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

So paul, I'm beginning to catch the hang of this evolutionary biology stuff,,, 1. insertion events only count when they quasi-support a evolutionary position and don't count the vast majority on time when they support a design position. 2. The equations of population genetics only count when they support and evolutionary position (for calculating obscene percentages of junk DNA) and don't count the vast majority of times when they support the design position., And 3. experimental evidence for knocking your beloved Junk DNA out, since you have no knock out experiments to point to (not even in the mice experiments), NEVER EVER counts against the evolutionary position. I think that pretty much sums it up. Did I miss anything Paul??? bornagain77

paulmc, Without an experiment that removes the alleged junk- I don't care how much they remove at a time- then there isn't any evidence that it is junk. You want an evidenced-based argument-> do the experiment. Short of that you don't have one. Joe

Haphazardly, like the majority of the insertions that occur that do have a notable phenotypic effect are deleterious, e.g. implicated in disease, and are not implicated in function. paulmc

Perhaps you could take it as an "admission" that I want to discuss the topic of junk DNA, not everything in evolutionary biology under the sun. If you have any points on the topic of this thread - great. Otherwise, see you. You can disagree with my explanation for not simply removing 90% of the genome and expecting the emergence of the same phenotypes. But perhaps it would be more civil to do so by way of a logical, evidence-based argument rather than resorting to calling me "afraid" and "whining". paulmc

see post 17 bornagain77

'haphazardly inserted' REALLY???

Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf

i.e. Why is it so important for you to believe, and push, that they were 'haphazardly inserted' unless you were, contrary to your denial, pushing a unfounded atheistic interpretation that is motivated by ideology rather than science??? notes:

On Not Reading Signature in the Cell: A Response to Francisco Ayala Excerpt: Contrary to Ayala’s claim, Alu sequences (and other mammalian SINEs) are not distributed randomly but instead manifest a similar “bar-code” distribution pattern along their chromosomes (Chen and Manuelidis, 1989; Gibbs et al., 2004; Korenberg and Rykowski, 1988). Rather like the distribution of the backslashes, semi-colons and spaces involved in the formatting of software code, the “bar-code” distribution of Alu sequences (and other SINEs) reflects a clear functional logic, not sloppy editing or random mutational insertions. For example, Alu sequences are preferentially located in and around protein-coding genes as befits their role in regulating gene expression (Tsirigos and Rigoutsos, 2009). They occur mainly in promoter regions–the start sites for RNA production–and in introns, the segments that break up the protein-coding stretches. Outside of these areas, the numbers of Alu sequences sharply decline. Further, we now know that Alu sequences are directed to (or spliced into) certain preferential hotspots in the genome by the protein complexes or the “integrative machinery” of the cell’s information processing system (Levy et al., 2010). This directed distribution of Alu sequences enhances the semantic and syntactical organization of human DNA. It appears to have little to do with the occurrence of random insertional mutations, contrary to the implication of Ayala’s “sloppy editor” illustration and argument. (page down for 33 references of ALU functionality) http://www.stephencmeyer.org/news/2010/03/_this_is_part_2.html

bornagain77

paulmc:

I understand that it suits you to believe this, but I have already answered this point. Changing the size of introns will mess with gene regulation, as intron length has the side effect of altering rates of expression.

Then those introns are NOT junk and you don't remove them. Geez all your whining about conducting an experiment exposes your anti-science agenda. Joe

As I said until you go about removing all that you consider junk and get a functional organism to develop, you don’t have anything but speculation.

You can repeat this ‘remove all the junk’ stuff as many times as you like, and it doesn’t help make it a better answer than it was when I wrote this (see last paragraph).

Whatever Paul. Until you or someone conducts that experiment the claim of the majority of our genome is junk is total BS.

And you can talk about speculation all you want, but it should be obvious to the informed reader that there is much more than ‘speculation’ going on; there are several strong, independent lines of evidence that support the junk DNA inference.

Yet there is ONLY ONE WAY to confirm that inference and apparently people are too afraid to perform the experiment.

Can your framework explain a) why one species of onion requires 4x as much DNA as a similar and closely related species of onion within the same genus; and b) why junk accumulation is proportional to mutation rate x effective population size?

Dude, your framwork can’t even explain onions, nor functional genomes. Perhaps you should focus on that. Or actually perform the experiment I mentioned.

Back on topic,...

I will take that as an admission that your position cannot explain anything beyond broken things. BTW if the experiment I ask for cannot be done then the claim of junk DNA being the majority of the genome is total BS. And your whining is not going to change that. Joe

REALLY??? Are we even on the same thread reading the same things??? Earth to paul,, WAKE UP!!!

I don't know. I think we're on a thread about junk DNA, you seem to think we're on a thread about anything you have a ready-made link for. paulmc

Speaking of 'uphill battles', how's that refutation of Abel's Null Hypothesis working out???

Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, Testable hypotheses about FSC What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses: Null hypothesis #1 Stochastic ensembles of physical units cannot program algorithmic/cybernetic function. Null hypothesis #2 Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function. Null hypothesis #3 Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function. Null hypothesis #4 Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time. We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified. http://www.tbiomed.com/content/2/1/29 The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html The Law of Physicodynamic Incompleteness - David L. Abel - August 2011 Summary: “The Law of Physicodynamic Incompleteness” states that inanimate physicodynamics is completely inadequate to generate, or even explain, the mathematical nature of physical interactions (the purely formal laws of physics and chemistry). The Law further states that physicodynamic factors cannot cause formal processes and procedures leading to sophisticated function. Chance and necessity alone cannot steer, program or optimize algorithmic/computational success to provide desired non-trivial utility. http://www.scitopics.com/The_Law_of_Physicodynamic_Incompleteness.html The GS (genetic selection) Principle – David L. Abel – 2009 Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.” http://www.bioscience.org/2009/v14/af/3426/3426.pdf

bornagain77

All you have is empty rhetoric describing my motivation as being 'atheist' and my reasoning as 'shallow excuses'. What part of the above very basic explanation do you find difficult to follow? Introns affect gene expression. We regularly identify new functional segments of DNA, something that won't slow down for a while. Both of these mean you can't simply remove 90% of the genome and expect no phenotypic effects. Neither of these things demonstrate function for a majority of the genome. Nor do they undermine the arguments for junk DNA. It simply means you can't do what you/Joe have proposed. Also, I'll ask you again, maybe you'll answer me this time: Can you explain how yet another copy of Alu haphazardly inserted in your genome would typically represent something functional? If you don’t think it would be functional, why do you believe something different for the other million copies of Alu? paulmc

as to,,, You are making the assumption that 10-15% of the genome is not enough, but providing no reason for this, only incredulity (e.g. “undreamt level of jaw-dropping complexity”). REALLY??? Are we even on the same thread reading the same things??? Earth to paul,, WAKE UP!!! more notes for you to ignore:

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 Life Leads the Way to Invention - Feb. 2010 Excerpt: a cell is 10,000 times more energy-efficient than a transistor. “ In one second, a cell performs about 10 million energy-consuming chemical reactions, which altogether require about one picowatt (one millionth millionth of a watt) of power.” This and other amazing facts lead to an obvious conclusion: inventors ought to look to life for ideas.,,, Essentially, cells may be viewed as circuits that use molecules, ions, proteins and DNA instead of electrons and transistors. That analogy suggests that it should be possible to build electronic chips – what Sarpeshkar calls “cellular chemical computers” – that mimic chemical reactions very efficiently and on a very fast timescale. http://creationsafaris.com/crev201002.htm#20100226a

Also of interest is that a cell apparently seems to be successfully designed along the very stringent guidelines laid out by Landauer's principle of 'reversible computation' in order to achieve such amazing energy efficiency, something man has yet to accomplish in any meaningful way for computers:

Notes on Landauer’s principle, reversible computation, and Maxwell’s Demon - Charles H. Bennett 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.hep.princeton.edu/~mcdonald/examples/QM/bennett_shpmp_34_501_03.pdf Programming of Life - Biological Computers - video http://www.youtube.com/user/Programmingoflife#p/c/AFDF33F11E2FB840/5/hRooe6ehrPs

further notes:

Michael Behe - Life Reeks Of Design - 2010 - video http://www.metacafe.com/watch/5066181

And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.

"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

The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,,

‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,,

Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,,

,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology

further note:

William Bialek - Professor Of Physics - Princeton University: Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," http://www.princeton.edu/~wbialek/wbialek.html

music:

Evanescence - Bring me to life (high quality) http://www.youtube.com/watch?v=9qlDveUeVNk

bornagain77

so when it suits your atheistic purposes DNA is 85 to 95% junk/garbage, but when push comes to shove to actually prove your point scientifically then you have all sorts of shallow excuses as to why it is not really garbage that you can just remove! The hypocrisy in your reasoning is just oozing out of you!!! bornagain77

Only in your imagination!

Not a blueprint: about the junk in your trunk Response to Jonathan Wells (when he wrote this). Population size, and the evolution of junk. Part I: Origins

As Joe said, if you can’t remove the 85% ‘garbage’ it ain’t junk! and It is thoroughly disingenuous of you to pretend that this basic fact does not undermine your whole contrived argument!

I understand that it suits you to believe this, but I have already answered this point. Changing the size of introns will mess with gene regulation, as intron length has the side effect of altering rates of expression. For this reason you cannot just remove them and expect no consequence. Also, there are unknown functional bits and pieces scattered through the genome - miRNAs and the like are regularly being discovered. Removing everything without known function will also remove these in the process. In other words, it is an experiment that will fail and it is not - nor has it ever been - a prediction of mine that such a thing could be soundly done. It is instead a ridiculous caricature of my position to claim that this is a sound avenue to test the junkiness of the mammalian genome. paulmc

paul, so you don’t find declaring that 85%, upwards to 95%, of the DNA to be ‘garbage’, to use PZ’s word, to be obscene???

No, it is not obscene to present the reasoned inference that 85-90% of mammalian genomes lack current function. You are making the assumption that 10-15% of the genome is not enough, but providing no reason for this, only incredulity (e.g. "undreamt level of jaw-dropping complexity"). One of the many uphill battles on your side would be to explain how yet another copy of Alu haphazardly inserted in your genome represents an untold wonder of function, masterfully crafted by The Designer. If you don't believe it does, why do you believe something different for the other million copies? paulmc

as to: there are several strong, independent lines of evidence that support the junk DNA inference. Only in your imagination! As Joe said, if you can't remove the 85% 'garbage' it ain't junk! and It is thoroughly disingenuous of you to pretend that this basic fact does not undermine your whole contrived argument! bornagain77

As I said until you go about removing all that you consider junk and get a functional organism to develop, you don’t have anything but speculation.

You can repeat this 'remove all the junk' stuff as many times as you like, and it doesn't help make it a better answer than it was when I wrote this (see last paragraph). And you can talk about speculation all you want, but it should be obvious to the informed reader that there is much more than 'speculation' going on; there are several strong, independent lines of evidence that support the junk DNA inference.

Can your framework explain a) why one species of onion requires 4x as much DNA as a similar and closely related species of onion within the same genus; and b) why junk accumulation is proportional to mutation rate x effective population size?

Dude, your framwork can’t even explain onions, nor functional genomes. Perhaps you should focus on that. Or actually perform the experiment I mentioned.

Back on topic, I'll take that to mean your framework can't explain a) or b). That's fine, just checking. paulmc

paul, so you don't find declaring that 85%, upwards to 95%, of the DNA to be 'garbage', to use PZ's word, to be obscene??? Actually from the choice of words I've could have used instead, considering the undreamt level of jaw-dropping complexity being discovered in DNA, that word was rather mild in response to your blatant materialistic delusions!!!,, Notes for you to ignore, and to pretend don't matter, once again:

Non-Local (beyong space and time) 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 Falsification Of Neo-Darwinism by Quantum Entanglement/Information https://docs.google.com/document/d/1p8AQgqFqiRQwyaF8t1_CKTPQ9duN8FHU9-pV4oBDOVs/edit?hl=en_US Scientists' 3-D View of Genes-at-Work Is Paradigm Shift in Genetics - Dec. 2009 Excerpt: Highly coordinated chromosomal choreography leads genes and the sequences controlling them, which are often positioned huge distances apart on chromosomes, to these 'hot spots'. Once close together within the same transcription factory, genes get switched on (a process called transcription) at an appropriate level at the right time in a specific cell type. This is the first demonstration that genes encoding proteins with related physiological role visit the same factory. http://www.sciencedaily.com/releases/2009/12/091215160649.htm 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 Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm

Of note: DNA repair machines 'Fixing every pothole in America before the next rush hour' is analogous to the traveling salesman problem. The traveling salesman problem is a NP-hard (read: very hard) problem in computer science; The problem involves finding the shortest possible route between cities, visiting each city only once. 'Traveling salesman problems' are notorious for keeping supercomputers busy for days.

NP-hard problem http://en.wikipedia.org/wiki/NP-hard

Since it is obvious that there is not a material CPU (central processing unit) in the DNA, or cell, busily computing answers to this monster logistic problem, in a purely 'material' fashion, then it is readily apparent that this monster 'traveling salesman problem', for DNA repair, is somehow being computed by 'non-local' quantum computation within the cell and/or within DNA; Of related interest:

DNA Computer Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today's most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours. http://www.tech-faq.com/dna-computer.html

Music and Verse:

Sarah McLachlan - Answer – http://www.youtube.com/watch?v=i8B1ai25lUo 2 Thessalonians 2:3 Let no man deceive you by any means: for that day shall not come, except there come a falling away first,,

bornagain77

junk DNA- yes if we take a 2 dimensional approach and say all DNA that does not code for some type of RNA is “junk”, then PaulMc, PZ, Larry Moran, et al., have a point.

