Denis Noble: Why talk about replacement of Darwinian evolution theory, not extension?

_{Denyse O'Leary

October 23, 2016

Darwinism, Evolution, Intelligent Design}

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In new book on the Royal Society’s Public Evolution Summit, Oxford’s Denis Noble explains,

The reasons I think we are talking about replacement rather than extension are several. The first is that the exclusion of any form of acquired characteristics being inherited was a central feature of the modern synthesis. In other words, to exclude any form of inheritance that was non-Mendelian, that was Lamarckian-like, was an essential part of the modern synthesis. What we are now discovering is that there are mechanisms by which some acquired characteristics can be inherited, and inherited robustly. So it’s a bit odd to describe adding something like to the synthesis ( i.e., extending the synthesis). A more honest statement is that the synthesis needs to be replaced.

By “replacement” I don’t mean to say that the mechanism of random change followed by selection does not exist as a possible mechanism. But it becomes one mechanism amongst many others, and those mechanisms must interact. So my argument for saying this is a matter of replacement rather than extension is simply that it was adirect intention of those who formulated the modern synthesis to exclude the inheritance of acquired characteristics. (p. 25)

That’s why the fat’s in the fire and smoking hot. Darwinism (or whatever the term du jour is) has been a totalistic system, enforced as such. But the evidence today simply doesn’t support it.

Reading Mazur’s book, I was struck by two things:

The genuinely interesting nature of alternative evolution proposals contrasts sharply with the science media release where fairly dull researchers have come up with a casuistical explanation of how Darwinism can account for various phenomena. And one realizes that for those individuals, that is evolution. That is science. Science is about reaffirming and finding evidence for the teachings of the Great One. And deploring or attacking anyone who doubts his teachings, irrespective of the state of the evidence.

The new approach is not exclusive or totalistic. It does not behave, as Darwinism does, as a metaphysic. Among many assemblies of evidence, some will naturally prevail, as more persuasive than others. But for once, evidence exists to understand living things better rather than to understand Darwin better.

Ladies and gentlemen, place your bets. This’ll be fun.

See also: What to expect from the Royal Society’s public evolution summit November 7-9

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Comments

"where do those quotes say that natural selection is not effective?" "“Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles." Further quotes from empirical and mathematical investigations that demonstrate the ineffectiveness of natural selection as the supposed 'designer substitute':
"We'll argue presently that, quite aside from the problems it has accommodating the empirical findings, the theory of natural selection is internally flawed; it's not just that the data are equivocal, it's that there's a crack in the foundations." Jerry Fodor and Massimo Piattelli-Palmarini - “What Darwin Got Wrong” Can Purifying Natural Selection Preserve Biological Information? - May 2013 - Paul Gibson, John R. Baumgardner, Wesley H. Brewer, John C. Sanford In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies [2–13]. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process.,,, http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0010 Selection Threshold Severely Constrains Capture of Beneficial Mutations - John C. Sanford – 2013 Concluding comments Our findings raise a very interesting theoretical problem — in a large genome, how do the millions of low-impact (yet functional) nucleotides arise? It is universally agreed that selection works very well for high-impact mutations. However, unless some new and as yet undiscovered process is operating in nature, there should be selection breakdown for the great majority of mutations that have small impact on fitness. We have now shown that this applies equally to both beneficial and deleterious mutations, and we have shown that selection interference is especially important when there are high-impact beneficial mutations. We conclude that only a very small fraction of all non-neutral mutations are selectable within large genomes. Our results reinforce and extend the findings of earlier studies [1–13], which in general employed many simplifying assumptions and rarely included more than a single source of biological noise. We show that selection breakdown is not just a simple function of population size, but is seriously impacted by other factors, especially selection interference. We are convinced that our formulation and methodology (i.e., genetic accounting) provide the most biologically-realistic analysis of selection breakdown to date. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0011 "many genomic features could not have emerged without a near-complete disengagement of the power of natural selection" Michael Lynch The Origins of Genome Architecture, intro "a relative lack of natural selection may be the prerequisite for major evolutionary advance" Mae Wan Ho Beyond neo-Darwinism Evolution by Absence of Selection “Darwinism provided an explanation for the appearance of design, and argued that there is no Designer -- or, if you will, the designer is natural selection. If that's out of the way -- if that (natural selection) just does not explain the evidence -- then the flip side of that is, well, things appear designed because they are designed.” Richard Sternberg - Living Waters documentary Whale Evolution vs. Population Genetics - Richard Sternberg and Paul Nelson - (excerpt from Living Waters video) https://www.youtube.com/watch?v=0csd3M4bc0Q Haldane's Pre-Cambrian Rabbit plus Natural Selection Falsified by Population Genetics - video https://youtu.be/zlGwjUJLgAE "We've been told by more than one of our colleagues that, even if Darwin was substantially wrong to claim that natural selection is the mechanism of evolution, nonetheless we shouldn't say so. Not, anyhow, in public. To do that is, however inadvertently, to align oneself with the Forces of Darkness, whose goal it is to bring Science into disrepute. Well, we don't agree. We think the way to discomfort the Forces of Darkness is to follow the arguments wherever they may lead, spreading such light as one can in the course of doing so. What makes the Forces of Darkness dark is that they aren't willing to do that. What makes science scientific is that it is." Jerry Fodor and Massimo Piattelli-Palmarini - “What Darwin Got Wrong” Quotes from Mazur’s Altenberg 16: “Oh sure natural selection’s been demonstrated … the interesting point, however, is that it has rarely if ever been demonstrated to have anything to do with evolution in the sense of long-term changes in populations. … Summing up we can see that the import of the Darwinian theory of evolution is just unexplainable caprice from top to bottom. What evolves is just what happens to happen [ellipsis in original]” (Stanley Salthe, p. 21). “Darwinism and the neo-Darwinian synthesis, last dusted off 70 years ago, actually hinder discovery of the mechanism of evolution” (Antonio Lima-de-Faria, p. 83). “Do I think natural selection should be relegated to a less import(ant) role in the discussion of evolution? Yes I do” (Scott Gilbert, p. 221). “She [Lynn Margulis] sees natural selection as ‘neither the source of heritable novelty nor the entire evolutionary process’ and has pronounced neo-Darwinism ‘dead’, since there’s no adequate evidence in the literature that random mutations result in new species” (Mazur, p. 257). “At that meeting [Francisco] Ayala agreed with me when I stated that this doctrinaire neo-Darwinism is dead. He was a practitioner of neo-Darwinism but advances in molecular genetics, evolution, ecology, biochemistry, and other news had led him to agree that neo-Darwinism’s now dead” (Lynn Margulis, p. 278). Can Darwinian Evolutionary Theory Be Taken Seriously? - Stephen L. Talbott - May 16, 2016 Excerpt: The influential Dutch botanist and geneticist, Hugo de Vries, framed the matter this way during the first decade of the twentieth century: Natural selection is