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Another Day; Another Bad Day for Darwinism: Pt. 43

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This is from a new study published in Nature Communications, and talked about at Phys.Org.

Oh, how difficult it is these days to be an “intellectually fulfilled” neo-Darwinian:

Humans don’t like being alone, and their genes are no different. Together we are stronger, and the two versions of a gene – one from each parent – need each other. Scientists at the Max Planck Institute for Molecular Genetics in Berlin have analysed the genetic makeup of several hundred people and decoded the genetic information on the two sets of chromosomes separately. In this relatively small group alone they found millions of different gene forms. The results also show that genetic mutations do not occur randomly in the two parental chromosome sets and that they are distributed in the same ratio in everyone.

Ouch!!!!!

The results show that most genes can occur in many different forms within a population: On average, about 250 different forms of each gene exist. The researchers found around four million different gene forms just in the 400 or so genomes they analysed. This figure is certain to increase as more human genomes are examined. More than 85 percent of all genes have no predominant form which occurs in more than half of all individuals. This enormous diversity means that over half of all genes in an individual, around 9,000 of 17,500, occur uniquely in that one person – and are therefore individual in the truest sense of the word.

Uh oh. What happened to “purifying selection”? Ouch!!!!

According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. “It’s amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula,” says Hoehe. The 60:40 distribution ratio appears to be essential for survival. “This formula may help us to understand how gene variability occurs and how it affects gene function.”

Double Ouch!!!!!

The gene, as we imagined it, exists only in exceptional cases. “We need to fundamentally rethink the view of genes that every schoolchild has learned since Gregor Mendel’s time. Moreover, the conventional view of individual mutations is no longer adequate. Instead, we have to consider the two gene forms and their combination of variants,” Hoehe explains. When analysing genomes, scientists should therefore examine each parental gene form separately, as well as the effects of both forms as a pair.

What’s that you say? Oh, you’re going to take your bat and go home now? I understand.

Yikes!!! Could it get any worse for the Darwinists? Just wait for tomorrow. . . . .

Comments
YOu forget that most mutations in exons are non-synonymous, for the difference in DNA-diversity and protein-diversity o occur you need (a) magic stopping non-synonymous mutations happening or (b) selection keeping them at low frequency. Charlesworth is talking about a different problem. When the population-mutation rate per site is high, the infinite allele model breaks down because the "same allele" can be created mulitple times. So, some nice pop gen results don't work anymore. The same problem doesn't arise when you define variants over long stretches of variable sites, because new mutations are making new alleles in those cases. Papers like Charlesworth's update our models, and make them applicable to cases they previously weren't. They don't require us to back up, burn The Origin and start again...wd400
December 2, 2014
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wd400: I wouldn't bad-mouth Max Planck Institute too much. Here's their "About Us" from the homepage:
he Max Planck Society is Germany's most successful research organization. Since its establishment in 1948, no fewer than 18 Nobel laureates have emerged from the ranks of its scientists, putting it on a par with the best and most prestigious research institutions worldwide. The more than 15,000 publications each year in internationally renowned scientific journals are proof of the outstanding research work conducted at Max Planck Institutes – and many of those articles are among the most-cited publications in the relevant field. What is the basis of this success? The scientific attractiveness of the Max Planck Society is based on its understanding of research: Max Planck Institutes are built up solely around the world's leading researchers. They themselves define their research subjects and are given the best working conditions, as well as free reign in selecting their staff. This is the core of the Harnack principle, which dates back to Adolph von Harnack, the first president of the Kaiser Wilhelm Society, which was established in 1911. This principle has been successfully applied for nearly one hundred years. The Max Planck Society continues the tradition of its predecessor institution with this structural principle of the person-centered research organization. The currently 82 Max Planck Institutes conduct basic research in the service of the general public in the natural sciences, life sciences, social sciences, and the humanities. Max Planck Institutes focus on research fields that are particularly innovative, or that are especially demanding in terms of funding or time requirements. And their research spectrum is continually evolving: new institutes are established to find answers to seminal, forward-looking scientific questions, while others are closed when, for example, their research field has been widely established at universities. This continuous renewal preserves the scope the Max Planck Society needs to react quickly to pioneering scientific developments.
