Uncommon Descent Serving The Intelligent Design Community

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

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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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Comments
bornagain77: Moreover, since DNA was not even discovered until 1953, which is a entire decade after your 1943 reference, I think I will trust my current references which show us that mutations to DNA are happening in a non-random fashion. No. The discovery of DNA does not contradict Delbrück & Luria. You might also want to look at Lederberg & Lederberg, Replica Plating and Indirect Selection of Bacterial Mutants, Journal of Bacteriology 1952.Zachriel
February 1, 2015
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sparc you state:
"You are obviously absolutely unaware of how cells deal with damaged DNA."
Multiple levels of sophisticated DNA repair mechanisms are contrary to what neo-Darwinism expected and needs in order to be viable as a hypothesis:
The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective – February 2011 Excerpt: “Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation.” http://benthamscience.com/open/toevolj/articles/V005/1TOEVOLJ.pdf Contradiction in evolutionary theory - video - (The contradiction between extensive DNA repair mechanisms and the necessity of 'random mutations/errors' for Darwinian evolution) http://www.youtube.com/watch?v=dzh6Ct5cg1o The Darwinism contradiction of repair systems Excerpt: The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma. https://uncommondescent.com/intelligent-design/the-darwinism-contradiction-of-repair-systems/
Moreover, DNA repair is a astonishing process that no one has a full handle on as to how it is actually accomplished
Protein Researchers Unravel the Molecular Dance of DNA Repair - March 2012 Excerpt: Using state-of-the-art technology, scientists at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen and their international collaborators have successfully obtained molecular snapshots of tens of thousands processes involved in DNA damage repair.,,, "We first damaged the DNA of cells using radiation or chemical drugs and then used a technique called mass spectrometry, which is a way of precisely determining the identity of proteins and their chemical modifications," Petra Beli says. "This allowed us to follow thousands of protein modifications that happened in the process of DNA repair, shedding new light on how the networks of biochemical signals are regulated and how the infrastructure of alerts works." The data from the experiments is so extensive that it will require much further work by researchers to fully understand the significance and impact of these newly identified signaling pathways. http://www.sciencedaily.com/releases/2012/03/120315123022.htm A Look at the Quality Control System in the Protein Factory - JonathanM - March 2012 Excerpt: The DNA damage response (DDR) system is like a cellular special ops force. The moment such damage is detected, an intricate network of communication and recruitment launches into action. If the cellular process for making proteins were a factory, this would be the most advanced quality-control system ever designed. http://www.evolutionnews.org/2012/03/a_look_at_the_q057791.html Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm
The extensive overlapping repair mechanisms for DNA include:
A proofreading system that catches almost all errors A mismatch repair system to back up the proofreading system Photoreactivation (light repair) Removal of methyl or ethyl groups by O6 – methylguanine methyltransferase Base excision repair Nucleotide excision repair Double-strand DNA break repair Recombination repair Error-prone bypass http://www.newgeology.us/presentation32.html
Moreover, since DNA was not even discovered until 1953, which is a entire decade after your 1943 reference, I think I will trust my current references which show us that mutations to DNA are happening in a non-random fashion:
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 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 Fully Random Mutations - Kevin Kelly - Jan. 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.,,, 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.,,, ,,,the lack of direct evidence for actual random mutations has now reached a stage where the idea needs to be retired. There are several related reasons why this unsubstantiated idea continues to be repeated without evidence. The first is fear that non-random mutations would be misunderstood and twisted by creationists,,, http://www.edge.org/responses/what-scientific-idea-is-ready-for-retirement also see James Shapiro, etc..,,
bornagain77
January 31, 2015
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BA77:
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.