a sieve. It creates nothing, as is so often assumed; it only sifts. It retains only what variability puts into the sieve. Whence the material comes that is put into it, should be kept separate from the theory of its selection. How the struggle for existence sifts is one question; how that which is sifted arose is another.34 It was de Vries who formulated the catchy phrasing that has since been repeated many times: “Natural selection may explain the survival of the fittest, but it cannot explain the arrival of the fittest”.35 It’s not a concern easily dismissed. Over subsequent decades other biologists have added their own accents: “The function of natural selection is selection and not creation. It has nothing to do with the formation of new variation”. (Reginald Punnett [1911], British geneticist who cofounded the Journal of Genetics; quoted in Stoltzfus 2006) Regarding specific traits, natural selection “might afford a reason for their preservation, but never provide the cause for their origin”. (Adolf Portmann [1967, p. 123], preeminent zoologist of the middle of the twentieth century) “Natural selection is the editor, rather than the composer, of the genetic message”. (Jack King and Thomas Jukes [1969], key developers of the idea of “neutral evolution”) “In evolution, selection may decide the winner of a given game but development non-randomly defines the players”. (Pere Alberch [1980], Spanish naturalist and embryologist, sometimes spoken of as the founder of Evo-Devo — evolutionary developmental biology) “Natural selection eliminates and maybe maintains, but it doesn’t create”. (Lynn Margulis [2011], microbiologist and botanist, pioneer in exploring the role of symbiosis in evolution, and co-developer of the Gaia hypothesis) The objection (to natural selection) these estimable biologists were raising has never gained the traction it deserves. ,,, On the other hand, it would have been hard to find even a slight blush of embarrassment when Stephen Jay Gould, countering the sort of doubt voiced above by his peers, asked, “Why was natural selection compared to a composer by Dobzhansky; to a poet by Simpson; to a sculptor by Mayr; and to, of all people, Mr. Shakespeare by Julian Huxley?” The answer, according to Gould, is that the allusions to poetry, musical composition, and sculpture helpfully underscore the “creativity of natural selection”: "The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies the raw material only. Natural selection directs the course of evolutionary change. It preserves favorable variants and builds fitness gradually".36 And so it is possible for leading theorists of evolution to declare an abstract algorithm — natural selection — a capable artist, even though the only place where we observe an actual creative and artistic activity going on is in the organism itself. And even though the explanatory appeal to natural selection simply hides the fact, as we saw above, that the explanation assumes this very same creative activity in the organism. ,,, What we do have is a god-like power of natural selection whose miracle-working activity in creating ever-new organisms is vividly clear to eyes of faith, but frustratingly obscure to mere empirical investigators. This is not a science ready for submission to a larger public along with a demand for acquiescence. Not if this public has yet to dull its sensitivity to fundamental questions in the way that the research community seems to have done. http://natureinstitute.org/txt/st/org/comm/ar/2016/teleology_30.htm
Darwin himself referred to Natural Selection as some type of master craftsman:
“It may be said that natural selection is daily and hourly scrutinizing, throughout the world, every variation, even the slightest; rejecting that which is bad preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life” - Darwin - Origin
Yet contrary to what Darwin and his modern day 'just so story tellers' may believe, Natural Selection as the designer substitute is not only blind but is dead:
The abject failure of Natural Selection on two levels of physical reality – video (2016) (princess and the pea paradox & quarter power scaling) https://youtu.be/ISu-09yq2Gc
bornagain77_{October 26, 2016
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ba77 - where do those quotes say that natural selection is not effective? Yes, they say we don't get selective sweeps and fixation, but I don't know any serious biologist who's claimed that natural selection has to lead to selective sweeps and fixation.Bob O'H_{October 26, 2016
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Bob states that "Your comments about me being “obfuscating and disingenuous” are not worth responding to." And yet Bob himself demonstrates the disingenuous nature in which conducts himself by his selective omission of what followed directly after his selected quote,,, specifically
, we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. On the basis of resequencing data from a single replicate population with accelerated development, as well as single nucleotide polymorphism data from individual flies from each replicate population, we infer little allele frequency differentiation between replicate populations within a selection treatment. Signatures of selection are qualitatively different than what has been observed in asexual species; in our sexual populations, adaptation is not associated with ‘classic’ sweeps whereby newly arising, unconditionally advantageous mutations become fixed. More parsimonious explanations include ‘incomplete’ sweep models, in which mutations have not had enough time to fix, and ‘soft’ sweep models, in which selection acts on pre-existing, common genetic variants. We conclude that, at least for life history characters such as development time, unconditionally advantageous alleles rarely arise, are associated with small net fitness gains or cannot fix because selection coefficients change over time.
The conclusion is more direct than the abstract:
“Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments.” http://www.homepages.ed.ac.uk/aspiliop//2010_2011/Burke%20et%20al%202010.pdf
I'll let the unbiased readers decide for themselves whether Bob provided the rope for his own hanging on the charge of being disingenuous towards the evidence!bornagain77_{October 26, 2016
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ba77 @ 38 - huh? That paper that you link to shows natural selection, at several dozen loci. From the abstract:
we identify several dozen genomic regions that show strong allele frequency differentiation between a pooled sample of five replicate populations selected for accelerated development and pooled controls. ... we infer little allele frequency differentiation between replicate populations within a selection treatment.
So there is both genotypic and phenotypic change, and this is repeatable across replicates. Your comments about me being "obfuscating and disingenuous" are not worth responding to.Bob O'H_{October 26, 2016
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I wonder whether rvb8 is actually a Turing test using a BA/PV app.
r - rare v - virus b - bot 8 - 8th iteration ?Vy_{October 25, 2016
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Arthur:
PaV,, regarding your resort to “the math”, i don’t think you have any idea what you are saying. You seem to be claiming, for example, that we have no idea about the mechanisms that underlie the origins of, say, the Hawaiian silverswords. That is more than wrong, it is silly. (I believe this subject has been broached before here, and the anti evolution crowd reflexively resorted to “no fair, they’re just plants”.).
You missed the part where I talked about Darwin describing "varieties" as "incipient species." This does get us back to "they're still just a [type of] plant." What Darwinism needs to demonstrate is still left for demonstration. Adaptation, and phenotypic diversity, is not "macroevolution." Simple as that. As to adaptive radiations, have you ever looked at Richard Goldschmidt's (1934?) "The Material Basis of Evolution"? There you will find that he determined that the one "new species" of moth that seemed to creep up at the end of one such 'radiation," was not due to 'genetics," but due to the type of soil. Guess what, even back then we were running into 'epigenetics': that is, environmental cues changing the regulatory mechanism of a 'genome.'
