Anything HGT does, Darwinian evolution did not do

_{Denyse O'Leary

August 13, 2015

horizontal gene transfer}

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Talk to the Fossils.jpg From Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more:

Richard Dawkins: For over a century, Darwinism was the “must be” explanation, the only “scientific one.” As Dawkins put it (p. 287, Blind Watchmaker, 1986):

My argument will be that Darwinism is the only known theory that is in principle capable of explaining certain aspects of life. If I am right it means that, even if there were no actual evidence in favour of the Darwinian theory (there is, of course) we should still be justified in preferring it over all rival theories.

But Darwinism is not “the only known theory that is in principle capable of explaining certain aspects of life.” Claims that were formerly merely preferred must be tested against HGT. True, some of the example findings given above may need revision or replacement. But many more will likely turn up, as research uncovers HGT in many genomes.

Anything HGT does, Darwinian evolution did not do. As more and more pieces are carved out of Darwin’s territory, just think of the impact on the vast project of “Darwinizing the culture.” More.

See also: Links to the rest of the series at Talk to the fossils: Let’s see what they say back

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Comments

Zach:
Box: 1. Assuming a self-replicator is assuming a lot.
It’s called an organism.
Indeed, and its existence is assumed by Darwin’s Evolutionary Theory — quite an assumption.
Zach:
Box: 2. By ‘viable’ is meant that a replicator miraculously doesn’t succumb to the second law (falls apart) before it replicates itself.
Entropy is not an impediment to life — life revels in it.

Staving off death is a thing that you have to work at. Left to itself - and that is what it is when it dies - the body tends to revert to a state of equilibrium with its environment. If you measure some quantity such as the temperature, the acidity, the water content or the electrical potential in a living body, you will typically find that it is markedly different from the corresponding measure in the surroundings. Our bodies, for instance, are usually hotter than our surroundings, and in cold climates they have to work hard to maintain the differential. When we die the work stops, the temperature differential starts to disappear, and we end up the same temperature as our surroundings. Not all animals work so hard to avoid coming into equilibrium with their surrounding temperature, but all animals do some comparable work. For instance, in a dry country, animals and plants work to maintain the fluid content of their cells, work against a natural tendency for water to flow from them into the dry outside world. If they fail they die. More generally, if living things didn't work actively to prevent it, they would eventually merge into their surroundings, and cease to exist as autonomous beings. That is what happens when they die. - - [Dawkins — The blind Watchmaker, p.10]
The question is of course: “what is working so hard to stave off death?”
Zach:
Box: 3. Not only is NS not creative, …
As already stated, it’s not variation or selection that is creative, but the interplay between the two, called evolution.
Nope, it’s chance that is creative and NS that is destructive.Box_{August 15, 2015
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Box: 1. Assuming a self-replicator is assuming a lot. It's called an organism. They can be observed commonly on the Earth. Box: 2. By ‘viable’ is meant that a replicator miraculously doesn’t succumb to the second law (falls apart) before it replicates itself. Entropy is not an impediment to life — life revels in it. Box: 3. Not only is NS not creative, ... As already stated, it's not variation or selection that is creative, but the interplay between the two.Zachriel_{August 15, 2015
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Darwin’s Evolution Theory breaks down like this:
(1). Assume a self-replicator. (2). Replication and the step-by-step filling of ‘viable self-replicator space’ by means of random mutations. (3). Viable self-replicators are situated in dynamic hostile surroundings that severely hamper the filling of ‘viable self-replicator space’. This obstruction is known as ‘natural selection’ (NS).
