In my last post, The Edge of Evolution?”, I drew readers’ attention to a 2011 paper by the Croatian biochemist Dr. Branko Kozulic, titled, Proteins and Genes, Singletons and Species, which argues that the presence of not one but literally hundreds of chemically unique proteins in each species is an event beyond the reach of chance, and that since these proteins exhibit specified complexity (as the amino acids which make up the polypeptide chain need to be in the correct order), each species must therefore be the result of intelligent planning. (A parallel argument can be made for de novo protein-coding genes.)
In this short post, I’d like to discuss a few falsifiable predictions which I believe are entailed by Dr. Kozulic’s hypothesis that Intelligent Design in Nature extends right down to the level of the species, in conjunction with his proposal that the concept of a species, which is defined in various ways in the field of biology, can best be defined in terms of the unique proteins and genes that characterize each species.
On a general level, the predictions made by Dr. Kozulic’s Intelligent Design model can be summed up in the following two propositions:
1. If two populations of organisms are known to share a common ancestry, and to have diverged from one another relatively recently, as a result of either unguided natural processes or human artificial selection, then there should not be any proteins or protein-coding genes that are unique to one of the two populations. (According to Dr. Kozulic’s Intelligent Design model, unguided processes are incapable of creating the hundreds of unique proteins and genes that characterize each species, within the time available; and of course, humans can’t accomplish this feat by selective breeding, either.)
2. If two populations of organisms are identified by biologists as distinct species on the basis of several independent criteria, then there should always be some proteins and protein-coding genes that are unique to each population. (According to Dr. Kozulic’s Intelligent Design model, each species of living organism can be characterized by proteins and genes that are unique to it.)
Falsification of proposition 1 would be absolutely fatal for Dr. Kozulic’s model of Intelligent Design. At the very least, it would mean that neither proteins nor protein-coding genes could be used to define the concept of a species, as he suggests. More importantly, it would also seem to imply that new proteins and protein-coding genes can originate as a result of unguided natural processes. (One might try to argue that perhaps the proteins and genes were originally present in both populations, but that some proteins and genes were subsequently lost from one population, but in my view, such an argument would be highly implausible. How could a population of organisms lose hundreds of proteins, as well as the genes that code for them?)
Falsification of proposition 2 would not be so serious: all it would mean is that the edge of evolution does not lie at the level of the species, as Dr. Kozulic hypothesizes, but at a higher taxonomic level – say, that of the genus. That should cause no alarm to Intelligent Design proponents, including those who profess to be old- or young-earth creationists. (Creationists entertain a wide variety of views as to what constitutes a “created kind”.)
Using Proposition 1, we can make the following predictions:
(a) If there are any genuine cases of ring species – and I say if because there are only four such species known in Nature, and some of the classic examples of ring species have recently been thrown into doubt – then there should be no proteins or genes which are unique to one population within that species;
(b) Domesticated animals should have the same proteins and protein-coding genes as their wild counterparts. For example, the domestic dog and its sole ancestor, the gray wolf (pictured above, courtesy of Wikipedia), should have the same proteins and genes.
(c) Man-made hybrid species, such as the mule, should not possess any proteins or protein-coding genes which are unique to that species.
Proposition 2 implies that any two species which are agreed by biologists to be genuinely distinct from one another should each possess (hundreds of) unique proteins and protein-coding genes.
The one case that I’d really like to see Intelligent Design biologists investigate is cichlid fish: a large family comprising up to 3,000 species, which are thought to have diverged within the last 10 million years. However, some of these species diverged much more recently, within the last few thousand years, making it very likely that their diversification was an unguided natural event. The question scientists need to examine is: which of these species possess unique proteins and protein-coding genes?
The following abstract by Barluenga et al. (“Sympatric speciation in Nicaraguan crater lake cichlid fish”, Nature, 2006 Feb 9; 439(7077): 719-723) illustrates what I’m getting at:
Sympatric speciation, the formation of species in the absence of geographical barriers, remains one of the most contentious concepts in evolutionary biology. Although speciation under sympatric conditions seems theoretically possible, empirical studies are scarce and only a few credible examples of sympatric speciation exist. Here we present a convincing case of sympatric speciation in the Midas cichlid species complex (Amphilophus sp.) in a young and small volcanic crater lake in Nicaragua. Our study includes phylogeographic, population-genetic (based on mitochondrial DNA, microsatellites and amplified fragment length polymorphisms), morphometric and ecological analyses. We find, first, that crater Lake Apoyo was seeded only once by the ancestral high-bodied benthic species Amphilophus citrinellus, the most common cichlid species in the area; second, that a new elongated limnetic species (Amphilophus zaliosus) evolved in Lake Apoyo from the ancestral species (A. citrinellus) within less than approximately 10,000 yr; third, that the two species in Lake Apoyo are reproductively isolated; and fourth, that the two species are eco-morphologically distinct.
If the two species Amphilophus citrinellus (pictured above, courtesy of Wikipedia and Omnitarian) and Amphilophus zaliosus are not only reproductively isolated but also eco-morphologically distinct, then we have multiple independent grounds for regarding them as bona fide species. In that case, Dr. Kozulic’s Intelligent Design model would predict that these species should each possess their own unique proteins and protein-coding genes. And if this turns out to be the case, then Kozulic’s model would imply that the daughter species did not arise as a result of ordinary natural processes, but as a result of intelligent manipulation of the ancestral species’ genome, less than 10,000 years ago. Obviously, there is a lot of research that needs to be done in this area.