This is not my position, nor is it PZ’s from his video, nor Larry’s from his writing.

So all DNA that doesn't code for some type of DNA is not junk?

For one, structural DNA does not fit under this description.

Can your position even explain structural DNA? Can it explain coding DNA? It sure seems good at explaining broken things.

For two, any definition should not include spurious, or junk transcripts – producing “some type of RNA” is not good enough.

That would be in addition to what I was talking about. The point being is there could be a basic need for stretches of DNA that do not code for any RNA.

There could be lots of things, but without evidence they remain idle speculation and peripheral to science.

Dude, the position the majority of our genome is junk and speculation and peripheral to science. As I said until you go about removing all that you consider junk and get a functional organism to develop, you don't have anything but speculation.

Can your framework explain a) why one species of onion requires 4x as much DNA as a similar and closely related species of onion within the same genus; and b) why junk accumulation is proportional to mutation rate x effective population size?

Dude, your framwork can't even explain onions, nor functional genomes. Perhaps you should focus on that. Or actually perform the experiment I mentioned. Joe

junk DNA- yes if we take a 2 dimensional approach and say all DNA that does not code for some type of RNA is “junk”, then PaulMc, PZ, Larry Moran, et al., have a point.

This is not my position, nor is it PZ's from his video, nor Larry's from his writing. For one, structural DNA does not fit under this description. For two, any definition should not include spurious, or junk transcripts - producing "some type of RNA" is not good enough.

The point being is there could be a basic need for stretches of DNA that do not code for any RNA.

There could be lots of things, but without evidence they remain idle speculation and peripheral to science. Can your framework explain a) why one species of onion requires 4x as much DNA as a similar and closely related species of onion within the same genus; and b) why junk accumulation is proportional to mutation rate x effective population size? paulmc

Obscene... interesting choice of words. If something about junk DNA offends you morally, I suspect that you are probably not in a good position to objectively evaluate the evidence! But thanks for the ironic bible quote - funny! paulmc

paul, and yet for all your denial, you still support that obscenely huge portions of the DNA is junk! Go figure!!!

2 Peter 1:16 For we did not follow cleverly devised tales when we made known to you the power and coming of our Lord Jesus Christ, but we were eyewitnesses.

bornagain77

junk DNA- yes if we take a 2 dimensional approach and say all DNA that does not code for some type of RNA is "junk", then PaulMc, PZ, Larry Moran, et al., have a point. HOWEVER Intelligent Design does NOT look at DNA in two dimensions as there are multiple levels of organization and information. Then there are structural constraints to be considered. The point being is there could be a basic need for stretches of DNA that do not code for any RNA. Joe

Now paulmc, I have put up with more than my fair share of malarkey from you with your 95% junk DNA tripe,, and have put some very compelling evidence for you to consider on the table that shows you to be completely off base.

I'm sure you actually believe that, too. Yet, for some reason you continue to link to news stories about adaptation and the limits of positive selection, showing you don't understand the argument being made at all. I've already explained how positive selection is completely unrelated to the argument for putative genomic junk. In other words, what you think is compelling is at best tangential, but mostly irrelevant.

the true rule for all biological adaptations falls under the rigid principle of genetic entropy not under your ‘religion’ of neo-Darwinism.

I follow neoDarwinism as a religion? Do I need to remind you that half of your posts end with bible quotes? This is not only a mischaracterisation of my position, but comically ironic. And there you go with adaptations again. FWIW, I am fairly sceptical of the classical neoDarwinian basis of adaptation, although I don't think Austin Hughes provides a particularly compelling case against it (much of his other work is excellent, however). There are arguments for non-adaptive origins of complexity. What more can I say - read Fernandez & Lynch (2011). paulmc

PaulMC, Thanks for responding. Is it safe to say that you and Francis Collins are not on the same page? Also, what do you think the teleological ramifications are for the junk DNA hypothesis. Do you think the science indicates that its all just a puddle of goo works very inefficiently and points to a random, purposeless history of life or is it too difficult to tell what any of it means, from a metaphysical viewpoint? Thanks in advance for your reply. wgbutler

paulmc, the true rule for all biological adaptations falls under the rigid principle of genetic entropy not under your 'religion' of neo-Darwinism. Moreover, the following is what the empirical evidence, not your imaginary models, actually dictates for all biological adaptations,,,

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

Moreover paulmc, the principle of genetic entropy is in full compliance with the second law of thermodynamics and with law of conservation of information, with what we witness in the fossil record, as well as with what we witness in genetic population studies:

EXPELLED - Natural Selection And Genetic Mutations - video http://www.metacafe.com/watch/4036840 "...but Natural Selection reduces genetic information and we know this from all the Genetic Population studies that we have..." Maciej Marian Giertych - Population Geneticist - member of the European Parliament - EXPELLED

The following 'should' interest you paulmc (though you will probably completely ignore it as you do with anything else that falsifies neo-Darwinism)

DNA Degeneration: Top Population Geneticists agree neo-Darwinism is not supported by the data - John Sanford http://www.youtube.com/watch?v=tYEkqwOXE5U

Now paulmc, I have put up with more than my fair share of malarkey from you with your 95% junk DNA tripe,, and have put some very compelling evidence for you to consider on the table that shows you to be completely off base. As far as I'm concerned I have made my case more than sufficiently, and will not play your stupid games anymore since you show no reasonableness to evidence.! bornagain77

Just when I thought you were making progress... so you accept the occurrence of slightly deleterious mutations and genetic entropy, but you don't accept the accumulation of junk DNA? Sincerely, what do you think happens at a population level? Do you think that neutral and nearly neutral mutations can fix in populations? If not, why not? And if so, why is junk DNA so hard to accept? paulmc

NO!

