Tibetans inherited gene for life at high altitudes from Denisovans?

_{Denyse O'Leary

July 14, 2014

Human evolution, News}

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From the BBC:

The variant of the EPAS-1 gene, which affects blood oxygen, is common in Tibetans – many of whom live at altitudes of 4,000m all year round.

But the DNA sequence matches one found in the extinct Denisovan people.

Many of us carry DNA from extinct humans who interbred with our ancestors as the latter expanded out of Africa.

Both the Neanderthals – who emerged around 400,000 years ago and lived in Europe and western Asia until 35,000 years ago – and the enigmatic Denisovans contributed DNA to present-day people.

From Nature:

As modern humans migrated out of Africa, they encountered many new environmental conditions, including greater temperature extremes, different pathogens and higher altitudes. These diverse environments are likely to have acted as agents of natural selection and to have led to local adaptations. One of the most celebrated examples in humans is the adaptation of Tibetans to the hypoxic environment of the high-altitude Tibetan plateau1, 2, 3. A hypoxia pathway gene, EPAS1, was previously identified as having the most extreme signature of positive selection in Tibetans4, 5, 6, 7, 8, 9, 10, and was shown to be associated with differences in haemoglobin concentration at high altitude. Re-sequencing the region around EPAS1 in 40 Tibetan and 40 Han individuals, we find that this gene has a highly unusual haplotype structure that can only be convincingly explained by introgression of DNA from Denisovan or Denisovan-related individuals into humans. Scanning a larger set of worldwide populations, we find that the selected haplotype is only found in Denisovans and in Tibetans, and at very low frequency among Han Chinese. Furthermore, the length of the haplotype, and the fact that it is not found in any other populations, makes it unlikely that the haplotype sharing between Tibetans and Denisovans was caused by incomplete ancestral lineage sorting rather than introgression. Our findings illustrate that admixture with other hominin species has provided genetic variation that helped humans to adapt to new environments. (paywall)

For an understandable reluctance to definitely classify the Denisovans as a separate “species,” see Neanderthal Man: The long-lost relative turns up again, this time with documents. A variety of terms is used in the BBC story; the notion of separate human “species” primarily meets psychological needs.