Notes: 1. Assuming a self-replicator is assuming a lot. See e.g. here 2. By ‘viable’ is meant that a replicator miraculously doesn’t succumb to the second law (falls apart) before it replicates itself. A replicator must be robust — “however many ways there may be of being alive, it is certain that there are vastly more ways of being dead” (Richard Dawkins). There is no materialistic explanation for robustness: “ (…) the question, rather, is why things don’t fall completely apart — as they do, in fact, at the moment of death. What power holds off that moment — precisely for a lifetime, and not a moment longer?” (Steve Talbott). 3. Not only is NS not creative, it severely hampers chance-driven evolution by eliminating viable organisms — NS does not produce information, but continuously destroys information. - - - - Bottom line: (2) would be better off without (3). IOW the ‘chance-driven filling of viable self-replicator space’ is not at all served by the effects of a restrictive hostile environment a.k.a. ‘natural selection’.Box_{August 15, 2015
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New Research Elucidates Directed Mutation Mechanisms - Cornelius Hunter - January 7, 2013 Excerpt: mutations don’t occur randomly in the genome, but rather in the genes where they can help to address the challenge. But there is more. The gene’s single stranded DNA has certain coils and loops which expose only some of the gene’s nucleotides to mutation. So not only are certain genes targeted for mutation, but certain nucleotides within those genes are targeted in what is referred to as directed mutations.,,, These findings contradict evolution’s prediction that mutations are random with respect to need and sometimes just happen to occur in the right place at the right time.,,, http://darwins-god.blogspot.com/2013/01/news-research-elucidates-directed.html Failed Darwinian Prediction - Mutations are not adaptive - Cornelius Hunter - 2015 In the twentieth century, the theory of evolution predicted that mutations are not adaptive or directed. In other words, mutations were believed to be random with respect to the needs of the individual. As Julian Huxley put it, “Mutation merely provides the raw material of evolution; it is a random affair, and takes place in all directions. … in all cases they are random in relation to evolution. Their effects are not related to the needs of the organisms.” (Huxley, 36) Or as Jacques Monod explained: chance alone is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, at the very root of the stupendous edifice of evolution: this central concept of modern biology is no longer one among other possible or even conceivable hypotheses. It is today the sole conceivable hypothesis, the only one that squares with observed and tested fact. And nothing warrants the supposition—or the hope—that on this score our position is likely ever to be revised. (Monod, 112) Ronald Fisher wrote that mutations are “random with respect to the organism’s need” (Orr). This fundamental prediction persisted for decades as a recent paper explained: “mutation is assumed to create heritable variation that is random and undirected.” (Chen, Lowenfeld and Cullis) But that assumption is now known to be false. The first problem is that the mutation rate is adaptive. For instance, when a population of bacteria is subjected to harsh conditions it tends to increase its mutation rate. It is as though a signal has been sent saying, “It is time to adapt.” Also, a small fraction of the population increases its mutation rates even higher yet. These hypermutators ensure that an even greater variety of adaptive change is explored. (Foster) Experiments have also discovered that duplicated DNA segments may be subject to higher mutation rates. Since the segment is a duplicate it is less important to preserve and, like a test bed, appears to be used to experiment with new designs. (Wright) The second problem is that organisms use strategies to direct the mutations according to the threat. Adaptive mutations have been extensively studied in bacteria. Experiments typically alter the bacteria food supply or apply some other environmental stress causing mutations that target the specific environmental stress. (Burkala, et. al.; Moxon, et. al; Wright) Adaptive mutations have also been observed in yeast (Fidalgo, et. al.; David, et. al.) and flax plants. (Johnson, Moss and Cullis) One experiment found repeatable mutations in flax in response to fertilizer levels. (Chen, Schneeberger and Cullis) Another exposed the flax to four different growth conditions and found that environmental stress can induce mutations that result in “sizeable, rapid, adaptive evolutionary responses.” (Chen, Lowenfeld and Cullis) In response to this failed prediction some evolutionists now are saying that evolution somehow created the mechanisms that cause mutations to be adaptive. References Burkala, E., et. al. 2007. “Secondary structures as predictors of mutation potential in the lacZ gene of Escherichia coli.” Microbiology 153:2180-2189. Chen, Y., R. Lowenfeld, C. Cullis. 2009. “An environmentally induced adaptive (?) insertion event in flax.” International Journal of Genetics and Molecular Biology 1:38-47. Chen, Y., R. Schneeberger, C. Cullis. 2005. “A site-specific insertion sequence in flax genotrophs induced by environment.” New Phytologist 167:171-180. David, L., et. al. 2010. “Inherited adaptation of genome-rewired cells in response to a challenging environment.” HFSP Journal 4:131–141. Fidalgo, M., et. al. 2006. “Adaptive evolution by mutations in the FLO11 gene.” Proceedings of the National Academy of Sciences 103:11228-11233. Foster, P. 2005. “Stress responses and genetic variation in bacteria.” Mutation Research / Fundamental and Molecular Mechanisms of Mutagenesis 569:3-11. Huxley, Julian. 1953. Evolution in Action. New York: Signet Science Library Book. Johnson, C., T. Moss, C. Cullis. 2011. “Environmentally induced heritable changes in flax.” J Visualized Experiments 47:2332. Monod, Jacques. 1971. Chance & Necessity. New York: Vintage Books. Moxon, E., et. al. 1994. “Adaptive evolution of highly mutable loci in pathogenic bacteria.” Current Biology 4:24-33. Orr, H. 2005. “The genetic theory of adaptation: a brief history.” Nature Review Genetics 6:119-127. Wright, B. 2000. “A biochemical mechanism for nonrandom mutations and evolution.” J Bacteriology 182:2993-3001. https://sites.google.com/site/darwinspredictions/mutations-are-not-adaptive
bornagain77_{August 14, 2015
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Mutations have causes, of course. Just like the outcomes of dice rolls and lottery draws have physical causes. But they are random with respect to fitness.wd400_{August 14, 2015
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as to wd400's claim:
"Nah — the mutations giving rise to adaptations arise by chance."
