Thursday, 21 August 2014

Pygmies - Another Big Problem for Creationists

Baka pygmies, West Africa
African pygmies evolved their short stature twice - health - 18 August 2014 - New Scientist

A paper published in PNAS last month is interesting for what it tells us of human evolution and of evolution in general, and it raises a major question for creationist loons to carefully avoid.

Significance

Tropical rainforest hunter-gatherer populations worldwide share the pygmy phenotype, or small human body size. The evolutionary history of this phenotype is largely unknown. Here we studied DNA from the Batwa, a rainforest hunter-gatherer population from east central Africa, to identify regions of the Batwa genome that underlie the pygmy phenotype. We then performed population genomic analyses to study the evolution of these regions, including comparisons with the Baka, a west central African rainforest hunter-gatherer population. We conclude that the pygmy phenotype likely arose due to positive natural selection and that it arose possibly multiple times within Africa. These results support longstanding anthropological hypotheses that small body size confers an important selective advantage for human rainforest hunter-gatherers.


Batwa pygmies, Uganda
The study found that two different groups of African pygmies had evolved independently. Examining the DNA from 169 Batwa pygmies from Uganda with that of 71 Baka from West Africa, the team found there was no overlap, showing that they had not acquired their short stature from a common ancestor. The team concluded that pygmyism had evolved at least twice and possibly multiple times due to positive natural selection in an environment which favoured small stature.

Quite what that advantage was is not certain but it could be, for example taking less energy to hunt in conditions where there are low branches such as in the rain forests where pygmies are normally found. It could also be an adaptation to an environment with many life-limiting hazards making it an advantage to stop growing and reach sexual maturity earlier.

If you're short, you find it much easier because you're bending much less to duck under branches. The shorter ones bend over less, sweat less and thereby expend less energy.

Luis Barreiro, University of Montreal, Quebec, Canada
Interesting though this is, it's easy to understand from an evolutionary point of view. The same or very similar environments acting on genetic variation will tend to converge on similar solutions to the same problems. What is not predictable however, is the precise nature of that variation given the randomness with which it arises. Anything which conveys an advantage in terms of the number of descendants will tend to be selected for and so will increase in the population.

There is no reason why the same genes or the same alleles of those genes should be involved in different populations so long as the effect is the same, and with about 16 areas of the human genome being associated with small stature, there is plenty to choose from. There are many ways to skin a cat and evolution has no preconceived notions about the best way to achieve it.

However, to fit these facts into an intelligent design model is a big problem for creationists. Why would an intelligent designer design multiple solutions to the same problem, or rather use multiple ways to achieve the same result, especially given exactly the same starting position?

Any creationist willing to solve this conundrum and suggest an explanation which is better than the scientific, Darwinian one, or is it to be ignored again like so many similar problems for the crackpot, evidence-free notion of intelligent design?

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18 comments :

  1. So how would you address those who would argue that this is only an example of "microevolution" which has occurred since God created homo-sapiens separately from the other great apes?

    Is there any genetic evidence for how recently these traits evolved?

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    1. By pointing out the ignorant stupidity of people who fall for the dishonest creationist pseudo-scientists' claim that there is a fundamental difference in the mechanism. See Creationist's Macro-Evolution Lie.

      I'm sorry if you are one or the other.

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  2. I don't think you understand what creation or ID biologists believe about evolution. They all agree that mutation and selection happen, some mutations are beneficial, and those mutations become fixed in populations through selection. That's how races came about, as well as the origin of lactose tolerance.

    The issue with evolution is the rate at which beneficial mutations arise and can become fixed in a population. All of our observations show us it's too slow. In 10^20 HIV we see several hundred mutations becoming selected and fixed in populations. It takes 10^20 malaria just to find the right four letters to gain chloro-quine resistance under strong selective pressure--and all other observations of microbial evolution in huge populations and under various selective pressures show only such very small gains. If this were not the case we would be talking about better results than it taking a trillion e coli just to duplicate their existing citrate gene a few times. :P

    Now compare that to evolution in mammals. There would've been about 10^20 or fewer mammals that ever lived since their shared common ancestor 200 million years ago. All mammals share about 5% DNA in common. We now know that genomes are mostly functional, which means that in the various mammal lineages you would need hundreds of billions of beneficial mutations to arise and become fixed.

