Some Altenberg 16 (= g’bye, Darwin, evolutionary biologists) have now organized the Oxford 50?

_{Denyse O'Leary

January 25, 2015

Darwinism, Intelligent Design, Science}

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Remember Suzan Mazur, who risked all on the Altenberg 16 and has a new book out on origin of life timewasters?

Well, it turns out that, in the era of genomics and epigenomics, lots of people besides us have gotten sick of Darwinblather, however inspired or funded. What’s not to get sick of?:

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process. The commonly accepted alternative is Neo-Darwinism, which is clearly naturalistic science but ignores much contemporary molecular evidence and invokes a set of unsupported assumptions about the accidental nature of hereditary variation. Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, 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.

And get this: A vehicle for new voices.

The web site therefore intends to present a wide variety of novel views about evolution but does not necessarily endorse any of them. Our goal is simply to make new thinking about evolution available in one place on the web.

Now, that’s revolutionary. It sounds like they are people who want to learn something rather than defend some dead idea.

Note: I had expected to continue religion coverage (it’s Sunday here in EST) but may choose to run those stacked stories later in the evening. They are interesting—but this feels much more so just now. Thoughts? – O’Leary for News

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Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information – September 2011 Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html Lenski's Long-Term Evolution Experiment: 25 Years and Counting - Michael Behe - November 21, 2013 Excerpt: Twenty-five years later the culture -- a cumulative total of trillions of cells -- has been going for an astounding 58,000 generations and counting. As the article points out, that's equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski's project the best, most detailed source of information on evolutionary processes available anywhere,,, ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, - http://www.evolutionnews.org/2013/11/richard_lenskis079401.html Multiple Mutations Needed for E. Coli - Michael Behe Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell. http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/ Rose-Colored Glasses: Lenski, Citrate, and BioLogos - Michael Behe - November 13, 2012 Excerpt: Readers of my posts know that I'm a big fan of Professor Richard Lenski, a microbiologist at Michigan State University and member of the National Academy of Sciences. For the past few decades he has been conducting the largest laboratory evolution experiment ever attempted. Growing E. coli in flasks continuously, he has been following evolutionary changes in the bacterium for over 50,000 generations (which is equivalent to roughly a million years for large animals). Although Lenski is decidedly not an intelligent design proponent, his work enables us to see what evolution actually does when it has the resources of a large number of organisms over a substantial number of generations. Rather than speculate, Lenski and his coworkers have observed the workings of mutation and selection.,,, In my own view, in retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski's work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient -- that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism. http://www.evolutionnews.org/2012/11/rose-colored_gl066361.html
bornagain77_{January 26, 2015
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DATCG: To be specific, the co-option model requires that a gene become duplicated, and then overexpressed before it can evolve some new function. A potentiating mutation followed by a gene duplication followed by optimizing mutations was observed by Lenski et al. in the E. coli long-term evolution experiment.Zachriel_{January 26, 2015
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as to:
"It’s been shown that at least some mutations are random with respect to fitness."
Actually, since the vast majority of mutations (i.e. changes to the genome) are shown to be happening in a non-random fashion before natural selection even has a chance to operate, as far as the theoretical construct of Darwinism is concerned, it is far more helpful to point out that, in regards to fitness and natural selection, that the vast majority of mutations that are happening in a non-random fashion in the genome reduce the fitness of the organism, i.e. to show that the vast majority of mutations are detrimental in regards to fitness!
Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006
And for the rare occasions that 'non-random' mutations do increase the fitness of the organism, it is found to come at a cost of the preexisting functional information that is already in the genome:
“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/
As to the distribution of 'non-random' mutations in regards to fitness, the following study shows that 'less fit' mutations are far more likely to be fixed than the 'slightly fitter' mutations.
Study demonstrates evolutionary ‘fitness’ not the most important determinant of success – February 7, 2014 – with illustration Excerpt: An illustration of the possible mutations available to an RNA molecule. The blue lines represent mutations that will not change its function (phenotype), the grey are mutations to an alternative phenotype with slightly higher fitness and the red are the ‘fittest’ mutations. As there are so few possible mutations resulting in the fittest phenotype in red, the odds of this mutation are a mere 0.15%. The odds for the slightly fitter mutation in grey are 6.7% and so this is far more likely to fix, and thus to be found and survive, even though it is much less fit than the red phenotype.,,, By modelling populations over long timescales, the study showed that the ‘fitness’ of their traits was not the most important determinant of success. Instead, the most genetically available mutations dominated the changes in traits. The researchers found that the ‘fittest’ simply did not have time to be found, or to fix in the population over evolutionary timescales. http://phys.org/news/2014-02-evolutionary-important-success.html
