“Junk DNA”’s defender doesn’t “do politeness”?

Fascinating to look back from 2019 at the exchanges. Bits of Junk DNA are now seen as food storage. No vestigials, no junk. Much egg on face. Belfast

That was supposed to be a quote:

Darwinism is unfalsifiable, because it can handle either extreme prediction.

-Q Querius

Timaeous @ 80 . . . Nicely put. Darwinism is unfalsifiable, because it can handle either extreme prediction. As well as almost anything else under investigation. The headlines are almost always, "Researchers surprised at X," Prominent evolutionary scientist n at i, attributes this finding to T: "What must have happened is that m and p, led to t, and this gives us new insight on how evolution works." The Theory of Evolution accommodates and explains everything, but predicts nothing. -Q Querius

Feynman lectures on how Science should be done. I'm afraid he would think Evo Bio is infested with "Cargo Cult" Scientists. http://www.youtube.com/watch?v=yvfAtIJbatg&feature=youtube_gdata_player ppolish

phoodoo (4): Good question, but jlafan is far too spineless to commit himself to a numerical prediction. After all, if the prediction were falsified, what would he do then? Darwinism is essentially unfalsifiable with reference to the amount of junk DNA. If there is lots of junk, the atheists and TEs will argue (as they have -- Miller, etc.): "and this is just what we would expect from a process like Darwinian evolution, which builds without plan or purpose in an ad hoc manner from whatever is lying around in the DNA junkyard." And if it turns out that 99% of DNA is functional, Darwinians can always change their argument to: "That's just what we would expect if natural selection is as strong as Darwin said it was! Selection would cause organisms not to waste energy conserving junk, and would tend over time to produce DNA that is nearly 100% functional." Darwinism is unfalsifiable, because it can handle either extreme prediction. On the other hand, if Darwinism were a precise enough theory to give a rough number range, say: "We predict that between 5% and 22% will be found useful to the organism," then Darwinism would be a scientific theory. Science has to have numbers attached to it. (Galileo.) To the extent that Darwinian theory can attach no numbers to its prediction of junk DNA, it is not a scientific theory. It's not surprising that jlafan gives no numbers; he hasn't taken a science course since 9th-grade biology. What is shocking is that professors of evolutionary biology at Harvard etc. aren't compelled to give numbers. If they have a viable scientific theory, they should be able to tell us roughly how much junk DNA we can expect. 10%? 50%? 80%? Not one of them will give a numerical prediction. No professor of experimental physics or chemistry could get away with avoiding numerical predictions like that. This shows how loose the scientific standards are in evolutionary biology. Timaeus

"Nothing in the recent research or commentary on the subject has challenged these observations." I would think challenges are a good thing. The writers of that paper (L.Moran et al) seem a bit defensive. A bit biased. That can't be good science. ppolish

wd400:

If you are “seriously looking for answers and open to truth”, you might want to do some research on the arguments for junk. here’s a place to start

"Yet, it is simply not true that potential functions for noncoding DNA were ignored until recently. In fact, various early commenters considered the notion that large swaths of the genome were nonfunctional to be “repugnant”, and possible functions were discussed each time a new type of nonprotein-coding sequence was identified..." But that didn't stop the atheists/materialists using "junk DNA" as an argument for materialism/atheism. "In this review, we examine several lines of evidence—both empirical and conceptual—that support the notion that a substantial percentage of the DNA in many eukaryotic genomes lacks an organism-level function and that the junk DNA concept remains viable post-ENCODE." Perhaps looking at the genome of the onion isn't the best way to determine how much "junk" there is in the human genome. So give ENCODE some credit, at least they are looking in the right place. Mung

Mung’s nearly neutral theory of dumpster diving. Dr JDD:

We are told that a random neutral mutation that confers no advantage can get fixed within the genome. Yet you are not affording the same possibility to a random neutral deletion.

It seems to me that by analogy you are asserting that we can’t argue for the accumulation of junk in the local landfill because we haven’t taken into account dumpster diving. Mung

I am using a bit of simplistic hyperbole when I say 98% is junk because many pro-evolutionists (several on here) will still state 98% is junk. So there is disparity within naturalists regarding this. I know full well many people do not consider 98% to be junk No one who knows what they are talking abuout thinks all non-coding sequences are junk. I don't know who made that claim here but they are obviously wrong. and some recently posted articles I posted in other threads show publications where secular scientists make statements that we know now a lot of apparent “junk” DNA is not junk after all. These people however tend to be not evolutionary biologists so they do not need to rely on there being junk present and it doesn’t bother their science as much thinking about the implications of much of non-coding DNA having function. It's true that the people who think genomes are near junless don't know much about evolution. It's not true that evolutionary biology "needs" a junky genome. We are told that a random neutral mutation that confers no advantage can get fixed within the genome. Yet you are not affording the same possibility to a random neutral deletion. This is my point – you cannot have it one way and say it cannot work the other way Right, so under neutrality both types of variant get fixed at the rate which they appear in individuals. Since the rate that junky sequences like ALUs and LINEs and (historically) all those now broken transposons get copied it much greater than they appear we have a ratchet by which junk can accrue. (Of course, some of the elements are later co-opted into functional genes, as we see in the human genome) Taking all the current evidence from ENCODE, FANTOM, recent findings about pseudogene function and lncRNAs Of course some non-coding DNA is functional, and the proportion of the genome assinged to biological function can only go up. But the bestfor junk DNA are not about the fact we can't assign most of the genome to biological function (and it's ignorant to pretent they are), so the slow trickle of functional elements (and the silly headlines from which ENCODE has quietly resiled) don't add up to much (all the lncRNAs, for instance, add up to less thatn one percent of the genome) wd400

For decades, there has been considerable interest in determining what role, if any, the majority of the DNA in eukaryotic genomes plays in organismal development and physiology. The ENCODE data are only the most recent contribution to a long-standing research program that has sought to address this issue. However, evidence casting doubt that most of the human genome possesses a functional role has existed for some time. This is not to say that none of the nonprotein-coding majority of the genome is functional—examples of functional noncoding sequences have been known for more than half a century, and even the earliest proponents of “junk DNA” and “selfish DNA” predicted that further examples would be found. Nevertheless, they also pointed out that evolutionary considerations, information regarding genome size diversity, and knowledge about the origins and features of genomic components do not support the notion that all of the DNA must have a function by virtue of its mere existence. Nothing in the recent research or commentary on the subject has challenged these observations.

The old "there is no non-functional DNA" straw-man. Mung

Querius, I agree completely. We should refer to these regions as non-classical coding DNA. They may well code for something or have function that involves a "code" however we have not fully ellucidated this yet. The problem is that low-hanging fruit looks the most tempting - and it is too easy for people to use unknown function to advance their theory of life. Sadly you are correct, much is antithetical in neo-Darwinism. wd400: I am using a bit of simplistic hyperbole when I say 98% is junk because many pro-evolutionists (several on here) will still state 98% is junk. So there is disparity within naturalists regarding this. I know full well many people do not consider 98% to be junk and some recently posted articles I posted in other threads show publications where secular scientists make statements that we know now a lot of apparent "junk" DNA is not junk after all. These people however tend to be not evolutionary biologists so they do not need to rely on there being junk present and it doesn't bother their science as much thinking about the implications of much of non-coding DNA having function.

Selection can only work on genetic variance withing on generation. The ~20% less junk version will never exist if mutations only come in the 0.0001% chunks you yourself admit will make no difference. At the same time mutations increasing junk in tiny chunks are almost undetectable, so we have ratchet by which junk can accumulate.