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Comments

So Dalai Lama was a GMO then?ChannaPrakash_{July 16, 2014
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Franklin: "Be forewarned to expect a multi=post link spam of articles from BA77…..few of which are pertinent to the topic and, IMO, far above BA77?s pay grade of understanding." What makes you conclude this?.... Oops. Spoke too soon. Maybe BA77 doesn't realize that most of us have full-time jobs. But beware. I have commented on his "bullsh_t baffles brains" approach and have been soundly chastised. Shunning will be next.Acartia_bogart_{July 15, 2014
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Franklin wrote: "Do you think there is a difference in the percentage of oxygen on the summit of Mt. Everest when compared to the percentage of oxygen at sealevel?" No difference in oxygen percentage, but a lower pressure at altitude (Everest's peak), thus less force for oxygen transfer in the lungs, and a resulting lower oxygen content in the blood. So your question has me wondering: Does this detail elicit further insight into the adaptive responses to high altitude in Tibetans, as compared to lowlanders? How does the Andeans function at altitude, inspite of their typical lowlander style 'compensatory mechanism' response, measure in respect to Tibetans or lowlanders?willh_{July 15, 2014
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bornagain77, I agree that the mutations discussed are well below the 500 bit threshold. Empirical evidence seems to support that natural causes did lead to a small gain of new information. Yet you imply this is not the case by saying "I would gladly concede that the adaptation to be a unambiguously information building beneficial mutation if it were so." I don't understand what your objection is in this example.rhampton7_{July 15, 2014
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BA77
goodnight Mr. franklin. I’m quite happy to let stand what I have stated and the evidence I have presented against your position.
but....but...but you haven't presented any evidence countering what I have pointed out. you seem to have missed this question (which pertains to the OP and what we are discussing): Do you think there is a difference in the percentage of oxygen on the summit of Mt. Everest when compared to the percentage of oxygen at sealevel?franklin_{July 14, 2014
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goodnight Mr. franklin. I'm quite happy to let stand what I have stated and the evidence I have presented against your position. A song to sleep on for you :) Come However You Are - City Harbor http://myktis.com/songs/come-however-you-are/bornagain77_{July 14, 2014
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I disagree. And I hold that a test for endurance between Tibetans and extremely fit individuals at normal altitude will bear out that the adaptation in Tibetans is deficient in a normal environment
Of course you disagree but it isn't because of the empirical data it is because you have no idea of what the underlying physiology and data indicates. the test was your idea. Why is it now up to me to conduct your proposed experiment? Is this characteristic of the ID camp where no experiments are ever conducted, no hypothesis are put forward, and no grant proposals are ever written to solicit funding to test their ideas/assertions? Here is a question for you, BA77. do you think the percentage of oxygen is different on the summit of Mt. Everest when compared to sealevel?franklin_{July 14, 2014
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I disagree. And I hold that a test for endurance between Tibetans and extremely fit individuals at normal altitude will bear out that the adaptation in Tibetans is deficient in a normal environment. Run the test and publish the results and get back to me! :) If you are correct you have finally shown a minor increase of functional information above and beyond what was already present. YAWN! Remind me to be impressed compared to what you have yet to explain. i.e. gigabytes on extremely sophisticated overlapping functional information! In the mean time, while you harp on this point as if it does your position any good in the grand scheme of things, you completely ignore the elephant in the living room that is absolutely devastating to your position. i.e. The overwhelming majority of mutations that are spreading throughout the human population are degrading the human genome! Dr. John Sanford: Genetic Entropy and the Mystery of the Genome - video https://www.youtube.com/watch?v=eY98io7JH-c Inside the Human Genome: A Case for Non-Intelligent Design - Pg. 57 By John C. Avise Excerpt: "Another compilation of gene lesions responsible for inherited diseases is the web-based Human Gene Mutation Database (HGMD). Recent versions of HGMD describe more than 75,000 different disease causing mutations identified to date in Homo-sapiens." I went to the mutation database website cited by John Avise and found: Mutation total (as of 2014-05-02) - 148,413 http://www.hgmd.cf.ac.uk/ac/ “Our Missing Genes” - The Scientist - February 18, 2012 Excerpt: On average, a person will have about 20 genes that are completely “lost”—meaning that both alleles have inactivating mutations. https://uncommondescent.com/genetics/at-least-1-percent-of-human-genes-can-be-shut-down-without-causing-serious-disease/ Human Genome in Meltdown - January 11, 2013 Excerpt: According to a study published Jan. 10 in Nature by geneticists from 4 universities including Harvard, “Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.”,,,: "We estimate that approximately 73% of all protein-coding SNVs [single-nucleotide variants] and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000 -10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes.",,, As for advantageous mutations, they provided NO examples,,, http://crev.info/2013/01/human-genome-in-meltdown/bornagain77_{July 14, 2014
