PZ Myers, the self-described Paris Hilton of atheists, on junk DNA

_{Denyse O'Leary

December 7, 2011

'Junk DNA', News}

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The authentic Word from Da Beard, and – as he isn’t a Christian Darwinist – you don’t need to start flinging sandals to hear it. (If you own any sandals.)

Here’s the real story on junk DNA.

Paris Hilton, in case you wondered. It could be your kid who gets … well, squished … in the cause of celebrity. What does that matter?

Comments

I'm sorry, but you haven't actually understood the words I've written. You keep sending me links about positive Darwinian selection! I don't have a clue why. That is very much the opposite of my argument, but you don't seem to get that - even though I've explictly outlined it already. You seem to think you can conflate a whole pile of separate ideas within population genetics, including conflating positive selection and weak purifying selection. OK - let me turn this around for a moment. Imagine I were to make a strong argument against - for example - CSI. Imagine we both agreed that it was a devastating case against CSI. I'm sure we would still both agree that in doing so I hadn't also made a strong argument against IC. Right? Assuming we can at least agree on that, unless you can make a compelling case against the population size effects on the strength of purifying selection, you have no case against the population genetics argument for the structure of the human genome. Positive selection is not even peripherally related to the argument. Also, as I've said a number of times, that is only one argument. There are independent lines of evidence supporting the concept of junk DNA, e.g. the genetic load argument.paulmc_{December 8, 2011
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paulmc so, just as one not concerned so much with truth, but in preserving your atheistic religion, you predictably danced around the fact that population genetics is completely ineffective for predicting overlapping complexity in the genome, you said that 'predicting junk' is unaffected in the equations, to I say 'fine prove it and cut out 95% of the genome!!!' Here are two more very specific examples of the failure of population genetics;
Waiting Longer for Two Mutations – Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that ‘for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years’ (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless “using their model” gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. http://www.discovery.org/a/9461 Whale Evolution Vs. Population Genetics – Richard Sternberg PhD. in Evolutionary Biology – video http://www.metacafe.com/watch/4165203
here is a very clear example as to exactly why population genetics will NEVER explain multiple layers of overlapping complexity:
Poly-Functional Complexity equals Poly-Constrained Complexity http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ
Paulmc, you then go on to offer very shallow excuses as to why you have no compelling experimental proof that shows the genomes are 95% 'garbage' as you adamantly contend. Well paul, I don't care!!! This is hard core science! This is not make gigantic concessions to paulmc's preferred atheistic beliefs!!!,,, As for you taking pot shots at IDists for the thoroughly unimpressive mice knockout experiments, here is what the authors themselves had to say about the experiments:
Jonathan Wells on Darwinism, Science, and Junk DNA - November 2011 Excerpt: Mice without “junk” DNA. In 2004, Edward Rubin?] and a team of scientists at Lawrence Berkeley Laboratory in California reported that they had engineered mice missing over a million base pairs of non-protein-coding (“junk”) DNA—about 1% of the mouse genome—and that they could “see no effect in them.” But molecular biologist Barbara Knowles (who reported the same month that other regions of non-protein-coding mouse DNA were functional) cautioned that the Lawrence Berkeley study didn’t prove that non-protein-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she said. “We don’t know if they have abnormalities that we don’t test for.”And University of California biomolecular engineer David Haussler? said that the deleted non-protein-coding DNA could have effects that the study missed. “Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argued. In 2010, Rubin was part of another team of scientists that engineered mice missing a 58,000-base stretch of so-called “junk” DNA. The team found that the DNA-deficient mice appeared normal until they (along with a control group of normal mice) were fed a high-fat, high-cholesterol diet for 20 weeks. By the end of the study, a substantially higher proportion of the DNA-deficient mice had died from heart disease. Clearly, removing so-called “junk” DNA can have effects that appear only later or under other circumstances. https://uncommondescent.com/intelligent-design/jonathan-wells-on-darwinism-science-and-junk-dna/
Moreover paulmc you have no substantiating empirical evidence whatsoever for your atheistic neo-Darwinian position in the first place:
Where's the substantiating evidence for neo-Darwinism? https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit?hl=en_US
So basically paulmc, all you have is a bunch of smoke and mirrors (and a huge condescending attitude) in order to make your case. Color me severely unimpressed by your theatrics!bornagain77_{December 8, 2011
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BA77 - While I appreciate that you've taken the time to find a paper that levels criticism at population genetics to support your case, this particular example isn't very helpful. Population genetics is a broad body of theory. As with all such bodies of theory, some of it may be right and some of it may be wrong. You cite a (quite informal) review paper that make a generic claim that: "If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions". The ability or otherwise of population genetics to to make quantitative predictions about three-locus quantitative traits does not in any way reflect on the role of effective population size and mutation rate on the accumulation of junk DNA. The two ideas are unrelated, and it is the latter that is of relevance here.
