Friday, 11 July 2014

Of Mice and Men and Evolution

Source: Iakes Ezkurdia, et. al., Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes*
Size of the human genome reduced to 19,000 genes - ScienceDaily

Just how close to other mammals are we? The answer is much closer than most people think and of course far closer than creationists will admit and which more sensible religious people like to imagine.

A detailed study led by Alfonso Valencia, Vice-Director of Basic Research at the Centro Nacional de Investigaciones Oncologicas (National Cancer Research Centre - CNIO) in Spain, and published in the journal Human Molecular Genetic found that about 90 percent of protein-coding genes found in humans are common to the earliest metazoans (multicellular organisms), that 99 percent of them pre-dated the emergence of the primates 50 million years ago.

They also found no protein-coding genes unique to Homo sapiens and not common to all primates.

Their work has reduced the size of the functional human genome by a further 1,700 to just 19,000 functional genes, on the basis of a functional gene being one which codes for a protein. This is well below the original estimate of around 100,000 genes.

Abstract*
Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein-coding potential is the detection of cellular protein expression through peptide mass spectrometry (MS) experiments. Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. We found a strong relationship between detection in proteomics experiments and both gene family age and cross-species conservation. Most of the genes for which we detected peptides were highly conserved. We found peptides for >96% of genes that evolved before bilateria. At the opposite end of the scale, we identified almost no peptides for genes that have appeared since primates, for genes that did not have any protein-like features or for genes with poor cross-species conservation. These results motivated us to describe a set of 2001 potential non-coding genes based on features such as weak conservation, a lack of protein features, or ambiguous annotations from major databases, all of which correlated with low peptide detection across the seven experiments. We identified peptides for just 3% of these genes. We show that many of these genes behave more like non-coding genes than protein-coding genes and suggest that most are unlikely to code for proteins under normal circumstances. We believe that their inclusion in the human protein-coding gene catalogue should be revised as part of the ongoing human genome annotation effort. [My emphasis]

Iakes Ezkurdia, David Juan, Jose Manuel Rodriguez, Adam Frankish, Mark Diekhans, Jennifer Harrow, Jesus Vazquez, Alfonso Valencia, and Michael L. Tress
Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes
Hum. Mol. Genet. first published online June 16, 2014 doi:10.1093/hmg/ddu309

Our figures indicate that the differences between humans and primates at the level of genes and proteins are very small. The number of new genes that separate humans from mice may even be fewer than ten.

David Juan (one of the authors)
Apart from its significance for the Human Genome Project, the interesting result from this study is just how few new proteins it takes to make a new species and even whole new orders and families. It is becoming increasingly clear that it is not the number of proteins and so the number of genes coding for those proteins which matters so far as the difference between taxons is concerned but how they are uses, and especially how the genes are controlled.

The minor anatomical and physiological differences between Homo sapiens, Pan troglodytes, P. paniscus and Gorilla gorilla is probably almost all down to how and when genes producing controlling protein enzymes were switched on or off during embryological development, resulting in relative differences in the sizes of the same basic skeletal elements, muscles, brain and other organs. The same goes for the differences between a mouse and a primate or between a mouse and any other mammal. In other words, the same basic recipe, varying the ingredients and cooking times slightly, can produce a different cake. There is no real increase in complexity involved.

This piece of research, and the fact that it does not cause major ripples in the world of evolutionary biology or taxonomy because anyone who knows anything about the subject understands how it merely confirms what was already understood, highlights how far evolutionary biology differs from what creationists pseudo-scientists tell their audience evolution is. Creationist continue to attack an increasingly surreal parody of evolution which has become almost unrecognisable even in parody.

Despite the growing evidence that evolution does not necessarily involve any increase in complexity, we still get this blatant lie from creationists:

The popular syndicated columnist, Sydney Harris, recently commented on the evolution/entropy conflict as follows:

There is a factor called "entropy" in physics, indicating that the whole universe of matter is running down, and ultimately will reduce itself to uniform chaos. This follows from the Second Law of Thermodynamics, which seems about as basic and unquestionable to modern scientific minds as any truth can be. At the same time that this is happening on the physical level of existence, something quite different seems to be happening on the biological level: structure and species are becoming more complex, more sophisticated, more organized, with higher degrees of performance and consciousness.

As Harris points out, the law of increasing entropy is a universal law of decreasing complexity, whereas evolution is supposed to be a universal law of increasing complexity. Creationists have been pointing out this serious contradiction for years, and it is encouraging that at least some evolutionists (such as Harris) are beginning to be aware of it.