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BA77<blockquote.No franklin, you are mistaken. Tell you what, let’s settle this disagreement empirically. Let’s have an extremely fit Tibetan compete against an extremely fit marathon runner at normal altitude and see who is found to be less fit in the contest!? Any bets?? No, I am not mistaken, BA77. As for your bet I would expect no differences in blood parameters of the Tibetan and any other healthy person on the planet. Any differences noted in marathon performance would be due to training not physiology. Do you think there would be a difference? If so why? Here is a question for you, BA77. do you think the percentage of oxygen is different on the summit of Mt. Everest when compared to sealevel?
But, as was already pointed out, this is all beside the point anyway
No it isn't beside the point. It is the point!
I would gladly concede this minor technicality to you but the evidence simply does not add up
it isn't a minor technicality and the evidence does add up but only if you have any idea of the subject matter at hand.franklin_{July 14, 2014
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No franklin, you are mistaken. Tell you what, let's settle this disagreement empirically. Let's have an extremely fit Tibetan compete against an extremely fit marathon runner at normal altitude and see who is found to be less fit in the contest!? Any bets??? :) But, as was already pointed out, this is all beside the point anyway. I would gladly concede this minor technicality to you but the evidence simply does not add up. The main point is that you refuse to address the elephant in the living room. i.e. Exactly how do you get gigabytes of extremely sophisticated overlapping functional information from a process that is overwhelmingly more likely to degrade information than build it up? Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. 38. Sanford J (2008) Genetic Entropy and the Mystery of the Genome. FMS Publications, NY. Pages 131–142. 39. Trifonov EN (1989) Multiple codes of nucleotide sequences. Bull of Mathematical Biology 51:417–432. 40. Trifanov EN (1997) Genetic sequences as products of compression by inclusive superposition of many codes. Mol Biol 31:647–654. 41. Kapranov P, et al (2005) Examples of complex architecture of the human transcriptome revealed by RACE and high density tiling arrays. Genome Res 15:987–997. 42. Birney E, et al (2007) Encode Project Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447:799–816. 43. Itzkovitz S, Hodis E, Sega E (2010) Overlapping codes within protein-coding sequences. Genome Res. 20:1582–1589. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Conclusions: Our analysis confirms mathematically what would seem intuitively obvious - multiple overlapping codes within the genome must radically change our expectations regarding the rate of beneficial mutations. As the number of overlapping codes increases, the rate of potential beneficial mutation decreases exponentially, quickly approaching zero. Therefore the new evidence for ubiquitous overlapping codes in higher genomes strongly indicates that beneficial mutations should be extremely rare. This evidence combined with increasing evidence that biological systems are highly optimized, and evidence that only relatively high-impact beneficial mutations can be effectively amplified by natural selection, lead us to conclude that mutations which are both selectable and unambiguously beneficial must be vanishingly rare. This conclusion raises serious questions. How might such vanishingly rare beneficial mutations ever be sufficient for genome building? How might genetic degeneration ever be averted, given the continuous accumulation of low impact deleterious mutations? http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006 Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637 In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read. Concluding powerpoint of the lecture (at the 1 hour mark): "Not only are there many different codes in the sequences, but they overlap, so that the same letters in a sequence may take part simultaneously in several different messages." Edward N. Trifonov - 2010 Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006bornagain77_{July 14, 2014
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BA7 my claim was modest
“Tibetans is don’t develop high red blood cells counts” and that high red blood cell counts are NORMALLY found to be good,,
no, this was your claim:
the ‘beneficial mutations’ that allow Tibetans to tolerate the low oxygen at high altitudes are actually found to be ‘slightly detrimnetal’ because they in fact result in a limit on the red cell blood count for Tibetans:
and you are wrong on all counts! There is nothing, from a physiological standpoint, limiting changes in the red cell counts of Tibetans despite your mistaken interpretation of the empirical data. To understand the data you first must understand why red cell counts increase in the first place and that seems to escape your grasp. BA77<blockquoteThus the point is simple. no, it isn't. BA77