Please read through my points about neutral evolution that I wrote in great simplification. Please think about random drift and neutral theory of evolution. You cannot say that something will not occur (deletion of useless DNA) when little advantage is gained when that is the arguing point of the greatest current advocates of naturalistic evolutionists. We are told that a random neutral mutation that confers no advantage can get fixed within the genome. Yet you are not affording the same possibility to a random neutral deletion. This is my point - you cannot have it one way and say it cannot work the other way. Especially given the amount of new information needed to be generated in evolution and apparently that just happens (de novo genes, etc). One of the greatest explanation for junk DNA being "ratched" into the genome as you say was pseudogenes. However time and time again we are finding function for these apparent pseudogenes. Therefore, the inference of non-coding DNA being left over from evolution is simply that - inference and assumptive. Our current trend of discovering roles for DNA implies that there is more function than we first attributed, not the other way around (despite the original estimates until about 15 years ago saying we should have a higher number of genes than we do). You make a very good point about genome size and selection pressure/population size. This is difficult to understand and certainly fits with the evolutionary mechanism to a degree as you describe. However many organisms much less complex than humans for example have more coding DNA (genes) than humans. The regulation is clearly different and this is something a bit difficult to understand for evolution to. Despite these seemingly odd large genome sizes (e.g. amoeba), I would still say it just shows how little we really know about DNA, genes, genetic coding and its complete function in an organisms lifecycle. I look forward to science that probes this further to try and interrogate why these genomes are so large, rather than simply assume it is a result of evolution (which it could well be - but the assumption I feel is dangerous). Thanks for the referenced article reviewing junk DNA. I will have a good read of it however it is likely to be very reactionary and biased against ENCODE's findings. These findings have quite annoyed evolutionary biologists it would seem. Taking all the current evidence from ENCODE, FANTOM, recent findings about pseudogene function and lncRNAs, I would say the overall evidence is pointing in a trend towards functionality for apparent non-coding DNA in more cases than we initially thought. I don't subscribe to the notion that ENCODE has proved there is no junk DNA. Nowhere have I said there cannot be junk DNA. I am simply saying we are seeing a trend towards identification of function where we previously did not see function and it would be wrong to assume junk when we are limited by our current understanding. Dr JDD

Dr JDD, Thanks for your cogent post in #64. This is also not in response to anything wd400 says. You wrote

What we should also consider, is that you can knock out plenty of proteins from mice and they look normal. That does not mean the protein is functionless. There are huge numbers of examples of this happening all the time. Therefore simply knocking out sections of non-coding DNA and seeing an apparent normal animal does not prove no function.

Then why not simply leave it at "non-coding DNA" rather than jumping to the conclusion that it's so much junk as Dr. Ohno did in his landmark paper? Proving something is "junk" is extremely difficult because you have to rule out all other possibilities: present, past, and in the case of "neutral" mutations, future. Jumping to unsupported conclusions might be common with Darwinism, but it's antithetical to the scientific method. -Q Querius

The irony- On one hand evos chide us for just giving up by reaching a design inference. Yet when it comes to alleged junk DNA it appears that they have just given up figuring out possible functions. However that is due to the limiting framework of their dogma. Joe

Does the guy who wrote a paper called "THe case for junk DNA" sound like an advocate for junk DNA? wd400

wd400: Of course “advocates for junk DNA do not claim all non-coding DNA is junk (and have never done so).” Gregory: Not only is “junk DNA” an inappropriate moniker for noncoding DNA in general...but it also has the unfortunate consequence of instilling a strong a priori assumption of total nonfunction. Does Gregory really sound like an advocate for junk DNA? Sounds to me like just the opposite. The quote is from Chapter 1 of the linked text, p. 30. Gregory is the editor of that volume, but also the author of chapter 1.

...dismissing it as no more than "junk" in the pejorative sense of "useless" or "wasteful" does little to advance the understanding of genome evolution. For this reason, the far less loaded term "noncoding DNA" is used throughout this chapter and is recommended in preference to "junk DNA" for future treatments of the subject. - p. 31

Mung

A somewhat neutral theory of junk DNA: Take a computer hard drive, for example. As you add data to it and delete data from it you can be left with segments that can be described as junk. How foolish is it to argue over the functionality of segments on a hard drive? Why is DNA so different from a hard drive? Mung

I presume so. Of course "advocates for junk DNA do not claim all non-coding DNA is junk (and have never done so)." wd400

wd400:

If you are “seriously looking for answers and open to truth”, you might want to do some research on the arguments for junk. here’s a place to start

Thank you for the link. Is that the same T. Ryan Gregory who wrote:

Not only is “junk DNA” an inappropriate moniker for noncoding DNA in general because of the minority status of pseudogenes within genome sequences, but it also has the unfortunate consequence of instilling a strong a priori assumption of total nonfunction.

Mung

Great writing, Dr. JDD. It is nice to have you here at UD. OldArmy94

You make several common mistakes here Given that apparently 98% of the genome is junk 98% of the genome is non-coding, advocates for junk DNA do not claim all non-coding DNA is junk (and have never done so). ... less chance of deleterious mutations (e.g. if the rate of mutation is 10e-8 then a genome of 10e10 will have more mutations than a genome of 10e8 by simple mathematics). Therefore this could be a small conferred advantage. If most of the genome is junk then the the total number of mutations doesn't make any difference - deleterious mutations can only fall in functional regions. Sure removing 0.0001% on one instance may not seem a advantage but what about the incremental deletion of that DNA to reach say, 20%? Selection can only work on genetic variance withing on generation. The ~20% less junk version will never exist if mutations only come in the 0.0001% chunks you yourself admit will make no difference. At the same time mutations increasing junk in tiny chunks are almost undetectable, so we have ratchet by which junk can accumulate. Interesting, the genomes of organisms with small population size (so weaker selection) are generally larger. And effect that fits with theory junk accumulates when the tiny differences in fitness an extra sequence might create can't be felt by selection. I think if you are seriously looking for answers and open to truth, then you will look at this problem of junk DNA and see how it does not quite make sense for it to be pure junk. ... That has been my argument here – my argument which some people have failed to understand is that junk DNA can be argued to not make much sense based on current evolutionary thinking and thinking about mutation events over vast periods of time. I'm afraid to make that argument you'd have to understand current evolutionary thinking more than you do. If you are "seriously looking for answers and open to truth", you might want to do some research on the arguments for junk. here's a place to start wd400