This following headline sums the preceding finding up very nicely:
Fittest Can’t Survive If They Never Arrive – February 7, 2014 http://crev.info/2014/02/fittest-cant-survive-if-they-never-arrive/
Needless to say, this is NOT the empirical evidence that Darwinism needs in order to be considered a viable candidate for explaining the optimal complexity being found in life. Such as the optimal complexity found in the vision cascade:
Evolution Vs. The Miracle Of The Eye - Vision Cascade Molecular Animation https://www.youtube.com/watch?v=AuLR0kzfwBU The Vision Cascade is Initiated Not by Isomerization but by Force Field Dynamics - July 2011 Excerpt: 'In addition to designing the opsin protein, evolution must now design the electric field surrounding the chromophore, and how it responds to photon interaction. And while it is busy with that task, it must also specify the correct amino acids at the correct locations within the opsin, that will be influenced by the chromophore’s dynamic electric field.' http://darwins-god.blogspot.com/2011/06/vision-cascade-is-initiated-not-by.html William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.html Eyeballing Design by Casey Luskin - December 2011 Excerpt:,,, the team of scientists who determined the function of glial cells concluded that the "retina is revealed as an optimal structure designed for improving the sharpness of images." http://www.salvomag.com/new/articles/salvo19/19luskin.php
The following article gives a small overview as to the astonishing complexity being dealt with in the vision cascade:
Could the eye have evolved by natural selection in a geological blink? March 18, 2013 Excerpt: Let us return to the question, how do we see? Although to Darwin the primary event of vision was a black box, through the efforts of many biochemists an answer to the question of sight is at hand. When light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein’s metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin. The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water. A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision. If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state; there are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration. However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration. Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall. Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate. The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon. Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle. To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol. Finally, a third enzyme removes the previously added hydrogen atoms to form 11-cis-retinal, and the cycle is complete. per: uncommondescent.com/intelligent-design/could-the-eye-have-evolved-by-natural-selection-in-a-geological-blink/
And please note, neo-Darwinists have yet to empirically demonstrate the origination of even one protein/gene of that jaw dropping complexity in this, or in any other, system!bornagain77_{January 26, 2015
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From another thread https://uncommondescent.com/news/proteins-are-defying-textbooks/#comment-544200
What isn’t criticized in any of these fields is the mention of evolutionary ideas as in the paper I have cited. This is because there is no uncertainty within these fields as to whether or not evolution has occurred. There are no serious problems with the theory, save for the fact that we understand only a fraction of the evolutionary process.
That seems like a standard response. No matter how discredited Neo-Darwinism becomes, they will be 'no uncertainty' that evolution occured. Even if nobody can explain the mechanisms - they will be certain that unguided, unintelligent, blind material forces did it. The fact that there will be conflicting new theories will still mean that 'there are no serious problems with the theory'.Silver Asiatic_{January 26, 2015
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From DATCG on #22: 'Massimo Pigliucci’s Altenberg colleagues are not all on the same page with his conservative thinking.' Conservative!!! Pretty ironical in the light of BA77's immediately-preceding post, especially the concluding paragraphs concerning falsifiability. Well, Pauli's point at the beginning, too.Axel_{January 26, 2015
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Some of the latest discussions on research by the Biological Institute LAB show what appear to be more limitations to Darwinian explanations such as co-option...
When Michael Behe published Darwin's Black Box in 1996, he outlined the concept of irreducible complexity as a biochemical challenge to Darwinian evolution. According to his argument, some structures require all of their parts (or a certain core minimum number) in order to function. In this game of all or nothing, such "irreducibly complex" structures cannot be built in the step-by-step manner of Darwinian evolution because they provide no advantage, of the kind evolution requires, until all their parts are present. At the time and since, evolutionists responded by arguing that irreducibly complex features can be built through co-option. Under this view, biological parts might exist elsewhere in an organism where they are used for a different function. Sometimes, when a gene is duplicated, the extra copy could then be borrowed, retooled, and "co-opted" to perform a new function in a new system.
Research scientist at Biologic Institute have been testing the co-option model of protein evolution. More discussion of the Research here.
To be specific, the co-option model requires that a gene become duplicated, and then overexpressed before it can evolve some new function. Thus, at least two more mutations are needed -- one to duplicate the gene and another to overexpress it.