In the high altitude Tibetans have traded off high red blood cell counts, which would normally be good at normal oxygen levels, for lower red blood cell counts at higher oxygen carrying capacity, in order to confer a benefit at high altitudes. At the most you could argue it was a tradeoff. You can’t argue that it is across the board beneficial since it will be a limiting factor for extremely fit individuals at normal altitude.
red cell number and hematocrit of Tibetans are anaagous to the rest of the worlds population. However, Tibetans Hb, due to mutational changes, has a higher oxygen binding affinity than the majority of the worlds population. This is why the Tibertans do not experience hypoxia at oxygen tensions that the rest of the worlds population would have great difficulty in saturating their hemoglobin with oxygen. There is no doubt that you could subject Tibetans to conditions their bodies would perceive as hypoxic and you would then see the same compensatory mechanisms kick in to help their body deal with the hypoxic conditions. Give it up, BA77, you are simply wrong and have no understanding of the subject matter......your comments make this abundantly clear. Do you know what polycythemia is and why it is a dangerous condition? Rhampton
Why is this not such a case? Isn’t this an example empirical evidence?
it is such a case and the empirical evidence bears this out,franklin_{July 14, 2014
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rhampton7, the limit is 500 bits of functional information generated by natural processes to falsify ID. A few mutations to a preexisting gene would hardly meet that limit: Intelligent Design: Required by Biological Life? K.D. Kalinsky - Pg. 10 - 11 Case Three: an average 300 amino acid protein: Excerpt: It is reasonable, therefore, to estimate the functional information required for the average 300 amino acid protein to be around 700 bits of information. I(Ex) > Inat and ID (Intelligent Design) is 10^155 times more probable than mindless natural processes to produce the average protein. http://www.newscholars.com/papers/ID%20Web%20Article.pdf Measuring the functional sequence complexity of proteins - Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors - 2007 Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families.,,, http://www.tbiomed.com/content/4/1/47 To clarify as to how the 500 bit universal limit is found for 'functional information': Dembski's original value for the universal probability bound is 1 in 10^150, 10^80, the number of elementary particles in the observable universe. 10^45, the maximum rate per second at which transitions in physical states can occur. 10^25, a billion times longer than the typical estimated age of the universe in seconds. Thus, 10^150 = 10^80 × 10^45 × 10^25. Hence, this value corresponds to an upper limit on the number of physical events that could possibly have occurred since the big bang. How many bits would that be: Pu = 10-150, so, -log2 Pu = 498.29 bits Call it 500 bits (The 500 bits is further specified as a specific type of information. It is specified as Complex Specified Information by Dembski or as Functional Information by Abel to separate it from merely Ordered Sequence Complexity or Random Sequence Complexity; See Three subsets of sequence complexity ) Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors http://www.tbiomed.com/content/2/1/29bornagain77_{July 14, 2014
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"I would gladly concede that the adaptation to be a unambiguously information building beneficial mutation if it were so." Why is this not such a case? Isn't this an example empirical evidence?rhampton7_{July 14, 2014
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franklin, my claim was modest: "Tibetans is don’t develop high red blood cells counts" and that high red blood cell counts are NORMALLY found to be good,, "Extremely fit individuals may have higher values—significantly more red cells in their bodies and significantly more oxygen-carrying capacity—but still maintain normal hematocrit values." Thus the point is simple. In the high altitude Tibetans have traded off high red blood cell counts, which would normally be good at normal oxygen levels, for lower red blood cell counts at higher oxygen carrying capacity, in order to confer a benefit at high altitudes. At the most you could argue it was a tradeoff. You can't argue that it is across the board beneficial since it will be a limiting factor for extremely fit individuals at normal altitude. Thus you have not proven your point that it was an increase of functional information over and above what is already present. But all this is beside the point anyway. I would gladly concede that the adaptation to be a unambiguously information building beneficial mutation if it were so.,,, The 'elephant in the living room point' that you, and other Darwinists, refuse to address honestly is the fact that all our empirical evidence shows (Behe) random mutations and natural selection are far more likely to degrade information than to build it up. That is what the empirical evidence I have already cited indicates, and you have yet to honestly address that point on its merits. Instead, you resort to bluff and bluster and ad hominem. Hardly endearing, nor convincing!bornagain77_{July 14, 2014
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BA77