    So if evolution is a lottery, after buying 10^20 tickets the various microbial species would've won between a few dollars and a few hundred. While mammals won hundreds of billions. Even though "the efficiency of natural selection declines dramatically between prokaryotes, unicellular eukaryotes, and multicellular eukaryotes", as Lynch says.

    So what about our Pygmies? I scanned the paper and they don't know what mutation is responsible for their shorter stature. But they say:

    "The identified genomic regions have multiple attributes that provide supporting evidence of genuine association
    with the pygmy phenotype, including enrichments for SNPs previously associated with stature variation in Europeans and for genes with growth hormone receptor and regulation functions."

    Which sounds an awful lot like mutations are knocking out (breaking) the binding of the growth hormones. Not surprising since most beneficial mutations give a gain by breaking something. "evolution in most of the lineages was apparently dominated by extensive loss of genes and introns" as Koonin published.

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    1. >I don't think you understand what creation or ID biologists believe about evolution.>

      I'm not concerned with creationist strawman parodies, lies, deliberate misrepresentations of ignorant assumptions. If what they believe differs from what science knows, then they are wrong. Knowledge is not a matter of belief.

      There really aren't fairies just because you might believe in them, because reality hasn't the slightest interest in your beliefs no matter how important you might think you are or how indignant you might be when reality fails to conform to your requirements.

      If ever evolution is refuted, it will be done by a scientist, not an idiot.

      I hope that helps.

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  3. Here are some links to articles that hopefully can shed light on creationist misrepresentations of what evolution is:

    1) http://www.oeb.harvard.edu/faculty/hanken/documents/Hanken%20and%20Wake%201993%20Ann%20Rev%20Ecol%20Syst.pdf .

    2) http://www.newscientist.com/article/dn13673-evolution-myths-mutations-can-only-destroy-information.html&.U9H0pfmSxmM#.U_enQfmSwQM

    3) http://aeon.co/magazine/science/vlatko-vedral-evolution-quantum-physics/

    4) http://aeon.co/magazine/science/kenneth-weiss-anne-buchanan-genetics/

    And now a specific answer to Joecoder7 who wrote: Not surprising since most beneficial mutations give a gain by breaking something. "evolution in most of the lineages was apparently dominated by extensive loss of genes and introns" as Koonin published.

    Link #2 provides an answer to (and refutation of) that claim; I quote:

    Most people lose the ability to digest milk by their teens. A few thousand years ago, however, after the domestication of cattle, several groups of people in Europe and Africa independently acquired mutations that allow them to continue digesting milk into adulthood. Genetic studies show there has been very strong selection for these mutations, so they were clearly very beneficial.

    Most biologists would see this as a gain in information: a change in environment (the availability of cow's milk as food) is reflected by a genetic mutation that lets people exploit that change (gaining the ability to digest milk as an adult). Creationists, however, dismiss this as a malfunction, as the loss of the ability to switch off the production of the milk-digesting enzyme after childhood.

    Rather than get bogged down trying to define what information is, let's just look at a few other discoveries made by biologists in recent years. For instance, it has been shown a simple change in gene activity in sea squirts can turn their one-chambered heart into a working two-chambered one. Surely this counts as increasing information?

    Some monkeys have a mutation in a protein called TRIM5 that results in a piece of another, defunct protein being tacked onto TRIM5. The result is a hybrid protein called TRIM5-CypA, which can protect cells from infection with retroviruses such as HIV. Here, a single mutation has resulted in a new protein with a new and potentially vital function. New protein, new function, new information.

    Although such an event might seem highly unlikely, it turns out that the TRIM5-CypA protein has evolved independently in two separate groups of monkeys. In general, though, the evolution of a new gene usually involves far more than one mutation. The most common way for a new gene to evolve is for an existing gene to be duplicated. Once there are two or more copies, each can evolve in separate directions.