PaV
December 2, 2014
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BTW, while I was looking around, I found this paper. The Abstract:
Some species exhibit very high levels of DNA sequence variability; there is also evidence for the existence of heritable epigenetic variants that experience state changes at a much higher rate than sequence variants. In both cases, the resulting high diversity levels within a population (hyperdiversity) mean that standard population genetics methods are not trustworthy. We analyze a population genetics model that incorporates purifying selection, reversible mutations and genetic drift, assuming a stationary population size. We derive analytical results for both population parameters and sample statistics, and discuss their implications for studies of natural genetic and epigenetic variation. In particular, we find that (1) many more intermediate frequency variants are expected than under standard models, even with moderately strong purifying selection (2) rates of evolution under purifying selection may be close to, or even exceed, neutral rates. These findings are related to empirical studies of sequence and epigenetic variation. Author: Brian Charlesworth------Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom Submitted July 2014
Does this man know nothing of modern evolutionary biology either? Yet, he's saying exactly what I'm saying, isn't he?PaV
December 2, 2014
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wd400: You're a handful! :)PaV
December 2, 2014
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wd400:
It’s simply not possible that the reduction in diverity of protein-types can be “attributed to how the alleles are being regulated”, because this paper is about genomic DNA, and does nothing to measure the results of the regulation of that DNA.
The only reason that I was speaking of “regulation” in the first place was because of your claim that there was “purifying selection.” I couldn’t begin to understand why you were making such a claim.
You are wrong that is only considers nsSNPS, you are wrong in claiming there are a “tremendous number of non-synonymous differences between alleles” (among those that vary at all they report 1.3–1.7 nsSNPs!), and you are wrong that it compares genomic results to proteomic ones. I’m not sure how more wrong you can be.
I still haven’t read the entire paper. Nor do I intend to. I was referring to the cumulative number of nsSNPs they found. It was in the millions across the genome. But, your numbers are right, and, yes, at the protein level, less variation is expressed. Yet, here is what they write:
Taken together, the diversity of haploid and diploid protein forms was much lower than their counterparts at the DNA sequence level. The absolute numbers were, however, still considerable, particularly of the protein diplotypes, up to 90% of which encoded two different proteins in the population. These can allow huge functional versatility of diploid genomes as an inherent key feature of diploidy and play an important role in biological variation within and between cells and organisms.
You’ve called this a form of “purifying selection.” I don’t agree. It’s just the difference between non-synonymous and synonymous substitutions. Differences at the molecular level don’t always show up as differences at the amino acid level. We all know this. And the fact that for 90% of ‘genes’ “two different proteins” are encoded seems like someone turned off the purifying selection. “Purifying selection” is meant to reduce deleterious alleles. But we find lots of allelic forms. That is the origin of my comment about “purifying selection.” I don’t see why you can’t acknowledge this. Here’s what they write:
The average number of haplotypes ‘per gene’ was between 3 and 22, much lower than the global averages described above (Supplementary Table 10c). These results demonstrate that the vast majority of genes, over 85%, do not encode one predominant haplotype. ‘Therefore, the concept that there is one predominant or ‘wild-type’ form of a gene and few rare or ‘mutant’ forms is overly simplistic and misleading’(quote from the study by Stephens et al.24).
wd400:
You don’t seem to understand what the 60:40 ratio is. It’s whether chemically altering (or just non-syn.) variant are present in both chromosomes, or only on one. The ratio is only “stable” when aggregated across whole genomes – i.e when you take thousands of draws from underlying distribution. Just like the mean of series of dice throws will converge on 3.5, the mean of this ratio will converge on the population-mean when you takes thousands of draws, so the spread (60–64% single-chromosomes) is not a surprise.
Here’s what the authors write:
Overall, cis configurations, leaving one form of the gene unperturbed, would be expected to occur more frequently in an individual genome to preserve organismal function. Thus, we determined the ratio of cis to trans configurations across all autosomal protein-coding genes for each individual genome in all sample sets (Methods). In fact, a striking phase imbalance was observed: without any exception, in each of the 14 molecularly phased genomes (Supplementary Table 16), 57CEU (Supplementary Table 14) and 372EUR statistically phased genomes, cis configurations of potentially perturbing mutations occurred significantly more frequently than trans configurations (Po7.68 10 8– 2.11 10 3), resulting in an overall ratio of about 60:40 (Table 1; Supplementary Note 4).