“the Tibertans have hemoglobin levels comparable to everyone else,,, far above BA77?s pay grade of understanding”
Thanks for the great example of a dishonest quote mine and removal of all context....that certainly underscores a major complaint the science community has with ID advocates and their less than honest representation on of others words/works.franklin_{July 14, 2014
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BA77
Mutation in key gene allows Tibetans to thrive at high altitude – 2010 Excerpt: “For Western people, after two to three weeks at altitude, the red blood cell count starts to increase. But Tibetans and Sherpas keep the same levels,” he said.
thanks for demonstrating my point, BA77. When people who lack the tibetan Hb properties experience hypoxia red cell counts do increase in an attempt of the body to increase oxygen saturation. However, the tibetans red cell count/hematocrit does not increase because their Hb is able to fully saturate with oxygen at the lower oxygen tensions found at high-altitude. In other words the Tibetans pysiology does not perceive the low oxygen tension at high altitude as being 'hypoxic'. BA77, pointing out something that is factual is not adhominum. As you jsut demostrated in your gross misinterpretation of the paper you cited. Everything I stated (in regards to Hb-oxygen equilibria) are textbook basics on the subject matter. Yu clearly aren't familiar with the subject matter. BA77
When looked at soberly, it is quite a modest adaptation in the grand scheme of the gigabytes of genomic information that has to be explained.
I'm sure all the dead and alive non-tibetan mountain climbers would sorely disagree with you on the magnitude of the adaptation.franklin_{July 14, 2014
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Is this a case of natural causes (a.k.a non-intelligent intervention) generating new information?rhampton7_{July 14, 2014
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franklin, without reference (and with ad hominem), states:
"the Tibertans have hemoglobin levels comparable to everyone else,,, far above BA77?s pay grade of understanding"
Yet the most recent study that I'm aware of states,,,
Mutation in key gene allows Tibetans to thrive at high altitude - 2010 Excerpt: "For Western people, after two to three weeks at altitude, the red blood cell count starts to increase. But Tibetans and Sherpas keep the same levels," he said. "I just summitted Everest a few weeks ago," added Dr Wang. He said the Sherpas and Tibetans were much stronger than the Westerners or lowland Chinese on the climb. "Their tissue oxygen concentration is almost the same as Westerners and Chinese but they are strong," he said "and their red blood cell count is not that high compared to people in Peru." "The remarkable thing about Tibetans is that they can function well in high altitudes without having to produce so much haemoglobin," said Prof Nielsen. "The entire mechanism is not well-understood – but is seems that the gene responsible is EPAS1." Nielsen said the gene is involved in regulating aerobic and anaerobic metabolism in the body (cell respiration with and without oxygen). "It may be that the [mutated gene] helps balance anaerobic versus aerobic metabolism in a way that is more optimal for the low-oxygen environment of the Tibetan plateau," he said. http://www.theguardian.com/science/2010/jul/02/mutation-gene-tibetans-altitude
Now I will, unlike Darwinists, be happy to admit I'm wrong in this instance if franklin cares to provide the proper reference refuting that paper. I have no particular axe to grind one way or the other on the Tibetan mutation issue. But what I would like to call attention to is the fact that IF this is truly a beneficial mutation then it is a very, very, lonely beneficial mutation indeed. Darwinists are hard pressed to cite truly beneficial mutations that do not degrade genetic information in one way or the other. Moreover, this adaptation in Tibetans is, as far as I can tell, the tweaking of an existing gene. No new proteins and/or genes were created! When looked at soberly, it is quite a modest adaptation in the grand scheme of the gigabytes of genomic information that has to be explained. More to the point, Dr. Behe has a paper out documenting the fact that the vast majority of mutations, even ones we once thought were beneficial, are in fact detrimental: “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Michael Behe: Intelligent Design – interview on radio program - ‘The Mind Renewed’ https://www.youtube.com/watch?v=H9SmPNQrQHE Thus, the problem for Darwinists is not the fact that a very few mutations may be beneficial. The insurmountable problem for Darwinists is the fact that the vast majority of mutations, even ones that confer a benefit, are found to be detrimental. i.e. It is simply ludicrous to believe we can gradually build the unfathomed complexity seen in the genomes of cells by breaking things. Random Mutation and Natural Selection is a lousy candidate for explaining the multiple layers of functional information we find in life. of related interest: A Key Inference of The Edge of Evolution Has Now Been Experimentally Confirmed - Michael Behe - July 14, 2014 (first of a three part essay) Excerpt: However, at the time the book's chief, concrete example,,, was an inference, not yet an experimentally confirmed fact.,, the deduction hadn't yet been nailed down in the lab. Now it has, thanks to Summers et al. 2014. It