Sandwalk: WikiPathways

Thursday, July 24, 2008

WikiPathways

Find a website with a correct citric acid cycle and win $1,000,000 or equivalent!NatureNews has an article on the growth of biological Wikis as a way of involving the molecular biology community in annotating genes, proteins, etc. [Molecular biology gets wikified]. I strongly support the work of Huss et al. (2008) as I described in a previous posting [A Gene Wiki].

Now Pico et al. (2008) have tried to do for metabolic pathways what Huss et al. did for genes. Unfortunately, WikiPathways isn't going to be successful for a number of reasons.

The idea is to create a Wiki for various pathways and allow the biological community to update and comment on the various entries. However, whereas Gene Wiki did the right thing by adding the human genes to Wikipedia, WikiPathways creates its own separate database. This makes it much less accessible since not only do you have to make an effort to find the Wiki, you also have to create an account to make changes.

That's not the only problem. Let's look at a familiar metabolic pathway on WikiPathways, the citric acid cycle. Right away you can see that there are no visible chemical reactions. Instead, you just see a pathway created by lines between boxes with the names of molecules. You don't even see that CO₂ and reducing equivalents are produced by this pathway! That's not going to be very useful.

Contrast the WikiPathways entry with the existing entry on Wikipedia [citric acdi cycle]. The Wikipedia entry is much more useful and, as it turns out, reasonably accurate. I'd be tempted to correct the Wikipedia entry but I'm not interested in doing all the work required to make the WikiPathways entry useful.

Speaking of corrections, when I teach my biochemistry course in the winter I challenge my students to find a single website that shows the citric acid cycle correctly. By that I mean a website where every single reaction is correctly balanced and all reactants and products are shown. The Wikipedia reactions are not correct and the sum of all reactions is incorrect, although in this case the only errors are in balancing the number of hydrogen atoms. Can anyone find the mistakes? Can anyone find a website that's correct? (You can't count any website that shows a figure from my textbook and you can't count the IUBMB website (e.g., citrate synthase). (The most serious error is in getting the products of the succinate dehydrogenase reaction wrong.)

The prize for finding a correct website is seeing your name in print on Sandwalk or $1,000,000 (one million dollars), whichever I think is the most valuable.

Huss III, J.W., Orozco, C., Goodale, J., Wu, C., Batalov, S., Vickers, T.J., Valafar, F., and Su, A.I. (2008) A Gene Wiki for Community Annotation of Gene Function. PLoS Biol 6(7): e175 [doi:10.1371/journal.pbio.0060175]

Pico, A.R., Kelder, T., van Iersel, M.P., Hanspers, K., Conklin, B.R., and Evelo, C. (2008) WikiPathways: Pathway Editing for the People. PLoS Biology, 6(7), e184. [DOI: 10.1371/journal.pbio.0060184]

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)

Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)

Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Peter Atkins

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake. Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory. Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change. Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance. Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change. Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat. Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is True

I once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000

It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma

One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick

There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner

An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins

Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod

The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.

Richard Lewontin

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Thursday, July 24, 2008

WikiPathways

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