This is not what they were expecting. Under random variation and negative selection, if anything, the ratio would be expected to be the reverse: trans:cis of 60:40. But, as usual, this doesn’t surprise you.
Finally, I don’t what you are on about with this fixation with wild types (for large genes made mostly of introns…). The paper finds something we’ve already known, and which is fairly obvious. If you take haplotypes that contain many variable sites then eventually no single haplotype will have a frequency > 0.5. Why do you think this is a problem. There is no “wild type genome”, or “wild type chromosome 12?, that there is no haplotype for some 20 kb gene with frequency > 0.5 hardly seems to matter.
Well, why don’t we listen to the authors. Perhaps you should write and inform them of the insignificance of their results. Here’s what they say (I’ve already quoted this, so, it apparently means little to you)
Our global view of haplotype/diplotype diversity in relation to population size suggests that current efforts are still far from capturing the majority of gene forms and that saturation may not even be achievable. The concept of a predominant, ‘wild-type’ form of ‘the’ gene appears obsolete for over 85% of genes, challenging traditional ‘Mendelian’ views. This highlights the need for an expansion of current concepts of ‘the’ gene, along with the development of appropriate documentation and language. The enormous diversity of haploid and diploid gene forms raises fundamental questions concerning the relationships between sequence(s), structure(s) and function(s).
It is obvious to the authors, and was obvious to me, that this ‘diversity’ of forms undermines conventional neo-darwinian presumptions. I take their statement about “saturation may not even be achievable” to mean that there are so many “forms” floating around in the genome that they might not ever be able to identify them all. This has to be a nightmare** [see the paper cited in my comment below]** for a traditionally-trained population geneticist. You fall in that camp. And yet you just wave away problem after problem. It reminds me of the string quartet playing away atop the Titanic.
So, I’m afraid it’s a matter of fact that you don’t understand the paper. As I’ve said from the start, that’s not really news, though it is still interesting that no one could pull you up on all these mistakes.
You might have just as well added this: “As I’ve said from the start, that’s not really news, though it is still interesting that no one could pull ‘the authors’ up on all these mistakes.” IOW, do you want to claim that the authors have no knowledge of modern evolutionary biology? It is them, and their results, that you protest, not mine. End of discussion.PaV
December 2, 2014
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wd400, so you consider Dawkins & Coyne & PZMyers (throw Tyson in there) to be heavyweights in science? :) Thanks for the laugh, I consider them to be nothing more than dogmatic atheists who have wrapped themselves in the cloak of science so as to promote their religion,,,, all the while ignoring, explaining away, and/or obfuscating (as you also do wd400), any and all contrary evidence that does not fit their preferred materialistic worldview,,, The only one who did anything of note in science was Dawkins with the 'polished' selfish gene, and even that idea is now considered bunk, even harmful to science, by many people in the field,, people like Shapiro, Sternberg, Nobel, Koonin, Trivonov etc.. etc.. No those atheists are certainly not heavyweights in science, not even close,,, they will soon quickly be forgotten when science moves on, perhaps a footnote for how Dawkins and Tyson misled science with false ideas, but that's about it.bornagain77
December 2, 2014
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Well, I don't know what' more ludicruous than a press release that doesn't describe the paper, and claims that paper is the end of Mendel. So I guess we just differ. I don't what the point of the rest of your comment is (some folks that spend their time defending evolutionary biology don't work on diseases so they are lightweights?), so let's call that an end.wd400
December 2, 2014
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The opening paragraph does not meet the definition of ludicrous sorry. And you now realize the Max Planck Institute is not a University as you earlier assumed. Margret Hoehe is also one sharp cookie. Fighting disease instead of wasting time fighting "creationists". Guys like Dawkins & Coyne & PZMyers are such lightweights.ppolish
December 2, 2014
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Well, starting from the start, the opening paragraph doesn't describe the paper. Even gpuccio agress the press release doesn't describe the paper very well. (By the way, there isn't a single Max Planck institute to call a world class outfit -- there are many across Germany and a few elsewhere, each with there own area of focus, including one of the leading centres for evolutionary anthropology).wd400
December 2, 2014
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What was ludicrous WD? Please cite a specific ludicrous sentence or two in the press release if you want. Maybe the German language statement is ludicrous, but the English version seems well written. World Class outfit over there at Max Planck.ppolish
December 2, 2014
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Max Planck institutes need promotion just like everyone else, why else would they have a PR office? Or create such a ludicrous release for that matter?wd400
December 2, 2014
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Wd400, I don't think "press officers promoting their University" is applicable here.. Max Planck Institute is not a University. They don't need promo like maybe your University does lol. A member there won this years Nobel though: http://www.mpg.de/8688233/nobel-prize-hell-2014ppolish
December 2, 2014
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Oh, on this
So, this is not about understanding the paper. This is about wd400 saying: (1) you can’t believe what’s put out in the press release (although in the paper they make this exact same claim), and (2) you should look to learned scientists to determine a paper’s worth, and (3) then you should follow their interpretation.
