Thoughts in a Haystack

[This is a potential entry in the Quote Mine Project:]

Quote #4.22

[Creation of new proteins by the undirected process of mutation and natural selection is a mystery]

The ultimate goal of gene family studies is an understanding of how duplicated genes have taken on novel biochemical and organismal functions. Domain shuffling aside, it remains a mystery how the undirected process of mutation, combined with natural selection, has resulted in the creation of thousands of new proteins with extraordinarily diverse and well-optimized functions. This problem is particularly acute for tightly integrated molecular systems that consist of many interacting parts, such as ligands, receptors, and the downstream regulatory factors with which they interact. In these systems, it is not clear how a new function for any protein might be selected for unless the other members of the complex are already present, creating a molecular version of the ancient evolutionary riddle of the chicken and the egg. - Joseph W. Thornton and Rob DeSalle, "Genomics Meets Phylogenetics," Annual Review of Genomics and Human Genetics, 2000. Vol. 1: 41–73

Representative quote miners: Post-Darwinist: Thinkquote of the day; Institute for Creation Research: The Egg/Chicken Conundrum; and Evolution-Facts.Org: Scientific Facts Against Evolution.

Let's look at what was omitted. Thornton and DeSalle also wrote, right at the end of the piece quoted above :

Detailed studies of gene family evolution promise to shed some light on the process by which changes at the genetic level have led to the diversification of function for members of such integrated molecular systems.

Let's also have a look at the abstract of the article:

With the advent of high-throughput DNA sequencing and whole-genome analysis, it has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. Because the hierarchy of genes, like that of living organisms, reflects an ancient and continuing process of gene duplication and divergence, many of the conceptual and analytical tools used in phylogenetic systematics can and should be used in comparative genomics. Phylogenetic principles and techniques for assessing homology, inferring relationships among genes, and reconstructing evolutionary events provide a powerful way to interpret the ever increasing body of sequence data. In this review, we outline the application of phylogenetic approaches to comparative genomics, beginning with the inference of phylogeny and the assessment of gene orthology and paralogy. We also show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of domain shuffling and lateral gene transfer, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.

Clearly, the authors do not doubt that evolution can explain the origin of new proteins with diverse and optimized functions in integrated molecular systems. It is this failure to point out that the authors do not perceive the problem the quoters are trying to convey which is the sort of dishonesty by omission that is the essence of quote mining.

Dr. DeSalle was contacted and gave this reply to the use of the quotation:

In this passage Dr. Thornton and I are trying to say that scientific tests of how novel proteins evolve have been lacking. We in no way wanted to suggest that we cannot test hypotheses about the origin of novel proteins because we can. This paper was written in 2000. Since then Dr. Thornton has shown quite clearly that there are evolutionary pathways that exist for the origin of new proteins and protein function. See his recent Science paper on steroid receptors.

The rhetoric we use here is common in scientific literature. We were pointing out an area of protein evolution that had not been addressed adequately, not because it couldn't be examined in an evolutionary context, but because we were just then in 2000 getting the data and the tools to examine the problem. Because scientists hadn't addressed the problem adequately is no a good reason to suggest that we can't explain the phenomenon in an evolutionary context. It just means that we haven't had the tools or the inclination to examine the problem. However when we do, the best explanation for things like the origin of novel protein function are ALWAYS ones placed into an evolutionary context.

- Leon Retief
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