you have chosen to ignore the many examples of stunning complexity in the DNA presented to you
What I have tried to do here was to present a number of independent lines of evidence that need to be addressed if someone is to make the positive claim that there is little or no junk DNA in the human genome. Incidentally, population genetics only underpins one of these lines of evidence. To date, these have not addressed.
if you have such great faith that you are correct, why don’t you go do the experiments and cut out the 95% of the genome that you and PZ think are ‘garbage’.
For quite a lot of reasons. Firstly, that is not my field, I don't have the expertise to do that experiment. Secondly, changing the size of introns will mess with gene regulation, as intron length has the side effect of altering rates of expression. Thirdly, there are undoubtedly unknown functional bits and pieces scattered through the genome that will be removed in the process, although they likely only amount ot a small fraction of total genome size; removing these will affect phenotypes. Fourthly - as with smaller experiments already done in mice - even when there are no observable effects, IDists will still claim it proves nothing because there could have been an unseen effect!paulmc_{December 8, 2011
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Well paulmc, I've been wondering as to how you can use the equations of population genetics to argue for massive amounts of junk in the DNA, when population genetics cannot even account for the multiple layers of overlapping complexity we find in DNA in the first place???
The next evolutionary synthesis: from Lamarck and Darwin to genomic variation and systems biology Excerpt: If more than about three genes (nature unspecified) underpin a phenotype, the mathematics of population genetics, while qualitatively analyzable, requires too many unknown parameters to make quantitatively testable predictions [6]. The inadequacy of this approach is demonstrated by illustrations of the molecular pathways that generates traits [7]: the network underpinning something as simple as growth may have forty or fifty participating proteins whose production involves perhaps twice as many DNA sequences, if one includes enhancers, splice variants etc. Theoretical genetics simply cannot handle this level of complexity, let alone analyse the effects of mutation. http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf
Now paul, if you had a solid foundation in science to make your conjectures from for Junk DNA, it would be a very different story, but you have chosen to ignore the many examples of stunning complexity in the DNA presented to you (of which many more examples could be presented), and have instead chosen to use population genetic equations, equations which very suspiciously can't even account for the overlapping complexity that we do know, for a fact exists, in the DNA, and have chosen these, for all practical purposes, ineffective equations to validate your claim for massive amounts of Junk in the DNA.!!! Do you see the problem here paul??? Or will you once again call us ignorant for not believing your baseless reasoning??? As was suggested earlier by Joe, if you have such great faith that you are correct, why don't you go do the experiments and cut out the 95% of the genome that you and PZ think are 'garbage'. Then you will have my complete attention, instead of having me question you ability to practice science impartially!!bornagain77_{December 8, 2011
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Fitting, yes, I particularly enjoyed the lyrics about organellar genomic structure.paulmc_{December 8, 2011
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In my opinion, Francis Collins has not provided a compelling argument against junk DNA. He appears to put a lot of value on the results of studies finding pervasive but low-level transcription, which if correct indicate the potential for wider function in the genome. However, those results are technique-specific, and alternatives like RNA-seq that are known to return fewer false positives indicate that pervasive transcription doesn't occur. Which is correct? I don't know, the two sides are still sorting this one out, and it is not my own area of research. Low-level transcription does occur throughout the genome by accident, and is predicted from what we know about transcription. There is a good chance they are simply junk transcripts. Regardless, we lack a reason why functional DNA would lack sequence specificity such that it is evolutionarily unconstrained (see Collins's quote from Language of God in your link). We know that only about 10% of the bases in our genome can be subject to purifying selection, which challenges the idea of function across the whole genome. Also, we expect genomes in relatively small populations, such as mammals, to accumulate junk DNA through ineffective purifying selection, as I've argued through this thread. Lastly - we know the origin of about half of our genome comes from transposable elements. Retrotransposons alone make up 40%, and when they duplicate themselves there is an entire copy inserted into the genome - making the genome highly repetitive. How likely is it that yet another copy of Alu, for example, is going to produce an essential RNA transcript?paulmc_{December 8, 2011