Nah. Here's the thing. You shouldn't believe what gets put in press releases, because the job of press officers is to promote their university, not communicate science. You don't have to trust other scientists on a papers worth, but, and this should hardly need saying, you should be skeptical of all results. Instead of credulously copy-paste-bolding sentences that you thought supported your own position, you should've read the paper, understood what they mean by "mutations" and the manner in which they were claiming they were non-random.wd400
December 2, 2014
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There is certainly no value in correcting all of your errors, PaV. But, since no IDers seems to want to, I'll correct the most glaring ones. It's simply not possible that the reduction in diverity of protein-types can be "attributed to how the alleles are being regulated", because this paper is about genomic DNA, and does nothing to measure the results of the regulation of that DNA. You are wrong that is only considers nsSNPS, you are wrong in claiming there are a "tremendous number of non-synonymous differences between alleles" (among those that vary at all they report 1.3--1.7 nsSNPs!), and you are wrong that it compares genomic results to proteomic ones. I'm not sure how more wrong you can be. You don't seem to understand what the 60:40 ratio is. It's whether chemically altering (or just non-syn.) variant are present in both chromosomes, or only on one. The ratio is only "stable" when aggregated across whole genomes - i.e when you take thousands of draws from underlying distribution. Just like the mean of series of dice throws will converge on 3.5, the mean of this ratio will converge on the population-mean when you takes thousands of draws, so the spread (60--64% single-chromosomes) is not a surprise. There's actually at least some suggestion of purifying selection in these results too, since the chemically altering variants have a high "single chromosome" frequency than normal nsSNPS (presumably because chemically altering variants are rarer than nsSNPs at large, which in turn are rarer than syn. SNPs). Finally, I don't what you are on about with this fixation with wild types (for large genes made mostly of introns...). The paper finds something we've already known, and which is fairly obvious. If you take haplotypes that contain many variable sites then eventually no single haplotype will have a frequency > 0.5. Why do you think this is a problem. There is no "wild type genome", or "wild type chromosome 12", that there is no haplotype for some 20 kb gene with frequency > 0.5 hardly seems to matter. So, I'm afraid it's a matter of fact that you don't understand the paper. As I've said from the start, that's not really news, though it is still interesting that no one could pull you up on all these mistakes.wd400
December 2, 2014
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wd400:
There is no point in my continuing to correct PaV’s errors – he/she is set in their position and no evidence will change it. But if ID has folks they really do know something about biology, shouldn’t they be able to set PaV straight?