They experimentally found that at least two mutations would be necessary to convert the most likely co-option candidates in this enzyme family to function like BioF2. But other mutations would be necessary as well -- at least one to duplicate the enzyme and another to overexpress it. This suggests at least four mutations would be required for this conversion.
Abstract for one of their recent papers...
Reeves MA, Gauger AK, Axe DD (2014) Enzyme families—Shared evolutionary history or shared design? A study of the GABA-aminotransferase family. BIO-Complexity 2014 (4):1?16.
The PDF is available for viewing or download at above link.DATCG_{January 26, 2015
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from Chicago biochemist James Shapiro's blog who is one of the scientist mentioned on The Third Way. Regarding "irreducible complexity." What Is the Best Way to Deal With Supernaturalists in Science and Evolution? He makes reasonable statements to engage ID theorist and Creationist. And he recognizes the interesting concept of irreducible complexity...
5. The newly discovered processes of genome change do indeed have the potential to generate "irreducibly complex" new functions. Such complex evolutionary inventions are at the center of the Intelligent Design critique of neo-Darwinian explanations, which are based exclusively on random genetic accidents and natural selection. Doubling the whole genome, distributing copies of mobile elements to different sites, and incorporating similar domains in different proteins provide the necessary raw materials for generating complex interactive networks in cells. A future task for experimental evolution science is to find out how this happens in real time.
DATCG_{January 26, 2015
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Suzan Mazur's credentials are fine. What some complain of is honest and open discussion of the failures of Neo-Darwinism to save Darwinism.
Regarding my journalistic credentials. I was an education major (Biology) for two years in college. I began my writing career as a science journalist 40 years ago at Hearst Magazines. Through the years I’ve contributed feature articles about science to The Economist, Financial Times, Archaeology, Omni, Connoisseur, Solar Age and others. Among the highlights: In the late 1970s, I investigated solar energy at the Kuwait Institute for Scientific Research. In 1980, I flew into Olduvai Gorge to interview paleoanthropologist Mary Leakey re evolution and interviewed scientists elsewhere in East and West Africa. In 1981, I interviewed scientists in subSaharan Africa. And at the French Space Agency in Paris. I reported on earthquakes and seismology in Guatemala. Archaeology in Colombia and Turkey. In the early 1980s, heading a solar energy film project, my crew and I were invited by the Swedish government and the Saudi Arabian National Center for Science and Technology to research a television documentary on solar energy villages in those two countries; I was a guest on Saudi-TV in Riyadh discussing the project. During the Gulf War I broke a fetal-to-fetal transplant [surgery] story. Etc. My book, The Altenberg 16: An Expose of the Evolution Industry (North Altantic Books), which includes the stories Pigliucci derides, has a cover endorsement by the world’s most respected public intellectual, Noam Chomsky, which reads as follows: “Very glad to see the book. I suspect it should have some (very much needed) influence now against the background of the “evo-devo revolution” and the belated recognition of Margulis’s work.” I’ve also covered the wars — Gulf War, Colombian Drug War, Sudan, Kashmir (from both sides of the CFL/LOC). Been a guest on McLaughlin, Charlie Rose and various Fox Television News shows. My television reports on human rights and politics have aired on PBS, CBC, MBC and Fox.
DATCG_{January 26, 2015
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bornagain77: Besides the fact that the vast majority of changes to the genome are accomplished via highly sophisticated molecular machines in a non-random fashion, even the ‘spontaneous’ mutations HAVE NOT been shown to be random in where they occur, how they occur, or when they occur. It's been shown that at least some mutations are random with respect to fitness. They are uncorrelated variables.Zachriel_{January 26, 2015
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Suzan Mazur's website shows interviews with Geneticist and Pioneers in Origin of Life research. Interview with Protocell Pioneer Matt Powner She defends herself well against accusations by Pigliucci... Interesting Developments of Pigliucci's About-Face
