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

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

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://uncommondesc.wpengine.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

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

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

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

"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

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-plasma Zachriel

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

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

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

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

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

"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

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

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

"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

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

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

You have a long wait ahead of you, considering everything. Petrushka

PaV, we're still waiting for rvb8 to respond to Brent's #17. Axel

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

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

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

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

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

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

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

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

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

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

Richard Lenski’s Long-Term Evolution Experiments with E. coli and the Origin of New Biological Information – September 2011 Excerpt: The results of future work aside, so far, during the course of the longest, most open-ended, and most extensive laboratory investigation of bacterial evolution, a number of adaptive mutations have been identified that endow the bacterial strain with greater fitness compared to that of the ancestral strain in the particular growth medium. The goal of Lenski’s research was not to analyze adaptive mutations in terms of gain or loss of function, as is the focus here, but rather to address other longstanding evolutionary questions. Nonetheless, all of the mutations identified to date can readily be classified as either modification-of-function or loss-of-FCT. (Michael J. Behe, “Experimental Evolution, Loss-of-Function Mutations and ‘The First Rule of Adaptive Evolution’,” Quarterly Review of Biology, Vol. 85(4) (December, 2010).) http://www.evolutionnews.org/2011/09/richard_lenskis_long_term_evol051051.html Lenski's Long-Term Evolution Experiment: 25 Years and Counting - Michael Behe - November 21, 2013 Excerpt: Twenty-five years later the culture -- a cumulative total of trillions of cells -- has been going for an astounding 58,000 generations and counting. As the article points out, that's equivalent to a million years in the lineage of a large animal such as humans. Combined with an ability to track down the exact identities of bacterial mutations at the DNA level, that makes Lenski's project the best, most detailed source of information on evolutionary processes available anywhere,,, ,,,for proponents of intelligent design the bottom line is that the great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions (Behe 2010). There have been no mutations or series of mutations identified that appear to be on their way to constructing elegant new molecular machinery of the kind that fills every cell. For example, the genes making the bacterial flagellum are consistently turned off by a beneficial mutation (apparently it saves cells energy used in constructing flagella). The suite of genes used to make the sugar ribose is the uniform target of a destructive mutation, which somehow helps the bacterium grow more quickly in the laboratory. Degrading a host of other genes leads to beneficial effects, too.,,, - http://www.evolutionnews.org/2013/11/richard_lenskis079401.html Multiple Mutations Needed for E. Coli - Michael Behe Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell. http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/ Rose-Colored Glasses: Lenski, Citrate, and BioLogos - Michael Behe - November 13, 2012 Excerpt: Readers of my posts know that I'm a big fan of Professor Richard Lenski, a microbiologist at Michigan State University and member of the National Academy of Sciences. For the past few decades he has been conducting the largest laboratory evolution experiment ever attempted. Growing E. coli in flasks continuously, he has been following evolutionary changes in the bacterium for over 50,000 generations (which is equivalent to roughly a million years for large animals). Although Lenski is decidedly not an intelligent design proponent, his work enables us to see what evolution actually does when it has the resources of a large number of organisms over a substantial number of generations. Rather than speculate, Lenski and his coworkers have observed the workings of mutation and selection.,,, In my own view, in retrospect, the most surprising aspect of the oxygen-tolerant citT mutation was that it proved so difficult to achieve. If, before Lenski's work was done, someone had sketched for me a cartoon of the original duplication that produced the metabolic change, I would have assumed that would be sufficient -- that a single step could achieve it. The fact that it was considerably more difficult than that goes to show that even skeptics like myself overestimate the power of the Darwinian mechanism. http://www.evolutionnews.org/2012/11/rose-colored_gl066361.html

bornagain77

DATCG: To be specific, the co-option model requires that a gene become duplicated, and then overexpressed before it can evolve some new function. A potentiating mutation followed by a gene duplication followed by optimizing mutations was observed by Lenski et al. in the E. coli long-term evolution experiment. Zachriel

as to:

"It’s been shown that at least some mutations are random with respect to fitness."

Actually, since the vast majority of mutations (i.e. changes to the genome) are shown to be happening in a non-random fashion before natural selection even has a chance to operate, as far as the theoretical construct of Darwinism is concerned, it is far more helpful to point out that, in regards to fitness and natural selection, that the vast majority of mutations that are happening in a non-random fashion in the genome reduce the fitness of the organism, i.e. to show that the vast majority of mutations are detrimental in regards to fitness!

Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 - May 2013 Excerpt: It is almost universally acknowledged that beneficial mutations are rare compared to deleterious mutations [1–10].,, It appears that beneficial mutations may be too rare to actually allow the accurate measurement of how rare they are [11]. 1. Kibota T, Lynch M (1996) Estimate of the genomic mutation rate deleterious to overall fitness in E. coli . Nature 381:694–696. 2. Charlesworth B, Charlesworth D (1998) Some evolutionary consequences of deleterious mutations. Genetica 103: 3–19. 3. Elena S, et al (1998) Distribution of fitness effects caused by random insertion mutations in Escherichia coli. Genetica 102/103: 349–358. 4. Gerrish P, Lenski R N (1998) The fate of competing beneficial mutations in an asexual population. Genetica 102/103:127–144. 5. Crow J (2000) The origins, patterns, and implications of human spontaneous mutation. Nature Reviews 1:40–47. 6. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. 7. Imhof M, Schlotterer C (2001) Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA 98:1113–1117. 8. Orr H (2003) The distribution of fitness effects among beneficial mutations. Genetics 163: 1519–1526. 9. Keightley P, Lynch M (2003) Toward a realistic model of mutations affecting fitness. Evolution 57:683–685. 10. Barrett R, et al (2006) The distribution of beneficial mutation effects under strong selection. Genetics 174:2071–2079. 11. Bataillon T (2000) Estimation of spontaneous genome-wide mutation rate parameters: whither beneficial mutations? Heredity 84:497–501. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006

And for the rare occasions that 'non-random' mutations do increase the fitness of the organism, it is found to come at a cost of the preexisting functional information that is already in the genome:

“The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain. http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/

As to the distribution of 'non-random' mutations in regards to fitness, the following study shows that 'less fit' mutations are far more likely to be fixed than the 'slightly fitter' mutations.

Study demonstrates evolutionary ‘fitness’ not the most important determinant of success – February 7, 2014 – with illustration Excerpt: An illustration of the possible mutations available to an RNA molecule. The blue lines represent mutations that will not change its function (phenotype), the grey are mutations to an alternative phenotype with slightly higher fitness and the red are the ‘fittest’ mutations. As there are so few possible mutations resulting in the fittest phenotype in red, the odds of this mutation are a mere 0.15%. The odds for the slightly fitter mutation in grey are 6.7% and so this is far more likely to fix, and thus to be found and survive, even though it is much less fit than the red phenotype.,,, By modelling populations over long timescales, the study showed that the ‘fitness’ of their traits was not the most important determinant of success. Instead, the most genetically available mutations dominated the changes in traits. The researchers found that the ‘fittest’ simply did not have time to be found, or to fix in the population over evolutionary timescales. http://phys.org/news/2014-02-evolutionary-important-success.html

This following headline sums the preceding finding up very nicely:

Fittest Can’t Survive If They Never Arrive – February 7, 2014 http://crev.info/2014/02/fittest-cant-survive-if-they-never-arrive/

Needless to say, this is NOT the empirical evidence that Darwinism needs in order to be considered a viable candidate for explaining the optimal complexity being found in life. Such as the optimal complexity found in the vision cascade:

Evolution Vs. The Miracle Of The Eye - Vision Cascade Molecular Animation https://www.youtube.com/watch?v=AuLR0kzfwBU The Vision Cascade is Initiated Not by Isomerization but by Force Field Dynamics - July 2011 Excerpt: 'In addition to designing the opsin protein, evolution must now design the electric field surrounding the chromophore, and how it responds to photon interaction. And while it is busy with that task, it must also specify the correct amino acids at the correct locations within the opsin, that will be influenced by the chromophore’s dynamic electric field.' http://darwins-god.blogspot.com/2011/06/vision-cascade-is-initiated-not-by.html William Bialek: More Perfect Than We Imagined - March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the smallest possible packages in which light comes wrapped. “Light is quantized, and you can’t count half a photon,” said William Bialek, a professor of physics and integrative genomics at Princeton University. “This is as far as it goes.” … In each instance, biophysicists have calculated, the system couldn’t get faster, more sensitive or more efficient without first relocating to an alternate universe with alternate physical constants. http://darwins-god.blogspot.com/2013/03/william-bialek-more-perfect-than-we.html Eyeballing Design by Casey Luskin - December 2011 Excerpt:,,, the team of scientists who determined the function of glial cells concluded that the "retina is revealed as an optimal structure designed for improving the sharpness of images." http://www.salvomag.com/new/articles/salvo19/19luskin.php