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Looking at PZ I doubt he could lift a sledge-hammer with one hand, let alone swing it. Oh wait, perhaps if he picked it up by the weighted end he could lift it- maybe. But there is no way he could lift it up over his head by grasping the bottom of the handle. But hey PZ, I have a 2 pound framing hammer that you may be able to lift but you may have problems trying to swing it.Joe_{December 8, 2011
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PaulMC, Is Francis Collins wrong in retreating from his earlier position on junk DNA (which as far as I can tell was the same as yours)? http://www.evolutionnews.org/2011/03/has_francis_collins_changed_hi044601.htmlwgbutler_{December 8, 2011
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paulmc, a fitting song,
Switchfoot - Meant To Live http://www.youtube.com/watch?v=VWkiFI5QwWE
bornagain77_{December 8, 2011
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ENV has a excellent article up that is of related interest,
A. L. Hughes's New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago - Wolf-Ekkehard Lönnig - December 2011 Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species' particular environment....By mutative reduction of the genetic potential, modifications became "heritable". -- As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The "remainder" has been lost by mutations (accumulation of slightly disadvantageous alleles) -- in the formation of secondary species. http://www.evolutionnews.org/2011/12/a_l_hughess_new053881.html
bornagain77_{December 8, 2011
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Of related note; Here are articles, and a audio interview, with Dr. Hunter, briefly summarizing the refusal of neo-Darwinists to submit the theory to a rigid criteria of falsification as all other robust theories of science do:
Darwin’s Predictions - Cornelius Hunter http://www.darwinspredictions.com/ Arsenic-Based Biochemistry: Turning Poison Into Wine - Cornelius Hunter - December 2010 http://darwins-god.blogspot.com/2010/12/arsenic-based-biochemistry-turning.html Darwin's Predictions With Cornelius Hunter - audio podcast part 1 http://intelligentdesign.podomatic.com/entry/eg/2009-11-04T16_03_23-08_00 The Religion and Failed Predictions of Evolutionists - Cornelius Hunter - audio podcast part 2 http://intelligentdesign.podomatic.com/player/web/2009-11-09T15_20_49-08_00
further note:
Falsification Of Neo-Darwinism by Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US
bornagain77_{December 7, 2011
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There you have it- one possible function that your position would never even consider. Then there is structural function- something I have never even heard your position consider. IOW Paul, you don't know what it takes to make a functioning metazoan genome so you don't know what is and isn't junk. But anyway please go into a lab and do the required knock-out experiments and get back to us.Joe_{December 7, 2011
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Thank you for that, but it seems my fumbling of my post has us talking past each other. My apologies.Upright BiPed_{December 7, 2011
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I would be happy to. A few years ago, I happily took the line that 'junk DNA' was an unhelpful term. I basically accepted the 'argument from ignorance' line and applied the precautionary principle :) For this reason, I don't believe I have any vested interest one way or the other in the argument. I am currently undertaking a PhD in evolutionary biology, studying what I might describe as evolutionary ecology - investigating ecological interactions with molecular phylogenetics. Through my course of study, I have had reason to learn much more than I previously knew about genomics. This has led me to reject the argument about the argument from ignorance... Once we understand a couple things, it becomes difficult to argue against the existence of a large amount of junk DNA. Several of these things have their basis in population genetics. In short, we need to understand how populations evolve, and we need to understand