I am not replying to Evolve or AVS as we disagree on a fundamental point thus they instantly nullify contemplating my point, but if anyone is interested in some non-linear critical thinking around the subject, perhaps this will interest them, perhaps not. Over millions of years, we would accept that DNA will undergo various changes ("mutations") that can be favourable, or deleterious. The truth is, most are deleterious so they do not get passed on. However we also know that any change that is neutral, can (not will, but can) get passed on. Simply speaking, what changes can occur? Well we can have point mutations, we can have frameshift mutations (deletion or addition of a base changing the reading frame - usually very deleterious), you can have recombination, horizontal gene transfer, you can have whole new chunks of DNA, but you can also have the revervse of modifications that add (duplication, recombination, etc) -i.e. deletions of segments of DNA. Now back to the millions of years time frame. As most mutations are deleterious, you have to go through a lot to get advantage where the gene is likely to be passed on. In that time, you are likely then to get deletion events. These could be single bases, they could be chunks or sections of DNA. Given that apparently 98% of the genome is junk (in humans, as an example - the point is the vast majority), it is likely that such deletions will occur in those non-coding regions. Such a deletion event will at least be neutral (if junk DNA theory is correct) but could be argued to confer advantage. Why? Because there is slightly less to copy, less energy used, less chance of deleterious mutations (e.g. if the rate of mutation is 10e-8 then a genome of 10e10 will have more mutations than a genome of 10e8 by simple mathematics). Therefore this could be a small conferred advantage. Given the number of steps positive evolution (i.e. in coding DNA where you need to mutate one duplicated gene for example into a completely new functional gene) must make, and where each new mutation is likely to either have no benefit (neutral) or very very slight benefit, it is at least equally probable to get the deletion events I describe above, of redundant, junk DNA. Therefore, if we see completely novel proteins that are said to come from mutated genes of other protein's DNA or code in an incremental step-wise fashion, why do we not see the removal of unnecessary DNA in stepwise fashion? Sure removing 0.0001% on one instance may not seem a advantage but what about the incremental deletion of that DNA to reach say, 20%? That is 10x more DNA than there is gene That would definitely be an advantage given the points I raise - less cellular expenditure in copying upon replication and less chance of deleterious mutation. We see the cell tries to avoid mutation - this is why we see events such as proof-reading polymerases and also enzymes to repair DNA. Therefore you have to ask the question, when something so simple as mutation to remove/delete unnecessary DNA is more likely (as it applies to 98% of the genome, not 2% therefore has higher chance of occurring here) does not remove it, yet the mutations in the 2% of coding regions do apparently with incremental steps create novel functionality and protein folds, how is that logical? And why are people using the argument that "if it is not advantagious to reproduction or survival of an organism it won't happen" yet advocating their gurus who claim neutral evolution rules? That simply there is a conflict. I think if you are seriously looking for answers and open to truth, then you will look at this problem of junk DNA and see how it does not quite make sense for it to be pure junk. It would make more sense to have function. And what I say above, and in coming to that conclusion is INDEPENDENT of OOL belief. The consequences of that conclusion have ramifications around OOL, but not the consideration itself. That has been my argument here - my argument which some people have failed to understand is that junk DNA can be argued to not make much sense based on current evolutionary thinking and thinking about mutation events over vast periods of time. You cannot say that the cell can randomly duplicate genes, introduce whole new sections of DNA and that results in functionality yet deny the process of deleting DNA that has no use or function in a similar mechanistic fashion. That makes no sense, and is not the critical thinking scientists should employ. What we should also consider, is that you can knock out plenty of proteins from mice and they look normal. That does not mean the protein is functionless. There are huge numbers of examples of this happening all the time. Therefore simply knocking out sections of non-coding DNA and seeing an apparent normal animal does not prove no function. Given species potential for diversification, given many genes' involvements with stress responses and other non "normal" or essential functions, we cannot conclusively say that removing something and seeing nothing wrong means no function - scientists (especially mouse geneticists) quite readily accept this already. If scientists did not let dogma about things unproven (naturalism) guide them, then the question would always be "why is this here?" or "why does this happen?" etc. That is what science is about. Instead of trying to determine function, naturalists are too keen to attribute something they don't understand, that could lend support to their belief system as a result of that belief system that science loses. Yet time and time again, as we probe deeper and deeper into our understanding of the complex cell (which we are barely scratching the surface, clearly), what we see is that things are there for a reason, there is usually purpose of function. Therefore the natural (logical based on evidence) hypothesis of things we do not initially see function for, is to assume we just do not yet know or cannot yet detect function, but we should certainly invest time and resource looking as it it likely to contain function. ID trumps naturalism time in time out in contribution towards scientific thinking when it comes to such issues around function. Dr JDD

Nothing tricky about it: Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.- Dr Behe in 1997 Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A bornagain77

@bornagain Look man, can you tone down the rhetoric here, please? Last I checked, trying to prove a negative is tricky business. VunderGuy

actually Darwinism is ALWAYS about story telling and never about empirically demonstrating! "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro, molecular biologist, National Review, Sept. 16, 1996 bornagain77

////But they are in competition with other cells to divide as fast and efficiently as possible. He who out-replicates the other wins. Natural Selection and Survival of the Fittest and and all that bs./// Wrong. They are in competition with other SPECIES who share the same resources to SURVIVE and REPRODUCE, not to set the Olympic record for the fastest reproduction! ///NSF Study on Green Algae Finds Darwin Was Wrong About Competition//// Did you actually read the title of the NSF article, which says it all: "Study suggests survival may not always be about competition". Nobody ever said that survival is ALWAYS about competition. That's unrealistic; there IS cooperation, symbiosis, mutualism, commensalism etc between species. Species can co-evolve instead of competing with each other. We've known that for many decades. The NSF study gives us one more example of cooperation, that's it. Evolve

further note: Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome - Oct. 2009 Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. http://www.sciencemag.org/cgi/content/abstract/326/5950/289 3-D Structure Of Human Genome: Fractal Globule Architecture Packs Two Meters Of DNA Into Each Cell - Oct. 2009 Excerpt: the information density in the nucleus is trillions of times higher than on a computer chip -- while avoiding the knots and tangles that might interfere with the cell's ability to read its own genome. Moreover, the DNA can easily unfold and refold during gene activation, gene repression, and cell replication. http://www.sciencedaily.com/releases/2009/10/091008142957.htm Moreover, since 'form' is not reducible to DNA sequences anyway, then Darwinism in reality has nothing to say about what the genome size should be in the first place, whereas, from a design point of view, we should rightly expect genome sizes to vary within design constraints. Constraints that would obviously be imposed in trying to achieve a ‘optimal design’ in any particular life-form that was designed; a few examples of such constraints,,: "There is strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus - which effects the rate of cell growth and division. Furthermore, in mammals there is a negative correlation between genome size and rate of metabolism. Bats have very high metabolic rates and relatively small genomes. In birds, there is a negative correlation between C-value and resting metabolic rate. In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration." Jonathan Wells - The Myth Of Junk DNA - page 85 THE ALLOMETRIC RELATIONSHIP BETWEEN GENOME SIZE (C-VALUE) AND TOTAL METABOLIC ENERGY PER LIFESPAN, PER UNIT BODY MASS IN ANIMALS Excerpt: this show(s) that,,, the higher total life energy per unit body mass leads to smaller C-value. http://www.sustz.com/Proceeding09/Papers/Medical%20Biology%20Studies/A_ATANASOV.pdf Chromosomes' Big Picture: Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place - 2011 Excerpt: "Basically what this all means is that if the chromosome number of a species can be given, the relative sizes of all the chromosomes can instantly be known," Yu said. "Also, if you tell me the genome size in the chromosome base pair, I can tell you the base pair length of each chromosome." According to Yu, the most surprising finding is the extremely consistent distribution pattern of the chromosomes, a result from comparing the full sets of chromosomes -- called genomes -- of the 68 random eukaryotes. The team found that nearly every genome perfectly formed an S-curve of ascending chromosomal lengths when placed on a standardized X-Y axis. That meant the genome from a species of rice expressed the same pattern as the genome from a species of maize, sorghum, fruit fly, dog, chimpanzee, etc.,,,, "We could not believe this the first time the plot was generated," said Chengsong Zhu, research associate in agronomy. http://www.sciencedaily.com/releases/2011/07/110706113450.htm The 's-curve' (1/4 power scaling) generated in the preceding paper can be seen here: http://images.sciencedaily.com/2011/07/110706113450-large.jpg As well, at the 7:00 minute mark of this following video, we find that ‘genome length vs. mass’ also gives a enigmatic 1/4 power scaling on the plotted graph for a wide range of different creatures. Thus, once again, giving strong indication of a design constraint that was/is imposed, top down, on genome length, and which is inexplicable from the neo-Darwinian framework: 4-Dimensional Quarter Power Scaling In Biology – video http://www.metacafe.com/watch/5964041/ bornagain77

Yes wd400, we are well aware that Darwinian evolution is great at breaking things and producing junk: 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 “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/ The problem for you is not to demonstrate that Darwinism produces junk. That is a given! The problem for you is to explain/demonstrate why we find complexity that our best computer programers and engineers can't come close to imitating: "Complexity Brake" Defies Evolution - August 2012 Excerpt: "This is bad news. 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.",,, Even with shortcuts like averaging, "any possible technological advance is overwhelmed by the relentless growth of interactions among all components of the system," Koch said. "It is not feasible to understand evolved organisms by exhaustively cataloging all interactions in a comprehensive, bottom-up manner." He described the concept of the Complexity Brake:,,, "Allen and Greaves recently introduced the metaphor of a "complexity brake" for the observation that fields as diverse as neuroscience and cancer biology have proven resistant to facile predictions about imminent practical applications. Improved technologies for observing and probing biological systems has only led to discoveries of further levels of complexity that need to be dealt with. This process has not yet run its course. We are far away from understanding cell biology, genomes, or brains, and turning this understanding into practical knowledge.",,, Why can't we use the same principles that describe technological systems? Koch explained that in an airplane or computer, the parts are "purposefully built in such a manner to limit the interactions among the parts to a small number." The limited interactome of human-designed systems avoids the complexity brake. "None of this is true for nervous systems.",,, to read more go here: http://www.evolutionnews.org/2012/08/complexity_brak062961.html Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.html bornagain77

If anyone wants to consider the evidence for the prevalence of junk in the genomes of most large eukaryotes, there was a review paper on just this published today wd400

Mung @45 noted

Trade-off is a design term.