Unexpectedly small effects of mutations in bacteria bring new perspectives - November 2010 Excerpt:,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed. http://www.physorg.com/news/2010-11-unexpectedly-small-effects-mutations-bacteria.html Scientists Map All Mammalian Gene Interactions – August 2010 Excerpt: Mammals, including humans, have roughly 20,000 different genes.,,, They found a network of more than 7 million interactions encompassing essentially every one of the genes in the mammalian genome. http://www.sciencedaily.com/releases/2010/08/100809142044.htm

bornagain77

Great - so am I take it from this that you now accept the argument for junk DNA? paulmc

paulmc, for crying out loud, if you can't prove even one instance of how complex functional information arises in genomes, with population genetics, why in blue blazes should I even give a hoot about anything else you have to say about what percentage of garbage you think is in the genomes??? You don't seem to have a very good grasp on what it takes to maintain coherent scientific integrity towards a point you are trying to make scientifically. Shoot paulmc, neo-Darwinism is SO GOOD at breaking things (Behe, 2010), I'm absolutely positive it is very easy for you, or anyone else, to, with a little slight of hand, 'mathematically' prove however much 'garbage' in the genomes they wanted to! But in the real world, using population genetics, with realistic rates of detrimental mutations compared to 'hypothetical' beneficial mutations, Dr. John Sanford, inventor of the 'gene gun, along with other top notch researchers in genetics, who have no hidden agenda, but only want to find the truth, developed a computer program that shows us exactly what will happen in a geneome in any size population you care to examine,, i.e. the answer is 'genetic entropy' in every case!

Using Computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load: Excerpt: We apply a biologically realistic forward-time population genetics program to study human mutation accumulation under a wide-range of circumstances.,, Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. http://bioinformatics.cau.edu.cn/lecture/chinaproof.pdf MENDEL’S ACCOUNTANT: J. SANFORD†, J. BAUMGARDNER‡, W. BREWER§, P. GIBSON¶, AND W. REMINE http://mendelsaccount.sourceforge.net http://www.scpe.org/vols/vol08/no2/SCPE_8_2_02.pdf Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086

So paulmc, you problem is not for you to prove that neo-Darwinism can break things, it does that extremely well thank you very much, your problem is to prove that it can do anything, whatsoever, as to building functional complexity/information!!! (Moreover, you have that little problem of being falsified by quantum information in DNA that, if you were honest, you need to be extremely concerned about!) notes:

The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www-qa.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html The Law of Physicodynamic Incompleteness - David L. Abel - August 2011 Summary: “The Law of Physicodynamic Incompleteness” states that inanimate physicodynamics is completely inadequate to generate, or even explain, the mathematical nature of physical interactions (the purely formal laws of physics and chemistry). The Law further states that physicodynamic factors cannot cause formal processes and procedures leading to sophisticated function. Chance and necessity alone cannot steer, program or optimize algorithmic/computational success to provide desired non-trivial utility. http://www.scitopics.com/The_Law_of_Physicodynamic_Incompleteness.html

bornagain77

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

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://uncommondesc.wpengine.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

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

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

Fitting, yes, I particularly enjoyed the lyrics about organellar genomic structure. paulmc

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

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

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.html wgbutler

paulmc, a fitting song,

Switchfoot - Meant To Live http://www.youtube.com/watch?v=VWkiFI5QwWE

bornagain77

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

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

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

Thank you for that, but it seems my fumbling of my post has us talking past each other. My apologies. Upright BiPed

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

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

Eric, clarity through and through, nice post! bornagain77

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

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

I will reply at the bottom - as I find I get a bit lost in this thread nesting. paulmc

...sorry

And for what it’s worth, I don’t self-identify with being dawkinsesque genetic determinist.

Upright BiPed

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. thanks Upright BiPed

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

bornagain77

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

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

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

So just to be clear - you're completely uninterested in talking on topic about junk DNA then? paulmc

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

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

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

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

paul, you ain't even in the right ballpark to play the game. You are operating off a antiquated foundation of genetic reductionism, yet epigenetics has rendered that entire position null and void of any true explanatory power within science:

https://uncommondesc.wpengine.com/junk-dna/pz-myers-the-self-described-paris-hilton-of-atheists-on-junk-dna/comment-page-1/#comment-411208

moreover:

The next evolutionary synthesis: Jonathan BL Bard Excerpt: We now know that there are at least 50 possible functions that DNA sequences can fulfill [8], that the networks for traits require many proteins and that they allow for considerable redundancy [9]. The reality is that the evolutionary synthesis says nothing about any of this; for all its claim of being grounded in DNA and mutation, it is actually a theory based on phenotypic traits. This is not to say that the evolutionary synthesis is wrong, but that it is inadequate – it is really only half a theory! http://www.biosignaling.com/content/pdf/1478-811X-9-30.pdf Astonishing DNA complexity update Excerpt: The untranslated regions (now called UTRs, rather than ‘junk’) are far more important than the translated regions (the genes), as measured by the number of DNA bases appearing in RNA transcripts. Genic regions are transcribed on average in five different overlapping and interleaved ways, while UTRs are transcribed on average in seven different overlapping and interleaved ways. Since there are about 33 times as many bases in UTRs than in genic regions, that makes the ‘junk’ about 50 times more active than the genes. http://creation.com/astonishing-dna-complexity-update DNA Computer Excerpt: DNA computers will work through the use of DNA-based logic gates. These logic gates are very much similar to what is used in our computers today with the only difference being the composition of the input and output signals.,,, With the use of DNA logic gates, a DNA computer the size of a teardrop will be more powerful than today’s most powerful supercomputer. A DNA chip less than the size of a dime will have the capacity to perform 10 trillion parallel calculations at one time as well as hold ten terabytes of data. The capacity to perform parallel calculations, much more trillions of parallel calculations, is something silicon-based computers are not able to do. As such, a complex mathematical problem that could take silicon-based computers thousands of years to solve can be done by DNA computers in hours. http://www.tech-faq.com/dna-computer.html Quantum Dots Spotlight DNA-Repair Proteins in Motion - March 2010 Excerpt: "How this system works is an important unanswered question in this field," he said. "It has to be able to identify very small mistakes in a 3-dimensional morass of gene strands. It's akin to spotting potholes on every street all over the country and getting them fixed before the next rush hour." Dr. Bennett Van Houten - of note: A bacterium has about 40 team members on its pothole crew. That allows its entire genome to be scanned for errors in 20 minutes, the typical doubling time.,, These smart machines can apparently also interact with other damage control teams if they cannot fix the problem on the spot. http://www.sciencedaily.com/releases/2010/03/100311123522.htm 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 "Today there is an explosion of knowledge going on in the study of gene regulatory networks. But it is not led, assisted, or even inspired by the theory of evolution. "We have little empirical knowledge on the evolutionary history of such networks."-- Dean, Antony M., Joseph W. Thornton. September 2007. Mechanistic approaches to the study of evolution: the functional synthesis. Nature Reviews Genetics, Vol. 8, pp. 675-688. http://www.newgeology.us/presentation32.html

The paradox between having elegant DNA repair mechanisms and the need for random mutations to 'drive evolution' is discussed here;

