Here:
The authentic Word from Da Beard, and – as he isn’t a Christian Darwinist – you don’t need to start flinging sandals to hear it. (If you own any sandals.)
Here’s the real story on junk DNA.
Paris Hilton, in case you wondered. It could be your kid who gets … well, squished … in the cause of celebrity. What does that matter?
notes:
The reports of my death have been greatly exaggerated – Mark Twain
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….
notes:
etc.. etc.. etc..
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 falsification for local realism (reductive materialism) was recently greatly strengthened:
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:
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 Entanglement/Information is confirmed in DNA by direct observation here;
The necessity of ‘transcendent’ information, to ‘constrain’ a cell, against thermodynamic effects is noted here:
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;,,,
,,,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:,,,
,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,
Further note:
The following describes how quantum entanglement is related to functional information:
Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;
A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:
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!
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!
verses and music:
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.
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.
A fundamentalist if I’ve ever seen one 🙂
As Philip Johnson said, atheism truly has morphed into the monster that is secular religion.
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.
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.
And your reply is ignorance battered in sarcasm.
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,
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:
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,,,
In fact Darwin’s entire theory turns out to be, at its core, a theological argument,,
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:
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.
Yeah, it’s EASY for YOU to claim I am ignorant but more importantly it is yet another one of your untestable claims.
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.
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:
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:
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:
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.
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.
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.
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, 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!!!!!!
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:
Presumably you’ve also looked at this discussion:
http://www.uncommondescent.com.....up-though/
Arguing for pervasive amounts of junk DNA is a fool’s errand.
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:
moreover:
The paradox between having elegant DNA repair mechanisms and the need for random mutations to ‘drive evolution’ is discussed here;
etc.. etc.. etc..
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.
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:
Further notes:
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.
So just to be clear – you’re completely uninterested in talking on topic about junk DNA then?
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!
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.
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.
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:
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:
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.
Quantum Action confirmed in DNA by direct empirical research;
Moreover a very high level of information processing suddenly disappears upon death of a organism
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
…sorry
I will reply at the bottom – as I find I get a bit lost in this thread nesting.
Eric @ 4.2.1.1
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.
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.
Eric, clarity through and through, nice post!
We agree on something 🙂
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.
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.
Thank you for that, but it seems my fumbling of my post has us talking past each other. My apologies.
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.
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:
further note:
ENV has a excellent article up that is of related interest,
paulmc, a fitting song,
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/2.....44601.html
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.
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?
Fitting, yes, I particularly enjoyed the lyrics about organellar genomic structure.
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???
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!!
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.
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.
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 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;
here is a very clear example as to exactly why population genetics will NEVER explain multiple layers of overlapping complexity:
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:
Moreover paulmc you have no substantiating empirical evidence whatsoever for your atheistic neo-Darwinian position in the first place:
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!
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, 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!
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:
Great – so am I take it from this that you now accept the argument for junk DNA?
NO!
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, 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,,,
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:
The following ‘should’ interest you paulmc (though you will probably completely ignore it as you do with anything else that falsifies neo-Darwinism)
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.!
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.
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.
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).
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.
paul, and yet for all your denial, you still support that obscenely huge portions of the DNA is junk! Go figure!!!
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!
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.
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?
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.
So all DNA that doesn’t code for some type of DNA is not junk?
Can your position even explain structural DNA? Can it explain coding DNA?
It sure seems good at explaining broken things.
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.
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.
Dude, your framwork can’t even explain onions, nor functional genomes.
Perhaps you should focus on that.
Or actually perform the experiment I mentioned.
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:
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.
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:
Music and Verse:
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.
Back on topic, I’ll take that to mean your framework can’t explain a) or b). That’s fine, just checking.
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!
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?
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
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.
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!!!
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:
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:
further notes:
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.
The following expert doesn’t even hide his very unscientific preconceived philosophical bias against intelligent design,,,
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,,,
further note:
music:
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?
Speaking of ‘uphill battles’, how’s that refutation of Abel’s Null Hypothesis working out???
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.
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.
Whatever Paul. Until you or someone conducts that experiment the claim of the majority of our genome is junk is total BS.
Yet there is ONLY ONE WAY to confirm that inference and apparently people are too afraid to perform the experiment.
Dude, your framwork can’t even explain onions, nor functional genomes.
Perhaps you should focus on that.
Or actually perform the experiment I mentioned.
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.
paulmc:
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.
‘haphazardly inserted’
REALLY???
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:
see post 17
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”.
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,
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.
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???