The following article gives a small overview as to the astonishing complexity being dealt with in the vision cascade:

Could the eye have evolved by natural selection in a geological blink? March 18, 2013 Excerpt: Let us return to the question, how do we see? Although to Darwin the primary event of vision was a black box, through the efforts of many biochemists an answer to the question of sight is at hand. When light strikes the retina a photon is absorbed by an organic molecule called 11-cis-retinal, causing it to rearrange within picoseconds to trans-retinal. The change in shape of retinal forces a corresponding change in shape of the protein, rhodopsin, to which it is tightly bound. As a consequence of the protein’s metamorphosis, the behavior of the protein changes in a very specific way. The altered protein can now interact with another protein called transducin. Before associating with rhodopsin, transducin is tightly bound to a small organic molecule called GDP, but when it binds to rhodopsin the GDP dissociates itself from transducin and a molecule called GTP, which is closely related to, but critically different from, GDP, binds to transducin. The exchange of GTP for GDP in the transducinrhodopsin complex alters its behavior. GTP-transducinrhodopsin binds to a protein called phosphodiesterase, located in the inner membrane of the cell. When bound by rhodopsin and its entourage, the phosphodiesterase acquires the ability to chemically cleave a molecule called cGMP. Initially there are a lot of cGMP molecules in the cell, but the action of the phosphodiesterase lowers the concentration of cGMP. Activating the phosphodiesterase can be likened to pulling the plug in a bathtub, lowering the level of water. A second membrane protein which binds cGMP, called an ion channel, can be thought of as a special gateway regulating the number of sodium ions in the cell. The ion channel normally allows sodium ions to flow into the cell, while a separate protein actively pumps them out again. The dual action of the ion channel and pump proteins keeps the level of sodium ions in the cell within a narrow range. When the concentration of cGMP is reduced from its normal value through cleavage by the phosphodiesterase, many channels close, resulting in a reduced cellular concentration of positively charged sodium ions. This causes an imbalance of charges across the cell membrane which, finally, causes a current to be transmitted down the optic nerve to the brain: the result, when interpreted by the brain, is vision. If the biochemistry of vision were limited to the reactions listed above, the cell would quickly deplete its supply of 11-cis-retinal and cGMP while also becoming depleted of sodium ions. Thus a system is required to limit the signal that is generated and restore the cell to its original state; there are several mechanisms which do this. Normally, in the dark, the ion channel, in addition to sodium ions, also allows calcium ions to enter the cell; calcium is pumped back out by a different protein in order to maintain a constant intracellular calcium concentration. However, when cGMP levels fall, shutting down the ion channel and decreasing the sodium ion concentration, calcium ion concentration is also decreased. The phosphodiesterase enzyme, which destroys cGMP, is greatly slowed down at lower calcium concentration. Additionally, a protein called guanylate cyclase begins to resynthesize cGMP when calcium levels start to fall. Meanwhile, while all of this is going on, metarhodopsin II is chemically modified by an enzyme called rhodopsin kinase, which places a phosphate group on its substrate. The modified rhodopsin is then bound by a protein dubbed arrestin, which prevents the rhodopsin from further activating transducin. Thus the cell contains mechanisms to limit the amplified signal started by a single photon. Trans-retinal eventually falls off of the rhodopsin molecule and must be reconverted to 11-cis-retinal and again bound by opsin to regenerate rhodopsin for another visual cycle. To accomplish this trans-retinal is first chemically modified by an enzyme to transretinol, a form containing two more hydrogen atoms. A second enzyme then isomerizes the molecule to 11-cis-retinol. Finally, a third enzyme removes the previously added hydrogen atoms to form 11-cis-retinal, and the cycle is complete. per: uncommondescent.com/intelligent-design/could-the-eye-have-evolved-by-natural-selection-in-a-geological-blink/

And please note, neo-Darwinists have yet to empirically demonstrate the origination of even one protein/gene of that jaw dropping complexity in this, or in any other, system! bornagain77

From another thread https://uncommondesc.wpengine.com/news/proteins-are-defying-textbooks/#comment-544200

What isn’t criticized in any of these fields is the mention of evolutionary ideas as in the paper I have cited. This is because there is no uncertainty within these fields as to whether or not evolution has occurred. There are no serious problems with the theory, save for the fact that we understand only a fraction of the evolutionary process.