Mung is correct in noting the way Darwinists disingenuously use the word chance,,,
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 “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. 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 other words, although the term “chance” can be defined as a mathematical probability, such as the chance involved in flipping a coin, when Darwinists use the term ‘random chance’, the vast majority of the time it’s substituting for a more precise word such as “cause”, especially when the cause, i.e. ‘mechanism’, is not known. Several people have noted this ‘shell game’ that is played with the word ‘chance’ and cause.
“To personify ‘chance’ as if we were talking about a causal agent,” notes biophysicist Donald M. MacKay, “is to make an illegitimate switch from a scientific to a quasi-religious mythological concept.” Similarly, Robert C. Sproul points out: “By calling the unknown cause ‘chance’ for so long, people begin to forget that a substitution was made. . . . The assumption that ‘chance equals an unknown cause’ has come to mean for many that ‘chance equals cause.’” The Universal Determinism Dichotomy (UDD) - David L. Abel - 2015 Excerpt: We sometimes appeal to yet-to-be-discovered laws when trying to explain what appears to be chance phenomena. Most theorists, however, attempt to reduce Chance Contingency to unknown and/or very complex physical causation, as summarized by Peale.12 Thus Chance Contingency as a true cause may be only “apparent.” Sproul argues effectively that chance is not a cause of anything. Chance is nothing more than a statistical description of unknown or complex physical causation. Chance, therefore, cannot have any physical effects, since it is not a physical cause. 13,,, 13. Sproul RC. - Not a Chance: the Myth of Chance in Modern Science and Cosmology. Grand Rapids, MI: Baker Books; 1994 https://www.academia.edu/12267097/The_Universal_Determinism_Dichotomy_UDD_
Thus to say 'it happened by chance', as it is usually used by Darwinists, is in reality a 'placeholder for ignorance' instead of being an appeal to a known cause. Moreover, it is now known that the vast majority of changes to the genome are being accomplished via sophisticated molecular machines and that the changes being implemented in the genome by those molecular machines are not happening in a random pattern as was presupposed by Darwinists.
"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 Duality in the human genome - Nov. 28, 2014 Excerpt: According to the researchers, mutations of genes are not randomly distributed between the parental chromosomes. They found that 60 percent of mutations affect the same chromosome set and 40 percent both sets. Scientists refer to these as cis and trans mutations, respectively. Evidently, an organism must have more cis mutations, where the second gene form remains intact. "It's amazing how precisely the 60:40 ratio is maintained. It occurs in the genome of every individual – almost like a magic formula," says Hoehe. http://medicalxpress.com/news/2014-11-duality-human-genome.html 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 Evolutionists Caught Again—But They Still Believe - Dr. Cornelius Hunter - May 2012 Excerpt: As a new paper now explains, under evolution we must believe that mutations rates have been “evolutionarily optimized.” That is, evolution is now so brilliant that it created the means to not only control, but to optimize the actual mutation rates.,,, (Here is how they put their findings) "Upon comparing 34 Escherichia coli genomes, we observe that the neutral mutation rate varies by more than an order of magnitude across 2,659 genes, with mutational hot and cold spots spanning several kilobases.,, Importantly, the variation is not random: we detect a lower rate in highly expressed genes and in those undergoing stronger purifying selection.,, Our observations suggest that the mutation rate has been evolutionarily optimized to reduce the risk of deleterious mutations.,, Current knowledge of factors influencing the mutation rate—including transcription-coupled repair and context-dependent mutagenesis—do not explain these observations, indicating that additional mechanisms must be involved. ,, The findings have important implications for our understanding of evolution and the control of mutations.,," Dr. Hunter then comments: "These findings have important implications for our understanding of evolution? Well sure, if by that they mean how absurd are evolution truth claims." http://darwins-god.blogspot.com/2012/05/evolutionists-caught-againbut-they.html
bornagain77_{August 14, 2015
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wd400:
Nah — the mutations giving rise to adaptations arise by chance.