Sophisticated mechanisms, indeed. Unfortunately they just don't work as you think. You are obviously absolutely unaware of how cells deal with damaged DNA. Even if you repeatedly introduce the very same ds breaks at exactly the same position in vivo (BTW, I doubt you know how to achieve this) there are different possible outcomes and it is impossible to predict which one will occur. In addition, I suggest that regarding the randomness of mutations you look up Delbrück & Luria (1943).sparc
January 30, 2015
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ppolish: Usually, but not always, the better design succeeds. What that means is that if there is variation in a population, the distribution of variation will change over time. If there is a source of novel variation, then it will be subject to the same process.Zachriel
January 29, 2015
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Natural Selection is "the name given to differential reproductive success," Yes, Petrushka, some live some die. Usually, but not always, the better design succeeds. Unlocking the secrets of Natural Design will have tremendous impact on medicine. Impact on a lot of things. ThirdWayEvolution is grasping this?ppolish
January 28, 2015
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"Natural selection is not a thing, so it cannot exist as a physical object" I agree with you there, Petrushka. But Natural Design DOES exist as a physical object. Plethora of examples and mountains of evidence. And "survival of the best design" is not even a tautalogy:) Furthermore, "Artificial Selection" is truly "Artificial Design". It's pretty obvious that unguided and purposeless are fail. Designer Dogs: http://theilovedogssite.com/10-most-popular-designer-dog-breeds/3/ppolish
January 28, 2015
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groovamos: I have never noticed that there is any believable grand story about how H2O was able to appear on our scorching hot young planet. It cooled. groovamos: Same goes for how the moon got into that ideal orbit for stabilizing the planetary axial tilt away from the orbital axis, causing the seasons. The mineral composition of the Moon supports that it was formed by a collision between the early Earth and another body. See Herwartz et al., Identification of the giant impactor Theia in lunar rocks, Science 2014. groovamos: Same with the molten core of the planet, is it radioactive decay, About half is radioactive decay; the rest is primordial. groovamos: and what elements are involved in this feature which is mandatory for life? Primarily uranium-238 and thorium-232, based on the detection of antineutrinos from the interior. See The KamLAND Collaboration, Partial radiogenic heat model for Earth revealed by geoneutrino measurements, Nature 2011. groovamos: Pat told him forcefully that he wanted to know why and how protons came into existence out of nothing. Quark soup. Scientists can make their own quark-gluon plasma, and from that they get protons (among a host of other particles). http://home.web.cern.ch/about/physics/heavy-ions-and-quark-gluon-plasmaZachriel
January 27, 2015
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skram: One step at a time. Nature has many sides. OK but I was looking for a little science in my asking for empiricism, as in: Are those many sides enumerated? The earth as a habitat is part of nature. We know pretty well how this part of nature developed over time. Oh, well I have never noticed that there is any believable grand story about how H2O was able to appear on our scorching hot young planet. A huge key to get life life here missing. Same goes for how the moon got into that ideal orbit for stabilizing the planetary axial tilt away from the orbital axis, causing the seasons. Same with the molten core of the planet, is it radioactive decay, and what elements are involved in this feature which is mandatory for life? In other words we "pretty well" do not know a lot of curcial things. But if you insist on having the Ultimate Answer to Life and Everything, then sorry, science does not deal with these kinds of questions. Not insisting because the mind has access to some marvelous realms without science. But saying science does not deal with these questions doesn't say it to Richard Dawkins. In a revealing exchange, Dawkins was being interviewed by Pat Buchanan on MSNBC more than 10 years ago. Pat told him forcefully that he wanted to know why and how protons came into existence out of nothing. Dawkins offered the promissory answer that is typical of people of faith: We almost have the answers to your question. Science has made great progress in this and is almost there. ---(I had a good laugh). They are too vague. OK And the answers provided by faith are not necessarily valid. A kind of vague pronouncement. I could use definitions of 'faith' and 'answers' as used on that one. And an identification of who makes a judgement on the 'validity' of the "answers".groovamos
January 27, 2015
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rvb8,
like Darwin I don’t like to comment much on OOL or what was before the before. That’s for scientists to reasonably speculate.
Seems like you're backtracking rather quickly. If you are called on your appeal to matter or nature creating itself and realize you don't have that option, then you're suddenly not that interested in OOL. You continue:
Perhaps all matter was energy and then energy being famously related to matter, did indeed explode into existence. Perhaps there is the multi-verse. Perhaps ‘big-bang then big crunch’ is an on going process.