took them years to get their results because they had to painstakingly develop a suitable test system where the malarial protein could be both effectively deployed and closely monitored for its relevant activity,,, Using clever experimental techniques they artificially mutated the protein in all the ways that nature has, plus in ways that produced previously unseen intermediates. One of their conclusions is that a minimum of two specific mutations are indeed required for the protein to be able to transport chloroquine.,,, The need for multiple mutations neatly accounts for why the development of spontaneous resistance to chloroquine is an event of extremely low probability -- approximately one in a hundred billion billion (1 in 10^20) malarial cell replications -- as the distinguished Oxford University malariologist Nicholas White deduced years ago. The bottom line is that the need for an organism to acquire multiple mutations in some situations before a relevant selectable function appears is now an established experimental fact. http://www.evolutionnews.org/2014/07/a_key_inference087761.htmlbornagain77_{July 14, 2014
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BA77: “the ‘beneficial mutations’ that allow Tibetans to tolerate the low oxygen at high altitudes are actually found to be ‘slightly detrimnetal’ because they in fact result in a limit on the red cell blood count for Tibetans:” What is detrimental under some conditions can be advantageous under others.
nah, this is just another case of BA77 not understanding what he is reading and the underlying physiology. What had long been hypothesized was that the Tibetans may have had increased numbers of erythrocytes (increased packed red cell volume) to compensate for the low-oxygen at high altitude. What has been found is that Tibetans have normal packed red cell volumes (hematocrit) and normal hemoglobin levels comparable to people living at lower elevations. What has changed in Tibetans is that the intrinsic oxygen binding of hemoglobin in these people has led to an increased affinity for oxygen which promotes full saturation at lower partial pressure of oxygen. It is a clear cut case of a beneficial adaptation with nothing deleterious at all about the change. Additionally, the Tibertans have hemoglobin levels comparable to everyone else. Hemotocrit may increase due to increased number of red cells, increased size of red cells, or acute stress-indiced splenic contraction. What is of primary concern to understanding blood-oxygen equilibrium and its relation to hemoglobin would be the size of the erythrocytes (MCV) and the hemoglobin content (MCHC) in the blood sample in addition to overall hemoglobin concentration in whole blood. There are also additional modifiers of hemoglobin-oxygen affinity that also shoulkd be be noted, i.e., NTP (nucleoside triphosphate) concentrations as well as other intrinsic modifiers of hemoglobin affinity for oxygen. Be forewarned to expect a multi=post link spam of articles from BA77.....few of which are pertinent to the topic and, IMO, far above BA77's pay grade of understanding.franklin_{July 14, 2014
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BA77: "the ‘beneficial mutations’ that allow Tibetans to tolerate the low oxygen at high altitudes are actually found to be ‘slightly detrimnetal’ because they in fact result in a limit on the red cell blood count for Tibetans:" What is detrimental under some conditions can be advantageous under others.Acartia_bogart_{July 14, 2014
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the 'beneficial mutations' that allow Tibetans to tolerate the low oxygen at high altitudes are actually found to be 'slightly detrimnetal' because they in fact result in a limit on the red cell blood count for Tibetans: Tibetans Developed Genes to Help Them Adapt to Life at High Elevations - May 2010 Excerpt: "What's unique about Tibetans is they don't develop high red blood cells counts," http://www.sciencedaily.com/releases/2010/05/100513143453.htm Yet high red blood cell counts are found to be good,, Extremely fit individuals may have higher values—significantly more red cells in their bodies and significantly more oxygen-carrying capacity—but still maintain normal hematocrit values. http://wiki.medpedia.com/Red_Blood_Cells#How_It_Works Moreover, the 'beneficial mutations' were not random, but were in fact 'directed' mutations: Another Darwinian “Prediction” Bites the Dust - PaV - August 2010 Excerpt: this means the probability of all three sites changing “at once” (6.25 X 10^-9)^2 = approx. 4 X 10^-17 specific bp change/ yr. IOW (In Other Words), for that size population, and this is a very reasonable guess for size, it would take almost twice the life of the universe for them to take place “at once”. Thus, the invocation of “randomness” in this whole process is pure nonsense. We’re dealing with some kind of programmed response if, in fact, “polygenic selection” is taking place. And, that, of course, means design. https://uncommondescent.com/intelligent-design/another-darwinian-prediction-bites-the-dust/#more-14516 supplemental notes: Critic ignores reality of Genetic Entropy - Dr John Sanford - 7 March 2013 Excerpt: Where are the beneficial mutations in man? It is very well documented that there are thousands of deleterious Mendelian mutations accumulating in the human gene pool, even though there is strong selection against such mutations. Yet such easily recognized deleterious mutations are just the tip of the iceberg. The vast majority of deleterious mutations will not display any clear phenotype at all. There is a very high rate of visible birth defects, all of which appear deleterious. Again, this is just the tip of the iceberg. Why are no beneficial birth anomalies being seen? This is not just a matter of identifying positive changes. If there are so many beneficial mutations happening in the human population, selection should very effectively amplify them. They should be popping up virtually everywhere. They should be much more common than genetic pathologies. Where are they? European adult lactose tolerance appears to be due to a broken lactase promoter [see Can’t drink milk? You’re ‘normal’! Ed.]