Thank you for your opinion. But opinion is just that: opinion. You say I don't understand the paper. But as I've said already, it is you who is coming along and "interpreting" the paper. You say there is "evidence" for "purifying selection," when there is no mention of this in the entire paper, and you base your 'evidence' on a Figure on the paper that basically proves the opposite: viz., that there are two 'forms' of the allele that are expressed as proteins. The fact that the cis:trans ratio is constant, you say is simply an artifact of the method they employ. But they say that it is a 'constant' ratio which indicates that "mutations" are NOT 'random.' You simply pooh-pooh this. So, this is not about understanding the paper. This is about wd400 saying: (1) you can't believe what's put out in the press release (although in the paper they make this exact same claim), and (2) you should look to learned scientists to determine a paper's worth, and (3) then you should follow their interpretation. Well, I don't care to follow your suggestion. Whatever your opinion of the paper, the authors have found that in only 15% of the genes is there something like what population geneticists would call a "wild-type" allele. The majority of the time there are AT LEAST two or more forms of the allele. This is molecular data. Say what you want, the data remains. And the data is a great big blow to neo-Darwinism/population genetics since many assumptions made since the discovery of Mendel's paper now need to be revisited and thought through again. Kimura found way, way more diversity within genes to continue with standard PG analyses, so he switched to his "neutral theory," and moving neutral drift to the forefront. Now, with this study, we're seeing a tremendous number of non-synonymous differences between alleles, alleles that are supposed to be "wild-type." This cannot be good news for PG since it becomes hard to explain the presence of this diversity, and because it indicates a more secondary role for genes. If you have problems with the paper, then write to Nature Communications and tell them about your concerns. When Nature Communications addresses those concerns, should they do that, then your opinion will have been validated, and I will then be happy to grapple with your understanding of the paper. Until such time, let's not waste any more of our valuable time discussing this.PaV
December 2, 2014
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Pachyaena 86
Non-IDers are trying to ... keep religious bunk and other woo out of science, ...while you IDers are trying to ‘wedge’ your religious bunk and other woo into science ...
Who owns science?Silver Asiatic
December 2, 2014
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Pachy, contrary to what you atheists believe, it is impossible to do science in the first place without presupposing 'purpose' on some level. Moreover, atheists live in denial of the 'purpose seeing' that is built into them: Design Thinking Is Hardwired in the Human Brain. How Come? – October 17, 2012 Excerpt: “Even Professional Scientists Are Compelled to See Purpose in Nature, Psychologists Find.” The article describes a test by Boston University’s psychology department, in which researchers found that “despite years of scientific training, even professional chemists, geologists, and physicists from major universities such as Harvard, MIT, and Yale cannot escape a deep-seated belief that natural phenomena exist for a purpose” ,,, Most interesting, though, are the questions begged by this research. One is whether it is even possible to purge teleology from explanation. http://www.evolutionnews.org/2012/10/design_thinking065381.html Children Act Like Scientists - October 1, 2012 Excerpt: New theoretical ideas and empirical research show that very young children’s learning and thinking are strikingly similar to much learning and thinking in science. Preschoolers test hypotheses against data and make causal inferences; they learn from statistics and informal experimentation, and from watching and listening to others. The mathematical framework of probabilistic models and Bayesian inference can describe this learning in precise ways. http://crev.info/2012/10/children-act-like-scientists/ Children are born believers in God, academic claims - 24 Nov 2008 Excerpt: "Dr Justin Barrett, a senior researcher at the University of Oxford's Centre for Anthropology and Mind, claims that young people have a predisposition to believe in a supreme being because they assume that everything in the world was created with a purpose." http://www.telegraph.co.uk/news/religion/3512686/Children-are-born-believers-in-God-academic-claims.html Geometric Principles Appear Universal in Our Minds - May 2011 Excerpt: Villagers belonging to an Amazonian group called the Mundurucú intuitively grasp abstract geometric principles despite having no formal math education,,, Mundurucú adults and 7- to 13-year-olds demonstrate as firm an understanding of the properties of points, lines and surfaces as adults and school-age children in the United States and France,,, http://www.wired.com/wiredscience/2011/05/universal-geometry/ “Geometry is unique and eternal, a reflection from the mind of God. That mankind shares in it is because man is an image of God.” – Johannes Kepler As well, biology is replete with teleology, i.e. with purpose. In fact, it is impossible to 'do biology' without using words that imply intentionality, functionality, strategy, and design. Life, Purpose, Mind: Where the Machine Metaphor Fails - Ann Gauger - June 2011 Excerpt: I'm a working biologist, on bacterial regulation (transcription and translation and protein stability) through signalling molecules, ,,, I can confirm the following points as realities: we lack adequate conceptual categories for what we are seeing in the biological world; with many additional genomes sequenced annually, we have much more data than we know what to do with (and making sense of it has become the current