The Rest of the Science Community Starting to Catch Up With ID on “Junk” DNA (It Ain’t)
| September 8, 2012 | Posted by Barry Arrington under Intelligent Design |
The ID community, including many writers here at UD, has been predicting for years that so-called junk DNA would be found to be functional. The Darwinists have scoffed. Now ID proponents are being vindicated. My prediction: The Darwinists will change their story to “we’ve been saying this all along.”
The Washington Post reports on the breakthrough research published in Nature.
Most of a person’s genetic risk for common diseases such as diabetes, asthma and hardening of the arteries appears to lie in the shadowy part of the human genome once disparaged as “junk DNA.”
Indeed, the vast majority of human DNA seems to be involved in maintaining individuals’ well being — a view radically at odds with what biologists have thought for the past three decades.
Those are among the key insights of a nine-year project to study the 97 percent of the human genome that’s not, strictly speaking, made up of genes.
The Encyclopedia of DNA Elements Project, nicknamed Encode, is the most comprehensive effort to make sense of the totality of the 3 billion nucleotides that are packed into our cells.
The project’s chief discovery is the identification of about 4 million sites involved in regulating gene activity. Previously, only a few thousand such sites were known. In all, at least 80 percent of the genome appears to be active at least sometime in our lives. Further research may reveal that virtually all of the DNA passed down from generation to generation has been kept for a reason.
“This concept of ‘junk DNA’ is really not accurate. It is an outdated metaphor,” said Richard Myers of the HudsonAlpha Institute for Biotechnology in Alabama.
Myers is one of the leaders of the project, involving more than 400 scientists at 32 institutions.
Another Encode leader, Ewan Birney of the European Bioinformatics Institute in Britain, said: “The genome is just alive with stuff. We just really didn’t realize that beforehand.”
“What I am sure of is that this is the science for this century,” he said. “In this century, we will be working out how humans are made from this instruction manual.”
The new insights are contained in six papers published Wednesday in the journal Nature. More than 20 related papers are appearing elsewhere. . .
The new research helps explain how so few genes can create an organism as complex as a human being. The answer is that regulation — turning genes on and off at different times in different types of cells, adjusting a gene’s output and coordinating its activities with other genes — is where most of the action is. . . .
In one paper, a team led by Thomas R. Gingeras of Cold Spring Harbor Laboratory in New York reported that three-quarters of the genome’s DNA is “transcribed” into a related molecule, RNA, at some point in life. A small amount of that RNA is then “translated” into protein. Much of the rest appears to have gene-regulating activities that remain to be discovered.
In a telephone conference call with reporters, several of the researchers likened the 4 million regulatory sites to electrical switches in a hugely complex wiring diagram.
By turning switches on and off, and varying the duration of their activity, a nearly infinite number of circuits can be formed. Similarly, by activating and modulating gene function, immensely complicated events such as the development of a brain cell or a liver cell from the same starting materials is possible.
119 Responses to The Rest of the Science Community Starting to Catch Up With ID on “Junk” DNA (It Ain’t)
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This paper is a bombshell. I like this quote from the following video:
The denial of this overwhelming evidence against Junk DNA, that I’ve seen thus far from Darwinists, really is illuminating as to revealing the dogmatic philosophical bias that Darwinists have as to ever evaluating the evidence fairly.
Around 9:30 minute mark of the following podcast, Casey Luskin speaks on this dogmatic ‘no concession’ policy of neo-Darwinists as to ever admitting they were wrong:
Very interesting quote:
“In a telephone conference call with reporters, several of the researchers likened the 4 million regulatory sites to electrical switches in a hugely complex wiring diagram.
By turning switches on and off, and varying the duration of their activity, a nearly infinite number of circuits can be formed. Similarly, by activating and modulating gene function, immensely complicated events such as the development of a brain cell or a liver cell from the same starting materials is possible.”
Emphasis mine. Does the phrase “immensely complicated events” ring a bell for us in ID? I bit ot does
Now our “friends” (the darwinists), in the spare time left by their unsuccessful attempts at explaining how the basic protein domains came into being, must also explain how the right circuits were generated among the search space of a “nearly infinite number of circuits”. I am not surprised that they are a little bit displeased…
I don’t believe I’ve ever seen a larger, more collective backtracking than I have when reading Darwinists’ reactions to the ENCODE Project’s discovery. This is unintentional comedy at it’s finest.
Backtracking? Pretty much everyone is saying the “80% functional” number is wrong. Even the project leader, Ewan Birney, more or less admitted it’s not credible for standard definitions of “functional”.
So it’s the ENCODE leaders that are backtracking, not the scientific community.
And, onion test. Answer it or you don’t have an argument.