Finally, I’d like to close with a brief discussion of Neanderthal man (depicted above, courtesy of UNiesert and Wikipedia), who is believed to have diverged from Homo sapiens somewhere between 350,000 and 700,000 years ago (when their presumed common ancestor, Heidelberg man, lived), but who is also thought to have interbred with modern human beings between 80,000 and 50,000 years ago, in Eurasia. (The skeleton of what is believed to have been a Neanderthal-Homo sapiens hybrid was found recently in Italy.) Neanderthal genes make up as much as 1 to 4% of the genome of Europeans living today. Despite his ability to inter-breed with modern man, many authorities classify Neanderthal man as a separate species, Homo neanderthalensis; however, others prefer to classify him as a subspecies, Homo sapiens neanderthalensis, placing modern man in the subspecies Homo sapiens sapiens. The ability to inter-breed does not necessarily indicate that Neanderthal man was the same species as we are; apparently, there are documented cases of two species hybridizing and producing fertile offspring and also of gene flow from one species into the gene pool of another by the repeated backcrossing of an interspecific hybrid with one of its parent species, so evidence of inter-breeding does not necessarily indicate that Neanderthal man was of the same species as we are.
Neanderthals had a brain the size of ours and are believed to have had a language, and they seem to have buried their dead with flowers, grave goods and ocher, although this remains controversial. On the other hand, the marked lack of innovation in their tool-making and the absence of conclusive evidence that Neanderthals created anything symbolic has led anthropologist Ian Tattersall, of the American Museum of Natural History, to doubt that they possessed the mental capacities that distinguish modern humans from other animals: “Burial in the simple Neanderthal style falls short of furnishing us with convincing proof of symbolic activity among these extinct hominids”, he declared in a recent interview. (Tattersall’s article, An Evolutionary Framework for the Acquisition of Symbolic Cognition by Homo sapiens, in Comparative Cognition and Behavior Reviews, 2008, Volume 3, pp 99-114, is also well worth reading.)
The question of whether Neanderthal man possessed unique proteins and genes is therefore one of vital importance for understanding who we are, and who this ancient human really was. As far as I can tell, he did possess a few unique genes. More information about Neanderthal genes can be found here, here, here and here. According to the study, A Draft Sequence of the Neandertal Genome by R. Green, D. Reich, S. Paabo et al. (Science, 7 May 2010: Vol. 328 no. 5979 pp. 710-722, DOI: 10.1126/science.1188021):
Features that occur in all present-day humans (i.e., have been fixed), although they were absent or variable in Neandertals, are of special interest. We found 78 nucleotide substitutions that change the protein-coding capacity of genes where modern humans are fixed for a derived state and where Neandertals carry the ancestral (chimpanzee-like) state (Table 2 and table S28). Thus, relatively few amino acid changes have become fixed in the last few hundred thousand years of human evolution; an observation consistent with a complementary study (57). We found only five genes with more than one fixed substitution changing the primary structure of the encoded proteins. One of these is SPAG17, which encodes a protein important for the axoneme, a structure responsible for the beating of the sperm flagellum (58). The second is PCD16, which encodes fibroblast cadherin-1, a calcium-dependent cell-cell adhesion molecule that may be involved in wound healing (59). The third is TTF1, a transcription termination factor that regulates ribosomal gene transcription (60). The fourth is CAN15, which encodes a protein of unknown function. The fifth is RPTN, which encodes repetin, an extracellular epidermal matrix protein (61) that is expressed in the epidermis and at high levels in eccrine sweat glands, the inner sheaths of hair roots, and the filiform papilli of the tongue.
For those readers who (like myself) dislike jargon, here’s a less technical summary by the Smithsonian National Museum of Natural History (Ancient DNA and Neanderthals, page 3):
Researchers found 78 sequence differences that would have affected proteins in which Neanderthals had the ancestral state and modern humans had a newer, derived state. Five genes had more than one sequence change that affected the protein structure. These proteins include SPAG17, which is involved in the movement of sperm, PCD16, which may be involved in wound healing, TTF1, which is involved in ribosomal gene transcription, and RPTN, which is found in the skin, hair and sweat glands. Scientists do not know the function of the CAN15 protein, which was also one of the differences. Other changes may affect regulatory regions in the human sequence. Some changes are in regions that code for microRNA molecules that regulate protein manufacture.
As far as I can tell (and I’m not a scientist), most of the differences referred to above would have involved modifications in existing proteins, rather than brand new ones appearing, although apparently Neanderthals were missing the protein repetin, making them better adapted to the cold, but less so to disease. However, one swallow does not make a summer, and geneticist Jeff Tomkins writes: “Modern humans and Neanderthals are essentially genetically identical.” It seems, then, that on Dr. Kozulic’s Intelligent Design model, modern humans and Neanderthals constitute a single species, which means that their divergence could have occurred as a result of ordinary natural processes.
Before I finish, I’d like to thank bornagain77 for having alerted me to the existence of ‘species specific’ alternative splicing codes, which are described in an article entitled, Evolution by Splicing by Ruth Williams (The Scientist, December 20, 2012):
A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?” said Ben Blencowe, a cell and molecular biology professor at the University of Toronto, who led one of the studies. A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge, biology and biological engineering professor at Massachusetts Institute of Technology and lead author of the second paper, found that gene expression is relatively conserved among species.
On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe. “Alternative splicing is evolving faster than gene expression,” concluded Tom Cooper, professor of pathology at Baylor College of Medicine in Houston, Texas, who was not involved in the work.
It would be interesting to see if alternative splicing patterns “carve up” species of organisms in the same way as Dr. Kozulic’s proposed method of using unique proteins and protein-coding genes as defining characteristics of species.
I shall stop here and throw the discussion open to readers. Can anyone think of some other testable predictions of Dr. Kozulic’s model of Intelligent Design? Over to you.