challenge); cells are staggeringly chock full of sophisticated technologies, which are exquisitely integrated; life is not dominated by a single technology, but rather a composite of many; and yet life is more than the sum of its parts; in our work, we biologists use words that imply intentionality, functionality, strategy, and design in biology--we simply cannot avoid them. Furthermore, I suggest that to maintain that all of biology is solely a product of selection and genetic decay and time requires a metaphysical conviction that isn't troubled by the evidence. Alternatively, it could be the view of someone who is unfamiliar with the evidence, for one reason or another. But for those who will consider the evidence that is so obvious throughout biology, I suggest it's high time we moved on. - Matthew http://www.evolutionnews.org/2011/06/life_purpose_mind_where_the_ma046991.html#comment-8858161 The 'Mental Cell': Let’s Loosen Up Biological Thinking! - Stephen L. Talbott - September 9, 2014 Excerpt: Many biologists are content to dismiss the problem with hand-waving: “When we wield the language of agency, we are speaking metaphorically, and we could just as well, if less conveniently, abandon the metaphors”. Yet no scientist or philosopher has shown how this shift of language could be effected. And the fact of the matter is just obvious: the biologist who is not investigating how the organism achieves something in a well-directed way is not yet doing biology, as opposed to physics or chemistry. Is this in turn just hand-waving? Let the reader inclined to think so take up a challenge: pose a single topic for biological research, doing so in language that avoids all implication of agency, cognition, and purposiveness1. One reason this cannot be done is clear enough: molecular biology — the discipline that was finally going to reduce life unreservedly to mindless mechanism — is now posing its own severe challenges. In this era of Big Data, the message from every side concerns previously unimagined complexity, incessant cross-talk and intertwining pathways, wildly unexpected genomic performances, dynamic conformational changes involving proteins and their cooperative or antagonistic binding partners, pervasive multifunctionality, intricately directed behavior somehow arising from the interaction of countless players in interpenetrating networks, and opposite effects by the same molecules in slightly different contexts. The picture at the molecular level begins to look as lively and organic — and thoughtful — as life itself. http://natureinstitute.org/txt/st/org/comm/ar/2014/mental_cell_23.htm Of supplemental note, Bruce Charlton's Miscellany - October 2011 Excerpt: I had discovered that over the same period of the twentieth century that the US had risen to scientific eminence it had undergone a significant Christian revival. ,,,The point I put to (Richard) Dawkins was that the USA was simultaneously by-far the most dominant scientific nation in the world (I knew this from various scientometic studies I was doing at the time) and by-far the most religious (Christian) nation in the world. How, I asked, could this be - if Christianity was culturally inimical to science? http://charltonteaching.blogspot.com/2011/10/meeting-richard-dawkins-and-his-wife.html Jerry Coyne on the Scientific Method and Religion - Michael Egnor - June 2011 Excerpt: The scientific method -- the empirical systematic theory-based study of nature -- has nothing to so with some religious inspirations -- Animism, Paganism, Buddhism, Hinduism, Shintoism, Islam, and, well, atheism. The scientific method has everything to do with Christian (and Jewish) inspiration. Judeo-Christian culture is the only culture that has given rise to organized theoretical science. Many cultures (e.g. China) have produced excellent technology and engineering, but only Christian culture has given rise to a conceptual understanding of nature. http://www.evolutionnews.org/2011/06/jerry_coyne_on_the_scientific_047431.html The truth about science and religion By Terry Scambray - August 14, 2014 Excerpt: In 1925 the renowned philosopher and mathematician, Alfred North Whitehead speaking to scholars at Harvard said that science originated in Christian Europe in the 13th century. Whitehead pointed out that science arose from “the medieval insistence on the rationality of God, conceived as with the personal energy of Jehovah and with the rationality of a Greek philosopher”, from which it follows that human minds created in that image are capable of understanding nature. The audience, assuming that science and Christianity are enemies, was astonished. http://www.americanthinker.com/blog/2014/08/the_truth_about_science_and_religion.htmlbornagain77
December 2, 2014
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Rec said, Remember you’re favoring the tiny side of functional sequence space to get to your big big numbers. So, as you crow about the diversity of functional sequences amounting to no single “wild type” sequence in human genes….. I say, This is an interesting comment. I wonder about the difference between the narrow side of functionality for proteins verses the apparent diversity in genes. Suppose there were only 1 protein that worked for a vital purpose but it could be built by 500 different genetic variants. This would seem to be an excellent mechanism for front-loading robustness into a "seed" cell you could pretty much guarantee that a given necessary protein would arise. Now imagine the opposite: 1 gene can build 500 different proteins. Now you have just made any kind of phenotypical continuity in a population nonexistent. If life existed at all it would appear random to us. Is there any physically necessary reason we should see one scenario and not the other? interesting peacefifthmonarchyman
December 2, 2014
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wd400:
The paper doesn’t claim mutations are non-random in the sense evolutionary biology assumes mutations are random.