Not really. Chance is not a cause of anything. "Chance" is just a word to be used in place of "we don't know how." If we knew how, appeals to "chance" would be superfluous. Ignorance is not an explanation. But evolution is a fact, Fact, FACT!Mung_{August 14, 2015
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wd400:
Selection means many individually-unlikely but beneficial traits can be brought together in a single lineage.
Beneficial is relative and changing. Natural selection is non-random in that not every individual has the same probability of being eliminated. There is still plenty of chance at play all throughout the process.Virgil Cain_{August 14, 2015
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Zachriel:
Evolution is creative, but it requires both variation and selection.
Your position offers variation and elimination.Virgil Cain_{August 14, 2015
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Well, how can I reply to such a cogent argument. I guess I withdraw.... (even your quote doesn't say what you seem to think it says)wd400_{August 14, 2015
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wd400: Selection means many individually-unlikely but beneficial traits can be brought together in a single lineage.
No, that's not the case.
wd400: So it’s more than chance that creates adaptations.
Nope
CHANCE ALONE, is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, is at the very root of the stupendous edifice of creation. [Jacques Monod]
Box_{August 14, 2015
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Nah -- the mutations giving rise to adaptations arise by chance. Selection means many individually-unlikely but beneficial traits can be brought together in a single lineage. So it's more than chance that creates adaptations.wd400_{August 14, 2015
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Zach: Evolution is creative, but it requires both variation and selection. It’s the interplay between the two that results in adaptation.
Nope, the adaptive organisms and their adaptive features are produced by chance alone. Because selection is not creation.Box_{August 14, 2015
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Box: All evolutionary theory has to offer is the concept that all life forms, and all its features, came into existence by chance alone... Selection is not creation. Evolution is creative, but it requires both variation and selection. It's the interplay between the two that results in adaptation.Zachriel_{August 14, 2015
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Zach: Evolutionary theory only explains how life how life has diversified (...)
All evolutionary theory has to offer is the concept that all life forms, and all its features, came into existence by chance alone. Natural selection hasn't caused the coming into existence of one single organism nor even one single feature of an organism. Selection is not creation.Box_{August 14, 2015
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Zachriel:
Evolutionary theory only explains how life how life has diversified
How life originated has a direct tie to how it diversified and evolutionism can't even explain how to get eukaryotes from populations of prokaryotes.Virgil Cain_{August 14, 2015
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Box: The main problem with Darwin’s evolution theory is that natural selection doesn’t do anything for the coming into existence of organisms. Sure. Evolutionary theory only explains how life how life has diversified, not its origin; just as gravitational theory only explains how masses interact, not their origin. Scientists continue to probe the question of how life began on Earth, but the circumstances are very ancient.Zachriel_{August 14, 2015
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The main problem with Darwin's evolution theory is that natural selection doesn't do anything for the coming into existence of organisms. Selection is NOT creation.
Jacques Monod: CHANCE ALONE, is at the source of every innovation, of all creation in the biosphere. Pure chance, absolutely free but blind, is at the very root of the stupendous edifice of creation.
