimensional structure of proteins. Look at the traditional depiction of the peptide bond in part (a) (top) of the figure on the left. It shows the actual peptide bond as a single bond and the bond between the carbon atom and the oxygen atom as a double bond. Note that the nitrogen atom has a pair of unshared electrons represented by the two red dots.

The middle structure shows that one electron from the nitrogen and carbon atoms can redistribute to form a double bond between C and N. This leaves an unshared pair of electrons on the oxygen atom. The actual bonding pattern is a mixture of these two resonance forms as shown in the bottom structure.

The partial double bond nature of the peptide bond has important consequences since it inhibits rotation around this bond. With a single bond there is free rotation so the groups on either side can adopt many different conformations. With a double bond there is very little rotation and the groups on either side are locked into the conformation that was formed when the bond is created.

The peptide bond has enough of a double bond characteristic to prevent rotation of the two newly joined amino acid residues. Thus, the O—C—N—H atoms around the peptide bond lie in a single plane shown in blue in the figure on the right.

What this means is the polypeptide chain is somewhat stiff and rigid. It can only adopt conformations that result from rotation around the other bonds in the chain. There are only two of these other bonds that can rotate. Looking at the central α₂ carbon atom above, you can see that there can be rotation around the N—C_α bond and around the C_α—C bond.

The angle of rotation around the N—C_α bond is called Φ (phi) and the angle around the C_α—C bond is called Ψ (psi). For each pair of amino acid residues, these two angles are all that's needed to specify the three-dimensional shape of the polypeptide backbone of the protein.

Not all angles are possible as shown on the left. If the two negatively charged oxygen atoms are too close together they will repel one another. This clash is called steric hindrance and it further limits the number of possible conformations of the polypeptide chain.

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Spring Is in the Air

 
The days are getting warmer and the snow is melting away. Spring is the time when a young person's fancy turns to .... poster presentations.

Every year at this time the lobby of my building fills up with poster presentations from undergraduate courses. Today it's the turn of a course called HMB322H "Human Diseases in our Society." This course is part of our "Human Biology" program. One of the assignments in the course is to shadow a health care professional (usually a researcher) and report on the kinds of things he/she does in a typical week.

The posters are supposed to explain the research/professional activity. Grades for the assignment are based on the quality of the poster as well as the explanation given by the student as the judges question them about their project.

The idea behind this assignment is to make 3rd year students familiar with the activities of a health care worker and provide them with an opportunity to practice their skills at presenting their findings to fellow students.

The Human Biology program¹ is run by a colleague of mine, Valerie Watt, and I'm a big fan of the innovative ideas she's trying out in the courses. Not all of them are going to work but at least she's trying to find new ways of teaching. The students I talked to seemed pretty excited about their shadowing experiences.

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1. I'm not a fan of the program, especially the sub-specialty called "Health & Disease" that these students are taking. I don't think that's an appropriate area of concentration for an Honors B.Sc. degree from the University of Toronto. I'd prefer to have them concentrate on basic fundamental science.

Tangled Bank #102

 
The latest issue of Tangled Bank is #102. It's hosted at Further Thoughts [Tangled Bank #102].

Welcome to the latest issue of The Tangled Bank, the blog carnival dedicated to the world of biology, medicine, natural history…and Sarah Silverman.

We’re all getting older. And as we get older, we lose the ability to hear some frequencies. Diane Kelly of Science Made Cool offers Is That…A Dog Whistle? – a tale of a test that lets you know just how much damage you did to your hearing back in your clubbing days…or will do when you finally finish grad school and are able to emerge onto the social scene ....

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If you want to submit an article to Tangled Bank send an email message to host@tangledbank.net. Be sure to include the words "Tangled Bank" in the subject line. Remember that this carnival only accepts one submission per week from each blogger. For some of you that's going to be a serious problem. You have to pick your best article on biology.

Botany Photo of the Day and the Nitrogen Cycle

 
Check out the Botany Photo of the Day and learn what this plant has to do with Australia, Argentina, Uruguay and The Nitrogen Cycle.

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The Guelph Creationists

 
The University of Guelph is located in southern Ontario (Canada) about 2 hours west of Toronto. It has recently gotten a lot of attention because of the presence of several Intelligent Design Creationists among its staff and students.

Here are the main players.

David K.Y. Chiu is Professor of Computing and Information Science and Professor of Biophysics Interdepartmental Group. He has a Ph.D. in Systems Design Engineering from the University of Waterloo (Canada).

Professor Chiu is head of the Pattern Learning Research Group. Most of his recent papers have to do with recognizing patterns in bioinformatics data.

Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007) Measuring the functional sequence complexity of proteins", Theoretical Biology and Medical Modelling 4:47. [doi:10.1186/1742-4682-4-47]

Chiu, D.K.Y. and K. Zhang (2007) Biomolecular data analysis: a post-genomic reflection. Biomolecular Engineering, 24:319-320.