The Evolutionary Dynamics of Digital and Nucleotide Codes: A Mutation Protection Perspective - February 2011 Excerpt: "Unbounded random change of nucleotide codes through the accumulation of irreparable, advantageous, code-expanding, inheritable mutations at the level of individual nucleotides, as proposed by evolutionary theory, requires the mutation protection at the level of the individual nucleotides and at the higher levels of the code to be switched off or at least to dysfunction. Dysfunctioning mutation protection, however, is the origin of cancer and hereditary diseases, which reduce the capacity to live and to reproduce. Our mutation protection perspective of the evolutionary dynamics of digital and nucleotide codes thus reveals the presence of a paradox in evolutionary theory between the necessity and the disadvantage of dysfunctioning mutation protection. This mutation protection paradox, which is closely related with the paradox between evolvability and mutational robustness, needs further investigation." http://www.arn.org/blogs/index.php/literature/2011/04/26/dna_repair_mechanisms_reveal_a_contradic

etc.. etc.. etc.. bornagain77

paulmc: Presumably you've also looked at this discussion: https://uncommondesc.wpengine.com/junk-dna/vidthe-debate-that-never-was-craig-vs-dawkins-junk-dna-does-show-up-though/ Arguing for pervasive amounts of junk DNA is a fool's errand. Eric Anderson

paulmc, so you are 100% certain, bet your life on it, that the DNA is mostly useless junk

What? Why should I be betting my life on it or be 100% certain? I am not 100% certain about any scientific inference. What I am certain about is this: the best, current, evidence-based explanation for the structure of the human genome and other eukaryotic genomes is genetic drift fixing slightly deleterious mutations, including duplicate retrotransposons. Large populations with more efficient purifying selection experience these fixations at much lower rates than small populations with weaker purifying selection. By small, we mean things like mammals, compared to things like bacteria. Look at what happens to genome content as genomes expands across the array of life's diversity. Coding sequences reach a maximum, which is never exceeded. Introns and retrotransposons continue to accumulate, dominating large genomes. Look at the types of organisms and think about what their relative population sizes are. It might indeed be wrong - of course it might - however it is the best answer with the current knowledge that we have and it is supported by a plethora of independent lines of evidence. paulmc

paulmc, so you are 100% certain, bet your life on it, that the DNA is mostly useless junk, i.e 'garbage', just as PZ claimed??? Frankly paulmc, not to be rude, but considering the multiple levels of functionality revealed thus far (in the 'linkfest' you refuse to consider), that is a fool's bet that I have never seen the likes of before!!!,,, No matter how much smarter you tyhink yourself to be over other people, that is the most foolish, ignorant, stupid, proclamation I've ever seen from neo-Darwinists!!!!!! bornagain77

I wonder why you've only addressed that comment to me and not to Joe, whose first comment to me was to dismiss me as being ignorant? Perhaps you are being selective in your criticism? I doubt I am the one being selective with the evidence, here. Where is the evidence for function that I have missed? Have you got a counterargument to any of this for example? paulmc

BA77, I have no interest in addressing your irrelevant linkfest. The argument for junk DNA is not intellectually related to claims of vestigial organs. There is positive evidence that the bulk of retrotransposon duplications that fix in populations happen through the escape from purifying natural selection, not from positive selection for function. Again, why not read a little Lynch before talking about arguments from ignorance. paulmc

Actually paulmc, I consider it you who is being very selective with the evidence you will consider, moreover I consider it extremely biased on your part to call others ignorant who don't subscribe to your extremely narrow and cheery picked view of the evidence. bornagain77

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. I have emphasised that these arguments are entirely independent of simply not knowing of function for those sequences. I have argued that there is an upper limit imposed by purifying selection on the number of bases that can be specified. This is in line with what we know about genome-wide sequence conservation. Importantly, the accumulation of junk across the diversity of life is extremely variable, but closely and predicatably linked to a) the effective population size and b) the mutation rate. Please read some Lynch. When you choose to *ignore* these lines of evidence, rather than address them and say things like "It could be that the argument for junk DNA- that is for junk DNA being the majority- is based on ignorance and is not testable. Other than that, good job." I interpret that as ignorance. paulmc

Moreover, aside from neo-Darwinists rushing to judgement to declare everything they don't understand to be junk, just so as to make their theologically based 'bad design' argument, the fact of the matter is that there are now some very strong lines of evidence that strongly indicate that the programming in DNA is far, far, more advanced than anything man has ever even dreamt of, much less anything he has actually implemented into a 'intelligently designed' code.

Human DNA is like a computer program but far, far more advanced than any software we've ever created. Bill Gates, The Road Ahead, 1996, p. 188

Bill Gates, in recognizing the superiority found in Genetic Coding compared to the best computer coding we now have, has now funded research into this area:

Welcome to CoSBi - (Computational and Systems Biology) Excerpt: Biological systems are the most parallel systems ever studied and we hope to use our better understanding of how living systems handle information to design new computational paradigms, programming languages and software development environments. The net result would be the design and implementation of better applications firmly grounded on new computational, massively parallel paradigms in many different areas. Do you believe Richard Dawkins exists? Excerpt: DNA is the best information storage mechanism known to man. A single pinhead of DNA contains as much information as could be stored on 2 million two-terabyte hard drives. http://creation.com/does-dawkins-exist 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 The multiple codes of nucleotide sequences. Trifonov EN. - 1989 Excerpt: Nucleotide sequences carry genetic information of many different kinds, not just instructions for protein synthesis (triplet code). http://www.ncbi.nlm.nih.gov/pubmed/2673451 "In the last ten years, at least 20 different natural information codes were discovered in life, each operating to arbitrary conventions (not determined by law or physicality). Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Donald E. Johnson – Programming of Life – pg.51 - 2010 DNA Caught Rock 'N Rollin': On Rare Occasions DNA Dances Itself Into a Different Shape - January 2011 Excerpt: Because critical interactions between DNA and proteins are thought to be directed by both the sequence of bases and the flexing of the molecule, these excited states represent a whole new level of information contained in the genetic code, http://www.sciencedaily.com/releases/2011/01/110128104244.htm Ends and Means: More on Meyer and Nelson in BIO-Complexity - September 2011 Excerpt: According to Garrett and Grisham's Biochemistry, the aminoacyl tRNA snythetase is a "second genetic code" because it must discriminate among each of the twenty amino acids and then call out the proper tRNA for that amino acid: "Although the primary genetic code is key to understanding the central dogma of molecular biology on how DNA encodes proteins, the second genetic code is just as crucial to the fidelity of information transfer." http://www.evolutionnews.org/2011/09/ends_and_means050391.html Histone Inspectors: Codes and More Codes - Cornelius Hunter - March 2010 Excerpt: By now most people know about the DNA code. A DNA strand consists of a sequence of molecules, or letters, that encodes for proteins. Many people do not realize, however, that there are additional, more nuanced, codes associated with the DNA. http://darwins-god.blogspot.com/2010/03/histone-inspectors-codes-and-more-codes.html Four More DNA Bases? - August 2011 Excerpt: As technology allows us to delve ever deeper into the inner workings of the cell, we continue to find layer-upon-layer of complexity. DNA, in particular, is an incredibly complex information-bearing molecule that bears the hallmarks of design. http://www.evolutionnews.org/2011/08/four_more_dna_bases049091.html "There is abundant evidence that most DNA sequences are poly-functional, and therefore are poly-constrained. This fact has been extensively demonstrated by Trifonov (1989). For example, most human coding sequences encode for two different RNAs, read in opposite directions i.e. Both DNA strands are transcribed ( Yelin et al., 2003). Some sequences encode for different proteins depending on where translation is initiated and where the reading frame begins (i.e. read-through proteins). Some sequences encode for different proteins based upon alternate mRNA splicing. Some sequences serve simultaneously for protein-encoding and also serve as internal transcriptional promoters. Some sequences encode for both a protein coding, and a protein-binding region. Alu elements and origins-of-replication can be found within functional promoters and within exons. Basically all DNA sequences are constrained by isochore requirements (regional GC content), “word” content (species-specific profiles of di-, tri-, and tetra-nucleotide frequencies), and nucleosome binding sites (i.e. All DNA must condense). Selective condensation is clearly implicated in gene regulation, and selective nucleosome binding is controlled by specific DNA sequence patterns - which must permeate the entire genome. Lastly, probably all sequences do what they do, even as they also affect general spacing and DNA-folding/architecture - which is clearly sequence dependent. To explain the incredible amount of information which must somehow be packed into the genome (given that extreme complexity of life), we really have to assume that there are even higher levels of organization and information encrypted within the genome. For example, there is another whole level of organization at the epigenetic level (Gibbs 2003). There also appears to be extensive sequence dependent three-dimensional organization within chromosomes and the whole nucleus (Manuelides, 1990; Gardiner, 1995; Flam, 1994). Trifonov (1989), has shown that probably all DNA sequences in the genome encrypt multiple “codes” (up to 12 codes). Dr. John Sanford; Genetic Entropy 2005

Besides multiple layers of 'classical information' embedded in overlapping layers throughout the DNA, there has now been discovered another layer of 'quantum information' embedded throughout the DNA:

Quantum Information In DNA & Protein Folding - short video http://www.metacafe.com/watch/5936605/

And, as pointed out previously, quantum information is not even within the materialistic framework of neo-Darwinism to consider in the first place! Thus clearly, for those who refuse to concede the falsification, neo-Darwinism is now overwhelmingly shown to be a position of dogmatic atheistic/materialistic religion instead of anything resembling honest inquiry! etc.. etc.. etc.. music and verse:

Grown Up Christmas List by Amy Grant http://www.godtube.com/watch/?v=JFC9MFNU Genesis 1:26-27 Then God said, "Let us make man in Our image, according to Our image, according to Our likeness; let them have dominion ..." So God created man in His own image; in the image of God He created him; male and female He created them.

bornagain77

Yeah, it's EASY for YOU to claim I am ignorant but more importantly it is yet another one of your untestable claims. Joe

Yet paulmc, the junk DNA argument is precisely a argument from ignorance. Just as with the now discredited vestigial organ argument,,, i.e. if neo-Darwinists were ignorant of a organs function they declared is useless, leftover, evolutionary garbage if you will,,, a false viewpoint that took a very, very, long time to overturn,

“The thyroid gland, pituitary gland, thymus, pineal gland, and coccyx, … once considered useless by evolutionists, are now known to have important functions. The list of 180 “vestigial” structures is practically down to zero. Unfortunately, earlier Darwinists assumed that if they were ignorant of an organ’s function, then it had no function.” "Tornado in a Junkyard" - book - by former atheist James Perloff

For a prime example of evolution's failed predictions of vestigial organs, recently in October 2007, the appendix has been found to have essential purpose in the human body:

Appendix has purpose: Excerpt: "The appendix acts as a good safe house for bacteria," said Duke surgery professor Bill Parker. http://en.wikinews.org/wiki/Scientists:_appendix_has_purpose Surgical removal of the tonsils and appendix associated with risk of early heart attack - June 2011 Excerpt: The surgical removal of the appendix and tonsils before the age of 20 was associated with an increased risk of premature heart attack in a large population study performed in Sweden. Tonsillectomy increased the risk by 44% (hazard ratio 1.44) and appendectomy by 33% (HR 1.33). The risk increases were just statistically significant, and were even higher when the tonsils and appendix were both removed. http://medicalxpress.com/news/2011-06-surgical-tonsils-appendix-early-heart.html#share

as well, to top matters off on this point, the junk DNA argument is in fact a Theologically based 'bad design' argument which has absolutely no business in science,,, i.e. Darwinists, arguing adamantly for 'junk' from such a position of ignorance, declare that God would not have done it that way therefore it must be a accidental product of blind evolution,,,

Refuting The Myth Of 'Bad Design' vs. Intelligent Design - William Lane Craig - video http://www.youtube.com/watch?v=uIzdieauxZg

In fact Darwin's entire theory turns out to be, at its core, a theological argument,,

Charles Darwin, Theologian: Major New Article on Darwin's Use of Theology in the Origin of Species - May 2011 Excerpt: I have argued that, in the first edition of the Origin, Darwin drew upon at least the following positiva theological claims in his case for descent with modification (and against special creation): 1. Human begins are not justfied in believing that God creates in ways analogous to the intellectual powers of the human mind. 2. A God who is free to create as He wishes would create new biological limbs de novo rather than from a common pattern. 3. A respectable deity would create biological structures in accord with a human conception of the 'simplest mode' to accomplish the functions of these structures. 4. God would only create the minimum structure required for a given part's function. 5. God does not provide false empirical information about the origins of organisms. 6. God impressed the laws of nature on matter. 7. God directly created the first 'primordial' life. 8. God did not perform miracles within organic history subsequent to the creation of the first life. 9. A 'distant' God is not morally culpable for natural pain and suffering. 10. The God of special creation, who allegedly performed miracles in organic history, is not plausible given the presence of natural pain and suffering. http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html From Philosopher to Science Writer: The Dissemination of Evolutionary Thought - May 2011 Excerpt: The powerful theory of evolution hangs on this framework of thought that mandates naturalism. The science is weak but the metaphysics are strong. This is the key to understanding evolutionary thought. The weak arguments are scientific and the strong arguments, though filled with empirical observation and scientific jargon, are metaphysical. The stronger the argument, the more theological or philosophical. http://darwins-god.blogspot.com/2011/05/from-philosopher-to-science-writer.html Peacefulness, in a Grown Man, That is Not a Good Sign - Cornelius Hunter - August 2011 Excerpt: Evolution cannot even explain how a single protein first evolved, let alone the massive biological world that ensued. From biosonar to redwood trees, evolution is left with only just-so stories motivated by the dogma that evolution must be true. That dogma comes from metaphysics, http://darwins-god.blogspot.com/2011/08/peacefulness-in-grown-man-that-is-not.html On the Vastness of the Universe Excerpt: Darwin’s objection to design inferences were theological. And in addition, Darwin overlooked many theological considerations in order to focus on the one. His one consideration was his assumption about what a god would or wouldn’t do. The considerations he overlooked are too numerous to mention here, but here’s a few:,,, - C.Yankee https://uncommondesc.wpengine.com/intelligent-design/on-the-vastness-of-the-universe/comment-page-2/#comment-362918