The first story post was March 4, 2008 (NZ time), titled “Altenberg! The Woodstock of Evolution?” with coverage of scientists invited to Altenberg and some leading scientists not invited, like Richard Lewontin, Niles Eldredge, Stuart Kauffman and Michael Lynch. The story that Massimo Pigliucci now describes as “hodge-podge” in his book on page 101, paragraph 2, reflects the widely different perspectives in evolutionary thinking among leading scientists. As complexity pioneer Stuart Kauffman told me: “There are people spouting off as if we know the answer [re the process of evolution]. We don’t know the answer.” “Altenberg! The Woodstock of Evolution?” story drew a large audience. And Pigliucci sent me an email shortly after the story posted saying the following: “Suzan very nice article indeed! Cheers, Massimo” (emphasis added) Some hours later when the intelligent design bloggers (some of the most vigorous re evolution) began to comment online about the piece, however, Pigliucci sent this email to all 16 invited Altenberg scientists with a CC to me: “All, well, it was inevitable, but Paul Nelson, of the ID “think tank” The Discovery Institute, picked up Suzan’s article and ran with it: https://uncommondescent.com/intelligent-design/-the-altenberg-sixteen/ Cheers, Massimo”
Some colleagues have other opinions as she points out...
Massimo Pigliucci’s Altenberg colleagues are not all on the same page with his conservative thinking. New York Medical College cell biologist Stuart Newman in an interview with me for Archaeology magazine said this: “I believe that the field will have to reorient I don’t by any means think the science that’s been done under the Darwinian paradigm will disappear or will be seen to be entirely invalid. But the Darwinian mechanism that’s used to explain all evolutionary change will be relegated, I believe, to being just one of the several mechanisms – maybe not even the most important when it comes to understanding macroevolution, the evolution of major transitions in body type.” And Richard Lewontin’s New York Review of Books article “Not So Natural Selection” commenting favorably on Jerry Fodor and Massimo Piattelli-Palmarini’s book What Darwin Got Wrong is also telling, a book Pigliucci termed “misguided” in his review in Nature magazine. In the NYRB article, Richard Lewontin also noted the lack of civility among evolutionary thinkers.
Yes, the times they are a changing.DATCG_{January 26, 2015
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Seversky at 1 quotes:
"One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process."
Actually, contrary to what is popularly believed, neo-Darwinism itself introduces a 'supernatural force' right into the middle of the 'evolution process':
Pauli’s ideas on mind and matter in the context of contemporary science - Harald Atmanspacher Excerpt: “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) http://www.igpp.de/english/tda/pdf/paulijcs8.pdf Evolution and the Illusion of Randomness - Talbott - Fall 2011 Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.” In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.” This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?” http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness
In fact the neo-Darwinian appeal to 'supernatual randomness' has been the primary obstacle to elucidating a rigid mathematical basis for Darwinism that can be potentially falsified (a falsification criteria as other theories of science, including ID, have:
“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.
And James Shapiro, one of the leading lights of 'The Third Way', has been fairly scathing towards the neo-Darwinian appeal to randomness:
"It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works' James Shapiro - Evolution: A View From The 21st Century - (Page 82) 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 How life changes itself: the Read-Write (RW) genome. - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611
Besides the fact that the vast majority of changes to the genome are accomplished via highly sophisticated molecular machines in a non-random fashion, even the 'spontaneous' mutations HAVE NOT been shown to be random in where they occur, how they occur, or when they occur.
WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Fully Random Mutations - Kevin Kelly - 2014 Excerpt: What is commonly called "random mutation" does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it. On the contrary, there's much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism's predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern. http://edge.org/response-detail/25264
Thus, since neo-Darwinism, as was formulated by Charles Darwin and as was laid out in the modern synthesis, relies on 'random variation' as its base postulate before Natural Selection even has a chance to operate, then neo-Darwinism is found to be false in its theoretical contstruct. I would also like to point our that, as far as empirical science itself is concerned, it is much easier to falsify ID than it is to falsify neo-Darwinism:
It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD https://www.youtube.com/watch?v=_T1v_VLueGk 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/9957206/The_Law_of_Physicodynamic_Incompleteness_Scirus_Topic_Page_
Since ID is much easier to falsify than neo-Darwinism is, according to Popper, ID 'speaks about reality' and Darwinism does not:
"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 http://izquotes.com/quote/147518
Verse and Music:
1 Thessalonians 5:21 but test everything; hold fast what is good. Alter Bridge – Rise Today http://www.youtube.com/watch?v=ZYG3BPvFOgs
