Front-Loading Prediction
August 16th, 2008 by 
Mike Gene
Over at Telic Thoughts, David E Levin writes:
It seems to me that front-loading of genetic information makes the very strong prediction that we should find in the genomes of simple species remnants of genes whose functions are specific to complex species. If all of the genetic information to make vertebrates (for example) was front-loaded into the earliest bacterial species, followed by functional loss of information from the genomes of species that did not need particular genes, we should see remnants of at least some of those lost genes. Are there, for example, remnants of metazoan-specific genes found in the genomes of protozoa or bacteria? As far as I am aware, there are not. For instance, a search of genomes for a large class of metazoan-specific genes that encode tyrosine kinase receptors, a distinctly metazoan innovation (from the evolutionary perspective), reveals nothing in the way of related pseudogenes or gene remnants in any bacterial or protozoan genome. This is the sort of evidence that one would have to produce for the idea of front-loading to be taken seriously. In the absence of evidential support for the idea, the rest of the discussion is meaningless. By contrast, there is plenty of evidence for the generation of new information through established evolutionary mechanisms, such as gene duplication (followed by mutational specialization), exon shuffling, and exonization of SINES, just to name a few. Where is the evidence for front-loading? Somebody help me to understand why this idea is worthy of serious consideration. (emphasis added)
Yes, mainstream evolutionary theory did predict that tyrosine kinases were indeed “a distinctly metazoan innovation.” And yes, if metazoans were front-loaded to appear, we would expect to find remnants of such genes in various unicellular organisms. But Levin is simply wrong in asserting “a search of genomes for a large class of metazoan-specific genes that encode tyrosine kinase receptors, a distinctly metazoan innovation (from the evolutionary perspective), reveals nothing in the way of related pseudogenes or gene remnants in any bacterial or protozoan genome.” On the contrary, scientists were surprised to find that single-celled choanoflagellates are loaded with tyrosine kinases and Tetrahymena possesses a receptor tyrosine kinase that probably responds to human insulin.
I will be adding some more neat stuff to the story about tyrosine kinases and front-loading shortly, but this example alone should help people to see why some of us do indeed think front-loading evolution, a hypothesis that has become steadily more plausible, is worthy of serious consideration. The sort of evidence that one would have to produce for the idea of front-loading to be taken seriously exists and continues to grow.
Relevant Reading:
Front-loading epithelial tissue
Posted in Front-loading | 
August 17th, 2008 at 8:02 am
David sent me an email that makes the same points he made in his reply over at Telic Thoughts. I suppose I should thus respond.
Given the way so many people engage in revisionism, it was refreshing to see one scientist acknowledge that the “evolutionary perspective” is (was) that tyrosine kinases are “a distinctly metazoan innovation.” But why dismiss the RTK example after bringing it up? His example wasn’t a good one, I suppose, because it turned out that I had the “sort of evidence that one would have to produce for the idea of front-loading to be taken seriously.” And there is a growing list of genes that were once thought to be distinctly metazoan innovations, co-evolving into existence along with the origin of metazoan. But as this blog has been documenting, more and more of these genes appear to be present in unicellular organisms, just as we would expect if evolution was front-loaded. Are we also supposed to ignore all these other examples?
As anyone who has read The Design Matrix knows, I dismiss the notion that you can front-load useless genes that will only become useful hundreds of millions of years later. And I do so for the very reason David cites - the issue of genomic decay that we know occurs in the absence of functional selection. The whole idea is how a designer would get around this problem and I outline the logic and solutions in chapter 7.
Why would anyone dismiss actual genes or domains, crucial to metazoans and previously thought to be metazoan innovations, and instead search for fragments of useless of pseudogenes? Remember that when we sequence the genomes of protozoa today, we are not sequencing the genomes of ancient, primitive organisms. We are sequencing the genomes of the evolved descendents of ancient ancestors. For example, metazoans are thought to have originated around 800 million years ago. If a unicellular organism from 800 million years ago had genes that can only be useful in a metazoan state, those genes would be pseudogenes in any protozoan and pseudogenes are completely erased over a time span of ca. 50 million years. What this means is that any remnants of metazoan-only genes in the lineage of Tetrahymena, for example, would have disappeared hundreds of millions of years ago.
On a final note, it is disappointing that Levin would mischaracterize my honest engagement as being dishonest. There is no need for this type of personal attack.