Chiu, D.K.Y. and Y. Wang (2006) Multipattern consensus regions in multiple aligned protein sequences and their segmentation. EURASIP Journal on Bioinformatics and Systems Biology, Vol.2006:1-8.

Ma, P.C.H., K.C.C. Chan, X. Yao and Chiu, D.K.Y. (2006) An evolutionary clustering algorithm for gene expression microarray data analysis. IEEE Trans. on Evolutionary Computation 10:296-314.

Hwang, C., Chiu, D.K.Y. and Sohn, I. (2005) Analysis of exon structure using PCA and ICA of short-time Fourier transform. L. Wang, K. Chen, and Y.S. Ong (Eds.): ICNC LNCS 3611, pp.306-315, 2005, Springer-Verlag Berlin Heidelberg 2005.(also Second Intern. Conf. on Fuzzy Systems and Knowledge Discovery, joint ICNC'05-FSKD'05, 27-29 Aug. 2005, Changsha, China.)

Durston, K. and Chiu, D.K.Y. (2005) A functional entropy model for biological sequences. in supplementary volume of the journal, Dynamics of Continuous, Discrete and Impulsive Systems, Series B, 2005 (also Proc. 4th Intern. Conf. on Engineering Applications and Computational Algorithms), pp.722-725.

Professor Chiu is a Fellow of the International Society for Complexity, Information, and Design. Other fellows include Michael Behe, Paul Nelson, Guillermo Gonzalez, William Dembski, Jonathan Wells and Scott Minnich.

Kirk Durston is National Director of the New Scholars Society whose aim is to "be a resource to those faculty and scholars who have an interest in developing the spiritual area of their lives from a Christian perspective." Durston has a B.Sc. in Physics from the University of Manitoba (Canada), a B.Sc. in Mechanical Engineering from the University of Manitoba (Canada) and an M.A. in Philosophy from the University of Manitoba (Canada). He is currently a Ph.D. candidate in the Biophysics Interdepartmental Group at the University of Guelph [Kirk Durston].

Durston's supervisor is David Chiu (see above). This is not a simple case of a graduate student falling under the influence of his supervisor since Durston was a well-known creationist even before he joined Chiu's group. It's just a coincidence that student and supervisor share the same views on religion and evolution since to suggest otherwise would be like accusing Chiu of selecting a student based on his religious views and not on the normal criteria. Intelligent Design Creationists are vehemently opposed to that kind of discrimination.

I'm sure Durston's previous degrees in physics, mechanical engineering, and philosphy made him well qualified to do Ph.D. research on the evolution of proteins in a bioinformatics lab.

Jack Trevors is a Professor in the Dept. of Environmental Biology [Jack Trevors] and he's also a member of the Biophysics Interdepartmental Group [Jack Trevors].

Professor Trevors has a B.Sc. and an M.Sc. from Acadia University (Canada) and a Ph.D. from the University of Waterloo (Canada). Most of his many publications are on various aspects of microbiology diversity and industrial applications but he is also interested in "Bacterial evolution with an emphasis on the origin and of the first bacterial cells and functional genetic instructions."

Trevors is famous in creationist circles for two papers he has published with David Abel, Director of The Gene Emergence Project at The Origin-of-Life Foundation, Inc. in Greenbelt, MD (USA). These papers are widely quoted as evidence that the origin of life cannot be explained by natural processes.

Abel and Trevors have also just published a paper with creationists Durston and Chiu.

Abel, D.L. and J.T. Trevors. (2006) Self-organization vs. self-ordering events in life-origin models. Physics of Life Reviews 3:211-228. [doi:10.1186/1742-4682-2-29]

Trevors, J.T. and Abel, D.L. (2004) Chance and necessity do not explain the origin of life. Cell Biology International 28:729-739. [doi:10.1016/j.cellbi.2004.06.006]

Durston, K.K., D.K.Y. Chiu, D.L. Abel and J.T. Trevors (2007) Measuring the functional sequence complexity of proteins. Theoretical Biology and Medical Modelling 4:47. [doi:10.1186/1742-4682-4-47]

Jack Trevors is not a creationist according to this profile at the University of Guelph. He's a "self-proclaimed atheist."

Take that question about the origins of life. It's hardly a new line of inquiry for Trevors, who was about 10 when he began wondering about the existence of God. He's still wondering. Indeed, it's a question that has consumed a fair amount of his own life recently, albeit now voiced in the language of a professional scientist: Where and how did the genetic code and its instructions arise?

No small question. “The origin of genetic instructions in the DNA is the most pressing question in science,” he says. “Genetic instructions don't write themselves, any more than a software program writes itself.”

He adds that the issue goes far beyond deciphering the recipes for making proteins. Given that our genetic material constitutes the stuff of our own identity, “it's the search for ourselves, our origins,” he says.