Exactly! Interestingly, in Genesis, the terms "good" and "very good" are used regarding creation, with one exception. But it never says "perfect. Dr JDD, Thank you for your great posts! They were very informative both in content and in what some of the embarrassingly desperate rhetorical responses reveals about the people who responded, as well as the dynamics of argumentation. Thanks for your patience, but we can all see how ideological contamination won't allow some people to appreciate the complexity of cellular processes, denigrating them in several ways. Evolve @ 53, You make an excellent demonstration on how your assumptions that the size of various genomes mean that they just gotta have alotta junk in them, and how this limits your imagination. How would you know that the Norway Spruce, various salamanders, and other living things with large genomes don't have a much greater ability to adapt, or a much greater ability to spawn new species, or were a true common ancestor to a wide range of species, or are the result of merging species, or something else? For all you know, the Norway Spruce can grow its own Christmas ornaments, candles and all. My point is that you don't know, and apparently wouldn't be interested in finding out, since you already have a made your conclusions. At least think about. -Q Querius

Evolve:

Cells are not in a race with themselves to divide as fast as possible or as efficiently as possible.

Well, duh. But they are in competition with other cells to divide as fast and efficiently as possible. He who out-replicates the other wins. Natural Selection and Survival of the Fittest and and all that bs. Or not. NSF Study on Green Algae Finds Darwin Was Wrong About Competition Mung

Dr JDD, you make me want to haul out my books on immunology! What a fascinating subject. kf, indeed! What we have in the cell is a manufacturing process. Wouldn't it be amazing if it were found to follow kanban principles, lo1! Weren't AVS or Evolve claiming that the cell isn't like a computer? hogwash. Wetware: A Computer in Every Living Cell Yes, that Dennis Bray. Mung

JDD, Cells are not in a race with themselves to divide as fast as possible or as efficiently as possible. As long as they can survive, metabolize and divide within the constraints of a given environment, cells wouldn't care how efficient those processes are. You're wrongly thinking that cellular processes are super-efficient. That's not the case. A good example of an inefficient process operating within the cell is pervasive transcription, which produces lots of RNA noise: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1000625 You're constantly failing to realize that regardless of the efficiency of the process, unless it is detrimental to the survival of the cell, natural selection won't be able to "see" it and get rid of it from the population. The cost associated with replicating excess DNA does not prevent the cell's metabolism or division. So it is "invisible" to natural selection. Thus it persists. This explains a lot of observations. We can delete large chunks from a mammalian genome and have a fully normal animal (see the Nature paper I quoted above). How's that possible if there's no such thing as junk DNA? We've species with gigantic genomes that won't make any sense unless most of their genome is junk. The Norway Spruce Christmas tree has a genome that's six times larger than a human's: http://www.huffingtonpost.com/2012/12/13/christmas-tree-genome-new-dna-study-conifers_n_2294265.html Various salamander species also have huge genomes, much larger than yours or mine: http://www.biology.colostate.edu/seminars/making-it-big-extreme-genome-sizes-in-salamanders/ But all this is dwarfed by the genome of a Japanese plant: http://www.sciencedaily.com/releases/2010/10/101007120641.htm Will you argue that, since there's no junk DNA, Christmas trees, plants and salamanders are more complex than humans? Evolve

Mung: Long time since I heard that word! Notice, the use of localised info -- codes! -- to control logistics flows and reduce inventory leading to lean manufacturing. KF kairosfocus

l decided to do a quick search and in 30 sec found a paper addressing this very issue AVS: http://m.jasn.asnjournals.org/content/17/7/1807.full note how they say "might seem wasteful but..." I will say it again, my initial point was that naturalists claim IDists limit scientific advance but by claiming something is likely to have function advances science more than the naturalist view that it is just the wastefulness of evolution. Dr JDD

Typing on phone so autocorrect - "nene fit" should be benefit. Dr JDD

Evolve I am not missing the point. You are. Let me rephrase it another way that you might understand it: Cellular energy and expendency is either linked to survival and reproduction or not. I am claiming it is - that we see generally a non-wasteful cell. It takes a lot of energy to copy a huge genome and when 98% is unnecessary, cutting that to 2% would be favourable to the cell as it could divide quicker thus favourable reproducibility trait. You happily admit that new genes can for by large reshuffling, duplications, extra fusions through chance with nene fit, yet you cannot envisage in that huge time period similar loss of non coding regions? If you cannot see how that could happen yet genes arise from seemingly nowhere, then you are more blind in your naturalistic religion than I thought. I will repeat what I said before - the junk in the garage is a poor analogy as you don't regularly remove and replace, or duplicate your garage. A cell does this lots. Perhaps extend your garage analogy then. What if you had to add new things to your garage - would you make it bigger or just remove the junk? Which requires more energy? That analogy is no worse than yours. Dr JDD

I am not too sure why i am bothering with someone who cannot grasp what i am saying, but anyway, what I actually said: "There is good evidence many RNA transcripts are rapidly translated and turned over..." I was saying it in that way to emphasise I am talking about the fact en a transcripts are rapidly translated (to proteins) and then degraded by the proteosome for a functional reason yet you claim i am making assertions about how efficient proteosomal degradation is. I am not. As you clearly cannot grasp simple science let me break it down for you: You say the cell is wasteful because it makes proteins that it simply degrades straight away. I say actually, there is purpose in making a protein to be directly degraded (eg for HLA presentation) therefore your claim that it is inefficient for the cell to make protein to just degrade is invalid. i then conclude that just because the cell does something that appears to be inefficient because we cannot understand function does not mean it is - it is just not currently understood why the cell does that. You then conclude I don't know what processes degrade proteins (laughable as I have published in several high impact peer-reviewed journals on the subject) and that i am speaking to how efficient the degradation system is. I am not. Anyone with half a brain can see i was a dressing cellular purpose and efficiency in why the cell might translate rna to simply degrade that protein product. " Dr JDD

Kanban Mung

AVS:

I am not saying that the degradation system itself is inefficient. I am saying that the overactivity of the degradation system produces inefficiency because it degrades proteins that should not be degraded. Yes the proteasome serves an important function in the immune system, but it also destroys correctly folded proteins that the cell just spent a good deal of energy synthesizing. This is a waste of energy = inefficiency.