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    1. Creationists either deliberately, or through ignorant stupidity, don't distinguish between information and meaning. Genetic information is given meaning by the environment. see Evolution - The Meaning of Information

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    2. Lactose tolerance is usually the first example I share when I'm asked for an example of a beneficial mutation in humans. The trait has even arose at least 3 separate times within thousands of years. This would be more remarkable if humans couldn't previously digest lactose, but all these mutations seem to do is disable the switch that normally shuts it off after nursing ends. I don't really consider that new information. But in my original post I shared examples where we did observe evolution creating new information, so I don't know why your whole post seems to be addressing me as if I claim the opposite?

      I found one paper on TRIM5 and it looks like this evolution was only inferred by comparing the differences between living old world monkeys, and not observed. If that's the case you may as well compare the human and platypus genomes, see they differ by about 3 billion bases, and say "look at all these differences evolution produced". The two-chambered sea-squirt heart appears to be laboratory induced through genetic engineering. Were the resulting sea-squirts more fit than their progenitors? Either way it's not observed evolution. I only read the summary.

      So let's get back to the real issue here. As I posted above:

      1. In 10^20 p. falciparum (human malaria) exposed to chloroquine, we saw a gain through 4 mutations.
      2. In 10^20 HIV, we've seen evolution produce thousands of likely (we'll assume they are) beneficial mutations. Some even created one or more new binding sites.
      3. In 10^20 mammals evolution would have had to create hundreds of billions of new beneficial gains through evolution.

      So we have a difference of about a hundred million fold, despite that mammals are a worst-case scenario for evolution due to the prominence of drift over selection.

      If you respond, please address this instead of pasting links and text from articles.

      Rosa Rubicondior, very very few random sequences of amino acids will fold together into a structured protein. Somewhere between one in 10 trillion or one in 10^64, depending on how you test and the size of the protein. So while environmental pressures fluctuate, the rules of chemistry that allow structured proteins do not. Information is when sequences that match the specification given to us by chemistry. After you get that far, environmental pressures will affect which proteins are functional.

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  4. I just found this newsletter in my mail box: https://ksj.mit.edu/tracker/2014/08/why-covering-creation-science-is-like-covering-cricket/ .

    A quote: The folks from the ICR [the Institute for Creation Research] take a literal view of the book of Genesis--"that argues humans lived alongside dinosaurs, that Noah loaded the adolescent Jurassic-era creatures on the ark in pairs with every other animal species on the planet, and that natural wonders like the Grand Canyon were formed in months instead of millions of years," Farwell writes. It shouldn't be too hard to distinguish these folks from scientists.

    [...]

    Farwell might have done better to quote, say, Laurence Krauss, a physicist who has spoken and written widely about creationism, and who says teaching it to kids "is child abuse." And he should have devoted far more of the article to the institute's critics.

    Farwell reports that the institute sued Texas to have its master's degree program certified; he doesn't say what happened. He repeats some of creationism's familiar "scientific" claims, including the assertion that spiral galaxies can't be billions of years old or that oceans should be saltier if they've been around a billion years. Farwell doesn't ask scientists to respond to these claims; they stand unchallenged in the story. And much has been written about what's wrong with them.

    [...]

    The issue here deals with more than evolution. We've seen the same thing with climate change--isolated scientists who claim a unique hold on a truth that clashes with nearly everyone else's. We've seen it with anti-vaccine campaigners.

    Farwell is sadly wrong on the details and wrong on the big picture. He's unfair to the scientists who should have been asked to respond to the claims the Institute for Creation Research made, and he is unfair to his readers, who will come away from the story with a blinkered and inaccurate view of "creation research."

    IN SUMMARY: You're MUCH NEEDED in this debate, Rosa.

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    1. It's easier for a camel to pass through the eye of a needle than to get a creationists to read a science book. :-)

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  5. @joecoder7: If you really have read the article "Genome reduction as the dominant mode of evolution" by Yuri I. Wolf and Eugene V. Koonin - see: http://onlinelibrary.wiley.com/doi/10.1002/bies.201300037/pdf - then I don't understand why you cite that article in the way you do.