As far as the alleged insufficiency of RM+NS, it is a fact that no antievolutionist has ever published any sort of well-controlled positive experimental evidence for this claim.
Well, in a way, I have. Look here (posts 46 and 48) and here. I predicted that the Adriatic lizard, Podacaris sicula, if fed the diet that the transplanted lizards encountered after transplantation to a new island in the lab would produce the same phenotypic changes that occurred. I suggested that this study be carried out. It was. I turned out to be correct. So, though I didn't publish it, the study was done and published. It's what Goldschmidt was saying 80 years ago.PaV_{October 25, 2016
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Querius
It seems like it would be good for someone to critique his material.
Agreed! He needs a tough-minded editor who wont' give him the chance to just keep replaying the same material. :-)Silver Asiatic_{October 25, 2016
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"your first link is dead." Indeed it is. Although the original article has apparently died and gone to internet heaven, here are some links that get the same point across
Long-Term Fruit Fly Experiment Raises Questions - October 6, 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments." http://darwins-god.blogspot.com/2010/10/long-term-fruit-fly-experiment-raises.html Genome-wide analysis of a long-term evolution experiment with Drosophila - 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments." http://www.homepages.ed.ac.uk/aspiliop//2010_2011/Burke%20et%20al%202010.pdf UCI scientists decode genomes of sexually precocious fruit flies - September 16, 2010 Excerpt: “This research really upends the dominant paradigm about how species evolve,” said ecology & evolutionary biology professor Anthony Long, the primary investigator. https://news.uci.edu/press-releases/uci-scientists-decode-genomes-of-sexually-precocious-fruit-flies/
Your critique of The Third Way is fuzzy to put it nicely. But I guess a Darwinist, who is purposely being obfuscating and disingenuous to the science at hand, would find it 'odd' that respected scientists, who have no theological axe to grind, would strenuously object to the mechanism of RM & NS on purely empirical grounds: These guys a pretty impressive in their work. One of the scientists listed on "The Third Way", who finds Darwinian explanations severely lacking, is Didier Raoult himself:
The "Most Productive and Influential Microbiologist in France" Is a Furious Darwin Doubter - March 2012 Excerpt: Controversial and outspoken, Raoult last year published a popular science book that flat-out declares that Darwin's theory of evolution is wrong. http://www.evolutionnews.org/2012/03/the_most_produc057081.html A New Model for Evolution: A Rhizome - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. - Didier Raoult http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html
bornagain77_{October 25, 2016
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ba77 @36 - your first link is dead. The Third Way group is odd - I suspect almost every evolutionary biologist would agree that "other mechanisms [than natural selection] are essential for a comprehensive understanding of evolutionary processes". That's why mutation, demography, drift, behaviour, and even (*gasp*) epigenetics are part of evolutionary biology. (although in fairness the evolutionary role of epigenetics is poorly understood)Bob O'H_{October 25, 2016
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as to this claim: "As far as the alleged insufficiency of RM+NS, it is a fact that no antievolutionist has ever published any sort of well-controlled positive experimental evidence for this claim." and yet we find,,,
Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) – October 2010 Excerpt: “Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.”,,, “This research really upends the dominant paradigm about how species evolve,” said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://eebweb.arizona.edu/nachman/Suggested%20Papers/Lab%20papers%20fall%202010/Burke_et_al_2010.pdf
Of note, it is hardly just 'anti-evolutionists' that find RM & NS severely wanting. "The Third Way" has a list of many distinguished scientists, who no doubt believe in some type of evolution, who find the mechanism of RM & NS severely wanting:
“some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis. Many scientists today see the need for a deeper and more complete exploration of all aspects of the evolutionary process.” http://www.thethirdwayofevolution.com/ List of people who are members of The Third Way http://www.thethirdwayofevolution.com/people
bornagain77_{October 24, 2016
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Silver Asiatic @ 21, Points taken. I got bored after a few minutes due to its slow pace and familiar approach. It seems like it would be good for someone to critique his material. The banana routine in another of his videos sounded like it came straight from an evolutionary argument in a Biology text. You know, like the goofy ones that try to trace the evolution of mustaches in men or that compare human blood to the sea water of ancient oceans. Now that film was a real corker! ;-) https://www.youtube.com/watch?v=32mHZbrVnuA -QQuerius_{October 24, 2016
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Marfin @17
rvb8- You also seem to have an aversion to answering straightforward questions. Any sign of that aversion going away and you answer my question re fossil ancestry.
So, you noticed that, too? All you read is Baseless Assertions and Pointless Vituperation. I wonder whether rvb8 is actually a Turing test using a BA/PV app. I once had had a similar experience when I was a kid trying to corner Eliza . . . -QQuerius_{October 24, 2016
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RM and NS is "not even wrong" Of note: The phrase "not even wrong" is generally attributed to theoretical physicist Wolfgang Pauli. Here is what Pauli said about evolution:
"In discussions with biologists I met large difficulties when they apply the concept of 'natural selection' in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely 'scientific' and 'rational,' they become actually very irrational, particularly because they use the word 'chance', not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word 'miracle.'" Wolfgang Pauli (pp. 27-28) - Letter by Pauli to Bohr of February 15, 1955
bornagain77_{October 24, 2016
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as to: " The fact is, RM+NS is all there is, and these mechanisms quite completely suffice to explain the variety of life as we know it." Dr. Sanford, among many others, begs to differ:
The waiting time problem in a model hominin population - 2015 Sep 17 John Sanford, Wesley Brewer, Franzine Smith, and John Baumgardner Excerpt: The program Mendel’s Accountant realistically simulates the mutation/selection process,,, Given optimal settings, what is the longest nucleotide string that can arise within a reasonable waiting time within a hominin population of 10,000? Arguably, the waiting time for the fixation of a “string-of-one” is by itself problematic (Table 2). Waiting a minimum of 1.5 million years (realistically, much longer), for a single point mutation is not timely adaptation in the face of any type of pressing evolutionary challenge. This is especially problematic when we consider that it is estimated that it only took six million years for the chimp and human genomes to diverge by over 5 % [1]. This represents at least 75 million nucleotide changes in the human lineage, many of which must encode new information. While fixing one point mutation is problematic, our simulations show that the fixation of two co-dependent mutations is extremely problematic – requiring at least 84 million years (Table 2). This is ten-fold longer than the estimated time required for ape-to-man evolution. In this light, we suggest that a string of two specific mutations is a reasonable upper limit, in terms of the longest string length that is likely to evolve within a hominin population (at least in a way that is either timely or meaningful). Certainly the creation and fixation of a string of three (requiring at least 380 million years) would be extremely untimely (and trivial in effect), in terms of the evolution of modern man. It is widely thought that a larger population size can eliminate the waiting time problem. If that were true, then the waiting time problem would only be meaningful within small populations. While our simulations show that larger populations do help reduce waiting time, we see that the benefit of larger population size produces rapidly diminishing returns (Table 4 and Fig. 4). When we increase the hominin population from 10,000 to 1 million (our current upper limit for these types of experiments), the waiting time for creating a string of five is only reduced from two billion to 482 million years. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4573302/ Genetic Entropy – peer reviewed references http://www.geneticentropy.org/#!properties/ctzx “The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the position of some people at the meeting, the answer can be given as a clear, No.” Roger Lewin - Historic Chicago 'Macroevolution' conference of 1980 "Evolutionary Theory Under Fire" Science, vol. 210, 21 November, p. 883
bornagain77_{October 24, 2016
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PaV,, regarding your resort to "the math", i don't think you have any idea what you are saying. You seem to be claiming, for example, that we have no idea about the mechanisms that underlie the origins of, say, the Hawaiian silverswords. That is more than wrong, it is silly. (I believe this subject has been broached before here, and the anti evolution crowd reflexively resorted to "no fair, they're just plants".). As far as the alleged insufficiency of RM+NS, it is a fact that no antievolutionist has ever published any sort of well-controlled positive experimental evidence for this claim. The fact is, RM+NS is all there is, and these mechanisms quite completely suffice to explain the variety of life as we know it. The summit we are talking about proposes new modes of heritable variation, but it doesn't seem to question this core pillar.Arthur Hunt_{October 24, 2016
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In fact, in so far as the math of population genetics can be applied to Darwinian claims, it has falsified natural selection, which was Darwin's primary claim to scientific fame, under the bus:
Majestic Ascent: Berlinski on Darwin on Trial - David Berlinski - November 2011 Excerpt: The publication in 1983 of Motoo Kimura's The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura's theories left the emergence of complex biological structures an enigma (since natural selection was no longer the supposed ‘designer substitute’), but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. "A critique of neo-Darwinism," the Dutch biologist Gert Korthof boasted, "can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science." By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian. http://www.evolutionnews.org/2011/11/berlinski_on_darwin_on_trial053171.html "many genomic features could not have emerged without a near-complete disengagement of the power of natural selection" Michael Lynch The Origins of Genome Architecture, intro "a relative lack of natural selection may be the prerequisite for major evolutionary advance" Mae Wan Ho Beyond neo-Darwinism Evolution by Absence of Selection “Darwinism provided an explanation for the appearance of design, and argued that there is no Designer -- or, if you will, the designer is natural selection. If that's out of the way -- if that (natural selection) just does not explain the evidence -- then the flip side of that is, well, things appear designed because they are designed.” Richard Sternberg - Living Waters documentary Whale Evolution vs. Population Genetics - Richard Sternberg and Paul Nelson - (excerpt from Living Waters video) https://www.youtube.com/watch?v=0csd3M4bc0Q
And whereas Darwinian evolution has no known law of nature to appeal to so as to establish itself as a proper, testable, science, Intelligent Design does not suffer from such a disconnect from physical reality. In other words, Intelligent Design can appeal directly to ‘the laws of conservation of information’ (Dembski, Marks, et al) in order to establish itself as a proper, testable, and rigorous science. https://uncommondescent.com/intelligent-design/consider-the-opossum-the-evidence-for-common-descent/#comment-609504 Moreover Lakatos, although he tipped toed around the failure of Darwinism to have a rigid demarcation criteria, he was brave enough to state that a good scientific theory will make successful predictions in science and a pseudo-scientific theory will generate ‘epicycle theories’ to cover up embarrassing failed predictions:
Science and Pseudoscience (transcript) - “In degenerating programmes, however, theories are fabricated only in order to accommodate known facts” – Imre Lakatos (November 9, 1922 – February 2, 1974) a philosopher of mathematics and science, , quote as stated in 1973 LSE Scientific Method Lecture http://www2.lse.ac.uk/philosophy/about/lakatos/scienceandpseudosciencetranscript.aspx Almost 20 years after Lakatos's 1973 challenge to the scientificity of Darwin, in her 1991 The Ant and the Peacock, LSE lecturer and ex-colleague of Lakatos, Helena Cronin, attempted to establish that Darwinian theory was empirically scientific in respect of at least being supported by evidence of likeness in the diversity of life forms in the world, explained by descent with modification. She wrote that “our usual idea of corroboration as requiring the successful prediction of novel facts...Darwinian theory was not strong on temporally novel predictions.” ... http://en.wikipedia.org/wiki/Imre_Lakatos#Darwin.27s_theory
And even by Lakatos's much softer falsification criteria, (a falsification criteria of just making successful predictions in science instead of subjecting a theory to direct empirical testing of its claims), we find that Darwinian evolution qualifies as a pseudo-science rather than qualifying as a hard science: Dr. Hunter comments here on Darwinism's failed predictions:
"Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought." ~ Cornelius Hunter "When their expectations turn out to be false, evolutionists respond by adding more epicycles to their theory that the species arose spontaneously from chance events. But that doesn’t mean the science has confirmed evolution as Velasco suggests. True, evolutionists have remained steadfast in their certainty, but that says more about evolutionists than about the empirical science." ~ Cornelius Hunter Here’s That Algae Study That Decouples Phylogeny and Competition - June 17, 2014 Excerpt: "With each new absurdity another new complicated just-so story is woven into evolutionary theory. As Lakatos explained, some theories simply are not falsifiable. But as a result they sacrifice realism and parsimony." - Cornelius Hunter http://darwins-god.blogspot.com/2014/06/heres-that-algae-study-that-decouples.html
And following in Lakatos footsteps, Dr. Hunter has compiled a list of many of the major false predictions generated by evolutionary theory. False predictions that are fundamental to evolutionary theory, i.e. go to the ‘core’ of the theory, and falsify it from the inside out as it were.