the consequences of mutation. First, natural selection (by which I mean purifying natural selection, which is the overwhelmingly most common form of natural selection) sets a limit on the amount of DNA that can be under purifying selection at any time. The limit relates to the mutation rate - each base in your genome is potentially subjected to mutation, so each additional, functional base bears the 'risk' of mutating and causing dysfunction, perhaps death. Because purifying selection works by eliminating individuals from the reproductive population, if we get to the point where all individuals are likely on balance to bear harmful mutations, then the population necessarily will begin to evolve to extinction. On this basis, Ohno (1972) made the argument that 90% of the genome was probably 'junk'. He didn't know what was in the majority of the genome, but it is still not an argument from ignorance but from inference. Second, we know purifying selection acts most efficiently in large populations (because mutations get 'tested' more times before going to fixation, meaning the importance of their selection coefficient is tested more times). Duplications of retrotransposons and expansions of introns run the risk of making DNA that in turn evolves into, e.g., spurious promoters that mess with normal function. Knowing this and knowing that the population-level retention of duplicate retrotransposons occurs in small not large populations, we can see that most additional copies are not likely to be there because of positive selection - rather the escape from selection that occurs in sufficiently small populations. These retained copies occasionally might evolve function. The jumping action of transposons in general always has the potential for this. But remember that about 40% of our genome is old copies of retrotransposons that have been broken by mutation. When we only need 2% our genome to make all the diversity of proteins we have, yet 40% of our genome is made up of repetitive self-replicating DNA, whose mode of replication is haphazard. It seems more plausible on balance that they are retained by chance rather than for function. Again, function for the odd duplicate might occur - but this is a numbers game and we are trying to explain the majority of our genome not the odd exception. I also make a case for a population genetics interpretation of junk DNA below by comparing animal and plant mitochondrial genomes. Hope this helps as a starting point for where I'm coming from.paulmc_{December 7, 2011
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Look Paul, your position doesn’t even recognize that living organisms contain software that is embedded IN the DNA.
We agree on something :)
That said you could be right and I readily admit that. However you still don’t have any way to test your claim.
I guess the problem is what each of us would accept as evidence. For example, I provisionally accept the strong inferential evidence of junk, as I've outlined.paulmc_{December 7, 2011
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Eric, clarity through and through, nice post!bornagain77_{December 7, 2011
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Actually, no Joe, claims about your ignorance are testable. For example, I have provided several lines of evidence that demonstrate the best interpretation of defective retrotransposons and long introns is that they are junk.
Yeah and long nerves are just a waste too- nothing to do with timing and nothing to do with holding software as does a RAM. Look Paul, your position doesn't even recognize that living organisms contain software that is embedded IN the DNA. That said until someone comes along, removes ALL of the alleged junk and still gets the organism to fully develop without any issues, we just don't know what is and isn't junk. Then given that we KNOW designed systems also have redundacies, well there is just no way to know what is and isn't junk. Add to that FUTURE functions and again all you have is ignorance. That said you could be right and I readily admit that. However you still don't have any way to test your claim.Joe_{December 7, 2011
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Eric @ 4.2.1.1
The argument for junk DNA does indeed rely in significant part on ignorance. Even if there is some demonstrated junk, the assumption that a large part of the remaining DNA is junk is an argument that, while perhaps based on evolutionary expectations, is based not on what we do know about that remaining DNA, but what we don’t know. We’ve barely scratched the surface of DNA and we have geniuses like PZ declaring that only 5% is not junk!? That is most certainly not an evidence-based declaration, so he must be declaring his faith in something else.
