The proof of the Truth is in the citation index…

A lost letter I came across in the historical archives dated November 30th 1871

Dear Gregor,

One of the hallmarks of science is that it is fruitful. A good scientific paper will usually lead to much work along the same lines, work that confirms and extends the results, and work that produces more new ideas inspired by the paper. Although citation counts are not completely reliable metrics for evaluating scientific papers, they do give some general information about what papers are considered important.

Pea factorization advocates like to point to lists of “peer-reviewed publications” advocating their position. Upon closer examination, their lists are misleading, packed with publications that are either not in scientific journals, or that appeared in venues of questionable quality, or papers whose relationship to pea factorization is tangential at best. Today, however, I’d like to look at a different issue: the fruitfulness pea factorization work. Let’s take a particular Pea factor publication, one that was trumpeted by a religious nutcase as a “breakthrough”, and see how much further scientific work it inspired.

The paper I have in mind is your paper Experiments on Plant Hybridization, which was published, amid some controversy, in the relatively obscure journal Proceedings of the Natural History Society of Brünn in 1865.

What I want to do here is look at every scientific publication that has cited your paper to determine whether your work can fairly said to be “fruitful”. I used the ISI Web of Science Database to do a “cited reference” search on your article. This database, which used to be called Science Citation Index, is generally acknowledged to be one of the most comprehensive available. The search I did included Science Citation Index Expanded, Social Sciences Citation Index, and Arts & Humanities Citation Index. Even such a search will miss some papers, of course, but it will still give a general idea of how much the scientific community has been inspired by your work.

I found exactly 0 citations to your paper in this database. Of these, counting generously, exactly 0 are scientific research papers that cite you approvingly!

I hope that you will see how foolish it is for religious nutcases to pretend to be involved in real science and that you will content yourself with simply growing peas and singing hymns in your monastery.

Yours scoffingly,

Jeff

The Lenski Experiments

In the Lenski experiment the E.Coli cells grown in the presence of oxygen gained the ability to transport citrate across the membrane. The allowed them to utilize citrate as a carbon source and provided a selective advantage in the conditions of the experiment.

In the absence of oxygen with another suitable source of energy the E.coli cells are able to transport and use citrate.

The mutation(s) that occurred in the Lenski experiment therefore allowed (unusually) the transport of citrate across the membrane in the presence of oxygen.

As far as I am aware the detailed molecular story of what happened in this particular case has yet to be unravelled. It seems that at least two different mutations must occur for this ability to be conferred.

As far as I am aware no new proteins are involved. The most likely explanations are a loss of the usual control of the anaerobic citrate transport system or a mutation in a protein that transports a similar molecule

What is significant from these results is that even for this small modification in an existing protein 31,500 generations were required with a population size of about 5 million. This was in the presence of the heaviest selection pressure possible.

Behe argues that this work is consistent with his arguments regarding the limit of evolution.

Behe’s discussion of the Lenski work.

A recent Scientific American article on the Lenski experiment. (HT to Psilo)

How big is the hole?

In an earlier post I likened the production of a protein with a new function to a blind man playing golf. One commenter wondered how large the hole was. I thought of this again while reading Stephen Meyer's recent book "Signature in the Cell". He presents the figure of 1 out of 10^74 as the number of possible proteins 150 amino acids long which have any function whatsoever. If this is correct then the hole is very small indeed...roughly equivalent to finding a single marked atom blindfold from all the atoms in the milky way. This figure also assumes that all the amino acids are left handed and only peptide bonds are formed.

Change in Comments Policy

Visitors will have noticed that there has not been much activity here for some time. This was because I have been unable to devote sufficient time to dealing with hostile comments. As a result of the increasingly unpleasant nature of these comments I have (reluctantly) decided to have only moderated comments.

For a comment to be published it must:
-be directly relevant to the post
-contain no bad language
-be polite

The God Delusion

I am reading Dawkin's book with the above title. A couple of thoughts occurred to me as I read the chapter entitled "Why there is almost certainly no God."

1. If Darwin was correct in highlighting the discovery of a complex organ which cannot be produced by numerous slight successive modifications as a real possible falsification of his theory then we cannot simply rule out any such proposed organ as a "God of the gaps" argument. If the God of he gaps protest is permitted then the possible falsification has gone. If the falsification is a genuine possible one then we must allow for the existence of real gaps.

2. Dawkins argues that an intelligent designer must be more complex than the evidence of his design and therefore requires a further explanation of an even higher level of complexity. He seems to indicate that this is a sort or killer punch as if the rule of the universe is that all complexity must necessarily come from simplicity. However the fact that he spends time on other arguments seems to indicate that he is not entirely happy that his killer blow has actually killed.