    Actually it's enough if you just read just the abstract to see that you have a biased view of the research that Wolf & Koonin have done and write about in their article. Let me quote from the abstract:

    A common belief is that evolution generally proceeds towards greater complexity at both the organismal and the genomic level, numerous examples of reductive evolution of parasites and symbionts notwithstanding. However, recent evolutionary reconstructions challenge this notion. Two notable examples are the reconstruction of the complex archaeal ancestor and the intron-rich ancestor of eukaryotes. In both cases, evolution in most of the lineages was apparently dominated by extensive loss of genes and introns, respectively. These and many other cases of reductive evolution are consistent with a
    general model composed of two distinct evolutionary phases: the short, explosive, innovation phase that leads to an abrupt increase in genome complexity, followed by a much longer reductive phase, which encompasses either a neutral ratchet of genetic material loss or adaptive genome streamlining. Quantitatively, the evolution of genomes appears to be dominated by reduction and simplification, punctuated by episodes of complexification.

    As far as I understand it, what Wolf & Koonin are saying is that quantitatively speaking you see an evolution of genomes dominated by reduction and simplification. But - and this is very important - you can also observe episodes of complexification.

    In other words: You're not telling all the truth, joecoder7, when you cite that article. Let me use a metaphor: Imagine the development of television sets. In the beginning they were big "colossuses". Then they successively became smaller and smaller. What I mean with this metaphor is that TV sets can become smaller although their complexity is increasing. That is, you can't look at evolution by just using a quantitative focus on the process. You must not forget the qualitative aspects.

    As far as I can understand it neither Wolf nor Koonin believe in creationism in spite of their findings of what the evolutionary process looks like. They apparently know that it's natural that simplification follows from a state of complexity and vice versa, all in a mutual/reciprocal way.

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    1. I wonder what these Dunning-Kruger simpletons imagine they are achieving by posing as experts. Do they think they are fooling anyone?

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    2. Yes, I read that part before I posted. Remember in my original post I'm comparing rates of observed evolution vs inferred rates in the past, and noting that there's a huge difference between what we see evolution doing today and what it must have done long ago.

      Koonin's text reinforces this. The "eposides of complexification" are not observed--only inferred because they compare genomes, see lots of adaptive differences, and chalk up every difference as a point for evolution. If you want to dispute this, please provide me an example where we've seen evolution produce hundreds of billions of adaptive gains in a population of 10^20. Or anything else anywhere close to that scale.

      Neither Wolf nor Koonin are creationists. I deliberately cite scientists from your own side as a testament against your claims. But if you'd prefer I can instead cite creationists who say the same thing :P

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    3. Evolution is not a process of 'complexification'. It may even involve LOSS of complexity but usually no increase at all. Could you remind us which serious biologist ever claimed we should be able to observe evolution occurring, please? Or are you just another creationist making ludicrous claims from carefully nurtured ignorance and challenging people to throw stones at your straw man?

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    4. Since "neither Wolf nor Koonin are creationists", a very relevant question to ask is this one: Why aren't they creationists. I can see two explanations: 1) They don't believe in their own research (which is very unlikely). Or, much more likely, they trust their own research but don't find their conclusions favoring creationism. And then I must ask you: Do you consider their research and conclusions as favoring and proving creationism? If your answer is yes, please try to explain why you're right and they're wrong.

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    5. This is JoeCoder again: I'm not sure why my name is being displayed as a long hexadecimal string. Perhaps a blogsot bug somewhere?

      Anyway, I think many disagree with my own conclusions because they see anything other than materialistic naturalism as a violation of scientific professionalism. As Lynn Margulis interviewed: "The critics, including the creationist critics, are right about their criticism. It’s just that they've got nothing to offer but intelligent design or 'God did it.' They have no alternatives that are scientific."

      Most are not as straightforward as Margulis, but I see the "anything except evolution is not science" perspective everywhere. However I can't speak directly for Koonin because I don't know whether he holds the same view.

      Biological systems contain complexity. By complexity I mean sequences that must be specific in order to function, and are not composed of trivial repeating patterns. So to accept evolutionary theory, evolution must be capable of both creating such sequences and creating them faster than it destroys them.

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    6. You forgot to say why you think evolution can't create complexity. You also forgot to say why complexity means 'sequences that must be specific in order to function'. Have you just been accepting what the frauds who push ID have been telling you?

      Your name is showing as your openid from Stackexchange.com because that's how you are logging on to Blogger, by the way.