bornagain77_{January 26, 2015
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DATCG
They’re breaking ranks with Neo-Darwinism and Dawkins’ absolutist position. This is a healthy step taking place, long overdue.
True. We still have absolutists posting here on UD. Others have quietly recognized the changing tide. As evidenced by responses to Susan Mazur's book though, there won't be a revolution and maybe not much of a media story. Perhaps 20 years after NDE is gone, magazines will point it out. But until then, it's a quiet shift to the idea that there are 'multiple mechanisms' and of course, 'no one has claimed that natural selection was a primary factor for decades'. It's a transition now. There's plenty of time to jump ship and grab a jumble of materialist-evolutionary ideas and then later claim 'we knew about this for years'.Silver Asiatic_{January 26, 2015
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There is exactly one way to explain physical existence; physically!
It's impossible to offer a physical explanation of anything. Explanations are not physical.Silver Asiatic_{January 26, 2015
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BA thanks for video post. Will watch when I have time. Think this is Denis Noble's video originally posted here in early January... take down of Neo-Darwinism Noble's subject in the lecture...
"All of these rules have been broken!" referring to Central Dogma of Neo-Darwinism failures. "Are mutations random?" Quoting biochemist James Shapiro, Evolution. A View from the 21st Century "It is difficult(if not impossible) to find a genome operator that is truly random in its action within the DNA of the cell where it works.(pg 82). All careful studies of mutagenesis find statistically significant non-random patters of change."
The march is on now to a different explanation. For those who a priori rule out a possible Design Inference, they're taking the "Third Way.' Was wondering when you guys would post it :) They're breaking ranks with Neo-Darwinism and Dawkins' absolutist position. This is a healthy step taking place, long overdue. Jeannie's Out of the Bottle Now Has been for some time. Eventually this will tumble over to the larger Media, then the Masses.DATCG_{January 26, 2015
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rvb8, You said:
There is exactly one way to explain physical existence; physically! Or naturally, if you will. Introducing phenomena, and the extra-natural is within the realm of childish wish fulfillment; no thank you!
So . . . the physical universe existed before it existed so that it could bring itself into existence. Right. And nature, which is a catch all of the physical universe, somehow worked on that which its meaning is derived from in order to bring that thing into existence so that it could get its meaning from that thing it brought into existence. Awesome. The whole thing sounds rather super-natural if you ask me, because we never expect nature or the physical universe to do these amazing things for us today. What was it you said about childish wish fulfillment?Brent_{January 26, 2015
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As to the gross inadequacy of unguided neo-Darwinian processes: Biological Information - Entire Lecture Series https://www.youtube.com/watch?v=vg_xp0dRUdM&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ&index=1bornagain77_{January 26, 2015
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No Mung that doesn't 'settle it'. Your implication that just because rvb8 said something then that 'settles it', is the typical poorly thought out 'toss away' non-answer we expect here. Please, please, please, at some point in the near future, please ID, do something! I have a notion that ID and Christianity lend themselves to one another because both love playing the 'victim'. This of course is a dangerous path because when it is clearly shown that your insignificance is due to your lack of work then victimhood remains the only answer. This again leads to paranoia and then to less productivity etc etc etc. It is not that 'I' say it. It is that science says it. I've googled Mazur. Loon, is the politest thing I could call her. Half baked quack, radical idealist, god bothering fanatic, unhinged fear dragon, moronic narcissitic rube, ego maniachal gas bag, also sprang to mind. Of course it is very strange that News finds her on the van guard of ID thought, or rather, a 'clear thinker', a 'defender of the trenches'. A revolutionary in the mould of Hamilton, Franklin, and Jefferson, or whichever other manufactured gods you care to name. Christ, give me a break! A red neck by any other name remains a denizen of the lower reaches of Alabami.rvb8_{January 25, 2015
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skram,
"We know pretty well how this part of nature developed over time."
Well, if you don't mind vague answers we do.
But if you insist on having the Ultimate Answer to Life and Everything, then sorry, science does not deal with these kinds of questions. They are too vague. And the answers provided by faith are not necessarily valid."
