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A Chimp’s Loss is Our Gain?

Patrick
March 1, 2006
Biology, Darwinism, Evolution
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http://www.umich.edu/news/index.html?Releases/2006/Feb06/r021406

Researchers who speculate about human origins have come up with three main scenarios for how we ended up with our unique traits, Zhang said. The first possibility is that we acquired completely new genes that other apes don’t have. Another is that some of our genes have taken on different functions through mutation.

It’s also possible that we humans lost some genes along the way, and those losses provided opportunities for changes that otherwise could not have occurred. For example, scientists have shown that over the course of evolution, humans lost a gene that produces a particular jaw muscle protein. Perhaps the loss of that gene gave us smaller jaw muscles, making room in our skulls for bigger brains.

That’s just speculation, and until now there was no concrete evidence for the “less is more hypothesis” that losing certain genes offered tangible benefits, Zhang said. “So we wanted to know how many genes have been lost and what kinds of genes have been lost in human evolution, and second, whether any of those gene losses was a good thing.”

Read the full thing for more.

On a side note would anyone happen to know whether anyone out there is claiming that chimps and humans are in fact NOT related and the similar features came about by convergent evolution? If there isn’t, why not?

Comments
Patrick, To answer your question, I have never heard anyone argue for convergent evolution of humans - an intering question in principle when you consider other instances of convergence. However, I did hear a programme on the BBC on the 'Aquatic Ape Hypothesis', presented by David Attenborough (funny, as he doesn't like ID but does like the AAH - both are fringe ideas in evolution). Here it is: http://www.bbc.co.uk/radio4/science/scarsofevolution.shtml In a nutshell, it argues that humans split from the other ape-like ancestors and evolved their traits in an aquatic environment. Something that I find interesting, having followed ID is that ID is not the only idea in evolution that has a dedicated debunking website devoted to it - see http://www.aquaticape.org/ for the 'Panda's Thumb' of the AAH The debunker is not an evolutionary biologist or even any scientist at all, but he sure seems to be a big fan of Darwin!! Funny.antg
March 5, 2006
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Alan Grey made a fairly rough estimate in order to get his point across but perhaps you could point that out to him if you want. Also it's a bit hard to take such randomness into account unless you assume such events must occur regularly.Patrick
March 5, 2006
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Patrick, Your calculation makes a crucial assumption: that each base pair difference represents an independent mutational event. That’s how you end up needing such a large number of mutations being fixed per generation. However, if a gene gets deleted or duplicated or viral DNA is inserted into the genome, then we are talking about single mutational events comprising perhaps thousands of base pairs. This should be taken into account in your calculation and clearly it tends to lower, perhaps greatly lower, your estimate of the number of mutations that have to be fixed per generation. Hanshanseconomist
March 5, 2006
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Scott, I'd agree it's not enough to explain the entirety of the complexity we find in nature but I'm hesitant to say it can NEVER produce "anything creative".Patrick
March 2, 2006
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I'm of the opinion that the Darwinian mechanism is incapable of anything creative. It maintains the status quo. NS can only apply selection pressures and "activate" information already present within the genome.Scott
March 2, 2006
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"Evolution" in general is a fact. The key point of contention is how far can things go with unguided natural processes. That's what needs to be discovered. It might be possible that under certain circumstances limited types of CSI can be created by unguided natural processes. Who knows.Patrick
March 2, 2006
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Joseph. I would be interested to get a reference to the paper about orangutan and humans. One thing I have learned when talking to an evolutionist is : small changes in genes = evolution moderate changes in genes = evolution big changes in genes = evolution no changes in genes = evolution convergent changes with supposed common ancestor = evolution convergent changes with different species = evolution it is a no-win battle!rb
March 2, 2006
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Actually science has demonstrated that convergent evolution can also be considered for genetic similarities. There was a paper that demonstrated that, for example, a human and an orangutan(sp?) shred the same alleged mutation, however, these organisms were not supposed to have a common ancestor- the alleged more recent common ancestors did not have the same muation. I will look for the paper...Joseph
March 2, 2006
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First off, I realize that. For example the horse has 64 pairs and donkeys 62. Problem is the 63 chromosome mule results in an incomplete reproductive system.

To save time I'll do a copy and paste job:

http://www.nature.com/nature/journal/v437/n7055/full/437047a.html

“Comparing the genetic code of humans and chimps will allow us to comb through each gene or regulatory region to find single changes that might have made a difference in evolution,” they say, but remind us that the oft-quoted 96%-similar-gene figure between chimps and humans must be seen in context: “At a conservative estimate we share about 88% of our genes with rodents and 60% with chickens. Applying a more liberal definition of similarity, up to 80% of the sea-squirt’s genes are found in humans in some form. So it’s no surprise that we are still asking, ‘What makes us human?’”

http://www.nature.com/nature/journal/v437/n7055/full/437050a.html

“The question of what genetic changes make us human is far more complex. Although the two genomes are very similar, there are about 35 million nucleotide differences, 5 million indels and many chromosomal rearrangements to take into account. Most of these changes will have no significant biological effect, so identification of the genomic differences underlying such characteristics of ‘humanness’ as large cranial capacity, bipedalism and advanced brain development remains a daunting task.”