Can you conceive of energy minus matter? Are you telling me energy is non-physical? Are you not aware that all you've done from your previous post is changed the names of the actors, but not the story? Energy is derived from the properties of objects. So now you have it, that, energy perhaps created that from which its very meaning is derived from, existing itself before that which gave it its meaning, so that it could get its meaning. Yeah. Perhaps there is the multi-verse, although there is no evidence for it, and it does nothing whatsoever to obviate the necessity for an ultimate beginning. Likewise, the Oscillating Universe hypothesis does nothing whatever to obviate an ultimate beginning. But why do you have this dilemma to begin with? You see, if you grasp onto any theory that does seem to dismiss the need for an ultimate beginning, you can be guaranteed it is incorrect. It CANNOT be true. As soon as you do that, you ipso facto introduce an eternal universe. An eternal universe is simply untenable, period. You cannot transverse the infinite. You cannot get to the present if there are an actual infinite number of seconds prior to this second, or events prior to this event. So, your problem is how to explain the physical, material universe that MUST have had a beginning, but without recourse to any physical, material cause, as that is the thing you are trying to explain. If you just say it's always been there, you run into the impossible problem of transversing the infinite. You continue:
All three of these are theories I prefer to your unsubstantiated wish fulfillment, of a divine (Christian?) interferer.
Hmm. One might be forgiven for accusing you of being a theist since you obviously hate God so much. And the way that is worded makes it sound as if you KNOW that those ideas you prefer are, well, ACTUALLY and TOTALLY unsubstantiated. But anyway, God is 'unsubstantiated' in your mind simply because of your demand that everything be physical. When you'll admit that this is simply impossible, you'll have no more reason to say that God's existing is unsubstantiated. It is very, very well substantiated.
What I do know is that yours and your friend’s introduction of super natural causation, or as is seriously sometimes mentioned as that insane, non-sequitur ‘the uncaused-cause’, is hopelessly childish wish fulfillment.
You obviously don't know anything. There is no serious recourse to anything but supernatural causation. Don't like it, go live somewhere else ;) . You can choose your favorite ice cream, not your favorite math. You don't have to like the fact that 2+2=4, but deny the fact at the risk of rightly received ridicule. Some things really are unavoidable. You cannot avoid the Uncaused-Cause no matter what you do. When you accept the One seeming contradiction, everything else makes perfect sense. When you reject that One seeming contradiction, everything else becomes actual contradiction.Brent
January 27, 2015
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bornagain77: I’m satisfied from the evidence presented thus far, and lack of any counter-evidence save for rhetoric That's right. We presented evidence: 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. You provided the rhetoric.Zachriel
January 27, 2015
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Zachriel, I'm satisfied from the evidence presented thus far, and lack of any counter-evidence save for rhetoric, that the unbiased reader can tell who is being fair with the evidence and who is being unfair. Thus I will retire from this thread. Thanks once again for being such a shining example for how empty the atheistic arguments truly are.bornagain77
January 27, 2015
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bornagain77: And the Saturn 5 rocket is just a elaborated bow and arrow. They work on somewhat different principles. The latter is ballistic, however, they are both projectiles. bornagain77: and once again to reiterate, citrate digestion is preexistent in e-coli, thus the adaptation is clearly the modification of a preexistent function. Disagree with that common sense fact? Sure. That's how evolution works, by gradual modification of existing structures. Why did you think otherwise? Behe: If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene-duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation. The novel phenotype was due to a gene-duplication with sequence divergence, hence, per Behe, it's a noteworthy gain-of-FCT mutation, i.e. what he terms Functional Coded elemenTs.Zachriel
January 27, 2015
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"Yes, as we said elaborated." And the Saturn 5 rocket is just a elaborated bow and arrow. :) and once again to reiterate, citrate digestion is preexistent in e-coli, thus the adaptation is clearly the modification of a preexistent function. Disagree with that common sense fact? then take it up with Dr. Behe Behe comments in more detail here:
"The gene duplication which brought an oxygen-tolerant promoter near to the citT gene did not make any new functional element. Rather, it simply duplicated existing features. The two FCTs comprising the oxygen tolerant citrate transporter locus -- the promoter and the gene -- were functional before the duplication and functional after. I had written in my review that one type of mutation that could be categorized as a gain-of-FCT was gene duplication with subsequent sequence modification, to allow the gene to specialize in some task. Venema thinks the mutation observed by Lenski is such an event. He has overlooked the fact that there was no subsequent sequence modification; a segment of DNA simply tandemly duplicated, bringing together two pre-existing FCTs. (It is true that the sequence of the protein coded by the duplicated gene includes a fragment from one of the nearby genes, but there is no evidence nor reason to think that the fused fragment is necessary for the activity of the protein.) In my review I classify that as a modification-of-function event. An example of a true gain-of-FCT by duplication cited in my review was the work of Olsthoorn and van Duin (1996) where a 14-nucleotide duplication led to the formation of new functional coded elements (it did not simply repeat pre-existing elements), so it is not just a modification-of-function mutation. The citrate mutation did nothing like that." http://www.evolutionnews.org/2012/11/rose-colored_gl066361.html
Thus no new genes, no new promoters, no new proteins, nothing of any new functional significance! It is sad that you would be reduced to defending this paltry and pathetic empirical evidence as some kind of proof that microbes can 'randomly' turn into man. Moreover, as if all that was not bad enough for you, the modification of function was actually accomplished in a 'non-random' fashion, via sophisticated molecular machinery, and is thus of no use for atheists in their desire to believe that they 'randomly' came to be for no reason at all:
Bacterial 'Evolution' Is Actually Design in Action by Brian Thomas, M.S. - Dec. 2012 Excerpt: So, the bacteria solved the problem of accessing an alternative food source by generating extra copies of the critical gene and by placing those copies under the control of an appropriate promoter. Does any of this resemble natural, undirected Darwinian evolution? Not at all. This amazing mechanism invented no new functional coded elements. It merely modified pre-existing elements. Therefore, not only did the Cit+ bacteria not evolve in the molecules-to-man direction, but they showed what could only be ingenious DNA rearrangement mechanisms. What mainstream headlines portrayed as evidence for evolution is actually the opposite.3 http://www.icr.org/article/bacterial-evolution-actually-design/
Moreover, Behe's argument is not that there are never any gain of function mutations, (in fact he cites a few gain of function mutations in his 2010 "The First Rule" paper in which deleted genes are compensated for), Behe's argument is that loss of function mutations, (i.e. mutations that gain an adaptive advantage by breaking something), greatly outnumber gain of function mutations, thus rendering neo-Darwinian explanations untenable:
Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information Excerpt: Even if there were several possible pathways by which to construct a gain-of-FCT mutation, or several possible kinds of adaptive gain-of-FCT features, the rate of appearance of an adaptive mutation that would arise from the diminishment or elimination of the activity of a protein is expected to be 100-1000 times the rate of appearance of an adaptive mutation that requires specific changes to a gene. (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).) The sort of loss-of-function examples seen in the Lenski's LTEE (Long Term Evolution Experiment) will never show that natural selection can increase high CSI. To understand why, imagine the following hypothetical situation. Consider an imaginary order of insects, the Evolutionoptera. Let’s say there are 1 million species of Evolutionoptera, but ecologists find that the extinction rate among Evolutionoptera is 1000 species per millennium. The speciation rate (the rate at which new species arise) during the same period is 1 new species per 1000 years. At these rates, every thousand years 1000 species of Evolutionoptera will die off, while one new species will develop–a net loss of 999 species. If these processes continue, in 1,000,001 years there will be no species of Evolutionoptera left on earth. http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html
Thus even if citrate digestion was a gain of function mutation it still would be of no help for you, (and your atheistic belief), since blind Darwinian processes are still far more likely to wind up stuck in useless dead ends than they are ever likely to wind up building even one molecular machine, (much less building a brain that is far more complex (i.e. elaborated :) ) than the entire internet combined).bornagain77
January 26, 2015
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bornagain77: Human brain has more switches than all computers on Earth Yes, as we said elaborated. Notably, you didn't respond concerning Behe's comment that if the phenotype is due to gene-duplication with sequence divergence, then it will be a noteworthy gain-of-FCT mutation.Zachriel
January 26, 2015