How do you know that it degrades proteins that should not be degraded? How do you know that this is a waste of energy? Mung

"That it’s not perfect, it doesn’t have a direction, and that there are trade-offs." Trade-off is a design term. Mung

A Darwinist claimed in this post,,, "Nothing is 100% efficient in the cell" Yet: Thermodynamic efficiency and mechanochemical coupling of F1-ATPase - 2011 Excerpt:F1-ATPase is a nanosized biological energy transducer working as part of FoF1-ATP synthase. Its rotary machinery transduces energy between chemical free energy and mechanical work and plays a central role in the cellular energy transduction by synthesizing most ATP in virtually all organisms.,, Our results suggested a 100% free-energy transduction efficiency and a tight mechanochemical coupling of F1-ATPase. http://www.pnas.org/content/early/2011/10/12/1106787108.short?rss=1 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 bornagain77

Now if only your position could account for DNA in the first place... Joe

See this Nature paper where they deleted 2.3 mb of DNA from a mouse's genome. And that didn't affect its viability! Megabase deletions of gene deserts result in viable mice. Abstract The functional importance of the roughly 98% of mammalian genomes not corresponding to protein coding sequences remains largely undetermined1. Here we show that some large-scale deletions of the non-coding DNA referred to as gene deserts2, 3, 4 can be well tolerated by an organism. We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome. Viable mice homozygous for the deletions were generated and were indistinguishable from wild-type littermates with regard to morphology, reproductive fitness, growth, longevity and a variety of parameters assaying general homeostasis. Further detailed analysis of the expression of multiple genes bracketing the deletions revealed only minor expression differences in homozygous deletion and wild-type mice. Together, the two deleted segments harbour 1,243 non-coding sequences conserved between humans and rodents (more than 100 base pairs, 70% identity). Some of the deleted sequences might encode for functions unidentified in our screen; nonetheless, these studies further support the existence of potentially ‘disposable DNA’ in the genomes of mammals. http://www.nature.com/nature/journal/v431/n7011/full/nature03022.html Evolve

DJDD, ///Evolve that is a poor example. Garages do not replicate. Replication requires energy and if 98% is unnecessary that is hugely inefficient for replication. I do not accept that as a good explanation and completely stand by what I said. We are to believe evolution can produce incredibly complex machineries like the 150+ protein complex spliceosome but just ignores the 98% of the genome of no use to it does not seem rational at all to a scientific mind./// It's not a poor example. You're failing to grasp the point that anything that doesn't affect the survival and reproduction of the cell will be ignored by selection and won't be weeded out. So while the cell may have to spend a bit more energy to replicate junk DNA, as long as that extra energy doesn't affect the cell's energy budget, it won't care. Evolve

"I said it degrades rna transcripts that had been translated." That's like saying "I drove my four wheels and a motor that has been assembled by Honda, to their house" AVS

"I did not say it degrades rna transcripts I said it degrades rna transcripts" Right. If you had knew what you were talking about you would have said it "degrades nascent polypeptide strands." You are completely missing my point. I am not saying that the degradation system itself is inefficient. I am saying that the overactivity of the degradation system produces inefficiency because it degrades proteins that should not be degraded. Yes the proteasome serves an important function in the immune system, but it also destroys correctly folded proteins that the cell just spent a good deal of energy synthesizing. This is a waste of energy = inefficiency. AVS

AVS please read what I said. I did not say it degrades rna transcripts I said it degrades rna transcripts that had been translated. And to be properly processed into the correct nonamers or octamers or decamers or whatever nmer the peptide is it likely has to be translated to a fully functional protein otherwise you might get peptides the thymus didn't display to T-cells and the immune system would see that cell as non-self and kill it. I just gave one example of why it may not be inefficient and again I stand by that example as a good, necessary example to balance recognising self and non-self by the immune system. My point remains - you see wastefulness where I see unknown function as yet. Which advances a investment more? That is my point with supposed junk DNA. It is also my point about the evolutionary outlook. In fact, as we advance our understanding I see in science that we show more and more function where it was previously assumed non-function. These processes simply add to that story. That is the trend we are observing therefore the rational extension is that where we have unknown function, we are most likely to expect it is simply unknown as of yet rather than no function and wasteful evolutionary processes. I get your resistance to that thinking though as accepting that puts a dent in the evidence an evolutionist likes to use. So i naturally expect such resistance from you over this point. Dr JDD

Yes, JDD, obviously there is a function for protein degradation. But the fact that this machinery often ends up degrading proteins that have just been correctly and fully synthesized by the cell, is an example of inefficiency. And the fact that this is continuously happening in trillions of cells many times per minute in each cell adds up to a large degree of inefficiency. Also, the proteasome does not degrade RNA transcripts as you said, that would be the various nucleases within the cell. AVS

Evolve that is a poor example. Garages do not replicate. Replication requires energy and if 98% is unnecessary that is hugely inefficient for replication. I do not accept that as a good explanation and completely stand by what I said. We are to believe evolution can produce incredibly complex machineries like the 150+ protein complex spliceosome but just ignores the 98% of the genome of no use to it does not seem rational at all to a scientific mind. Dr JDD

Yes Evolve, unguided evolution is good at breaking things and collecting junk. Too bad it cannot account for DNA in the first place. Joe

AVS:

At the nanoscale level these processes can approach 100% efficiency much more easily than at the macroscopic.

Ah, that's why we humans go on building inefficient macroscopic machines, and do not build cells. We like challenges, and we are bored of simple things! Now I understand. gpuccio

Dr.JDD ///I would be interested to hear a rational explanation for junk DNA remaining in such vast quantities within the genome by a naturalist. I have yet to hear a convincing argument./// You're not thinking enough. Cells will accumulate junk DNA as long as they have little to no deleterious effect on the ability to survive and reproduce. Such DNA is essentially invisible to selection. So they'll persist. One can draw an analogy to the junk accumulating in your garage. You may ignore it for years because it doesn't affect your day-to-day life in any significant manner. Evolve

The changes that are made are undirected, the changes that increase efficiency are kept in successive generations. Changes that increase efficiency would include perfectly functional proteins that have been synthesized. They why is this process not kept in successive generations? You noted earlier that it's one of the things that are problematic for cell biology. It is still illogical to believe that an undirected process will cause change for the better. Because obviously it's not doing that. Barb

AVS - perhaps you are assuming inefficiency with again, misunderstanding a process. Perhaps I suggest, not definite. I am merely saying consider it. Many of the cellular machines we find hard to point to inefficiencies. Often where we see inefficiency we just don't understand. Take for example, the fish movement has recently been shown by engineers to rewrite our understanding of optimal speed, direction and manoeuvrability. Prior to this, it seemed inefficient. You quote making proteins to simply just degrade it off the top of your head. Have you considered there is purpose to this? Have you considered the immune system, which we barely understand (I think I have the right to say that as an Immunologist) has a purpose for this? Our body relies on presenting short peptide fragments on HLA molecules (MHC complex) to recognise as self. This is important in both evading foreign infection but also in things like avoiding cancer. There is good evidence many RNA transcripts are rapidly translated and turned over (degraded by the proteasome etc) to have peptides presented on the cell surface as a role in adaptive immunity. Again, to prove my point - you take a process, assume it has no function as you don't see function, so attribute it to wasteful evolution. Therefore the possibility there is function is ignored to advance your favoured OOL theory and once again, science does not progress. Yet the irony is you claim IDists hinder progress in science! Again I emphasise. Irony. JD Dr JDD

The fact that you think removing 50% of an organism's genome and it not being able to function, "falsifies evolution" tells us quite a bit about how you understand and perceive science phoo. AVS

JLAfan2001, What does slight or medium function mean? Now you want to have an out by saying whilst we may find purpose to more of the genome, you can claim its not an important function? Ok then, simple, lets try removing 50% of any organisms genome, and see if it can still function at all. If it can't will you agree that Darwinian evolution has been falsified? phoodoo

The changes that are made are undirected, the changes that increase efficiency are kept in successive generations. This is the simplest form of evolution. The fact that I have to explain this to you is telling. Although not surprising. AVS

How can something be efficient, or work towards better efficiency if it's undirected? That is entirely illogical. That you refuse to acknowledge this point is telling. Barb

That it's not perfect, it doesn't have a direction, and that there are trade-offs Barb, did you have a point? AVS

degradation of perfectly functional proteins that have just been synthesized What does this say about the efficiency of evolution? Barb