No. The argument doesn't rely in any significant way on ignorance. For example, the accumulation of duplicates of retrotransposons only occurs in sufficiently small populations. The composite variable Neu (Ne, effective population size; u mutation rate) describes the behaviour of selection when new mutations enter a population. In large populations, or those with high mutation rates, there is a reasonably strong selective 'pressure' to remove duplications. This is because purifying selection works more efficiently in large populations, and because new DNA sequences from duplications creates new material that are subject to mutation and therefore may have deleterious consequences. A line of evidence in support of this idea is that plants and animals have roughly comparable population sizes - overalapping at least. The nuclear genomes of both have comparable mutation rates. We see quite similar genomic composition in these two eukaryotic lineages in terms of introns and retrotransposons for nuclear DNA. However, when we look at the mitochondrial genomes of these two lineages the story changes. Plants have mt genomes that are loaded with introns. Animals have highly efficient mt genomes with no introns at all. From an anti-junk line of argument, we would be forced to conclude that plants have far better and more complex mitochondria than animals - despite the much greater energy demand that animals have!! In fact what appears to be happening is this: plants have a 100x lower mutation rate than animals in their mt genomes. This means than genomic expansions in plants are less likely to be deleterious, so purifying selection is less efficient at removing these variants. Eventually some drift to fixation and we get expanding plant mt genomes. In animals, with 100x high mutation rates, these changes and expansions are strongly selected against. We still see a high rate of nucleotide substitution because of this mutation rate, however, introns do not form. This seems like a much better explanation. And rather than being based on ignorance, it is based on strong and consistent inferences that result from population genetics.paulmc_{December 7, 2011
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I will reply at the bottom - as I find I get a bit lost in this thread nesting.paulmc_{December 7, 2011
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...sorry
And for what it’s worth, I don’t self-identify with being dawkinsesque genetic determinist.
Upright BiPed_{December 7, 2011
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Hello paulmc, Can you talk about this a bit; just wondering what your background thinking is, and what you think the key issues/distinctions are. thanksUpright BiPed_{December 7, 2011
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paulmc, once again, you ain't even in the right ballpark! First your are using a reductive materialistic (genetic reductionism) view of life as your foundation for reasoning. and Yet reductive materialism, your foundation for reasoning, whether you admit it or not, is falsified by the finding of non-local, beyond space and time, quantum entanglement/information in life. Moreover this quantum information, which cannot be reduced to a material basis (in fact material is now shown to be reducible to quantum information), is found to 'run the show' in life. i.e. it is the 'top tier' which governs life! To show how pervasive this transcendent quantum information is in life I refer to 4-dimensional quarter power scaling: notes:
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 “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
Moreover, at the 7:00 minute mark of this following video, after numerous examples of 1/4 power scaling, we find that ‘genome length vs. mass’ 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/
Though Jerry Fodor and Massimo Piatelli-Palmarini rightly find it inexplicable for 'random' Natural Selection to be the rational explanation for the scaling of the physiology, and anatomy, of living things to four-dimensional parameters, they do not seem to fully realize the implications this 'four dimensional scaling' of living things presents. This 4-D scaling is something we should rightly expect from a Intelligent Design perspective. This is because Intelligent Design holds that ‘higher dimensional transcendent information’ is more foundational to life, and even to the universe itself, than either matter or energy are. This higher dimensional 'expectation' for life, from a Intelligent Design perspective, is directly opposed to the expectation of the Darwinian framework, which holds that information, and indeed even the essence of life itself, is merely an 'emergent' property of the 3-D material realm.
Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. http://journals.witpress.com/paperinfo.asp?pid=420 Quantum entanglement holds together life’s blueprint - 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours. “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/ The relevance of continuous variable entanglement in DNA - July 2010 Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix. http://arxiv.org/abs/1006.4053v1 Quantum Information/Entanglement In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/ Quantum Computing in DNA – Stuart Hameroff Excerpt: Hypothesis: DNA utilizes quantum information and quantum computation for various functions. Superpositions of dipole states of base pairs consisting of purine (A,G) and pyrimidine (C,T) ring structures play the role of qubits, and quantum communication (coherence, entanglement, non-locality) occur in the “pi stack” region of the DNA molecule.,,, We can then consider DNA as a chain of qubits (with helical twist). Output of quantum computation would be manifest as the net electron interference pattern in the quantum state of the pi stack, regulating gene expression and other functions locally and nonlocally by radiation or entanglement. http://www.quantumconsciousness.org/views/QuantumComputingInDNA.html
Quantum Action confirmed in DNA by direct empirical research;
DNA Can Discern Between Two Quantum States, Research Shows - June 2011 Excerpt: -- DNA -- can discern between quantum states known as spin. - The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team's results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property. http://www.sciencedaily.com/releases/2011/03/110331104014.htm Does DNA Have Telepathic Properties?-A Galaxy Insight - 2009 Excerpt: The recognition of similar sequences in DNA’s chemical subunits, occurs in a way unrecognized by science. There is no known reason why the DNA is able to combine the way it does, and from a current theoretical standpoint this feat should be chemically impossible.