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Brent, like Darwin I don't like to comment much on OOL or what was before the before. That's for scientists to reasonably speculate. Perhaps all matter was energy and then energy being famously related to matter, did indeed explode into existence. Perhaps there is the multi-verse. Perhaps 'big-bang then big crunch' is an on going process. All three of these are theories I prefer to your unsubstantiated wish fulfillment, of a divine (Christian?) interferer. What I do know is that yours and your friend's introduction of super natural causation, or as is seriously sometimes mentioned as that insane, non-sequitur 'the uncaused-cause', is hopelessly childish wish fulfillment. Yeah BA ooooh, look how many synapses there are, that proves god. Rats have synapses as does all animal life, we have more, what's your frustrating point?rvb8
January 26, 2015
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"After all, humans are ‘just’ elaborated deuterostomes: a tube with appendages to stuff food into one end. Microevolution." LOL, and yet:
Human brain has more switches than all computers on Earth - November 2010 Excerpt: They found that the brain's complexity is beyond anything they'd imagined, almost to the point of being beyond belief, says Stephen Smith, a professor of molecular and cellular physiology and senior author of the paper describing the study: ...One synapse, by itself, is more like a microprocessor--with both memory-storage and information-processing elements--than a mere on/off switch. In fact, one synapse may contain on the order of 1,000 molecular-scale switches. A single human brain has more switches than all the computers and routers and Internet connections on Earth. http://news.cnet.com/8301-27083_3-20023112-247.html "Complexity Brake" Defies Evolution - August 8, 2012 Excerpt: Consider a neuronal synapse -- the presynaptic terminal has an estimated 1000 distinct proteins. Fully analyzing their possible interactions would take about 2000 years. Or consider the task of fully characterizing the visual cortex of the mouse -- about 2 million neurons. Under the extreme assumption that the neurons in these systems can all interact with each other, analyzing the various combinations will take about 10 million years..., even though it is assumed that the underlying technology speeds up by an order of magnitude each year. http://www.evolutionnews.org/2012/08/complexity_brak062961.html
I rest my case! Music:
I Am Not Alone – Kari Jobe https://www.youtube.com/watch?x-yt-cl=84503534&v=bfveawSAHJA&x-yt-ts=1421914688
bornagain77
January 26, 2015
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bornagain77: Moreover, it is interesting to note the flexibility to which Darwinists define functionality. Actually, Behe defined it so in the paper you cited. Do you disagree? bornagain77: Moreover, we presently have Zachriel, a Darwinist, While natural selection is essential for adaptation, there's a lot more to evolution than adaptation. bornagain77: trying to relabel what is clearly a minor modification of a preexistent function (citrate digestion) as a major new function. After all, humans are 'just' elaborated deuterostomes: a tube with appendages to stuff food into one end. Microevolution.Zachriel
January 26, 2015
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To reiterate what is obvious, since ‘E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available)’ then the adaptation is clearly the result of modification of a preexistent function. Moreover, it is interesting to note the flexibility to which Darwinists define functionality. Zachriel is more than ready to label this minor modification in functionality as a major gain in functionality so as to try to lend credence to Darwinism. Yet, when it suits Darwinian purposes, even something that demonstrates clear biochemical activity is deemed non-functional. This 'flip-flop' in the definition of functional importance was made clear in the recent ENCODE study which found over 80% functionality for the genome.
Junk No More: ENCODE Project Nature Paper Finds "Biochemical Functions for 80% of the Genome" - Casey Luskin - September 5, 2012 Excerpt: The Discover Magazine article further explains that the rest of the 20% of the genome is likely to have function as well: "And what's in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project's Lead Analysis Coordinator and self-described "cat-herder-in-chief". He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. "It's likely that 80 percent will go to 100 percent," says Birney. "We don't really have any large chunks of redundant DNA. This metaphor of junk isn't that useful."" We will have more to say about this blockbuster paper from ENCODE researchers in coming days, but for now, let's simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA. ENCODE researchers use words like "surprising" or "unprecedented." They talk about of how "human DNA is a lot more active than we expected." But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted. http://www.evolutionnews.org/2012/09/junk_no_more_en_1064001.html
Atheists/Darwinists did not like that ENCODE result one bit so Darwinists said that functionality, (i.e. biochemical activity), does not really determine if a sequence is actually functional, only evolutionary 'conservation of sequence' determines what is actually functional:
DNA mostly 'junk?' Only 8.2 percent of human DNA is 'functional', study finds - July 24, 2014 Excerpt: To reach their (8.2%) figure, the Oxford University group took advantage of the ability of evolution to discern which activities matter and which do not. They identified how much of our genome has avoided accumulating changes over 100 million years of mammalian evolution -- a clear indication that this DNA matters, it has some important function that needs to be retained. http://www.sciencedaily.com/releases/2014/07/140724141608.htm