Darwin's (failed) Predictions - Cornelius G. Hunter - 2015 This paper evaluates 23 fundamental (false) predictions of evolutionary theory from a wide range of different categories. The paper begins with a brief introduction to the nature of scientific predictions, and typical concerns evolutionists raise against investigating predictions of evolution. The paper next presents the individual predictions in seven categories: early evolution, evolutionary causes, molecular evolution, common descent, evolutionary phylogenies, evolutionary pathways, and behavior. Finally the conclusion summarizes these various predictions, their implications for evolution’s capacity to explain phenomena, and how they bear on evolutionist’s claims about their theory. *Introduction Why investigate evolution’s false predictions? Responses to common objections *Early evolution predictions The DNA code is not unique The cell’s fundamental molecules are universal *Evolutionary causes predictions Mutations are not adaptive Embryology and common descent Competition is greatest between neighbors *Molecular evolution predictions Protein evolution Histone proteins cannot tolerate much change The molecular clock keeps evolutionary time *Common descent predictions The pentadactyl pattern and common descent Serological tests reveal evolutionary relationships Biology is not lineage specific Similar species share similar genes MicroRNA *Evolutionary phylogenies predictions Genomic features are not sporadically distributed Gene and host phylogenies are congruent Gene phylogenies are congruent The species should form an evolutionary tree *Evolutionary pathways predictions Complex structures evolved from simpler structures Structures do not evolve before there is a need for them Functionally unconstrained DNA is not conserved Nature does not make leaps *Behavior Altruism Cell death *Conclusions What false predictions tell us about evolution https://sites.google.com/site/darwinspredictions/home Why investigate evolution’s false predictions? Excerpt: The predictions examined in this paper were selected according to several criteria. They cover a wide spectrum of evolutionary theory and are fundamental to the theory, reflecting major tenets of evolutionary thought. They were widely held by the consensus rather than reflecting one viewpoint of several competing viewpoints. Each prediction was a natural and fundamental expectation of the theory of evolution, and constituted mainstream evolutionary science. Furthermore, the selected predictions are not vague but rather are specific and can be objectively evaluated. They have been tested and evaluated and the outcome is not controversial or in question. And finally the predictions have implications for evolution’s (in)capacity to explain phenomena, as discussed in the conclusions. https://sites.google.com/site/darwinspredictions/why-investigate-evolution-s-false-predictions
Moreover, as bad as all of the preceding is for people who prefer to believe in Darwinian evolution no matter what the evidence says to the contrary, being a pseudo-science is not the worse failing of Darwinian evolution. The worst failing of Darwinian evolution is its naturalistic basis. Simply put, if we try to use naturalism as our basis for understanding the universe, and for practising science, then everything within that atheistic/naturalistic worldview, (i.e. sense of self. observation of reality, beliefs about reality, free will, even reality itself), collapses into self refuting, unrestrained, flights of fantasy and imagination.
Darwinian evolution, and atheism/naturalism in general, are built entirely upon a framework of illusions and fantasy Excerpt: Thus, basically, without God, everything within the atheistic/naturalistic worldview, (i.e. supposed evidence for Darwinian evolution, observations of reality, beliefs about reality, sense of self, free will, even reality itself), collapses into self refuting, unrestrained, flights of fantasy and imagination. It would be hard to fathom a more unscientific worldview than Darwinian evolution and Atheistic materialism/naturalism in general have turned out to be. Scientists should definitely stick with the worldview that brought them to the dance! i.e Christianity! https://docs.google.com/document/d/1Q94y-QgZZGF0Q7HdcE-qdFcVGErhWxsVKP7GOmpKD6o/edit
Verse:
1 Thessalonians 5:21 but test everything; hold fast what is good.
bornagain77_{October 24, 2016
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Art Hunt says that it is hard for him to see how anything that is being brought up in the conference would be a challenge to the theoretical core of Darwinian evolution. And he is right to claim that it hard to see how anything can be a challenge to Darwinian evolution. It should be very hard for anyone to see how anything can ever really be a challenge to the theoretical core of Darwinian evolution since Darwinian evolution does not even have a hard core to be challenged in the first place:
A Philosophical Question...Does Evolution have a Hard Core ? Some Concluding Food for Thought In my research on the demarcation problem, I have noticed philosophers of science attempting to balance (usually unconsciously) a consistent demarcation criteria against the disruptive effects that its application might have with regard to the academic status quo (and evolution in particular)… Few philosophers of science will even touch such matters, but (perhaps unintentionally) Imre Lakatos does offer us a peek at how one might go about balancing these schizophrenic demands (in Motterlini1999: 24) “Let us call the first school militant positivism; you will understand why later on. The problem of this school was to find certain demarcation criteria similar to those I have outlined, but these also had to satisfy certain boundary conditions, as a mathematician would say. I am referring to a definite set of people to which most scientists as well as Popper and Carnap would belong. These people think that there are goodies and baddies among scientific theories, and once you have defined a demarcation criterion. you should divide all your theories between the two groups. You would end up. for example, with a goodies list including Copernicus’s (Theory1), Galileo’s (T2), Kepler’s (T3), Newton’s (T4) … and Einstein’s (T5), along with (but this is just my supposition) Darwin’s (T6). Let me just anticipate that nobody to date has yet found a demarcation criterion according to which Darwin can be described as scientific, but this is exactly what we are looking for.” So basically, the demarcation problem is a fun game philosophers enjoy playing, but when they realize the implications regarding the theory of evolution, they quickly back off… http://www.samizdat.qc.ca/cosmos/philo/hardcore_pg.htm
Basically, Lakatos was referring to the fact that Darwinian evolution is not scientifically falsifiable. That it to say, there is no test that someone can perform in the lab that has the potential to directly falsify evolution. And since it is not falsifiable, then it does not qualify as a science but is more realistically classified as a pseudo-science along the lines of tea leaf reading:
“In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality.” Karl Popper – The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge “On the other hand, I disagree that Darwin’s theory is as `solid as any explanation in science.; Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?” – Berlinski, D., “A Scientific Scandal?: David Berlinski & Critics,” Commentary, July 8, 2003
J. B. S. Haldane himself, one of the main founders of population genetics, basically agreed with the point that Darwinian evolution is untestable in the lab, and therefore unfalsifiable, when he offered up the laughable ‘pre-cambrian rabbit’ as a supposed test that could falsify evolution:
Haldane’s Pre-Cambrian Rabbit plus Natural Selection Falsified by Population Genetics – video https://youtu.be/zlGwjUJLgAE