There is nothing in the cell that "we struggle to say it is even less than 100% efficient as a machine." Nothing is 100% efficient in the cell, there is always energy lost. At the nanoscale level these processes can approach 100% efficiency much more easily than at the macroscopic. There are also many examples of the cell being quite inefficient and wasting a good deal of energy, abortive transcripts and degradation of perfectly functional proteins that have just been synthesized are a couple off the top of my head. AVS

Very well said Dr JDD bornagain77

I would be interested to hear a rational explanation for junk DNA remaining in such vast quantities within the genome by a naturalist. I have yet to hear a convincing argument. When we consider our current state of understanding complex proteinacious molecular machineries made up of in some cases, even > 100 components what we find is incredible efficiency so much so that we struggle to say it is even less than 100% efficient as a machine. Even a single protein enzyme can have incredible complex tertiary and quaternary structures and have the appearance of perfect efficiency. We used to see different isoforms of a protein where one seemed more or very important for function of the cell or a process within the cell but an isoform appeared "redundant". However in time, function was determined and it often had a very unique or tissue specific role which is why the elucidation of the role was not as straightforward. Therefore, one thing we seem to learn about the cell is incredible efficiency - energy is not generally wasted in unnecessary processes. As whenever evolutionists are confronted with such findings, they merely state how incredibly efficient evolution is in finding the best route to achieve such high efficiency, it seems at conflict or rather even against much apparent evolutionary evidence to say that 98% of the genome is junk and the wastelands of evolution. If there is no function, the cell is incredibly wasteful in having so much DNA that it must replicate with each division. That goes against every other understood processes in the cell. It is hugely inefficient and expends unnecessary energy. One would predict evolution should expelled junk regions of DNA as a result. However I feel the low hanging fruit was too tempting to those wishing to easily use unexplainable presence of apparent information, as the wasteful product of evolution as this was an easy rebuttal to a design hypothesis. Given what we know about how efficient the cell is, regardless of your OOL view, I would say the most sensible view of "non-coding" DNA is to expect functionality of some type. The issue with that approach however is it lends more to a designer hypothesis than a random one. It is sad when this bias limits scientific understanding and advancement, but this is an emerging case as such. JD Dr JDD

phoodoo I would guess greater than 50% or 60% functional not 19%. I'm talking actual function not "slight or medium or a hint or possibly" but actual "it does somthing important" functional. JLAfan2001

JLAfan2001, How much? What percentage supports the theory of evolution, and what % is evidence against it? I can understand you reluctance to answer the question, but your dodging is evidence itself of the emptiness of your theory. phoodoo

Graur is right in this respect: ““I believe science is a search for the truth, not a lesson in manners…” However, if scientific truth shows that most of DNA is functional, then what? Do the Darwinists revise their hypothesis (which is how science should work) or do they claim that Darwinian evolution predicted this all along? I find it telling that I quoted a scientist who decried ideology driving science, and yet no Darwinist posting on this blog acknowledges that point. Susumu Ohno is credited with coining the term “junk DNA” in his paper So Much ‘Junk’ DNA in Our Genome. He wrote that the remaining sequences of DNA “are the remains of nature’s experiments which failed. The earth is strewn with fossil remains of extinct species; is it a wonder that our genome too is filled with the remains of extinct genes?” This affected the subsequent study of genetics. Molecular biologist Wojciech Makalowski says that such thinking “repelled mainstream researchers from studying noncoding [junk] DNA,” with the exception of a small number of scientists, who, “at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA . . . began to change in the early 1990s.” Now, he adds, biologists generally regard what was called junk “as a genomic treasure.” [“Not Junk After All,” Science, Vol. 300(5623): (May 23, 2003).] The junk DNA analysis is a classic example of scientific tradition ignoring—or derailing—objective analysis of the facts. The latter would, of course, lead to the truth, as Graur points out. This isn’t just a little mistake, either. Truth in science should be determined on the basis of evidence, not by popular vote. Barb

JLAfan2001: OK, but the ENCODE data still show activity for 80% of DNA. Nothing has changed. We will see how much of that is confirmed as functional in independent ways. Science must be patient. gpuccio

gpuccio 19% functional is long cry from 80%. JLAfan2001

My question to Darwinists is if DNA is mostly non-functional, how in blue blazes did it know about reversible computation? Also of interest is that the integrated coding between the DNA, RNA and Proteins of the cell apparently seem to be ingeniously programmed along the very stringent guidelines laid out by Landauer’s principle, by Charles Bennett from IBM of Quantum Teleportation fame, for ‘reversible computation’ in order to achieve such amazing energy/metabolic efficiency. Logical Reversibility of Computation* - C. H. Bennett - 1973 Excerpt from last paragraph: The biosynthesis and biodegradation of messenger RNA may be viewed as convenient examples of logically reversible and irreversible computation, respectively. Messenger RNA. a linear polymeric informational macromolecule like DNA, carries the genetic information from one or more genes of a DNA molecule. and serves to direct the synthesis of the proteins encoded by those genes. Messenger RNA is synthesized by the enzyme RNA polymerase in the presence of a double-stranded DNA molecule and a supply of RNA monomers (the four nucleotide pyrophosphates ATP, GTP, CTP, and UTP) [7]. The enzyme attaches to a specific site on the DNA molecule and moves along, sequentially incorporating the RNA monomers into a single-stranded RNA molecule whose nucleotide sequence exactly matches that of the DNA. The pyrophosphate groups are released into the surrounding solution as free pyrophosphate molecules. The enzyme may thus be compared to a simple tape-copying Turing machine that manufactures its output tape rather than merely writing on it. Tape copying is a logically reversible operation. and RNA polymerase is both thermodynamically and logically reversible.,,, http://www.cs.princeton.edu/courses/archive/fall04/cos576/papers/bennett73.html Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett - September 2003 Excerpt: Of course, in practice, almost all data processing is done on macroscopic apparatus, dissipating macroscopic amounts of energy far in excess of what would be required by Landauer’s principle. Nevertheless, some stages of biomolecular information processing, such as transcription of DNA to RNA, appear to be accomplished by chemical reactions that are reversible not only in principle but in practice.,,,, http://www.sciencedirect.com/science/article/pii/S135521980300039X Logically and Physically Reversible Natural Computing: A Tutorial - 2013 Excerpt: This year marks the 40th anniversary of Charles Bennett’s seminal paper on reversible computing. Bennett’s contribution is remembered as one of the first to demonstrate how any deterministic computation can be simulated by a logically reversible Turing machine. Perhaps less remembered is that the same paper suggests the use of nucleic acids to realise physical reversibility. In context, Bennett’s foresight predates Leonard Adleman’s famous experiments to solve instances of the Hamiltonian path problem using strands of DNA — a landmark date for the field of natural computing — by more than twenty years. http://link.springer.com/chapter/10.1007%2F978-3-642-38986-3_20 The amazing energy efficiency possible with ‘reversible computation’ has been known about since Charles Bennett laid out the principles for such reversible programming in 1973, but as far as I know, due to the extreme level of complexity involved in achieving such ingenious ‘reversible coding’, has yet to be accomplished in any meaningful way for our computer programs even to this day: Reversible computing Excerpt: Reversible computing is a model of computing where the computational process to some extent is reversible, i.e., time-invertible.,,, Although achieving this goal presents a significant challenge for the design, manufacturing, and characterization of ultra-precise new physical mechanisms for computing, there is at present no fundamental reason to think that this goal cannot eventually be accomplished, allowing us to someday build computers that generate much less than 1 bit's worth of physical entropy (and dissipate much less than kT ln 2 energy to heat) for each useful logical operation that they carry out internally. http://en.wikipedia.org/wiki/Reversible_computing#The_reversibility_of_physics_and_reversible_computing bornagain77

OldArmy94, JLAfan2001: Flames everywhere! :) I hope we can go on discussing, before everything burns. gpuccio