http://www.nature.com/nature/journal/v437/n7055/full/nature04000.html

A third of apparent segmental duplications in the human genome (defined by more than 94% sequence identity) are not found in the chimp genome. This team compared the two genomes, and figured that this required a duplication rate of 4 to 5 million bases per million years since humans and chimps parted evolutionary ways. Most of the changes, surprisingly, deal with chromosome structure. No clear picture emerges for how or why these differences arose: “It is unknown whether slow rates of deletion, high rates of duplication or gene conversion are largely responsible for the evolutionary maintenance of these duplicates.” A surprising conclusion is that “when compared to single-base-pair differences, which account for 1.2% genetic difference, base per base, large segmental duplication events have had a greater impact (2.7%) in altering the genomic landscape of these two species.”

A couple points to keep in mind:

Epigenetics: Genes cannot be telling the whole story. There’s a lot more going on to make us human than just genes. If two mice species that look similar have just as much genetic difference (4%) as humans and chimps, and if dogs, from great danes to chihuahuas, have far less genetic difference (0.15%), then clearly phenotypic difference (outward appearance) is not a linear function of genotypic distance. Just look into the research being done on mRNA and all the “junk” DNA. After all, those systems control the expression of genes. You have to look at the entirety of the system and not just a section. It’s almost like if I were to look at someone’s source code and try to figure it how it works by focusing in on the variables and ignoring the majority of the functions. Though some scientists might find this comparison insulting, I liken geneticists to the “script-kiddies” of software engineering since they modify already functioning code without knowing what they’re doing in order to discover how it works.

Inconsequential Differences: Why should genes differ so widely that are only concerned with chromosome structure? Why should there be so many segmented duplication differences, and “neutral” differences? Darwinists wanted to find clear evidence of positive selection leading to upright posture, language and culture. Although such studies are just beginning, they only have a paltry few to suggest so far, and those are ambiguous.

Phenotypic Revolutions: Humans exhibit several profound anatomical differences shared by no other primate: upright posture, ability to do long-distance running, naked skin with thermoregulatory function, prolonged maturation, vocal apparatus suited for language, a very large brain relative to body size, and much more. Could this much interrelated change occur by undirected, accidental mutations over a few “short” millions of years? Where is the evidence for strong positive selection in the DNA?

http://alangrey.blogspot.com/2005/09/science-chimp-dna-fully-sequenced.html

“Another interesting thing to note. Despite the similarities in human and chimp genomes, the scientists identified some 40 million differences among the three billion DNA molecules, or nucleotides, in each genome.

Since we apparently diverged from a common ancestor 6 million years ago, that is roughly 6.6 mutations per year that get fixed within the genome (or 3.3 per year if you divide them equally amongst the 2 branching species). Given a conservative estimate of average generational time of 10 years, this means that 33 new mutations had to be fixed within the population every generation.

This seems fairly high to me. The current human mutation rate is around 3 or 4 mutations per organism. It becomes a very messy math exercise to test whether this rate is even possible, but you can be sure of one thing - the evolutionists won’t bother studying this scientific question unless they are pushed by those anti-science creationists who want to stop all science being done.

Update: Most of the news articles I read state the size of the chimp genome at 3 billion base pairs (BP) (the same number as humans are reported to have), yet checking into the actual values of the two species makes this claim of equal sized genomes as false. The human genome (homo sapiens) has a CV of 3.5, which equates to roughly 3.423 Billion BP. The chimp genome (pan troglodytes) has a CV of 3.76, which equates to roughly 3.6773 Billion BP. (although there is a range of CV figures from 3.63 to 3.85 - this range equates to 3.55 billion BP to 3.77 billion BP)

So at the outset, the chimpanzee genome has 250 (or taking the lowest of the range 122) MILLION additional base pairs over the human genome. So why is the difference only reported only 40 million? It seems the difference MUST be a lot higher than commonly referred to. This would also make the required mutation rate about 3 to 6 times higher as well.”

Patrick
March 1, 2006
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Chromosome number is not that constant. Different "subspecies" (house mice have been studied a lot in this respect) can differ in chromosome number and this may prevent them from "merging" again because hybrids usually lack essential genes or have too many of them. It might be an important postzygotic isolation mechanism.Raevmo
March 1, 2006
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I'm not talking about a scenario where Pan troglodytes and Homo sapiens came about by vastly disparate lines (as is claimed to be the case with many, many other instances of convergent evolution). I'm talking about having a common ancestor a bit further back and then the morphological similarities for both came about by convergent evolution. Also, when it comes to genetic similarities chromosome number is probably more constant, however, than any other single morphological characteristic that is available for species identification since it determines how DNA is stored. And going by that we're more closely related to the potato. :)Patrick
March 1, 2006
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My guess is that so far convergent evolution can only account for morphological similarities (like whales and fish) and maybe a gene type here or there. But I don't think anyone believes convergent evolution can account for sharing massive amounts of coding and noncoding DNA, combined with morphological similarities. Therefore it's probably not considered a possible source for high degrees of similarities like those between a chimp and a human.

Fross
March 1, 2006
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