The reason why Darwinian evolution, as it is presently configured, is a unfalsifiable pseudo-science is because it has no rigid mathematical basis to test against (As say Quantum Theory and General Relativity have a rigid mathematical basis to test against):
Deeper into the Royal Society Evolution Paradigm Shift Meeting – 02/08/2016 Suzan Mazur: Peter Saunders in his interview comments to me said that neo-Darwinism is not a theory, it’s a paradigm and the reason it’s not a theory is that it’s not falsifiable. http://www.huffingtonpost.com/suzan-mazur/john-dupre-interview-deep_b_9184812.html Peter Saunders is Co-Director, Institute of Science in Society, London; Emeritus professor of Applied Mathematics, King’s College London. Peter Saunders has been applying mathematics in biology for over 40 years, in microbiology and physiology as well as in development and evolution. He has been a critic of neo-Darwinism for almost as long. Evolution is Missing a Mathematical Formula Excerpt: Virtually all scientists acknowledge that mathematics is the real language of science. Every theory uses words to describe and postulate the theory, but the true test of a theory is numbers and mathematics. It is numbers and mathematical formulae that distinguish true science from hocus-pocus.,,, Every scientific theory that has been promoted to the status of being a scientific law has been quantified and/or embodied into one or more mathematical formulae that make accurate predictions. But no scientist has been able to derive any working formula from the Theory of Evolution and no one has been able to quantify its dictums. Millions of scientists have tried to quantify the Theory of Evolution and they have all failed to do so. http://darwinconspiracy.com/article_1_rev2.php
The primary reason why no scientist has been able to ‘quantify its dictums’ is because there are no known laws of nature for Darwinists to appeal to to base their math on. In other words, there is no known ‘law of evolution’, such as there is a ‘law of gravity’, within the physical universe for us to test against:
“It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109. The Evolution of Ernst: Interview with Ernst Mayr – 2004 Excerpt: biology (Darwinian Evolution) differs from the physical sciences in that in the physical sciences, all theories, I don’t know exceptions so I think it’s probably a safe statement, all theories are based somehow or other on natural laws. In biology, as several other people have shown, and I totally agree with them, there are no natural laws in biology corresponding to the natural laws of the physical sciences. ,,, And so that’s what I do in this book. I show that the theoretical basis, you might call it, or I prefer to call it the philosophy of biology, has a totally different basis than the theories of physics. per scientific american WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Evolution is True – Roger Highfield – January 2014 Excerpt:,,, Whatever the case, those universal truths—’laws’—that physicists and chemists all rely upon appear relatively absent from biology. Little seems to have changed from a decade ago when the late and great John Maynard Smith wrote a chapter on evolutionary game theory for a book on the most powerful equations of science: his contribution did not include a single equation. http://www.edge.org/response-detail/25468
In fact, not only does Evolution not have any universal law to appeal to as other overarching theories of science have, Entropy, a law with great mathematical explanatory power in science, almost directly contradicts Darwinian claims that increases in functional complexity can be easily had (Granville Sewell, Andy McIntosh). Moreover, empirical evidence is also overwhelmingly telling us that Genetic Entropy, as an overriding principle for biology, i.e. genomic decay, holds for biology (Michael Behe, First Rule of Evolution, John Sanford, Genetic Entropy)
“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/ Dr. John Sanford "Genetic Entropy and the Mystery of the Genome" – video https://www.youtube.com/watch?v=eY98io7JH-c Genetic Entropy – peer reviewed references http://www.geneticentropy.org/#!properties/ctzx
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Dennis Noble: By “replacement” I don’t mean to say that the mechanism of random change followed by selection does not exist as a possible mechanism. If the mechanism of random change followed by selection DOESN'T EXIST, what's the alternative professor Noble? Give us a few hints other than the ones you don't want to admit.J-Mac_{October 24, 2016
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Arthur: RM+NS couldn't explain evolution before. [What I mean is that look wherever you like, you will not find a sustained mathematical argument for how species arise. The argument is always that inheritable nucleotides can change from one generation to another, and that these nucleotide changes can become 'fixed.' What is left out, however, is how, over time, through numerous 'generations,' new 'species' arise. There is no 'proof,' but only 'conjecture.' And the 'conjecture' is rather sweeping, and un-detailed.] The situation is now worse in terms of "genetic load." We now have three levels of inheritance that can only be 'filtered' via mortality, or, genetic load. As to the two pillars, I grant you number (1), given that you've used the word ancestry and not inheritance. But number (2) was unsupported before, and now only becomes more problematic. If one looks at a 'trend line,' so to speak, the 'trend' is in the direction of finding more and more interactions--something that implies more and more types of feedback: i.e., complexity. More complexity is the friend of ID, and the enemy of Darwinism. Alas, as you know I've said, "another day, and another bad day for Darwinism." This trending increase in complexity is exactly what I have in mind when I write this phrase. Just like on Wall Street, "the trend is your friend!"PaV_{October 24, 2016
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I think sometime sit is useful to review just what Darwinism is, and what the significant revision adds. The two pillars of Darwin's theory: 1. All life shares a common ancestry. 2. The different forms of life arose (and arise) via natural selection acting on heritable phenotypic variability. The addition: The different forms of life arose (and arise) via the dual proceesss of fixation of random heritable variation and of natural selection acting on heritable phenotypic variability. It is hard to see how this summit changes either of these, at all. Fantastic and sweeping claims that these fundamentals are in some way being challenged are wrong. Just plain wrong.Arthur Hunt_{October 24, 2016
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I can't because you haven't fully explained your disagreement. That's what I'm urging you to do. State the case for why the medical and scientific community is wrong on this too.AhmedKiaan_{October 24, 2016
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AK: Stop playing a game. If you have issues with those who disagree with the HIV consensus, then state it in simple language.PaV_{October 24, 2016
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PaV, you've said that the HIV medical industry has serious fundamental problems, and the basic science is incoherent and wrong. Please explain those problems on a dedicated thread. It would be great to find out what all these issues are. If scientists are being deceptive like they are with evolution and global warming, lets get it out in the open and discuss it.AhmedKiaan_{October 24, 2016
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Commenters who have not read Mazur's Public Evolution Summit interviews are urged to do so. For the first time, the Darwinsmoke cleared and one was listening to modern-day evolutionary biology. People like Coyne are noisy relics now. Dawkins is running an anti-God crusade. I don;t think PZ Myers has invented a new swear word in the last decade. More later, be sure of it.News_{October 24, 2016
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Querius
The video looks pretty good from what I’ve seen of it.