That seems like a standard response. No matter how discredited Neo-Darwinism becomes, they will be 'no uncertainty' that evolution occured. Even if nobody can explain the mechanisms - they will be certain that unguided, unintelligent, blind material forces did it. The fact that there will be conflicting new theories will still mean that 'there are no serious problems with the theory'. Silver Asiatic

From DATCG on #22: 'Massimo Pigliucci’s Altenberg colleagues are not all on the same page with his conservative thinking.' Conservative!!! Pretty ironical in the light of BA77's immediately-preceding post, especially the concluding paragraphs concerning falsifiability. Well, Pauli's point at the beginning, too. Axel

Some of the latest discussions on research by the Biological Institute LAB show what appear to be more limitations to Darwinian explanations such as co-option...

When Michael Behe published Darwin's Black Box in 1996, he outlined the concept of irreducible complexity as a biochemical challenge to Darwinian evolution. According to his argument, some structures require all of their parts (or a certain core minimum number) in order to function. In this game of all or nothing, such "irreducibly complex" structures cannot be built in the step-by-step manner of Darwinian evolution because they provide no advantage, of the kind evolution requires, until all their parts are present. At the time and since, evolutionists responded by arguing that irreducibly complex features can be built through co-option. Under this view, biological parts might exist elsewhere in an organism where they are used for a different function. Sometimes, when a gene is duplicated, the extra copy could then be borrowed, retooled, and "co-opted" to perform a new function in a new system.

Research scientist at Biologic Institute have been testing the co-option model of protein evolution. More discussion of the Research here.

To be specific, the co-option model requires that a gene become duplicated, and then overexpressed before it can evolve some new function. Thus, at least two more mutations are needed -- one to duplicate the gene and another to overexpress it.

They experimentally found that at least two mutations would be necessary to convert the most likely co-option candidates in this enzyme family to function like BioF2. But other mutations would be necessary as well -- at least one to duplicate the enzyme and another to overexpress it. This suggests at least four mutations would be required for this conversion.

Abstract for one of their recent papers...

Reeves MA, Gauger AK, Axe DD (2014) Enzyme families—Shared evolutionary history or shared design? A study of the GABA-aminotransferase family. BIO-Complexity 2014 (4):1?16.

The PDF is available for viewing or download at above link. DATCG

from Chicago biochemist James Shapiro's blog who is one of the scientist mentioned on The Third Way. Regarding "irreducible complexity." What Is the Best Way to Deal With Supernaturalists in Science and Evolution? He makes reasonable statements to engage ID theorist and Creationist. And he recognizes the interesting concept of irreducible complexity...

5. The newly discovered processes of genome change do indeed have the potential to generate "irreducibly complex" new functions. Such complex evolutionary inventions are at the center of the Intelligent Design critique of neo-Darwinian explanations, which are based exclusively on random genetic accidents and natural selection. Doubling the whole genome, distributing copies of mobile elements to different sites, and incorporating similar domains in different proteins provide the necessary raw materials for generating complex interactive networks in cells. A future task for experimental evolution science is to find out how this happens in real time.

DATCG

Suzan Mazur's credentials are fine. What some complain of is honest and open discussion of the failures of Neo-Darwinism to save Darwinism.