Box_{August 14, 2015
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It still sounds like a materialist account of evolution. Did News mean to suggest it isn't?rhampton7_{August 14, 2015
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Also of note: Even many supposed viral sequences, that are held, by Darwinists, to have been gained by horizontal gene transfer to humans, are now called into question:
Refutation Of Endogenous Retrovirus - ERVs - Richard Sternberg, PhD Evolutionary Biology - video http://www.youtube.com/watch?v=SrEOe2E0Euc Sternberg, R. v. & J. A. Shapiro (2005). How repeated retroelements format genome function. Cytogenet. Genome Res. 110: 108-116. Excerpt: Employing an information science model, the "functionalist" perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization. http://www.ncbi.nlm.nih.gov/pubmed/16093662 Shapiro and Sternberg Anticipated the Fall of Junk DNA - Douglas Axe - September 13, 2012 Excerpt: "In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled "Why repetitive DNA is essential to genome function." These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for "guilt-by-association" claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written. The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful." - James Shapiro http://www.evolutionnews.org/2012/09/shapiro_and_ste064291.html Endogenous retroviruses regulate periimplantation placental growth and differentiation - 2006 http://www.pnas.org/content/103/39/14390.abstract. Retrovirus in the Human Genome Is Active in Pluripotent Stem Cells - Jan. 23, 2013 Excerpt: "What we've observed is that a group of endogenous retroviruses called HERV-H is extremely busy in human embryonic stem cells," said Jeremy Luban, MD, the David L. Freelander Memorial Professor in HIV/AIDS Research, professor of molecular medicine and lead author of the study. "In fact, HERV-H is one of the most abundantly expressed genes in pluripotent stem cells and it isn't found in any other cell types. http://www.sciencedaily.com/releases/2013/01/130123133930.htm Here is Another Retrovirus With an Important Function - Cornelius Hunter - March 9, 2015 Excerpt: Yet another retrovirus function was published last fall in a study out of Canada. This retrovirus works with several proteins in human embryonic stem cells and without it the stem cells lose their key functionalities. "Human endogenous retrovirus subfamily H (HERVH) is a class of transposable elements expressed preferentially in human embryonic stem cells (hESCs). Here, we report that the long terminal repeats of HERVH function as enhancers and that HERVH is a nuclear long noncoding RNA required to maintain hESC identity. Furthermore, HERVH is associated with OCT4, coactivators and Mediator subunits. Together, these results uncover a new role of species-specific transposable elements in hESCs." As with previous human retrovirus examples, this finding forced evolutionists to hypothesize that the retrovirus, unbelievably, played a crucial role human evolution. As one report explained: "According to the study's lead author, Xinyi Lu, a postdoctoral researcher in Ng's laboratory, the emergence of the regulatory activities executed by HERV-H could represent an important step in the evolution of our early ancestors. "HERV-H first integrated into the primate genome around 45 million years ago and is only found in the primate genome," says Lu, "and so it may contribute to some of the differences between primates and other mammals."" How curious this is. A retrovirus is supposed to have evolved, and then it just happened to play an important role in the construction of humans. This is yet another example of the incredible serendipity that evolutionists envision at work in their theory. Do they ever wonder at the likelihood of a retrovirus just luckily fitting in to the evolutionary process, and serving in an important role in the production of increasingly complex organisms? With evolution, science becomes not a search for how nature works, or what likely occurred in the past, but rather bizarre, unlikely tales that cannot be proven wrong. http://darwins-god.blogspot.com/2015/03/here-is-another-retrovirus-with.html The definitive response on Endogenous Retroviruses (ERV’s), with Dr. Jean Lightner http://www.youtube.com/watch?v=feHYEgzaGkY etc.. etc..
bornagain77_{August 14, 2015
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Or related note, one method of horizontally transferring genetic material is with the bacteriophage virus. Yet, the “horizontal” gene transferring bacteriophage virus is far more complex than many people have imagined it ever would be, as these following videos and article clearly point out:
Virus - Assembly Of A Nano-Machine - video https://www.youtube.com/watch?v=Ofd_lgEymto Bacteriophage T4 DNA Packing https://www.youtube.com/watch?v=wNQQz0NGUNQ The amazing design of bacteriophage viruses and its DNA packaging motor http://reasonandscience.heavenforum.org/t2134-the-amazing-design-of-bacteriophage-viruses-and-its-dna-packaging-motor
Here is a short video of the Bacteriophage 'landing' on a bacterium:
Bacteriophage T4 - landing - video https://www.youtube.com/watch?v=kdz9VGH8dwY
The first thought I had when I first saw the bacteriophage virus is that it looks very similar to the lunar lander of the Apollo program. The comparison is not without merit considering some of the relative distances to be traveled and the virus must somehow possess, as of yet un-elucidated, orientation, guidance, docking, unloading, loading, etc... mechanisms. And please remember this level of complexity exists in a world that is far too small to be seen with the naked eye. As well, horizontal gene transfer is far more tenuous as a 'mechanism of evolution' than many Darwinists are apparently willing to admit:
Evolutionists Celebrated This Prediction But When it Later Failed They Didn’t Care - Cornelius Hunter - April 2012 Excerpt: Sometimes their use of this lateral or horizontal gene transfer mechanism is a real stretch. And in any case, their story calls for evolution to have created this incredible mechanism which then was so important for adaptation and the supposed subsequent evolution. In other words, evolution created evolution.,,, In some cases evolutionists have no idea, beyond pure speculation, about how it could have happened. As they admit in one paper: "An alternative and more plausible possibility is that the STC gene has been laterally transferred among phylogenetically diverged eukaryotes through an unknown mechanism." http://darwins-god.blogspot.com/2012/04/evolutionists-celebrated-this.html Horizontal Gene Transfer 5-16-2015 by Paul Giem - video https://www.youtube.com/watch?v=W6X5sJ62NbE
Here is a recent article (2015) by Jeffrey Tomkins which shows that the mechanism of Horizontal Gene Transfer falls far short of being a satisfactory explanation.