The first 30 minutes are good - although even that went on too long, a lot was repeated. I object to the part at about 41:20 where Mr. Comfort interviews a Catholic student and starts giving him his theological views. From that point on for the next 25 minutes it's all basically Christian preaching in the style of Ray Comfort (which I don't like and don't agree with). Interviewing a Catholic in a movie directed at "the Atheist Delusion" was tasteless and demeaning, but that's very much in the style of Ray Comfort as I see him. An edited version with just the ID parts (maybe 20 minutes max) would be great. If not, it's more like something oriented to Evangelical church ministry, and that's certainly ok for its purpose. But even there, I enjoy watching David Rives who does a Creation Ministry program - very similar to Ray Comfort but more appealing in my opinion. But it's a different kind of ID than I'm familiar with, very Biblically based as the starting point. The science seems good. But they actually oppose ID because it doesn't name the designer as the God of Christian Faith. I always appreciate BA77's links - which come from a variety of sources, including atheists who support ID, so I hope we don't view my comments as a criticism of him or the great job he does in providing resources! And, in fact, I'm very glad to have heard about this video in the first place, so thank you!Silver Asiatic_{October 24, 2016
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OT: Dr. Paul Giem wraps up his review of Doug Axe's book 'Undeniable'
Undeniable (Part 9 - Chapters 13 & 14) 10-22-2016 by Paul Giem https://www.youtube.com/watch?v=k-dZ-7Ff8D0&index=9&list=PLHDSWJBW3DNUx3ngrgTIQyl-B2TaQBoq8
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Bob O'H: I linked to a post pointing out the surprise finding of how ds-RNA migrates into the new gamete. If you look at the short video, it is quite remarkable. This is no small amount of ds-RNA that is being transferred. This is an additional mechanism. It further dilutes RM+NS. And it is always at the level of 'adaptation,' not 'innovation.' neo-Darwinism has always limped. Now it is in a wheelchair. William Provine, THE historian of neo-Darwinism, as his final work, decimates the underpinnings of the MS. He points out, over and over, that genetic changes in small populations occur not because of “random genetic drift,” but because of “inbreeding.” Neo-Darwinism is defective at its core. I am still stunned, now about seven or eight years later, that Fisher's "Fundamental Theorom of Natural Selection" comes from differentiating two equations used for actuarial tables (i.e., how to calculate the rate of death), and then equating the differentials! Wow! That's the "fundamental theorom"? Oh, my. And, of course, his "equation" finds great use in "statistical mechanics." You might as well say that increasing entropy causes evolution! Oh, wait. They do! Oh, my. Just go to your nearest 'heat bath' and see what nature has produced!PaV_{October 24, 2016
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Bob O'H, you are picking at inconsequential details in Noble's broad historical outline, Details that Noble purposely skipped over in order to make his presentation short and sweet so as too be able to highlight the more important empirical falsifications of neo-Darwinism in his short lecture. Moreover, you are apparently ignoring the much more important 'elephant in the living room' empirical falsifications against neo-Darwinism that Noble presented in his talk in order to focus on inconsequential historical details. It does not reflect well on you to be so disingenuous to the science at hand. As to your attempted, half hearted, defence of Dawkins, that is simply inexcusable. IMHO, Dawkins is almost single handedly responsible for leading the entire field of molecular biology down a blind path for decades with his 'selfish gene' concept: At the 10:30 minute mark of the following video, Dr. Trifonov states that the concept of the selfish gene 'inflicted an immense damage to biological sciences', for over 30 years:
Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://www.youtube.com/watch?v=fDB3fMCfk0E
also of note
Die, selfish gene, die - The selfish gene is one of the most successful science metaphors ever invented. Unfortunately, it’s wrong - Dec. 2013 Excerpt: But 15 years after Hamilton and Williams kited [introduced] this idea, it was embraced and polished into gleaming form by one of the best communicators science has ever produced: the biologist Richard Dawkins. In his magnificent book The Selfish Gene (1976), Dawkins gathered all the threads of the modern synthesis — Mendel, Fisher, Haldane, Wright, Watson, Crick, Hamilton, and Williams — into a single shimmering magic carpet (called the selfish gene). Unfortunately, say Wray, West-Eberhard and others, it’s wrong. https://uncommondescent.com/darwinism/epigenetics-dawkins-selfish-gene-discredited-by-still-more-scientists-you-should-have-heard-of/
Of related note: It is certainly not your grandfather's selfish gene any more
Genes and Organisms: Improvising the Dance of Life - Stephen L. Talbott - Nov. 10, 2015 Excerpt: The performances of countless cells in your body are redirected and coordinated as part of a global narrative for which no localized controller exists. This redirection and coordination includes a unique choreography of gene expression in each individual cell. Hundreds or thousands of DNA sequences move (or are moved) within vast numbers of cell nuclei, and are subjected to extraordinarily nuanced, locally modulated chemical activity so as to contribute appropriately to bodily requirements that are nowhere codified — least of all in those DNA sequences.,,, DNA in its larger matrix You may recall from my earlier article, “Getting Over the Code Delusion” (Talbott 2010), that packing DNA into a typical cell nucleus is like packing about 24 miles of very thin, double-stranded string into a tennis ball, with the string cut up (in the normal human case) into 46 pieces, corresponding to our 46 chromosomes. To locate a protein-coding gene of typical size within all that DNA is like homing in on a one-half-inch stretch within those 24 miles. Or, rather, two relevant half-inch stretches located on different pieces of string, since we typically have two copies of any given gene. Except that sometimes one copy differs from the other and one version is not supposed to be expressed, or one version needs to be expressed more than the other, or the product of one needs to be modified relative to the other. So part of the job may be to distinguish one of those half-inch stretches from the other. “Decisions” everywhere, it seems. But no such decisions are made in a vacuum. As it happens, the chromosome does not consist of a naked DNA double helix. Our DNA, rather, is bound up with a massive, intricate, and dynamic protein-RNA-small molecule complex (called chromatin) that is as fully “informative” for the cell as the DNA sequence itself — and, you might say, much more active and directive.,,, the cell, by managing the shifting patterns of the chromatin infrastructure within which DNA is embedded, brings our chromosomes into movement on widely varying scales. These include large looping movements that put particular genes into connection with essential regulatory sequences and with other, related genes (that is, with other one-half inch stretches of our “24 miles of string in a tennis ball”).,,, A gene is not in any case the kind of rigidly defined entity one might hope to calculate with. As a functional unit appropriate to current circumstances, it must be cobbled together by the cell according to the needs of the moment. There is no neatly predefined path to follow once the cell has located the “right” half inch or so of string, or once it has done whatever is necessary to bring that locus into proper relation with other chromosomal loci participating in the same “dance”. One issue has to do with the fact that there are two strands in the DNA double helix and, starting from any particular point, it is possible to transcibe either of two DNA sequences in either of two directions: “forward” along one strand, or “backward” along the other. This yields two completely different products. One of them is very likely not even a protein-coding RNA, and yet it may still play a vital role in gene expression and in cellular processes more generally. And even when the cell would proceed in one particular direction, it must “choose” the exact point in the genetic sequence at which to begin. Different starting points can yield functionally distinct results. “Many studies focusing on single genes have shown that the choice of a specific transcription start site has critical roles during development and cell differentiation, and aberrations in . . . transcription start site use lead to various diseases including cancer, neuropsychiatric disorders, and developmental disorders”.8,,, The (protein) enzyme that transcribes DNA into RNA is RNA polymerase12. The enzyme certainly does not work alone, however, and its task is by no means cut-and-dried. To begin with, its critical interactions with various elements of the pre-initiation