See Fig. 1, here: http://www.pnas.org/content/111/17/6131/F1.expansion.html gpuccio

JLAfan2001: The last ENCODE paper gives as most likely functional about 20% of the whole genome, based on either evolutionary evidence (conservation) or genetic evidence (relationship to phenotype) or biochemical evidence (high level of activity according to ENCODE). Considering that some (but not all) of that 20% are protein coding genes (let's say about 1%), that still leaves at least 19% of the genome which is non coding and almost certainly functional. There is another 30-40% of the genome which has medium level of activity according to ENCODE, and another part which has low level of activity. Summing all three levels of activity in ENCODE. we get more or less the famous 80%. So, let's say that at least 19% of non coding genome is almost certainly functional. That percentage can only grow. gpuccio

I can't wait until Encode comes back and says "Sorry, DNA is junk after all." I am stocking up on my beer and nachos to watch the ship going down in flames that is ID. JLAfan2001

JLAFan, ///In fact it’s what we would expect with ID. It can’t be falsified./// Their designer is capable of anything, never underestimate him! No junk DNA? That's exactly what ID predicts - our great omnipotent designer will never make a bad design. If it is there, it has to have a function. Full of junk DNA? No problem, that's how the designer did it. After all, bad design doesn't mean no design, you see! Evolve

Anyone who thinks that DNA is mostly junk is not dealing with a full deck Ah, but the average Darwinian has a wonderfully flexible deck can use for the game; one card or 52, it doesn't matter as long as they can rewrite the rules per their whims. OldArmy94

Here is another ‘horrendously complex’ metabolic pathway chart: Map Of Major Metabolic Pathways In A Cell - Diagram http://www.sigmaaldrich.com/img/assets/4202/MetabolicPathways_6_17_04_.pdf Part of the ‘horrendous complexity’ inherent in metabolic pathways is gone over here: The 10 Step Glycolysis Pathway In ATP Production: An Overview – video http://www.youtube.com/watch?v=8Kn6BVGqKd8 At the 14:00 minute mark of the following video, Chris Ashcraft, PhD – molecular biology, gives us an overview of the Citric Acid Cycle, which is, after the 10 step Glycolysis Pathway, also involved in ATP production: Evolution vs ATP Synthase – Chris Ashcraft - video - citric acid cycle at 14:00 minute mark https://www.youtube.com/watch?feature=player_detailpage&v=rUV4CSs0HzI#t=746 The Citric Acid Cycle: An Overview - video http://www.youtube.com/watch?v=F6vQKrRjQcQ Glycolysis and the Citric Acid Cycle: The Control of Proteins and Pathways - Cornelius Hunter - July 2011 http://darwins-god.blogspot.com/2011/07/glycolysis-and-citric-acid-cycle.html Moreover, Metabolic pathways are found to be 'optimal' Optimal Design of Metabolism - Dr. Fazale Rana - July 2012 Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition. http://www.reasons.org/articles/the-optimal-design-of-metabolism Moreover, as if that were not ‘horrendously’ bad enough for Darwinists, metabolic pathways are found to operate on ‘Quarter Power Scaling’. i.e. Metabolic Pathways operate as if they were ‘four-dimensional’ Kleiber’s law Excerpt: Kleiber’s law,[1] named after Max Kleiber’s biological work in the early 1930s, is the observation that, for the vast majority of animals, an animal’s metabolic rate scales to the 3/4 power of the animal’s mass. http://en.wikipedia.org/wiki/Kleiber%27s_law 4-Dimensional 'Quarter Power Scaling' In Biology – video http://www.metacafe.com/w/5964041/ The predominance of quarter-power (4-D) scaling in biology Excerpt: Many fundamental characteristics of organisms scale with body size as power laws of the form: Y = Yo M^b, where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent. A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling. per nceas Jerry Fodor and Massimo Piatelli-Palmarini put the problem that Quarter Power Scaling presents to Darwinism this way: “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 i.e. The reason why ’4-Dimensional’ metabolic pathways are impossible for Darwinism to explain is that Natural Selection operates on the 3-Dimensional phenotypes of an organism. ’4-Dimensional’ metabolic pathways are simply ‘invisible’ to natural selection. The fact that 4-Dimensional things are completely invisible to 3-Dimensional things is best illustrated by ‘flatland’: Flatland – 3D to 4D shift – Carl Sagan – video http://www.youtube.com/watch?v=UnURElCzGc0 bornagain77

Here is another ‘horrendously complex’ metabolic pathway chart: Map Of Major Metabolic Pathways In A Cell - Diagram http://www.sigmaaldrich.com/img/assets/4202/MetabolicPathways_6_17_04_.pdf Part of the ‘horrendous complexity’ inherent in metabolic pathways is gone over here: The 10 Step Glycolysis Pathway In ATP Production: An Overview – video http://www.youtube.com/watch?v=8Kn6BVGqKd8 At the 14:00 minute mark of the following video, Chris Ashcraft, PhD – molecular biology, gives us an overview of the Citric Acid Cycle, which is, after the 10 step Glycolysis Pathway, also involved in ATP production: Evolution vs ATP Synthase – Chris Ashcraft - video - citric acid cycle at 14:00 minute mark https://www.youtube.com/watch?feature=player_detailpage&v=rUV4CSs0HzI#t=746 The Citric Acid Cycle: An Overview - video http://www.youtube.com/watch?v=F6vQKrRjQcQ Glycolysis and the Citric Acid Cycle: The Control of Proteins and Pathways - Cornelius Hunter - July 2011 http://darwins-god.blogspot.com/2011/07/glycolysis-and-citric-acid-cycle.html Moreover, Metabolic pathways are found to be 'optimal' Optimal Design of Metabolism - Dr. Fazale Rana - July 2012 Excerpt: A new study further highlights the optimality of the cell’s metabolic systems. Using the multi-dimension optimization theory, researchers evaluated the performance of the metabolic systems of several different bacteria. The data generated by monitoring the flux (movement) of compounds through metabolic pathways (like the movement of cars along the roadways) allowed researchers to assess the behavior of cellular metabolism. They determined that metabolism functions optimally for a system that seeks to accomplish multiple objectives. It looks as if the cell’s metabolism is optimized to operate under a single set of conditions. At the same time, it can perform optimally with relatively small adjustments to the metabolic operations when the cell experiences a change in condition. http://www.reasons.org/articles/the-optimal-design-of-metabolism Moreover, as if that were not ‘horrendously’ bad enough for Darwinists, metabolic pathways are found to operate on ‘Quarter Power Scaling’. i.e. Metabolic Pathways operate as if they were ‘four-dimensional’ Kleiber’s law Excerpt: Kleiber’s law,[1] named after Max Kleiber’s biological work in the early 1930s, is the observation that, for the vast majority of animals, an animal’s metabolic rate scales to the 3/4 power of the animal’s mass. http://en.wikipedia.org/wiki/Kleiber%27s_law 4-Dimensional 'Quarter Power Scaling' In Biology – video http://www.metacafe.com/w/5964041/ The predominance of quarter-power (4-D) scaling in biology Excerpt: Many fundamental characteristics of organisms scale with body size as power laws of the form: Y = Yo M^b, where Y is some characteristic such as metabolic rate, stride length or life span, Yo is a normalization constant, M is body mass and b is the allometric scaling exponent. A longstanding puzzle in biology is why the exponent b is usually some simple multiple of 1/4 (4-Dimensional scaling) rather than a multiple of 1/3, as would be expected from Euclidean (3-Dimensional) scaling. http://www.nceas.ucsb.edu/~drewa/pubs/savage_v_2004_f18_257.pdf Jerry Fodor and Massimo Piatelli-Palmarini put the problem that Quarter Power Scaling presents to Darwinism this way: “Although living things occupy a three-dimensional space, their internal physiology and anatomy operate as if they were four-dimensional. Quarter-power scaling laws are perhaps as universal and as uniquely biological as the biochemical pathways of metabolism, the structure and function of the genetic code and the process of natural selection.,,, The conclusion here is inescapable, that the driving force for these invariant scaling laws cannot have been natural selection.” Jerry Fodor and Massimo Piatelli-Palmarini, What Darwin Got Wrong (London: Profile Books, 2010), p. 78-79 i.e. The reason why ’4-Dimensional’ metabolic pathways are impossible for Darwinism to explain is that Natural Selection operates on the 3-Dimensional phenotypes of an organism. ’4-Dimensional’ metabolic pathways are simply ‘invisible’ to natural selection. The fact that 4-Dimensional things are completely invisible to 3-Dimensional things is best illustrated by ‘flatland’: Flatland – 3D to 4D shift – Carl Sagan – video http://www.youtube.com/watch?v=UnURElCzGc0 bornagain77