Another Horizontal Gene Transfer Fairy Tale by Jeffrey P. Tomkins, Ph.D. - April 6, 2015 Excerpt: First, the researchers found unique genes in a variety of fruit flies, worms, primates, and humans that had no clear evolutionary ancestry. In other words, each of these genes is specific to a certain type of creature. Scientists have previously termed these "orphan genes"—a unique type of gene that provides a clear anti-evolutionary enigma I have discussed in previous reports.3,4 Some claim these novel orphan sequences evolved suddenly out of non-coding DNA while others, such as the authors of this new report, claim they were derived from HGT. The major problem with claiming that these alleged HGT genes are imported or "foreign" (i.e., transferred into the genome from some other creature), is that many of them encode important enzymatic proteins and are key parts of the interconnected gene networks and complex biochemical pathways that are essential to the very life of the organism. The researchers stated, "The majority of these genes are concerned with metabolism." Clearly, the genes are not foreign at all, but designed to function as key parts of essential biologically complex systems. Second, the approach to supposedly identifying many of the foreign genes in animals as microbial in origin was not even based on actual complete gene sequence, but depended upon isolated regions of similarity in the proteins they encode. In mammals, genes are quite complex, and on average only about 10% of the entire gene sequence actually codes for protein, the rest contains a large diversity of regulatory sequences that determine how the gene is to function and its various types of products. In contrast, microbial genes are typically much less complex and lack these intricate and intervening regulatory regions found in animal genes. If the researchers had actually compared the genomic DNA, very little similarity would have been discovered—in other words, they didn't do their homework correctly. In fact, they admitted their claim that the gene was foreign—or where it originated from—was purely hypothetical, when they stated that "absolute certainty in the assignment of most HGT is unachievable." Third, no mechanism of HGT for any of the hundreds of alleged "foreign genes" they found was either discovered or even suggested. This is due to the fact that the only cases where such gene transfer occurs in nature typically involves a clear host-parasite relationship. Not only that, but the cells of the germline (those that produce sperm and egg) must be specifically targeted or the introgressed genes (those that were incorporated from one species into the genome of another) will not be inherited. Unfortunately, evolutionary biologists constantly resort to fictional stories cloaked in technical terminology to escape the straightforward conclusion that the genomes of different creatures were purposefully crafted. Because of their unwavering commitment to evolution, all ideas about these cleverly designed and network-integrated gene sequences being engineered by a Creator are not considered—at least not openly. http://www.icr.org/article/another-horizontal-gene-transfer-fairy
I would be shocked that such slipshod science, as Dr. Tomkins highlighted, could be practiced by Darwinists. But after many years of seeing how Darwinists constantly practice their brand of 'science', never allowing the core of their theory to be challenged by empirical evidence, such shenanigans by Darwinists has come to be expected by me. Apparently it is the only way that they can keep their supposedly 'scientific' theory afloat amongst all the contradictory evidence that comes along.bornagain77_{August 14, 2015
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Zachriel:
Evolutionary theory has...
Gone missing- no one can find this alleged evolutionary theory. And there isn't any way to test the claim that humans share a common ancestry with other apes. The claim is out of the realm of science.Virgil Cain_{August 14, 2015
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BA77 @7 'Cruise Control permeating the whole of the protein structure? This is an absolutely fascinating discovery. The equations of calculus involved in achieving even a simple process control loop, such as a dynamic cruise control loop, are very complex. In fact it seems readily apparent to me that highly advanced mathematical information must reside ‘transcendentally’ along the entirety of the protein structure, in order to achieve such control of the overall protein structure. This fact gives us clear evidence that there is far more functional information residing within, and along, protein chains than meets the eye. Moreover this ‘oneness’ of cruise control, within the protein structure, can only be achieved through quantum computation/entanglement principles, and is inexplicable to the reductive materialistic approach of neo-Darwinism! And indeed we find quantum information/entanglement residing along the entirety of protein molecules:' Nothing to see here. Move along. No design involved. Just random chance in deep time.Axel_{August 14, 2015
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News: Sorry, Darwin, it’s not your evolution any more Evolutionary theory has undergone constant change as the field has expanded and matured. It hasn't been Darwin's original theory for a long time. Horizontal gene transfer between widely separated taxa isn't consistent with branching descent. That doesn't mean humans don't share common ancestry with other apes, but it does mean some human genetic material may come from other sources, as well, such as viruses.Zachriel_{August 14, 2015
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No problem ppolish.
Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, http://www.ncbi.nlm.nih.gov/pubmed/19765975 "Shared Evolutionary History or Shared Design?" - Ann Gauger - January 1, 2015 Excerpt: The waiting time required to achieve four mutations is 10^15 years. That's longer than the age of the universe. The real waiting time is likely to be much greater, since the two most likely candidate enzymes failed to be coopted by double mutations. http://www.evolutionnews.org/2015/01/happy_new_year092291.html Can Even One Polymer Become a Protein in 13 billion Years? – Dr. Douglas Axe, Biologic Institute - June 20, 2013 - audio http://radiomaria.us/discoveringintelligentdesign/2013/06/20/june-20-2013-can-even-one-polymer-become-a-protein-in-13-billion-years-dr-douglas-axe-biologic-institute/
Moreover, not only are the unguided material processes of neo-Darwinism grossly inadequate to explain how a billion-trillion protein molecules can possibly cohere as a single unified whole in the single human body for a life time,,,
The Vitruvian Man - Leonardo da Vinci - Drawing https://upload.wikimedia.org/wikipedia/commons/thumb/2/22/Da_Vinci_Vitruve_Luc_Viatour.jpg/441px-Da_Vinci_Vitruve_Luc_Viatour.jpg One Body - animation - video http://www.youtube.com/watch?v=pDMLq6eqEM4 HOW BIOLOGISTS LOST SIGHT OF THE MEANING OF LIFE — AND ARE NOW STARING IT IN THE FACE - Stephen L. Talbott - May 2012 Excerpt: “If you think air traffic controllers have a tough job guiding planes into major airports or across a crowded continental airspace, consider the challenge facing a human cell trying to position its proteins”. A given cell, he notes, may make more than 10,000 different proteins, and typically contains more than a billion protein molecules at any one time. “Somehow a cell must get all its proteins to their correct destinations — and equally important, keep these molecules out of the wrong places”. And further: “It’s almost as if every mRNA [an intermediate between a gene and a corresponding protein] coming out of the nucleus knows where it’s going” (Travis 2011),,, Further, the billion protein molecules in a cell are virtually all capable of interacting with each other to one degree or another; they are subject to getting misfolded or “all balled up with one another”; they are critically modified through the attachment or detachment of molecular subunits, often in rapid order and with immediate implications for changing function; they can wind up inside large-capacity “transport vehicles” headed in any number of directions; they can be sidetracked by diverse processes of degradation and recycling . . . and so on without end. Yet the coherence of the whole is maintained. The question is indeed, then, “How does the organism meaningfully dispose of all its molecules, getting them to the right places and into the right interactions?” The same sort of question can be asked of cells, for example in the growing embryo, where literal streams of cells are flowing to their appointed places, differentiating themselves into different types as they go, and adjusting themselves to all sorts of unpredictable perturbations — even to the degree of responding appropriately when a lab technician excises a clump of them from one location in a young embryo and puts them in another, where they may proceed to adapt themselves in an entirely different and proper way to the new environment. It is hard to quibble with the immediate impression that form (which is more idea-like than thing-like) is primary, and the material particulars subsidiary. Two systems biologists, one from the Max Delbrück Center for Molecular Medicine in Germany and one from Harvard Medical School, frame one part of the problem this way: "The human body is formed by trillions of individual cells. These cells work together with remarkable precision, first forming an adult organism out of a single fertilized egg, and then keeping the organism alive and functional for decades. To achieve this precision, one would assume that each individual cell reacts in a reliable, reproducible way to a given input, faithfully executing the required task. However, a growing number of studies investigating cellular processes on the level of single cells revealed large heterogeneity even among genetically identical cells of the same cell type. (Loewer and Lahav 2011)" ,,, And then we hear that all this meaningful activity is, somehow, meaningless or a product of meaninglessness. This, I believe, is the real issue troubling the majority of the American populace when they are asked about their belief in evolution. They see one thing and then are told, more or less directly, that they are really seeing its denial. Yet no one has ever explained to them how you get meaning from meaninglessness — a difficult enough task once you realize that we cannot articulate any knowledge of the world at all except in the language of meaning.,,, http://www.netfuture.org/2012/May1012_184.html#2
Not only are the 'bottom up' unguided material processes of neo-Darwinism grossly inadequate to explain how a billion-trillion protein molecules can possibly cohere as a single unified whole in a single human body for a life time, but the unguided material processes of neo-Darwinism are also grossly inadequate to explain how even a single protein can possibly cohere as a single unified whole.