Moreover a very high level of information processing suddenly disappears upon death of a organism
The Unbearable Wholeness of Beings - Steve Talbott Excerpt: Virtually the same collection of molecules exists in the canine cells during the moments immediately before and after death. But after the fateful transition no one will any longer think of genes as being regulated, nor will anyone refer to normal or proper chromosome functioning. No molecules will be said to guide other molecules to specific targets, and no molecules will be carrying signals, which is just as well because there will be no structures recognizing signals. Code, information, and communication, in their biological sense, will have disappeared from the scientist’s vocabulary. http://www.thenewatlantis.com/publications/the-unbearable-wholeness-of-beings
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Thanks, paulmc. If I get a chance I'll read through your link in the next day or so, particularly to see if there is much empirical evidence beyond knockout studies, which I have already discussed. Just quickly, however: - The argument for junk DNA does indeed rely in significant part on ignorance. Even if there is some demonstrated junk, the assumption that a large part of the remaining DNA is junk is an argument that, while perhaps based on evolutionary expectations, is based not on what we do know about that remaining DNA, but what we don't know. We've barely scratched the surface of DNA and we have geniuses like PZ declaring that only 5% is not junk!? That is most certainly not an evidence-based declaration, so he must be declaring his faith in something else. - Functions without known causes does not depend on some kind of absolute genetic determinism. It does depend on what we do know about the systems we have elucidated (which, almost without exception, are extremely integrated and tightly controlled systems), together with a basic understanding of what is required to build and maintain systems. There is no evidence that complex functional integrated systems come together without detailed programming and operational instructions. The alternative to functions without a DNA-based cause is not an explanation, but a vague appeal to some as-yet-undiscovered property of matter or physics that simply causes things to arise. You are of course free to repose your faith in the promissory note of finding such a property down the road. I prefer to put my faith in what we do know about chemistry, physics, engineering and systems programming. - Finally, as to your last sentence, I don't argue that the existence of complex functional integrated systems logically mean that there cannot be any junk. There may be some. But everything in our experience should give us pause before thinking there are large amounts of junk. Is there anything else in biology that is mostly junk? Any other system? The heart, lungs, respiratory system, eyes, hearing, muscular system, etc. -- are any of them characterized by mostly junk with a few islands of function? Of course not. There are multiple levels of organized functional complexity and the pervasive reality from top to bottom is function, not junk. Same goes for our human technology. Now logically it is possible that DNA -- the most sophisticated piece of technology ever discovered -- just happens to go against this overwhelming trend and is mostly junk, with islands of function peeking out from the detritus, but anyone who stands on that side of the equation is, in my estimation, standing on the wrong side of both history and empirical data.Eric Anderson_{December 7, 2011
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If you can show me where any of my reasoning has relied on positive Darwinian selection of the type described in the article about the Oxford job, then you mght have a point. If you instead understood that the argument I made above was actually based on Kimura's neutral theory, rather than challenged by it, perhaps we wouldn't be having this conversation. Your ability to link to a video on whale evolution does not have any bearing on the strong evidence provided in the Lynch review article I have linked to several times in this thread, but that you have not read.paulmc_{December 7, 2011
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Let's see paulmc, you state population genetics is a major cornerstone of your reasoning, and I showed population genetics to be void of explanatory power for neo-Darwinism. Perhaps you and Lynch should go apply for the job in Oxford to 'fix' the problems with the population genetic equations since you think you know more than the rest of us as to what constitutes a solid foundation for reasoning!bornagain77_{December 7, 2011
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So just to be clear - you're completely uninterested in talking on topic about junk DNA then?paulmc_{December 7, 2011