Keep on fiddling JLAFan. Your paradigm is aflame, friend. OldArmy94

Anyone who thinks that DNA is mostly junk is not dealing with a full deck: Demonstrating, Once Again, the Fantastic Information-Storage Capacity of DNA - January 29, 2013 Excerpt: Gigabytes have become commonplace, and now we're warming up to terabytes. Ready for petabytes? That's a thousand terabytes and a million gigabytes. It's the new lingo that will migrate from geek to street, if DNA hard drives become a reality.,,, Last year, researchers led by bioengineers Sriram Kosuri and George Church of Harvard Medical School reported that they stored a copy of one of Church's books in DNA, among other things, at a density of about 700 terabits per gram, more than six orders of magnitude more dense than conventional data storage on a computer hard disk. Now, researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, UK, report online today in Nature that they've improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.,,, This is truly a profound achievement of human intelligent design. Why wouldn't the same be true of natural DNA? ,,, There's far more information in our DNA than the UK team embedded in theirs -- layers and layers of coding that regulate gene expression and respond interactively to signals in a vast network of complex feedback loops. It's a whole system of information. To clinch the comparison, natural DNA also has elaborate error correction, proofreading and repair systems that can copy all that information with extremely high fidelity. As the Shakespearean sonnets in DNA point to intelligent design, the functional information in natural DNA points to intelligent design. It would be foolish to ascribe the superior information to blind, unguided processes. http://www.evolutionnews.org/2013/01/how_do_you_peta068641.html Bioinformatics: The Information in Life - Donald Johnson - video http://vimeo.com/11314902 On a slide in the preceding video, entitled 'Information Systems In Life', Dr. Johnson points out that: * the genetic system is a pre-existing operating system; * the specific genetic program (genome) is an application; * the native language has codon-based encryption system; * the codes are read by enzyme computers with their own operating system; * each enzyme’s output is to another operating system in a ribosome; * codes are decrypted and output to tRNA computers; * each codon-specified amino acid is transported to a protein construction site; and * in each cell, there are multiple operating systems, multiple programming languages, encoding/decoding hardware and software, specialized communications systems, error detection/correction systems, specialized input/output for organelle control and feedback, and a variety of specialized “devices” to accomplish the tasks of life. Cells Are Like Robust Computational Systems, - June 2009 Excerpt: Gene regulatory networks in cell nuclei are similar to cloud computing networks, such as Google or Yahoo!, researchers report today in the online journal Molecular Systems Biology. The similarity is that each system keeps working despite the failure of individual components, whether they are master genes or computer processors. ,,,,"We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail." http://www.sciencedaily.com/releases/2009/06/090616103205.htm Systems biology: Untangling the protein web - July 2009 Excerpt: Vidal thinks that technological improvements — especially in nanotechnology, to generate more data, and microscopy, to explore interaction inside cells, along with increased computer power — are required to push systems biology forward. "Combine all this and you can start to think that maybe some of the information flow can be captured," he says. But when it comes to figuring out the best way to explore information flow in cells, Tyers jokes that it is like comparing different degrees of infinity. "The interesting point coming out of all these studies is how complex these systems are — the different feedback loops and how they cross-regulate each other and adapt to perturbations are only just becoming apparent," he says. "The simple pathway models are a gross oversimplification of what is actually happening." http://www.nature.com/nature/journal/v460/n7253/full/460415a.html ExPASy - Biochemical Pathways - interactive schematic http://web.expasy.org/cgi-bin/pathways/show_thumbnails.pl I showed that particular biochemical pathway chart to a Darwinist once when he asked me for ANY evidence of intelligent design in biology. His response upon seeing it was something along the lines of, ‘Just because it is horrendously complex does not prove it was designed.’. ,,, Well maybe so, but such ‘horrendous complexity’ certainly does not give comfort to the notion that such ‘horrendous complexity’ can be the accumulation of random genetic accidents either! bornagain77

Barb Read the OP. Encode has recanted the 80% claim. It seems to me that this claim has to be re-evaluated. JLAfan2001

JLAfan2001, How much junk does Darwinian evolution predict? Is it any number from 1-99.99% What number refutes its prediction? Or do you just enjoy the privilege of allowing Darwinian evolution to be the most malleable, and undefined theory in the history of theories? phoodoo

JLAfan2001:

It seems to me that one of ID’s predictions is starting to crumble. You were all celebrating this finding and now it’s beginning to look like the “80%” claim wasn’t as accurate as you all thought.

As you can tell from my post, initially it was thought that 98% of human DNA was junk. ENCODE initially thought it might be closer to 80%. That's one of ID's predictions coming true.

Now, you have to back track and use some propaganda news pieces to save face.

Much like Darwinists do all the time.

I predict once Encode comes back and says that there is junk DNA after all, the IDist will try to say that the finding doesn’t refute ID at all. In fact it’s what we would expect with ID. It cna’t be falsified.

There probably is junk DNA, but not 98% of the human DNA is junk. Read my post and tell me why the scientist quoted is wrong when he describes ideology driving Darwinian evolution. And ID can be falsified. Read the FAQ sometime. But quit spewing nonsense. It's getting boring.

The good thing about ID is that it drives real science so that they can be proven wrong. Keep up the pseudoscience guys. Refuting you is how we are learning.

Yawn. Boring atheist troll is boring. Barb

It seems to me that one of ID's predictions is starting to crumble. You were all celebrating this finding and now it's beginning to look like the "80%" claim wasn't as accurate as you all thought. Now, you have to back track and use some propaganda news pieces to save face. I predict once Encode comes back and says that there is junk DNA after all, the IDist will try to say that the finding doesn't refute ID at all. In fact it's what we would expect with ID. It cna't be falsified. The good thing about ID is that it drives real science so that they can be proven wrong. Keep up the pseudoscience guys. Refuting you is how we are learning. JLAfan2001

Evolutionary theory has led other researchers to false conclusions. Look at the concept of "vestigial organs"; early Darwinists classified certain organs, such as the appendix, the pituitary gland, and the tonsils, as vestigial. They considered them to be evolutionary leftovers because these organs seemed no longer to have any function. In time, however, the important role of these organs came to light. Evolutionists, therefore, had to discard their earlier views. A similar development recently occurred in the field of genetics. Early research suggested that about 98 percent of the DNA in humans and other organisms had no function. Hence, many who were influenced by the theory of evolution assumed that this DNA was “evolutionary junk”—a view that quickly became orthodox. Once again, however, an assumption rooted in Darwinism proved to be false. Recently, scientists have discovered that “junk” DNA plays a vital role in the body by yielding special forms of RNA (ribonucleic acid) that are vital for life. John S. Mattick, director of the Institute for Molecular Bioscience at the University of Queensland in Australia, feels that the hasty acceptance of the “junk” DNA theory is “a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century.” This failure, he adds, “may well go down as one of the biggest mistakes in the history of molecular biology.” Barb