In what way does evolutionary biology assume mutations are random?
What’s more, when evolutionary biologists say mutations are random when mean random with respect to fitness — not “distributed in the same ration in everyone”.
That is incorrect. Random wrt biology means accidental as "random wrt fitness" is nonsense because it doesn't say if the mutations were directed or not.Joe
December 2, 2014
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Dionisio said: "You and your fellow travelers have revealed your motivations already. They are obvious to any observer." As are yours. Non-IDers are trying to educate IDers and others and keep religious bunk and other woo out of science, education, and public policies, while you IDers are trying to 'wedge' your religious bunk and other woo into science, education, and public policies. You and other IDers seem to think that all observers (or "onlookers") are IDers or are open to ID. Imagining that likely gives you comfort but you might want to look around and see what kind of reputation ID and this blog have before you get too comfy.Pachyaena
December 1, 2014
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as to: "The paper doesn’t claim mutations are non-random in the sense evolutionary biology assumes mutations are random." give me a break, having extremely sophisticated molecular machines direct mutations to DNA in a overarching pattern is completely antithetical to the original Darwinian assumption of 'random, accidental' mutations,,, Shapiro created quite a few waves by pointing this now accepted fact out: Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigenetic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism.bornagain77
December 1, 2014
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wd400 is all over this one....but geez the paper and PaV's hype are 180 degrees away. Also, even within the human population, where you might define a narrow tiny bulls-eye of function in sequence space, what do we find? Enormous diversity of functional sequences. Remember you're favoring the tiny side of functional sequence space to get to your big big numbers. So, as you crow about the diversity of functional sequences amounting to no single "wild type" sequence in human genes.....REC
December 1, 2014
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I’m not sure where the ideas that you would call “anti-science” come from but when they are flippantly dismissed instead of addressed straightforwardly they tend to coalesce.