Regarding my journalistic credentials. I was an education major (Biology) for two years in college. I began my writing career as a science journalist 40 years ago at Hearst Magazines. Through the years I’ve contributed feature articles about science to The Economist, Financial Times, Archaeology, Omni, Connoisseur, Solar Age and others. Among the highlights: In the late 1970s, I investigated solar energy at the Kuwait Institute for Scientific Research. In 1980, I flew into Olduvai Gorge to interview paleoanthropologist Mary Leakey re evolution and interviewed scientists elsewhere in East and West Africa. In 1981, I interviewed scientists in subSaharan Africa. And at the French Space Agency in Paris. I reported on earthquakes and seismology in Guatemala. Archaeology in Colombia and Turkey. In the early 1980s, heading a solar energy film project, my crew and I were invited by the Swedish government and the Saudi Arabian National Center for Science and Technology to research a television documentary on solar energy villages in those two countries; I was a guest on Saudi-TV in Riyadh discussing the project. During the Gulf War I broke a fetal-to-fetal transplant [surgery] story. Etc. My book, The Altenberg 16: An Expose of the Evolution Industry (North Altantic Books), which includes the stories Pigliucci derides, has a cover endorsement by the world’s most respected public intellectual, Noam Chomsky, which reads as follows: “Very glad to see the book. I suspect it should have some (very much needed) influence now against the background of the “evo-devo revolution” and the belated recognition of Margulis’s work.” I’ve also covered the wars — Gulf War, Colombian Drug War, Sudan, Kashmir (from both sides of the CFL/LOC). Been a guest on McLaughlin, Charlie Rose and various Fox Television News shows. My television reports on human rights and politics have aired on PBS, CBC, MBC and Fox.

DATCG

bornagain77: Besides the fact that the vast majority of changes to the genome are accomplished via highly sophisticated molecular machines in a non-random fashion, even the ‘spontaneous’ mutations HAVE NOT been shown to be random in where they occur, how they occur, or when they occur. It's been shown that at least some mutations are random with respect to fitness. They are uncorrelated variables. Zachriel

Suzan Mazur's website shows interviews with Geneticist and Pioneers in Origin of Life research. Interview with Protocell Pioneer Matt Powner She defends herself well against accusations by Pigliucci... Interesting Developments of Pigliucci's About-Face

The first story post was March 4, 2008 (NZ time), titled “Altenberg! The Woodstock of Evolution?” with coverage of scientists invited to Altenberg and some leading scientists not invited, like Richard Lewontin, Niles Eldredge, Stuart Kauffman and Michael Lynch. The story that Massimo Pigliucci now describes as “hodge-podge” in his book on page 101, paragraph 2, reflects the widely different perspectives in evolutionary thinking among leading scientists. As complexity pioneer Stuart Kauffman told me: “There are people spouting off as if we know the answer [re the process of evolution]. We don’t know the answer.” “Altenberg! The Woodstock of Evolution?” story drew a large audience. And Pigliucci sent me an email shortly after the story posted saying the following: “Suzan very nice article indeed! Cheers, Massimo” (emphasis added) Some hours later when the intelligent design bloggers (some of the most vigorous re evolution) began to comment online about the piece, however, Pigliucci sent this email to all 16 invited Altenberg scientists with a CC to me: “All, well, it was inevitable, but Paul Nelson, of the ID “think tank” The Discovery Institute, picked up Suzan’s article and ran with it: https://uncommondesc.wpengine.com/intelligent-design/-the-altenberg-sixteen/ Cheers, Massimo”

Some colleagues have other opinions as she points out...

Massimo Pigliucci’s Altenberg colleagues are not all on the same page with his conservative thinking. New York Medical College cell biologist Stuart Newman in an interview with me for Archaeology magazine said this: “I believe that the field will have to reorient I don’t by any means think the science that’s been done under the Darwinian paradigm will disappear or will be seen to be entirely invalid. But the Darwinian mechanism that’s used to explain all evolutionary change will be relegated, I believe, to being just one of the several mechanisms – maybe not even the most important when it comes to understanding macroevolution, the evolution of major transitions in body type.” And Richard Lewontin’s New York Review of Books article “Not So Natural Selection” commenting favorably on Jerry Fodor and Massimo Piattelli-Palmarini’s book What Darwin Got Wrong is also telling, a book Pigliucci termed “misguided” in his review in Nature magazine. In the NYRB article, Richard Lewontin also noted the lack of civility among evolutionary thinkers.

Yes, the times they are a changing. DATCG

Seversky at 1 quotes:

"One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process."