Call it looking for God in our DNA — or at least that's how a person of faith might phrase it. Trevors, a self-proclaimed atheist, is more circumspect. “If you're a religious person, you say God. If you're an evolutionist, you say evolution.”

He notes, however, that not even evolution deigns to tell us where or how life itself first came about or how DNA's instructions came to be. Perhaps the birthplace of those instructions — like the very creation of the universe itself — is, in Trevors' words, both “unknowable and ‘undecidable' at this point in time.”

The same profile article describes his association with David Abel ...

It's a million-dollar question, literally. That's the size of the prize in a contest being run by the Origin-of-Life Foundation based near NASA's Goddard Space Flight Centre in Maryland. All the winner needs to do to claim the reward — actually annual instalments of $50,000 for 20 years — is to explain how the initial genetic code arose — or, in the words of the contest rules, provide "a highly plausible mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life."

The Gene Emergence Project is a program of the foundation, a scientific and educational body of about 200 scientists in 40 countries.

"We want the international scientific community to help us prove that genetic instructions don't write themselves," says Trevors, who got involved by contacting David Abel, the project's program director, two years ago.

"Jack relentlessly looks for evolutionary explanations for everything we observe in biology," says Abel, adding that his Guelph colleague helps ensure that "life-origin theory" remains empirically responsible, or answerable to the test of repeated observation. "He likes to include the full gamut of microbiological phenomena to make sure our models are explaining all aspects of genetic control."

Trevors has written on the topic, including a paper last year with Abel called: "Chance and Necessity Do Not Explain the Origin of Life." There and in a more recent piece, they frame the genesis-of-life discussion in terms that might resonate with a computer programmer, including referring to genes as linear strings of digital instructions and describing DNA's four nucleotide building blocks as four-way switches. If genes are merely algorithms, albeit highly sophisticated ones, another obvious question occurs, says Trevors. “Computer programs don't write themselves. Why would scientists or anyone else think genetic programs write themselves? The question has to be asked and examined from a scientific perspective.”

I don't know about the rest of you but I don't often hear atheists say things like that. Maybe he's thinking of aliens who write genetic programs? I also don't know too many atheists who would publish papers with known creationists who use the data to support their religious agenda.

The Origin-of-Life Prize has a complicated set of rules that must be followed in order to claim victory. The organization has posted a list of suggested texts that candidates should be familiar with (see sidebar on their website). That list is very revealing. There are books by well-known scientists like Michael Behe, Hubert P. Yockey, Walter James ReMine, William Dembski, and David Berlinski.

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First Sex?

 
Here's the opening paragraphs from a news item on the National Geographic website ["First Sex" Found in Australian Fossils?].

Sex is part of the "oldest profession" and often called the subject of the "world's oldest joke." Now scientists think they've found evidence of the oldest known creatures to engage in sexual reproduction.

A new study suggests that nature's first sexual encounter took place among tubular invertebrates called Funisia dorothea, which lived about 565 million years ago.

This is an example of bad science writing. Sexual reproduction is a phenomenon seen in many bacteria and in all eukaryotes (with minor exceptions). Animals are not the only eukaryotes that have sex. Plants, do it; fungi do it; and so do all single-cell eukaryotes.

The ancestors of these tube worms were having sex for at least a billion years before the Neoproterozoic. The idea that these organisms were "nature's first sexual encounter" is silly.

Who is responsible for this misrepresentation of the evolution of sex? The paper by Droser and Gehling (2008) was published in Science last week. The only reference to sex in the peer-reviewed paper is the following ....

The branching patterns and rarity of branching of Funisia is consistent with metazoan asexual budding. The consistency of tube widths on individual bedding surfaces (Fig. 1, A, I, and J), the densely packed nature of the attachment structures, and the clustering pattern of developmental stages of attachment structures on individual bedding planes suggests that the juveniles settled as aggregates in a series of limited cohorts.

These solitary organisms thus exhibit growth by addition of serial units to tubes and by the division of tubes, and dispersed propagation by the production of spats. Among living organisms, spat production is almost ubiquitously the result of sexual reproduction but is known to occur rarely in association with asexual reproduction (8). Hence, despite its morphological simplicity the Neoproterozoic F. dorothea provides evidence of a variety of growth modes and a complex arrangement for the propagation of new individuals. In living organisms, synchronous aggregate growth may result from a variety of factors—including response to competition, sediment disturbance, and heterogeneity of the substrate—and has the advantage of reducing competition for space between clones and can also decrease gamete wastage (9, 10).

There's nothing in the paper about these organisms being the first to reproduce sexually—that wouldn't have survived the reviews. The only remaining question is why did the author (Droser) allow herself to be quoted in a press release when she must have known that it was misrepresenting the paper?

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Droser, M.L. and Gehling, J.G. (2008) Synchronous Aggregate Growth in an Abundant New Ediacaran Tubular Organism. Science 319:1660-1662. DOI: 10.1126/science.1152595