. African resistance to malaria is due to a broken hemoglobin protein [see Sickle-cell disease. Also, immunity of an estimated 20% of western Europeans to HIV infection is due to a broken chemokine receptor—see CCR5-delta32: a very beneficial mutation. Ed.] Beneficials happen, but generally they are loss-of-function mutations, and even then they are very rare! http://creation.com/genetic-entropy Human Genetic Variation Recent, Varies Among Populations - (Nov. 28, 2012) Excerpt: Nearly three-quarters of mutations in genes that code for proteins -- the workhorses of the cell -- occurred within the past 5,000 to 10,000 years,,, "One of the most interesting points is that Europeans have more new deleterious (potentially disease-causing) mutations than Africans,",,, "Having so many of these new variants can be partially explained by the population explosion in the European population. However, variation that occur in genes that are involved in Mendelian traits and in those that affect genes essential to the proper functioning of the cell tend to be much older." (A Mendelian trait is controlled by a single gene. Mutations in that gene can have devastating effects.) The amount variation or mutation identified in protein-coding genes (the exome) in this study is very different from what would have been seen 5,000 years ago,,, The report shows that "recent" events have a potent effect on the human genome. Eighty-six percent of the genetic variation or mutations that are expected to be harmful arose in European-Americans in the last five thousand years, said the researchers. The researchers used established bioinformatics techniques to calculate the age of more than a million changes in single base pairs (the A-T, C-G of the genetic code) that are part of the exome or protein-coding portion of the genomes (human genetic blueprint) of 6,515 people of both European-American and African-American decent.,,, http://www.sciencedaily.com/releases/2012/11/121128132259.htm Scientists Discover Proof That Humanity Is Getting Dumber, Smaller And Weaker By Michael Snyder, on April 29th, 2014 Excerpt: An earlier study by Cambridge University found that mankind is shrinking in size significantly. Experts say humans are past their peak and that modern-day people are 10 percent smaller and shorter than their hunter-gatherer ancestors. And if that’s not depressing enough, our brains are also smaller. The findings reverse perceived wisdom that humans have grown taller and larger, a belief which has grown from data on more recent physical development. The decline, said scientists, has happened over the past 10,000 years. http://thetruthwins.com/archives/scientists-discover-proof-that-humanity-is-getting-dumber-smaller-and-weakerbornagain77_{July 14, 2014
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Another feat of engineering genius. One whereby blind undirected forces, as an explanation, borders on the insane.humbled_{July 14, 2014
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The chunk of DNA around the tibetan allele is very different from anything else in modern humans -- 40 mutations in a 33Kb block. The number of differences between the Denisovan sequence and the Tibetan one are also about what you'd expect given the age of the Denisovan fossil.wd400_{July 14, 2014
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I wonder, how different these alleles are. The video hints it's only a single base mutation. If so, the evidence for inherritance from Denisovans would be very weak.Kajdron_{July 14, 2014
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@willh: jucging from Wikipedia: 1 yes; 2 so probably yes; 3 noKajdron_{July 14, 2014
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... Thankyou for any response.willh_{July 14, 2014
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A quick question for them that's knows. I was under the impression, that the EPAS 1 gene was something to do with the regulation of the blood cell count. From the short video above, it seems to allude to the properties of the 'oxygen capture' in the blood. Cannot expect much from such a simplified explanation, but if someone could please clarify: 1/ Is my first assumption of EPAS 1 affecting blood cell count correct? 2/ If so, is an interpretation of 'oxygen capture' more to the gas transfer efficiency, rather than a straight blood cell count. 3/ Or are my assumptions totally on the wrong track? Had this subject of Tibetan EPAS 1 evolution presented to me a while back. But my limited reading brought up suggestions of a broken gene, rather than a discovery of an adaptation explaining why Tibetans without heightened cell count, function so well at altitude.willh_{July 14, 2014
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