Proteins with cruise control provide new perspective: "A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order." http://www.princeton.edu/main/news/archive/S22/60/95O56/
Cruise Control permeating the whole of the protein structure? This is an absolutely fascinating discovery. The equations of calculus involved in achieving even a simple process control loop, such as a dynamic cruise control loop, are very complex. In fact it seems readily apparent to me that highly advanced mathematical information must reside 'transcendentally' along the entirety of the protein structure, in order to achieve such control of the overall protein structure. This fact gives us clear evidence that there is far more functional information residing within, and along, protein chains than meets the eye. Moreover this ‘oneness’ of cruise control, within the protein structure, can only be achieved through quantum computation/entanglement principles, and is inexplicable to the reductive materialistic approach of neo-Darwinism! And indeed we find quantum information/entanglement residing along the entirity of protein molecules:
Classical and Quantum Information Channels in Protein Chain - Dj. Koruga, A. Tomi?, Z. Ratkaj, L. Matija - 2006 Abstract: Investigation of the properties of peptide plane in protein chain from both classical and quantum approach is presented. We calculated interatomic force constants for peptide plane and hydrogen bonds between peptide planes in protein chain. On the basis of force constants, displacements of each atom in peptide plane, and time of action we found that the value of the peptide plane action is close to the Planck constant. This indicates that peptide plane from the energy viewpoint possesses synergetic classical/quantum properties. Consideration of peptide planes in protein chain from information viewpoint also shows that protein chain possesses classical and quantum properties. So, it appears that protein chain behaves as a triple dual system: (1) structural - amino acids and peptide planes, (2) energy - classical and quantum state, and (3) information - classical and quantum coding. Based on experimental facts of protein chain, we proposed from the structure-energy-information viewpoint its synergetic code system. http://www.scientific.net/MSF.518.491
Moreover, this quantum information/entanglement which gives the protein a 'unity of form' so as to enable it to function as a cohesive whole as is witnessed with 'cruise control', is also found in DNA molecules:
Classical and Quantum Information in DNA – Elisabeth Rieper – video (Longitudinal Quantum Information along the entire length of DNA discussed at the 19:30 minute mark; at 24:00 minute mark Dr Rieper remarks that practically the whole DNA molecule can be viewed as quantum information with classical information embedded within it) https://youtu.be/2nqHOnVTxJE?t=1176
bornagain77_{August 14, 2015
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Thanks BA77. Meyers/Axe: "Unguided purposeless NS could not do a Cambrian in 500 trillion years" PZMeyers/Dawkins: "Blind Watchmaker had eons and eons. 30+ million years" Math was never a Dawkins strongpoint. Or rationality & logic for that matter:(ppolish_{August 13, 2015
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wd400, and your real time empirical evidence that unguided material processes can create any non-trivial functional information/complexity at all is where exactly? Stephen Meyer Critiques Richard Dawkins's "Mount Improbable" Illustration https://www.youtube.com/watch?v=7rgainpMXa8bornagain77_{August 13, 2015
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Anything meiosis did Dariwnian evolution didn't do! Evolution did nothing at all because genes get passed on... or something? Makes as much sense as this.wd400_{August 13, 2015
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Dawkins is wrong. there is NO biological scientific evidence for a false hypthesis on biological origin processes. Anyways. As people get smarter in this stuff it will be that other mechanisms are found for biological changes. We must all explain human "race looks" differences. for example. So indeed other mechanisms be seized by evolutionists as needed. its a prediction. indeed other threads here show non creationist scientists looking for a third way. because THEY NEED ANOTHER WAY cause old man chuck ain't working in a modern world.Robert Byers_{August 13, 2015
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Darwinian evolution has pretty much been relegated to high school biology textbooks and Richard Dawkins twitter feed. And wherever baby science or pseudo science is located.ppolish_{August 13, 2015
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