Actually, contrary to what is popularly believed, neo-Darwinism itself introduces a 'supernatural force' right into the middle of the 'evolution process':

Pauli’s ideas on mind and matter in the context of contemporary science - Harald Atmanspacher Excerpt: “In discussions with biologists I met large difficulties when they apply the concept of ‘natural selection’ in a rather wide field, without being able to estimate the probability of the occurrence in a empirically given time of just those events, which have been important for the biological evolution. Treating the empirical time scale of the evolution theoretically as infinity they have then an easy game, apparently to avoid the concept of purposesiveness. While they pretend to stay in this way completely ‘scientific’ and ‘rational,’ they become actually very irrational, particularly because they use the word ‘chance’, not any longer combined with estimations of a mathematically defined probability, in its application to very rare single events more or less synonymous with the old word ‘miracle.’” Wolfgang Pauli (pp. 27-28) http://www.igpp.de/english/tda/pdf/paulijcs8.pdf Evolution and the Illusion of Randomness - Talbott - Fall 2011 Excerpt: The situation calls to mind a widely circulated cartoon by Sidney Harris, which shows two scientists in front of a blackboard on which a body of theory has been traced out with the usual tangle of symbols, arrows, equations, and so on. But there’s a gap in the reasoning at one point, filled by the words, “Then a miracle occurs.” And the one scientist is saying to the other, “I think you should be more explicit here in step two.” In the case of evolution, I picture Dennett and Dawkins filling the blackboard with their vivid descriptions of living, highly regulated, coordinated, integrated, and intensely meaningful biological processes, and then inserting a small, mysterious gap in the middle, along with the words, “Here something random occurs.” This “something random” looks every bit as wishful as the appeal to a miracle. It is the central miracle in a gospel of meaninglessness, a “Randomness of the gaps,” demanding an extraordinarily blind faith. At the very least, we have a right to ask, “Can you be a little more explicit here?” http://www.thenewatlantis.com/publications/evolution-and-the-illusion-of-randomness

In fact the neo-Darwinian appeal to 'supernatual randomness' has been the primary obstacle to elucidating a rigid mathematical basis for Darwinism that can be potentially falsified (a falsification criteria as other theories of science, including ID, have:

“It is our contention that if ‘random’ is given a serious and crucial interpretation from a probabilistic point of view, the randomness postulate is highly implausible and that an adequate scientific theory of evolution must await the discovery and elucidation of new natural laws—physical, physico-chemical, and biological.” Murray Eden, “Inadequacies of Neo-Darwinian Evolution as a Scientific Theory,” Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution, editors Paul S. Moorhead and Martin M. Kaplan, June 1967, p. 109.

And James Shapiro, one of the leading lights of 'The Third Way', has been fairly scathing towards the neo-Darwinian appeal to randomness:

"It is difficult (if not impossible) to find a genome change operator that is truly random in its action within the DNA of the cell where it works' James Shapiro - Evolution: A View From The 21st Century - (Page 82) Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf How life changes itself: the Read-Write (RW) genome. - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611

Besides the fact that the vast majority of changes to the genome are accomplished via highly sophisticated molecular machines in a non-random fashion, even the 'spontaneous' mutations HAVE NOT been shown to be random in where they occur, how they occur, or when they occur.

WHAT SCIENTIFIC IDEA IS READY FOR RETIREMENT? Fully Random Mutations - Kevin Kelly - 2014 Excerpt: What is commonly called "random mutation" does not in fact occur in a mathematically random pattern. The process of genetic mutation is extremely complex, with multiple pathways, involving more than one system. Current research suggests most spontaneous mutations occur as errors in the repair process for damaged DNA. Neither the damage nor the errors in repair have been shown to be random in where they occur, how they occur, or when they occur. Rather, the idea that mutations are random is simply a widely held assumption by non-specialists and even many teachers of biology. There is no direct evidence for it. On the contrary, there's much evidence that genetic mutation vary in patterns. For instance it is pretty much accepted that mutation rates increase or decrease as stress on the cells increases or decreases. These variable rates of mutation include mutations induced by stress from an organism's predators and competition, and as well as increased mutations brought on by environmental and epigenetic factors. Mutations have also been shown to have a higher chance of occurring near a place in DNA where mutations have already occurred, creating mutation hotspot clusters—a non-random pattern. http://edge.org/response-detail/25264

Thus, since neo-Darwinism, as was formulated by Charles Darwin and as was laid out in the modern synthesis, relies on 'random variation' as its base postulate before Natural Selection even has a chance to operate, then neo-Darwinism is found to be false in its theoretical contstruct. I would also like to point our that, as far as empirical science itself is concerned, it is much easier to falsify ID than it is to falsify neo-Darwinism:

It’s (Much) Easier to Falsify Intelligent Design than Darwinian Evolution – Michael Behe, PhD https://www.youtube.com/watch?v=_T1v_VLueGk The Law of Physicodynamic Incompleteness - David L. Abel Excerpt: "If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise." If only one exception to this null hypothesis were published, the hypothesis would be falsified. Falsification would require an experiment devoid of behind-the-scenes steering. Any artificial selection hidden in the experimental design would disqualify the experimental falsification. After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: "No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone." https://www.academia.edu/9957206/The_Law_of_Physicodynamic_Incompleteness_Scirus_Topic_Page_

Since ID is much easier to falsify than neo-Darwinism is, according to Popper, ID 'speaks about reality' and Darwinism does not:

"In so far as a scientific statement speaks about reality, it must be falsifiable; and in so far as it is not falsifiable, it does not speak about reality." Karl Popper - The Two Fundamental Problems of the Theory of Knowledge (2014 edition), Routledge http://izquotes.com/quote/147518

Verse and Music:

1 Thessalonians 5:21 but test everything; hold fast what is good. Alter Bridge – Rise Today http://www.youtube.com/watch?v=ZYG3BPvFOgs

bornagain77

DATCG

They’re breaking ranks with Neo-Darwinism and Dawkins’ absolutist position. This is a healthy step taking place, long overdue.

True. We still have absolutists posting here on UD. Others have quietly recognized the changing tide. As evidenced by responses to Susan Mazur's book though, there won't be a revolution and maybe not much of a media story. Perhaps 20 years after NDE is gone, magazines will point it out. But until then, it's a quiet shift to the idea that there are 'multiple mechanisms' and of course, 'no one has claimed that natural selection was a primary factor for decades'. It's a transition now. There's plenty of time to jump ship and grab a jumble of materialist-evolutionary ideas and then later claim 'we knew about this for years'. Silver Asiatic

There is exactly one way to explain physical existence; physically!

It's impossible to offer a physical explanation of anything. Explanations are not physical. Silver Asiatic

BA thanks for video post. Will watch when I have time. Think this is Denis Noble's video originally posted here in early January... take down of Neo-Darwinism Noble's subject in the lecture...

"All of these rules have been broken!" referring to Central Dogma of Neo-Darwinism failures. "Are mutations random?" Quoting biochemist James Shapiro, Evolution. A View from the 21st Century "It is difficult(if not impossible) to find a genome operator that is truly random in its action within the DNA of the cell where it works.(pg 82). All careful studies of mutagenesis find statistically significant non-random patters of change."

The march is on now to a different explanation. For those who a priori rule out a possible Design Inference, they're taking the "Third Way.' Was wondering when you guys would post it :) They're breaking ranks with Neo-Darwinism and Dawkins' absolutist position. This is a healthy step taking place, long overdue. Jeannie's Out of the Bottle Now Has been for some time. Eventually this will tumble over to the larger Media, then the Masses. DATCG

rvb8, You said:

There is exactly one way to explain physical existence; physically! Or naturally, if you will. Introducing phenomena, and the extra-natural is within the realm of childish wish fulfillment; no thank you!

So . . . the physical universe existed before it existed so that it could bring itself into existence. Right. And nature, which is a catch all of the physical universe, somehow worked on that which its meaning is derived from in order to bring that thing into existence so that it could get its meaning from that thing it brought into existence. Awesome. The whole thing sounds rather super-natural if you ask me, because we never expect nature or the physical universe to do these amazing things for us today. What was it you said about childish wish fulfillment? Brent

As to the gross inadequacy of unguided neo-Darwinian processes: Biological Information - Entire Lecture Series https://www.youtube.com/watch?v=vg_xp0dRUdM&list=PLHDSWJBW3DNUUhiC9VwPnhl-ymuObyTWJ&index=1 bornagain77

No Mung that doesn't 'settle it'. Your implication that just because rvb8 said something then that 'settles it', is the typical poorly thought out 'toss away' non-answer we expect here. Please, please, please, at some point in the near future, please ID, do something! I have a notion that ID and Christianity lend themselves to one another because both love playing the 'victim'. This of course is a dangerous path because when it is clearly shown that your insignificance is due to your lack of work then victimhood remains the only answer. This again leads to paranoia and then to less productivity etc etc etc. It is not that 'I' say it. It is that science says it. I've googled Mazur. Loon, is the politest thing I could call her. Half baked quack, radical idealist, god bothering fanatic, unhinged fear dragon, moronic narcissitic rube, ego maniachal gas bag, also sprang to mind. Of course it is very strange that News finds her on the van guard of ID thought, or rather, a 'clear thinker', a 'defender of the trenches'. A revolutionary in the mould of Hamilton, Franklin, and Jefferson, or whichever other manufactured gods you care to name. Christ, give me a break! A red neck by any other name remains a denizen of the lower reaches of Alabami. rvb8

skram,

"We know pretty well how this part of nature developed over time."