If you consider sound, deductive, necessarily true answers vague (and then, additionally, become somehow suddenly unwilling to countenance a dirty, 'vague', answer).Brent_{January 25, 2015
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"One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process." Ie, sure looks like this is the best explanation, but it isn't because it is philosophically not permitted.Moose Dr_{January 25, 2015
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If your claim there is "ultimate value, purpose, meaning and hope" we'll need more evidence than the fact that you need there to be. And if there is a God what makes you think that we are His ultimate purpose? As another OP points out, this is a very big universe and it may not be the only one, either. This is classical wish fulfillment at its best.Seversky_{January 25, 2015
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skram 7 "But if you insist on having the Ultimate Answer to Life and Everything, then sorry, science does not deal with these kinds of questions. They are too vague." How did space/time, matter/energy arise from themselves? Too vague. How did life arise from non-life? Too vague. How did the incredible machinery in every cell arise by unguided process? Too vague. How did the incredibly complex codes (yes, they are plural) within DNA arise by unguided processes? Too vague. Why does the fossil record not match Darwin's Tree of Life? Too vague. How did most of the major phyla arise abruptly in the Cambrian without visible antecedents? Too vague. Why do we never observe fruit flies becoming something other than fruit flies, no matter how much we mutate them? Too vague. All I can say is, nice work if you can get it!anthropic_{January 25, 2015
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From the naturalists give in this thread it's no wonder why I consider atheism an emotional worldview moreso then a rational one . What makes it even more irrational is that they dogmatically want to believe that there is no ultimate value, purpose, meaning and hope , even though they can't give us evidence for it . This is classical insanity at its bestwallstreeter43_{January 25, 2015
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Funny, without God there would be no science and yet science cannot tell us anything about God? Methinks the good Dr. be blind!bornagain77_{January 25, 2015
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ThirdWayEvolution website launched last May? I check on it every couple months or so - not a lot of activity posted there. Although it seems they have picked up some additional members since the launch.ppolish_{January 25, 2015
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groovamos, One step at a time. Nature has many sides. The earth as a habitat is part of nature. We know pretty well how this part of nature developed over time. But if you insist on having the Ultimate Answer to Life and Everything, then sorry, science does not deal with these kinds of questions. They are too vague. And the answers provided by faith are not necessarily valid.skram_{January 25, 2015
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rvb8: There is exactly one way to explain physical existence; physically! Or naturally, if you will. Please rvb8, "explain" to us the natural origins for nature. It would be great if you would include some empiricism in your 'explanation', or the history of such.groovamos_{January 25, 2015
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rvb8: The “16?, were squarely in the realm of science. Mazur is squarely in the realm of ‘loon’. Will that settles it then!Mung_{January 25, 2015
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There is exactly one way to explain physical existence; physically! Or naturally, if you will. Introducing phenomena, and the extra-natural is within the realm of childish wish fulfillment; no thank you! The "16", were squarely in the realm of science. Mazur is squarely in the realm of 'loon'.rvb8_{January 25, 2015
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"..there are only two alternative ways to explain the origins of biological diversity." Strikes me as begging the question from the start. Diversity isn't really what most people are trying to explain anyway. Life itself is what most people want to explain. And genomics is telling us STRONGLY that life is NOT diverse. Every new finding leads irresistibly to a SINGLE complete original plan, started at exactly one time, with each life form losing or varying or temporarily switching off various parts of the single complete plan. If we encountered this arrangement in architecture, as in a Levittown development, we wouldn't call it diversity. We'd call it uniformity plus decorations.polistra_{January 25, 2015
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Ive read plenty of papers by neo darwinists that discuss hgt, not really sure what theyre talking about. Also did you miss the part about creationism? Thats bad for you guys.Starbuck_{January 25, 2015
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