So basically, in order to counter the ENCODE findings for widespread functionality, according to Darwinian reasoning, functionality does not determine if a sequence is actually functional. Only if Darwinian evolution is assumed as true, and a sequence is 'conserved' across different species will Darwinists be willing to accept that a given sequence of 'junk' DNA may be functional! That is called 'assuming your conclusion into your premise' and is absolutely horrible science! Moreover, we presently have Zachriel, a Darwinist, trying to relabel what is clearly a minor modification of a preexistent function (citrate digestion) as a major new function. Yet, according to the Darwinian reasoning to counter the ENCODE findings of widespread functionality, the modification, since it is not a 'conserved sequence' is not functional. Thus, when it suits Darwinian purposes to try to prove evolution is true, every little modification of any function is of immense functional importance, and, on the other hand, when it suits Darwinian purposes to try to keep Darwinism from being falsified, nothing in the genome is to be considered functionally important, even though it exhibits functionality (i.e. biochemical activity), except for what is evolutionarily conserved across different species! Only in Darwinian science is such flexibility of definitions, ('functionality' in this case), tolerated. As I've heard said before, the only actual evidence we have for Darwinian evolution happening is within the theory itself. The theory is endlessly plastic, forever morphing itself into whatever shape it needs to so as to 'explain away' difficult, and even completely contradictory, findings:
"Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought." ~ Cornelius Hunter
bornagain77
January 26, 2015
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You have a long wait ahead of you, considering everything.Petrushka
January 26, 2015
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PaV, we're still waiting for rvb8 to respond to Brent's #17.Axel
January 26, 2015
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Natural selection is not a thing, so it cannot exist as a physical object. It is not a force, so it is not like gravity. It is the name given to differential reproductive success, As Darwin noted more than a hundred and fifty years ago, it is most nearly like Adam Smith's Invisible hand. I find it odd that anti-evolutionists become believers in central planning of economies when they think about biology.Petrushka
January 26, 2015
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rvb8: Does natural selection exist? If it doesn't exist, then why do we talk about it? If it exists, is it physical? If it exists and is not physical, what is the material explanation for it?PaV
January 26, 2015
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bornagain77: Thanks once again You're welcome. We're more than happy to point out your misunderstanding of evolution. We cited Behe's claim that if the phenotype were due to gene-duplication with sequence divergence, then it will be a noteworthy gain-of-FCT mutation. Perhaps you disagree, but you didn't present such an argument in your last comment.Zachriel
January 26, 2015
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LOL, Thanks once again Zachriel for showing unbiased readers how irrational Darwinists can be in defending their base atheistic worldview when confronted with brute empirical facts that directly contradict their claims that all life, in all its wondrous and unfathomed complexity, arose via unguided processes. Like I said the other day, you are much better at apologetics than most theists! :)bornagain77
January 26, 2015
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bornagain77: Actually, since ‘E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available)’ then the adaptation is clearly the result of modification of a preexistent function. That's how most evolution works, for instance, the trunk of the elephant is an adaptation of the nose and upper lip. In the fetus, the upper lip and trunk are not yet fused. But it's still a nose!!Zachriel
January 26, 2015
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Actually, since 'E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available)' then the adaptation is clearly the result of modification of a preexistent function. Moreover, the modification of the preexistent function happened via sophisticated molecular machines in response to a 'citrate enhanced' environmental factor, (i.e. via a epigenomic modification). Thus, once again, the adaptation is of no help for the neo-Darwinist in his bid to say that unguided processes can create the sophisticated molecular machines that we find brimming in life. Even more crushing evidence against neo-Darwinism can be gleaned from Lenski’s long term evolution experiment on E-coli. Upon even closer inspection, it seems Lenski’s ‘cuddled’ E. coli are actually headed for genetic meltdown instead of ever evolving into something, anything, better than what they originally were, since the e-coli lost its ability to repair its DNA properly.