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  6. @Rosa: After reading your excellent blog article Evolution - The Meaning of Information (see: http://rosarubicondior.blogspot.co.uk/2011/12/evolution-meaning-of-information.html ) I came to remember the so-called Neuronal Recycling Hypothesis, which was proposed by Stanislas Dehaene around soon a decade ago. See: http://en.wikipedia.org/wiki/Neuronal_Recycling_Hypothesis .

    Let me quote from that Wikipedia article:

    QUOTE #1: This hypothesis was formulated in response to the 'reading paradox', which states that these cognitive processes are cultural inventions too modern to be the products of evolution. The paradox lies within the fact that cross-cultural evidence suggests specific brain areas are associated with these functions. The concept of neuronal recycling resolves this paradox by suggesting that novel functions actually utilize and 'recycle' existing brain circuitry. Once these cognitive functions find a cortical area devoted to a similar purpose, they can invade the existing circuit. Through plasticity (an ongoing characteristic of the brain's cortical structure to change and reorganize through learning), the cortex can adapt in order to accommodate for these novel functions.

    QUOTE #2: The concept of neuronal recycling is similar to exaptations in evolutionary theory, which states that several evolved functions are simply byproducts of an ancient biological mechanism.[1] This process, however, is the reuse of biological mechanisms that occur as a result of brain plasticity, rather than evolutionary pressures on a population. Neuronal recycling produces changes in a matter of weeks to years which don't require a change in genome like evolutionary exaptations do.

    QUOTE #3: The neuronal recycling hypothesis relies on the following assumptions:

    i) The organization of the human brain is subject to anatomical constraints from evolution and thus is not infinitely plastic. Neural maps are present in infancy which biases subsequent learning.

    ii) Cultural tools like reading and writing are not present in the brain at birth, but rather must find a neuronal niche in the brain whose circuit is set up to perform a similar function and is sufficiently plastic to reorient itself enough to accommodate this novel use.

    iii) The original organization of the cerebral cortex is never fully erased once these cultural tools invade the cortical areas. Instead, these initial neural constraints exert a powerful influence on what can be learned.

    QUOTE #4: In response to these criticisms, Cohen & Deheane proposed there is a functional specialization in the visual word form area for reading, which is reproducible across subjects and cultures. They do not believe there is specific selectivity for word recognition because it is activated by other stimuli, such as the aforementioned object recognition and naming tasks. This can, however, be explained by the fact that this cortical area was recycled in order to accommodate reading functions, and thus it is not unlikely to be activated in other, similar tasks.

    If Stanislas Dehaene is right, then evolution of new cognitive traits and qualities obviously can occur without directly involving genes by recycling of one or more cortical areas in the brain.

    Did you find this information interesting, fascinating and useful? Then I recommend you to also click this link: http://readinginthebrain.pagesperso-orange.fr/figures.htm . There you'll find a very good summary of Stanislas Dehaene's book "Reading in the Brain" from 2009.

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  7. A very common debate technique among creationists seems to be creating false dichotomies. They attack the evolution paradigm thus apparently believing that by casting suspicion upon evolution they automatically strengthen the creationism paradigm.

    That's an unfair and very biased way of debating if creationism has better explanation and probability powers than evolution.

    That's why I find it a legitimate question to ask: Why haven't Wolf and Koonin become creationists, since their research is promoted and cited by so many creationists as evidence of biblical creationism? I smell more than one rat here, i.e. it seems likely to believe that creationists misinterpret their research and conclusions.

    BTW, here are two articles about genes and DNA: 1) http://aeon.co/magazine/science/kenneth-weiss-anne-buchanan-genetics/ (Title: Things genes can’t do. Simplistic ideas of how genes ‘cause’ traits are no longer viable: life is an orderly collection of uncertainties.); and 2) http://aeon.co/magazine/science/does-our-genetic-heritage-lie-under-a-pile-of-junk-dna/ (title: Life doesn’t make trash. A genome is not a blueprint for building a human being, so is there any way to judge whether DNA is junk or not?).

    Both of these articles contain many facts that reasonably must be extremely difficult for creationists to explain away. If God created life, then God must have been a nutty engineer or geneticist, since the genomes look like a patchwork. An omniscient God? Forget it!

    ReplyDelete

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