Well, if you don't mind vague answers we do.

But if you insist on having the Ultimate Answer to Life and Everything, then sorry, science does not deal with these kinds of questions. They are too vague. And the answers provided by faith are not necessarily valid."

If you consider sound, deductive, necessarily true answers vague (and then, additionally, become somehow suddenly unwilling to countenance a dirty, 'vague', answer). Brent

"One way is Creationism that depends upon intervention by a divine Creator. That is clearly unscientific because it brings an arbitrary supernatural force into the evolution process." Ie, sure looks like this is the best explanation, but it isn't because it is philosophically not permitted. Moose Dr

If your claim there is "ultimate value, purpose, meaning and hope" we'll need more evidence than the fact that you need there to be. And if there is a God what makes you think that we are His ultimate purpose? As another OP points out, this is a very big universe and it may not be the only one, either. This is classical wish fulfillment at its best. Seversky

skram 7 "But if you insist on having the Ultimate Answer to Life and Everything, then sorry, science does not deal with these kinds of questions. They are too vague." How did space/time, matter/energy arise from themselves? Too vague. How did life arise from non-life? Too vague. How did the incredible machinery in every cell arise by unguided process? Too vague. How did the incredibly complex codes (yes, they are plural) within DNA arise by unguided processes? Too vague. Why does the fossil record not match Darwin's Tree of Life? Too vague. How did most of the major phyla arise abruptly in the Cambrian without visible antecedents? Too vague. Why do we never observe fruit flies becoming something other than fruit flies, no matter how much we mutate them? Too vague. All I can say is, nice work if you can get it! anthropic

From the naturalists give in this thread it's no wonder why I consider atheism an emotional worldview moreso then a rational one . What makes it even more irrational is that they dogmatically want to believe that there is no ultimate value, purpose, meaning and hope , even though they can't give us evidence for it . This is classical insanity at its best wallstreeter43

Funny, without God there would be no science and yet science cannot tell us anything about God? Methinks the good Dr. be blind! bornagain77

ThirdWayEvolution website launched last May? I check on it every couple months or so - not a lot of activity posted there. Although it seems they have picked up some additional members since the launch. ppolish

groovamos, One step at a time. Nature has many sides. The earth as a habitat is part of nature. We know pretty well how this part of nature developed over time. But if you insist on having the Ultimate Answer to Life and Everything, then sorry, science does not deal with these kinds of questions. They are too vague. And the answers provided by faith are not necessarily valid. skram

rvb8: There is exactly one way to explain physical existence; physically! Or naturally, if you will. Please rvb8, "explain" to us the natural origins for nature. It would be great if you would include some empiricism in your 'explanation', or the history of such. groovamos

rvb8: The “16?, were squarely in the realm of science. Mazur is squarely in the realm of ‘loon’. Will that settles it then! Mung

There is exactly one way to explain physical existence; physically! Or naturally, if you will. Introducing phenomena, and the extra-natural is within the realm of childish wish fulfillment; no thank you! The "16", were squarely in the realm of science. Mazur is squarely in the realm of 'loon'. rvb8

"..there are only two alternative ways to explain the origins of biological diversity." Strikes me as begging the question from the start. Diversity isn't really what most people are trying to explain anyway. Life itself is what most people want to explain. And genomics is telling us STRONGLY that life is NOT diverse. Every new finding leads irresistibly to a SINGLE complete original plan, started at exactly one time, with each life form losing or varying or temporarily switching off various parts of the single complete plan. If we encountered this arrangement in architecture, as in a Levittown development, we wouldn't call it diversity. We'd call it uniformity plus decorations. polistra

Ive read plenty of papers by neo darwinists that discuss hgt, not really sure what theyre talking about. Also did you miss the part about creationism? Thats bad for you guys. Starbuck

This sounds like a good idea. The group is still clearly promoting evolution and rejecting any sort of supernatural explanation.

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.

Seversky