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Thanks for the link, I have now read it. You make two basic arguments: (1) there is little evidence for junk DNA; and (2) secondly that there is evidence against the position that much junk DNA exists. On (1), I would say that you are either mistaken or unaware of the evidence. Here I provide four reasons to expect the majority of the genome to be junk. Ohno's (1972) argument is quite compelling if you have an understanding of population genetics. I am also in the middle of two part post about the population genetics argument for junk DNA, part one here. On (2) the first point (vestigial organs) is irrelevant, because the argument for junk does not rely on an argument from ignorance. The second point (functions without known causes) relies on a degree of genetic determinism for which there is no evidence at all, only an engineering assumption for how the genome should work if it were designed. The third point (to summarise, organisms are complex and work well) is again, a non-argument. That does not in any way preclude a large amount of junk.paulmc_{December 7, 2011
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Further notes:
Oxford University Admits Darwinism's Shaky Math Foundation - May 2011 Excerpt: However, mathematical population geneticists mainly deny that natural selection leads to optimization of any useful kind. This fifty-year old schism is intellectually damaging in itself, and has prevented improvements in our concept of what fitness is. - On a 2011 Job Description for a Mathematician, at Oxford, to 'fix' the persistent mathematical problems with neo-Darwinism within two years. http://www.evolutionnews.org/2011/05/oxford_university_admits_darwi046351.html Majestic Ascent: Berlinski on Darwin on Trial - David Berlinski - November 2011 Excerpt: The publication in 1983 of Motoo Kimura's The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura's theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. "A critique of neo-Darwinism," the Dutch biologist Gert Korthof boasted, "can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science." By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian. http://www.evolutionnews.org/2011/11/berlinski_on_darwin_on_trial053171.html Bernard d'Abrera on Butterfly Mimicry and the Faith of the Evolutionist - October 5, 2011 Excerpt: For it to happen in a single species once through chance, is mathematically highly improbable. But when it occurs so often, in so many species, and we are expected to apply mathematical probability yet again, then either mathematics is a useless tool, or we are being criminally blind.,,, Evolutionism (with its two eldest daughters, phylogenetics and cladistics) is the only systematic synthesis in the history of the universe that proposes an Effect without a Final Cause. It is a great fraud, and cannot be taken seriously because it outrageously attempts to defend the philosophically indefensible. http://www.evolutionnews.org/2011/10/in_this_excerpt_from_the051571.html
bornagain77_{December 7, 2011
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Buddy, despite what you may think of yourself, the very words you write testify that you are a died in the wool, card totin, reductive genetic determinist!,,, as to 'ignores population genetics'??? funny, it seems to me that neo-Darwinists are the ones who are purposely ignoring population genetics, especially when it suits their atheistic/materialistic purpose, just so to arrive at the conclusion they desire beforehand:
Experimental Evolution in Fruit Flies (35 years of trying to force fruit flies to evolve in the laboratory fails, spectacularly) - October 2010 Excerpt: "Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles.,,, "This research really upends the dominant paradigm about how species evolve," said ecology and evolutionary biology professor Anthony Long, the primary investigator. http://www.arn.org/blogs/index.php/literature/2010/10/07/experimental_evolution_in_fruit_flies Waiting Longer for Two Mutations - Michael J. Behe Excerpt: Citing malaria literature sources (White 2004) I had noted that the de novo appearance of chloroquine resistance in Plasmodium falciparum was an event of probability of 1 in 10^20. I then wrote that 'for humans to achieve a mutation like this by chance, we would have to wait 100 million times 10 million years' (1 quadrillion years)(Behe 2007) (because that is the extrapolated time that it would take to produce 10^20 humans). Durrett and Schmidt (2008, p. 1507) retort that my number ‘is 5 million times larger than the calculation we have just given’ using their model (which nonetheless "using their model" gives a prohibitively long waiting time of 216 million years). Their criticism compares apples to oranges. My figure of 10^20 is an empirical statistic from the literature; it is not, as their calculation is, a theoretical estimate from a population genetics model. http://www.discovery.org/a/9461 Whale Evolution Vs. Population Genetics - Richard Sternberg PhD. in Evolutionary Biology - video http://www.metacafe.com/watch/4165203
bornagain77_{December 7, 2011
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Another linkfest? Really? Epigenetics is an interesting field, sure (OT, a very interesting recent find here). And for what it's worth, I don't self-identify with being dawkinsesque genetic determinist. But neither of these ideas are going to explain away the population-level retention of defective retrotransposons. The last link of yours is the closest to being on topic. However, it ignores population genetics. I'll say it again: please read some Lynch - links above. Lynch unifies population genetics with the genome structure. This is about the effectiveness of purifying selection.paulmc_{December 7, 2011
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