And the theological 'bad design' argument, which Darwinists unwittingly continually use to try to make their case, is actually its own independent discipline of study within Theology itself called Theodicy:

Is Your Bod Flawed by God? - Feb. 2010 Excerpt: Theodicy (the discipline in Theism of reconciling natural evil with a good God) might be a problem for 19th-century deism and simplistic natural theology, but not for Biblical theology. It was not a problem for Jesus Christ, who was certainly not oblivious to the blind, the deaf, the lepers and the lame around him. It was not a problem for Paul, who spoke of the whole creation groaning and travailing in pain till the coming redemption of all things (Romans 8). http://www.creationsafaris.com/crev201002.htm#20100214a Did God Create Evil? (William Dembski) – video http://www.youtube.com/watch?v=cCVYqg6TFmA

Little do most atheists realize that the existence of evil itself necessitates the existence of Good. i.e. you cannot disprove God by pointing to evil. All a atheist does when he points to evil in this world is to point out the fact that this world is not perfectly good, Yet Christianity never claimed we were in heaven in the first place. i.e. by pointing to evil (the absence of good), the atheist actually affirms the Christian belief that we are in a fallen world. bornagain77

And your reply is ignorance battered in sarcasm. paulmc

It could be that the argument for junk DNA- that is for junk DNA being the majority- is based on ignorance and is not testable. Other than that, good job. Joe

Is there anything of substance in particular about the argument for junk DNA that PZ Myers makes that you find objectionable, or is it simply his style? I have attempted serious discussions about junk DNA on UD before, and have raised several independent lines of argument - including directly addressing claims made by Jonathan Wells - but have not had the points raised adequately addressed. I have also written about this elsewhere a couple of times. paulmc

A fundamentalist if I've ever seen one :) As Philip Johnson said, atheism truly has morphed into the monster that is secular religion. Stu7

Paris Hilton is a known air-head. PZ is admiting that he is an air-head of atheism. heh-heh Also what is up with these allged "skeptics"? They should apply their skepticism towards their position- that is why those alleged skeptics get a load of stuff on the internet. Joe

bornagain77, thanks for watching and taking notes. There is no way I could have watched that thing -- weak stomach and all that, you know . . . PZ Myers needs some serious help. In addition to being a ranting, unstable guy, he doesn't know that much about biology. Pretty sad. Oh well, this video will give us something to point to in coming years as his assessment (already way off) continues to be more and more laughable. By the way, I'm going to proclaim myself the Anti-Myers. He claims 5% is not junk? I've stated openly on this blog that, at most, 5-10% of DNA will turn out to be junk. Eric Anderson

The following describes how quantum entanglement is related to functional information:

Quantum Entanglement and Information Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. http://plato.stanford.edu/entries/qt-entangle/

Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;

Quantum Entanglement and Teleportation – Anton Zeilinger – video http://www.metacafe.com/watch/5705317/

A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:

Quantum Teleportation Excerpt: To perform the teleportation, Alice and Bob must have a classical communication channel and must also share quantum entanglement — in the protocol we employ*, each possesses one half of a two-particle entangled state. http://www.cco.caltech.edu/~qoptics/teleport.html

And quantum teleporation has now shown that atoms, which are suppose to be the basis from which ALL functional information ‘emerges’ in the atheistic neo-Darwinian view of life, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of in the first place!

Ions have been teleported successfully for the first time by two independent research groups Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,, http://www.rsc.org/chemistryworld/Issues/2004/October/beammeup.asp Atom takes a quantum leap – 2009 Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,, “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second. http://www.freerepublic.com/focus/news/2171769/posts

Thus the burning question, that is usually completely ignored by the neo-Darwinists that I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA, or any other atoms, when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments? i.e. It is simply 'COMPLETELY IMPOSSIBLE' for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ‘emerge’ from, any material basis of particles! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a trivial matter in the least as far as developments in science have gone!

Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff - video (notes in description) http://vimeo.com/29895068 non-local ‘epigenetic’ information is implicated in controlling the 3-D spatial organization of body plans; https://docs.google.com/document/d/1iNy78O6ZpU8wpFIgkILi85TvhC9mSqzUSE_jzbksoHY/edit?hl=en_US

verses and music:

John 1:1-3 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. 1 Corinthians 2:14 The natural person does not accept the things of the Spirit of God, for they are folly to him, and he is not able to understand them because they are spiritually discerned. Brooke Fraser – Lord of Lords(Legendado Português) - http://www.youtube.com/watch?v=rkF3iVjOZ1I

bornagain77

Quantum Entanglement/Information is confirmed in DNA by direct observation here;

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 Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/ Quantum states in proteins and protein assemblies: The essence of life? - STUART HAMEROFF, JACK TUSZYNSKI Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign. http://www.tony5m17h.net/SHJTQprotein.pdf Myosin Coherence Excerpt: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. Living systems have mastered the making and breaking of chemical bonds, which are quantum mechanical phenomena. Absorbance of frequency specific radiation (e.g. photosynthesis and vision), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects. http://www.energetic-medicine.net/bioenergetic-articles/articles/63/1/Myosin-Coherence/Page1.html

The necessity of 'transcendent' information, to ‘constrain’ a cell, against thermodynamic effects is noted here:

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

i.e. It is very interesting to note, to put it mildly, that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! ,,,To refute this falsification of neo-Darwinism, one must overturn Alain Aspect, and company’s, falsification of local realism (reductive materialism) ! ================= Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007 ================= And to dovetail into Dembski and Marks’s previous work on Conservation of Information;,,,

LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information William A. Dembski and Robert J. Marks II http://evoinfo.org/publications/lifes-conservation-law/

,,,Encoded ‘classical’ information such as what Dembski and Marks demonstrated the conservation of, and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of ‘transcendent’ (beyond space and time) quantum entanglement/information by the following method:,,,

,,,This following research provides solid falsification for the late Rolf Landauer’s decades old contention that the information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it; Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm

,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,

Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html

Further note:

Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC (Functional Sequence Complexity). FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, Testable hypotheses about FSC What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses: Null hypothesis #1 Stochastic ensembles of physical units cannot program algorithmic/cybernetic function. Null hypothesis #2 Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function. Null hypothesis #3 Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function. Null hypothesis #4 Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time. We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified. http://www.tbiomed.com/content/2/1/29

bornagain77

Actually Joe, to be fair, PZ just declared Dembski's prediction that most of the DNA would exhibit functionality 'FALSIFIED', and did not declare the entire ID framework falsified. But even in that modest claim for falsification, PZ has greatly overstated his case and has come no where near the rigor required for genuine 'falsification' of that particular prediction;, Indeed there is much evidence that argues forcefully against each point he brought up!!!,, Whereas, on the other hand, the fact that the genetic reductionism model, which PZ is working from in the first place, is 'falsified', is coming into general acceptance with the gradual realization of just how pervasive, and foundational, epigenetics is. (as briefly noted),, Moreover, the fact that non-local, beyond space and time, quantum entanglement/information is now found in molecular biology, on a massive scale,,, far from the superficial falsification PZ thought he had achieved, goes all the way down to the foundation of reality itself to rigorously FALSIFY the materialistic foundation upon which the entire neo-Darwinian framework is built!!! notes: Falsification Of Neo-Darwinism by Quantum Entanglement/Information Neo-Darwinian evolution purports to explain all the wondrously amazing complexity of life on earth by reference solely to chance and necessity processes acting on energy and matter (i.e. purely material processes). In fact neo-Darwinian evolution makes the grand materialistic claim that the staggering levels of unmatched complex functional information we find in life, and even the ‘essence of life’ itself, simply ‘emerged’ from purely material processes. And even though this basic scientific point, of the ability of purely material processes to generate even trivial levels of complex functional information, has spectacularly failed to be established, we now have a much greater proof, than this stunning failure for validation, that ‘put the lie’ to the grand claims of neo-Darwinian evolution. This proof comes from the fact that it is now shown from quantum mechanics that ‘information’ is its own unique ‘physical’ entity. A physical entity that is shown to be completely independent of any energy-matter space-time constraints, i.e. it does not ‘emerge’ from a material basis. Moreover this ‘transcendent information’ is shown to be dominant of energy-matter in that this ‘information’ is shown to be the entity that is in fact constraining the energy-matter processes of the cell to be so far out of thermodynamic equilibrium. First, Here is the falsification of local realism (reductive materialism). Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:

The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video http://www.metacafe.com/w/4744145

The falsification for local realism (reductive materialism) was recently greatly strengthened:

'Quantum Magic' Without Any 'Spooky Action at a Distance' - June 2011 Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically. http://www.sciencedaily.com/releases/2011/06/110624111942.htm Physicists close two loopholes while violating local realism – November 2010 Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview. http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009 Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/releases/2009/07/090722142824.htm

of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light. This following video illustrates just how 'spooky', to use Einstein’s infamous word, this quantum action truly is:

Light and Quantum Entanglement Reflect Some Characteristics Of God – video http://www.metacafe.com/watch/4102182/

And yet, this ‘spooky’ quantum entanglement, which rigorously falsified local realism (reductive materialism) as the ‘true’ description of reality, is now found in molecular biology on a massive scale!

Quantum Information/Entanglement In DNA & Protein Folding – short video http://www.metacafe.com/watch/5936605/ 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 (arxiv.org/abs/1006.4053v1). “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

bornagain77

notes:

Human Genome “Infinitely More Complex” Than Expected - April 2010 Excerpt: Hayden acknowledged that the “junk DNA” paradigm has been blown to smithereens. “Just one decade of post-genome biology has exploded that view,” she said,,,, Network theory is now a new paradigm that has replaced the one-way linear diagram of gene to RNA to protein. That used to be called the “Central Dogma” of genetics. Now, everything is seen to be dynamic, with promoters and blockers and interactomes, feedback loops, feed-forward processes, and “bafflingly complex signal-transduction pathways.” http://www.creationsafaris.com/crev201004.htm#20100405a Deep Genomics: In the Case of DNA, the Package Can Be as Important as Its Contents, New Work With Fruit Flies Reveals - January 2011 http://www.sciencedaily.com/releases/2011/01/110113102158.htm The Origin at 150: is a new evolutionary synthesis in sight? - Koonin - Nov. 2009 Excerpt: The edifice of the modern synthesis has crumbled, apparently, beyond repair. http://www.arn.org/blogs/index.php/literature/2009/11/18/not_to_mince_words_the_modern_synthesis With a Startling Candor, Oxford Scientist Admits a Gaping Hole in Evolutionary Theory - November 2011 Excerpt: As of now, we have no good theory of how to read [genetic] networks, how to model them mathematically or how one network meshes with another; worse, we have no obvious experimental lines of investigation for studying these areas. There is a great deal for systems biology to do in order to produce a full explanation of how genotypes generate phenotypes,,, http://www.evolutionnews.org/2011/11/with_a_startling_candor_oxford052821.html What Do Organisms Mean? Stephen L. Talbott - Winter 2011 Excerpt: But it’s obvious enough that a section of a DNA molecule does not “sculpt” anything. In fact, the research emphasis today is in the reverse direction: how proteins and the overall activity of the cell sculpt the genes and chromosomes. ,,, The activity of individual genes reflects the choreography of chromosomes, which reflects the larger choreography of the nucleus, which reflects the choreography of the cell and organism as a whole. Who, then, is sculpting whom?,,, http://www.thenewatlantis.com/publications/what-do-organisms-mean Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf

etc.. etc.. etc.. bornagain77

Yes BA77, they have indeed falsified their strawman version of ID. They hung it out, beat the crap out of it and now they say they are laying it to rest. My bet is they will resurrect it again and again just so they can falsify it some more.... Joe

notes:

26:00 minute mark PZ states '5% of the genome is not junk'; 29:00 minute mark, 'fire the guy' for 'bad design', 'stupid function' for repeat 10%; 31:00 minute mark: LINE segments, 21%, PZ staes they 'do nothing for the cell', states LINEs are 'viral relics', 'useless',,, SINE's and ERV's both declared useless waste,,, PZ's final pronouncement at 35:30 mark is,,, 45% known, parasitic junk DNA 10% structural DNA 5% functional DNA paraphrase,,, We 'know' half of DNA is garbage,,, 36:15, PZ 'predicts' most of the remaining 'unknown' DNA will be found to be 'garbage', although he concedes 'some surprises'; ,,,mentions 'Onion test' Declares ID 'FALSIFIED' at 41:00 minute mark.

The reports of my death have been greatly exaggerated - Mark Twain bornagain77