I don't know how I can be more straightforward about PaV's mistakes. The paper doesn't claim mutations are non-random in the sense evolutionary biology assumes mutations are random. The diversity of diplotyes (combinations of two haplotypes) is no suprising given haplotypes are diverse. The data presented in the paper shows strong evidence for purifying selection, despite the OP's claim the paper was evidence against the operation of this process in our genome. None of this mystical stuff about regulation of alternative haplotypes has any basis in a result in the paper. That's just the OP. How can I be more straightforward in pointing out the mistakes?wd400
December 1, 2014
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footnote to 80: Sam Harris's Free Will: The Medial Pre-Frontal Cortex Did It - Martin Cothran - November 9, 2012 Excerpt: There is something ironic about the position of thinkers like Harris on issues like this: they claim that their position is the result of the irresistible necessity of logic (in fact, they pride themselves on their logic). Their belief is the consequent, in a ground/consequent relation between their evidence and their conclusion. But their very stated position is that any mental state -- including their position on this issue -- is the effect of a physical, not logical cause. By their own logic, it isn't logic that demands their assent to the claim that free will is an illusion, but the prior chemical state of their brains. The only condition under which we could possibly find their argument convincing is if they are not true. The claim that free will is an illusion requires the possibility that minds have the freedom to assent to a logical argument, a freedom denied by the claim itself. It is an assent that must, in order to remain logical and not physiological, presume a perspective outside the physical order. http://www.evolutionnews.org/2012/11/sam_harriss_fre066221.htmlbornagain77
December 1, 2014
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Wd400 says, (as to why I’m here — I find it really interesting to know where anti-science ideas come from and how they coalesce into broader movements/belief systems) I say, I'm not sure where the ideas that you would call "anti-science" come from but when they are flippantly dismissed instead of addressed straightforwardly they tend to coalesce. I'm not saying you need to beat a dead horse but surely you should at least make sure it is not still charging at you. From this side it looks like you did a little quick hand waving about the article and then just proceeded to try and belittle the apposition for not acquiescing to you and the powers that be. Just my opinion peacefifthmonarchyman
December 1, 2014
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as to: "I find it really interesting to know where anti-science ideas come from and how they coalesce into broader movements/belief systems" Yet, amazingly, you are a dedicated proponent of 'anti-science' with your relentless promotion of neo-Darwinism,,, For instance of the anti-science inherent in neo-Darwinism, if the atheistic/materialistic version of neo-Darwinism were actually true it would lead to the epistemological failure of science itself,,, Evolutionary Argument Against Naturalism (An Introduction) - video https://www.youtube.com/watch?v=vpQ1-AGPysM Scientific Peer Review is in Trouble: From Medical Science to Darwinism - Mike Keas - October 10, 2012 Excerpt: Survival is all that matters on evolutionary naturalism. Our evolving brains are more likely to give us useful fictions that promote survival rather than the truth about reality. Thus evolutionary naturalism undermines all rationality (including confidence in science itself). Renown philosopher Alvin Plantinga has argued against naturalism in this way (summary of that argument is linked on the site:). Or, if your short on time and patience to grasp Plantinga's nuanced argument, see if you can digest this thought from evolutionary cognitive psychologist Steve Pinker, who baldly states: "Our brains are shaped for fitness, not for truth; sometimes the truth is adaptive, sometimes it is not." Steven Pinker, evolutionary cognitive psychologist, How the Mind Works (W.W. Norton, 1997), p. 305. http://blogs.christianpost.com/science-and-faith/scientific-peer-review-is-in-trouble-from-medical-science-to-darwinism-12421/ Quote: "In evolutionary games we put truth (true perception) on the stage and it dies. And in genetic algorithms it (true perception) never gets on the stage" Donald Hoffman PhD. - Consciousness and The Interface Theory of Perception - 7:19 to 9:20 minute mark - video https://www.youtube.com/watch?feature=player_detailpage&v=dqDP34a-epI#t=439bornagain77
December 1, 2014
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Fifth, I don't claim IDers are stupid. But most IDers (and most pro-evolutionary biology folks on the internet for that matter) don't know much about modern biology. I think it's very strange that people who think we should throw out most of modern biology don't first educate themselves on what biology actually is. This thread started with PaV misunderstanding a press release, and has got worse from there. There is no point in my continuing to correct PaV's errors - he/she is set in their position and no evidence will change it. But if ID has folks they really do know something about biology, shouldn't they be able to set PaV straight? (as to why I'm here -- I find it really interesting to know where anti-science ideas come from and how they coalesce into broader movements/belief systems)wd400
December 1, 2014
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Wd400, It's common practice for critics to claim that folks with ID sympathies are stupid and uneducated. For all I know this may be a valid critique especially in my case. I am definitely not the brightest bulb in the pack But it is a very poor way to win hearts and minds to your cause. If you want to change minds I would think a better approach would be to demonstrate where your opponent is mistaken. Maybe that's not your intention here. If not I have no clue what it is. I know I'm here to sharpen my own ideas but I can't believe that is your purpose, peacefifthmonarchyman
December 1, 2014
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Wd400:
Here’s your test ID movement — who can save PaV from his/her self?
We need a new Intelligence Design Lab, or genetics will soon make no sense to almost everyone.Gary S. Gaulin
December 1, 2014
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Here's your test ID movement -- who can save PaV from him/her self?wd400
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