New Work by Richard Lenski: - 2009 Excerpt: Interestingly, in this paper they report that the E. coli strain became a “mutator.” That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal. http://www.evolutionnews.org/2009/10/new_work_by_richard_lenski.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.,,, ,,,its mutation rate has increased some 150-fold. As Lenski's work showed, that's due to a mutation (dubbed mutT) that degrades an enzyme that rids the cell of damaged guanine nucleotides, preventing their misincorporation into DNA. Loss of function of a second enzyme (MutY), which removes mispaired bases from DNA, also increases the mutation rate when it occurs by itself. However, when the two mutations, mutT and mutY, occur together, the mutation rate decreases by half of what it is in the presence of mutT alone -- that is, it is 75-fold greater than the unmutated case. Lenski is an optimistic man, and always accentuates the positive. In the paper on mutT and mutY, the stress is on how the bacterium has improved with the second mutation. Heavily unemphasized is the ominous fact that one loss of function mutation is "improved" by another loss of function mutation -- by degrading a second gene. Anyone who is interested in long-term evolution should see this as a baleful portent for any theory of evolution that relies exclusively on blind, undirected processes. ,,,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
also of note, combining the top five 'beneficial' mutations in Lenski's e-coli surprisingly led to 'negative epistasis', instead of enhanced function, which is certainly not good news for the committed atheistic Darwinist, (such as Zachriel), who desparately wants unguided material processes to be the reason why he exists:
Mutations : when benefits level off - June 2011 - (Lenski's e-coli after 50,000 generations) Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually. http://www2.cnrs.fr/en/1867.htm?theme1=7 New Research on Epistatic Interactions Shows "Overwhelmingly Negative" Fitness Costs and Limits to Evolution - Casey Luskin June 8, 2011 Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn't run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does? http://www.evolutionnews.org/2011/06/new_research_on_epistatic_inte047151.html
bornagain77
January 26, 2015
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BA77 Blount et al. 2012 ("et al." includes Lenski) don't mention Behe in the article, so they can't have reported that he was "largely right". Maybe Gauger herself draws such a wishful conclusion from their analysis, but she should not have put her own interpretation in the authors' mouths. Here's the conclusion of the article, in full (emphasis added):
The evolution of citrate use in an experimental E. coli population provided an unusual opportunity to study the multi-step origin of a key innovation. Comparative studies have shown that gene duplications have an important creative role in evolution by generating redundancies that allow neo-functionalization [5,6,8–10]. Our findings highlight the less-appreciated capacity of duplications to produce new functions by promoter capture events that change gene regulatory networks [38]. The evolution of citrate use also highlights that such actualizing mutations are only part of the process by which novelties arise. Before a new function can arise, it may be essential for a lineage to evolve a potentiating genetic background that allows the actualizing mutation to occur or the new function to be expressed. Finally, novel functions often emerge in rudimentary forms that must be refined to exploit the ecological opportunities. This three-step process -- in which potentiation makes a trait possible, actualization makes the trait manifest, and refinement makes it effective -- is probably typical of many new functions.
Piotr
January 26, 2015
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bornagain77: Innovation or Renovation? Behe: If the phenotype is due to one or more mutations that result in, for example, the addition of a novel genetic regulatory element, gene-duplication with sequence divergence, or the gain of a new binding site, then it will be a noteworthy gain-of-FCT mutation. Well, it turns out it was due to gene-duplication with sequence divergence. This directly undermines the claim made above about gene duplications.Zachriel
January 26, 2015
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Innovation or Renovation? By Ann Gauger - Sept. 24, 2012 Excerpt: But how significant was this innovation (citrate; Lenski)? In his paper in Quarterly Review of Biology, Dr. Michael Behe pointed out that E. coli was already capable of using citrate for anaerobic growth (when no oxygen was available). He postulated that a change in gene regulation could turn on citrate transport and permit growth on citrate under aerobic conditions. After an enormous amount of work, having sequenced the genomes of many clones along the lineages that led to the ability to use citrate, as well as lineages that never did, and testing the phenotypes of identified mutations, Blount et al. have now reported that Behe was largely right. The key innovation was a shift in regulation of the citrate operon, caused by a rearrangement that brought it close to a new promoter. http://www.biologicinstitute.org/post/32246480851/innovation-or-renovation?og=1
bornagain77
January 26, 2015
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bornagain77: Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. The novel trait was due to "a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter". See Blount, Genomic analysis of a key innovation in an experimental Escherichia coli population, Nature 2012.Zachriel
January 26, 2015
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