complex help determine whether and exactly where transcription will begin, if it is to begin at all. Then, after those “decisions” have been made, RNA polymerase moves along the double helix transcribing the sequence of genetic “letters” into the complementary sequence of an RNA. Throughout this productive journey, which is called elongation, the RNA polymerase still keeps good and necessary company. Certain co-activators modify it during its transit of a genetic locus, and these modifications not only enable transcription elongation to begin, but also provide binding sites for yet other proteins that will cooperate throughout the transcription journey.,,, Finally — and mirroring all the possibilities surrounding initiation of gene transcription — there are the issues relating to its termination. Again, they are far too many to mention here. Transcription may conclude at a more or less canonical terminus, or at an alternative terminus, or it may proceed altogether past the gene locus, even to the point of overlapping what, by usual definitions, would be regarded as a separate gene farther “downstream”. The cell has great flexibility in determining what, on any given occasion, counts as a gene, or transcriptional unit. The last part of the transcribed gene is generally non-protein-coding, but nevertheless contains great significance. Examining this region in a single gene, a research team recently identified “at least 35 distinct regulatory elements” to which other molecules can bind.13 Further regulatory potentials arise from yet more binding sites on the customized “tail” that the cell adds to the RNA immediately upon conclusion of its transcription. Proteins and other molecules that bind to the various regulatory elements of the non-protein-coding portion of the transcript do so in a context-sensitive manner, where cell and tissue type, phase of the cell cycle, developmental stage, location of the RNA within the cell, and environmental factors, both intra- and extra-cellular, may all play a role. These converging influences can change the stability of the RNA, change its localization within the cell, and change the efficiency of its translation into protein, among other possibilities.,,, What is generally considered the post-transcriptional modulation of gene expression actually begins during transcription proper. A prime example has to do with what happens partly as a result of the pauses during elongation. Cells don’t just passively accept the RNAs that emerge from the transcription process, but rather “snip and stitch” them via an elaborate procedure known as RNA splicing. It happens that the cutting out and knitting together of selected pieces typically begins before the RNA is fully transcribed, and the rhythm of pauses during elongation has an important influence upon which pieces form the mature transcript. This splicing operation, which is applied to nearly all human RNAs, is performed by the spliceosome, consisting of a few non-protein-coding RNAs and over 300 cooperating proteins, and is hardly less exacting in its requirements than, say, brain surgery. For the vast majority of human genes the operation can be performed in different ways, yielding distinct proteins (called isoforms) from a single RNA derived from a single DNA sequence. This is called alternative splicing, and it would be hard to find anything in human development, disease etiology, or normal functioning that is not dependent in one way or another on the effectiveness of this liberty the cell takes with its gene products. But RNA splicing is hardly the end of it. Through RNA editing the cell can add, delete, or substitute individual “letters” of the RNA sequence.15 Or, leaving the letters in place, the cell can chemically modify them in any of over one hundred different ways.16 ,,, Eventually, a protein-coding RNA needs to be translated into protein. This happens by means of large molecular complexes called “ribosomes”. Just as with gene transcription, there are many associated factors that must work together to bring about the initiation of translation, many that cooperate with the ribosome during translation, and yet others that play a role in modifying, localizing, or otherwise regulating the newly produced protein. The overall picture of gene expression is one of unsurveyable complexity in the service of remarkably effective living processes.,,, A decisive problem for the classical view of DNA is that “as cells differentiate and respond to stimuli in the human body, over one million different proteins are likely to be produced from less than 25,000 genes”.30 Functionally, in other words, you might say that we have over a million genes.,,, http://www.natureinstitute.org/txt/st/org/comm/ar/2015/genes_29.htm
bornagain77_{October 24, 2016
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rvb8- You also seem to have an aversion to answering straightforward questions. Any sign of that aversion going away and you answer my question re fossil ancestry.Marfin_{October 24, 2016
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rvb8, since you can not be bothered to watch the new Ray Comfort video because of your aversion to him making an erroneous claim of evidential support in the past from a banana, (which is a surprising aversion on your part since the history of Darwinian evolution is chock full of egregious and erroneous claims of evidential support in the past, (i.e. see junk DNA, vestigial organs, etc... etc... also see Cornelius Hunter's page "Darwin's Predictions"),,, anyways,, since your refined scientific sensibilities prevent you from ever watching a Ray Comfort video then I will ask you the main simple question from the video. OK, pretend you are holding, say, an evolutionary biology textbook in your hands and that you are thumbing through all the rich texts and pictures of the book. OK, got it?, now,, "Do you believe the book wrote itself by accident or do you believe that a person intentionally wrote that book?" And if you rightly, and sanely, believe that a person wrote that book, then do you also rightly, and sanely, believe that the information in DNA, (which is orders, upon orders, more complex and extensive than the information in the book is), is also written by a person? All the college kids in the video, who were atheistic at the beginning of the video, rightly agreed that it is impossible for unguided processes to write the information in the book and thus, by default, they also agreed that it is also impossible for the much more extensive and complex information in DNA to be written by accident, i.e. they agreed that a person had to intentionally write the information in DNA. In fact, no one has EVER seen unguided material processes created non-trivial information. Every time we see information generated in the world we invariably trace its source back to an intelligent agent! In fact, if you, or any Darwinists, can come up with just one example of unguided material processes creating non-trivial information then you would falsify ID and possibly net yourself up to 3 million dollars.
The Law of Physicodynamic Incompleteness - David L. Abel Excerpt: "If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise." If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: "No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone." https://www.academia.edu/Documents/in/The_Law_of_Physicodynamic_Incompleteness The Origin of Information: How to Solve It - Perry Marshall Where did the information in DNA come from? This is one of the most important and valuable questions in the history of science. Cosmic Fingerprints has issued a challenge to the scientific community: “Show an example of Information that doesn’t come from a mind. All you need is one.” “Information” is defined as digital communication between an encoder and a decoder, using agreed upon symbols. To date, no one has shown an example of a naturally occurring encoding / decoding system, i.e. one that has demonstrably come into existence without a designer. A private equity investment group is offering a technology prize for this discovery (up to 3 million dollars). We will financially reward and publicize the first person who can solve this;,,, To solve this problem is far more than an object of abstract religious or philosophical discussion. It would demonstrate a mechanism for producing coding systems, thus opening up new channels of scientific discovery. Such a find would have sweeping implications for Artificial Intelligence research. http://cosmicfingerprints.com/solve/
Moreover, ID uses the exact same method of science as Darwin himself used, i.e. presently acting cause known to produce the effect in question, thus if you try to say that ID is unscientific, then you are also, by default, saying that Darwinian evolution itself is unscientific:
Stephen Meyer: Charles Darwin's Methods, Different Conclusion https://www.youtube.com/watch?v=iqq6JP5gE0E
verse:
John 1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. All things were made through him; and without him was not anything made that hath been made. In him was life; and the life was the light of men.
bornagain77_{October 24, 2016
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