How can the forces of biological development and the forces of physical degeneration be operating at cross purposes? It would take, of course, a far greater mind than mine even to attempt to penetrate this riddle. I can only pose the question - because it seems to me the question most worth asking and working upon with all our intellectual and scientific resources.

This, indeed, is a good question, and one for which evolutionists so far have no answer. Some have tried to imagine exceptions to the Second Law at some time or times in the past, which allowed evolution to proceed in spite of entropy, but such ideas are nothing but wishful thinking.


The late Henry M. Morris, PhD, a hydrology engineer, not a biologist, was co-founder of the Institute for Creation Research. Sydney Harris was a journalist for the Chicago Daily News with no scientific training or qualifications. Despite the fact that this argument is easy to refute, and has not been revised since the 1980s, it is still trotted out regularly by creationist pseudo-scientists to misinform their audiences. A hydrolics engineer quoting a scientifically ignorant journalist and pronouncing authoritatively on biology and physics is considered perfectly good science in creationist circles, apparently.

Entropy, of course, only applies to a closed system which, for all practical purposes means the entire Universe. There is nothing in the Second Law of Thermodynamics which precludes a decrease in entropy in an open system if energy is supplied to the system, as it is with a biological organism in the form of nutrients and oxygen - energy which derives ultimately from the sun. It's as simple as that. If you want it said in a more detail see PZ Myer's blog, Entropy and Evolution.

With typical dishonesty, playing to the scientific ignorance of his audience, Morris waved aside this fundamental principle of science with:

It is amazing how many anti-creationist debaters and writers try to "sidestep" this serious problem with such a simplistic cliché as this. Creationists who cite the entropy principle against the evolutionary philosophy are, time and again, dismissed as either ignorant of thermodynamics or dishonest in their use of the second law. Such charges are inappropriate, to say the least.

In the first place, the entropy principle applies at least as much to open systems as to closed systems... [My emphasis]

Henry M. Morris, PhD; Op. cit.

He then follows this with an almost surreal piece of misinformation about thermodynamics followed by almost equally surreal display of misinformation about evolution:

Thus entropy in an open system always at least tends to increase, no matter how much external energy is available to it from the sun or any other source. To offset this tendency, the external energy must somehow be supplied to it, not as raw energy (like a bull in a china shop) but as organizing information. If the energy of the sun somehow is going to transform the non-living molecules of the primeval soup into intricately complex, highly organized, replicating living cells, and then to transmute populations of simple organisms like worms into complex, thinking human beings, then that energy has to be stored and converted into an intricate array of sophisticated machinery by an intricate array of complex codes and programs. If such codes and mechanisms are not available on the earth, then the incoming heat energy will simply disintegrate any organized systems that might accidentally have shown up there. [My emphasis]

Henry M. Morris, PhD; Op. cit.

And so the late Dr Henry M. Morris, spiritual founder of modern Young-Earth Creationism, displayed his dishonesty, prowess at building straw men, almost complete ignorance of basic physics and a cavalier attitude to the truth - to put it mildly. It's hard to imagine that even someone with an engineering degree would not have a grounding in basic science.

But all that is irelevent, and another creationist straw man anyway, because, as we are now understanding, there need be no increase in complexity whatsoever in evolution. All that is needed is a small change in the way genes are controlled by other genes. Studies such as that by the Spanish CNIO team are showing that the difference between related taxons are actually very small and more apparent than real. Most shockingly for creationists and religious people who like to flatter themselves with the thought that they are so important a god must have created a Universe just so it had somewhere to put its special creation, human beings, science is increasingly showing that we are simply another evolved species and very little different to any other evolved species.

*© The Author 2014. Published by Oxford University Press.
Reproduced for non-commercial re-use under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/)


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2 comments :

  1. According to this article, The Norway spruce genome sequence and conifer genome evolution (see: http://www.nature.com/nature/journal/v497/n7451/full/nature12211.html ), the genome sequencers have identitied almost 29,000 functional (= protein-coding) genes, compared with 19,000 functional genes in the human genome.

    And the total genome of the Norwegian spruce is SEVEN times bigger than the human genome.

    All this makes me wonder: Why did God create the Norwegian spruce with so many functional genes and such a big genome? Does it mean that conifers are the crowning work of God's creation? Instead of Adam and Eve?

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    1. Interesting, and might well be material for another blog. Also the fact that some salamanders have a vastly larger genome than humans, giving the lie to creationist assertions that science claims evolution always involves increasing complexity.

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