http://www.genomicron.evolverz.....nion-test/
I like this article:
Nick as to the onion test, let’s see if you can detach your ‘intellectual inertia’ for a moment:
Nick, as with you philosophically (and dogmatically) driven belief in Junk DNA, human ignorance for why the genomes are the varying sizes they are is not a actual argument for the Darwinian origin of those varying sizes! In fact some very credible reasons have been put forth for why it would make ‘engineering sense’ to vary genome sizes as such:
i.e. There is no logical ‘evolutionary progression’ to be found for the amount of DNA in less complex animals to the size of genomes found in more complex animals. In fact the genome sizes are known to vary widely between Kinds/Species despite their differences in complexity and this mystery is known as the c-value enigma:
C-value enigma
Excerpt: it was soon found that C-values (genome sizes) vary enormously among species and that this bears no relationship to the presumed number of genes (as reflected by the complexity of the organism). For example, the cells of some salamanders may contain 40 times more DNA than those of humans. Given that C-values were assumed to be constant because DNA is the stuff of genes, and yet bore no relationship to presumed gene number, this was understandably considered paradoxical;
http://en.wikipedia.org/wiki/C-value_enigma
And yet, even though this C-value enigma is somewhat (very?) paradoxical to the materialistic, neo-Darwinian, point of view, since information is presupposed to simply ‘emerge’ from a material basis and there clearly is no linear correlation to amount of material present and amount of information expressed, from a design point of view we should rightly expect genome sizes to vary within design constraints. Constraints that would obviously be imposed in trying to achieve a ‘optimal design’ for any particular life-form that was designed; For examples of such constraints,,:
“There is strong positive correlation, however, between the amount of DNA and the volume of a cell and its nucleus – which effects the rate of cell growth and division. Furthermore, in mammals there is a negative correlation between genome size and rate of metabolism. Bats have very high metabolic rates and relatively small genomes. In birds, there is a negative correlation between C-value and resting metabolic rate. In salamanders, there is also a negative correlation between genome size and the rate of limb regeneration.”
Jonathan Wells – The Myth Of Junk DNA – page 85
Similarities Found in Genomes Across Multiple Species; Platypus Still out of Place – July 2011
Excerpt: “Basically what this all means is that if the chromosome number of a species can be given, the relative sizes of all the chromosomes can instantly be known,” Yu said. “Also, if you tell me the genome size in the chromosome base pair, I can tell you the base pair length of each chromosome.”
http://pos-darwinista.blogspot.....evela.html
THE ALLOMETRIC RELATIONSHIP BETWEEN GENOME SIZE (C-VALUE) AND TOTAL METABOLIC ENERGY PER LIFESPAN, PER UNIT BODY MASS IN ANIMALS
Excerpt: this show(s) that,,, the higher total life energy per unit body mass leads to smaller C-value.
http://www.sustz.com/Proceedin.....ANASOV.pdf
As well, at the 7:00 minute mark of this following video, 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/
Chargaff’s “Grammar of Biology”: New Fractal-like Rules – 2011
Excerpt from Conclusion: It was shown that these rules are valid for a large set of organisms: bacteria, plants, insects, fish and mammals. It is noteworthy that no matter the word length the same pattern is observed (self-similarity). To the best of our knowledge, this is the first invariant genomic properties publish(ed) so far, and in Science invariant properties are invaluable ones and usually they have practical implications.
http://arxiv.org/ftp/arxiv/pap.....2.1528.pdf
Why the “Onion Test” Fails as an Argument for “Junk DNA” – Jonathan M. – November 2, 2011
Excerpt: The so-called onion test, or indeed the “C-value enigma,” is predicated on unsupportable assumptions about the physiological effects of — and/or requirements for — larger genomes, many of which are contradicted by the scientific evidence.
http://www.evolutionnews.org/2.....52321.html
So aside from this being yet another failed Darwinian prediction, what’s the big deal? Can someone please explain what’s going on in simple terms?
Thanks.
The rate-independent symbol structures make life and evolution possible. Deal with it, or you don’t have an argument.
Nick is in full spin mode. Here is my prediction. Nick and his buddies will say ENCODE isn’t really saying what you think they are saying until that becomes totally unsupportable. Then they will start saying that they never really believed most of the DNA was junk. In fact, Darwinian theory predicts exactly what ENCODE has found.
The whole thing is like the husband who was caught by his wife in flagrante delicto carrying on with another woman. The man tries to brass it out and denies the affair. The wife says “but I caught you in the very act,” to which the man replies “who are you going to believe, me or your own eyes?” Nick asks us to believe him and not our own eyes.
Nick, no amount of spin on your part is going to make this anything other than a devastating loss of the “junk DNA” crowd. Why don’t you show a little class and fess up that you and your buddies have been wrong all along when you claimed the vast majority of human DNA is junk.
Here ya go Nick.
just say it wasn’t you
Hey Barry. Answer me this:
1. What definition of “function” did ENCODE use?
2. Is that a good definition, in accord with standard English usage?
3. Why isn’t it valid to point out that even the project leader, Ewan Birney, expressed qualms about the 80% number and chose it mostly to get attention?
4. If most of our DNA is functional, why do some other vertebrates (and plants) make a vertebrate with 10 times less DNA, and other vertebrates use 10 times more? We all have about the same number of genes, the differences are due mostly to repetitive elements. Why isn’t it reasonable to think that the minimal genomes contain what is actually needed, and the critters with 10 times bigger genomes (us) and 100 times bigger genomes (e.g. salamanders) have a lot of DNA that it pretty much dispensable, i.e., junk?
Nick,
I will not rise to your bait. Your attempt to deflect from the fundamental findings at ENCODE are sad.
Tell you what. I will answer your questions just as soon as you admit that everyone who said the vast majority of human DNA is “junk” was wrong. Again, I won’t be holding my breath.
Nick Matzke:
LoL! the first part “If most of our DNA is functional…” has nothing to do with the second. Desperation is not a good position to argue from, Nick.
But anyway- Why do old computers contain many more discrete components than their modern counterparts? Why are old computer languages more cumbersome and contain more coding lines than their modern counterparts?
BTW Nick, how many different proteins do we have compared with the number of genes?
I used to work for a computer/ technology company that used redundancy- every board was backed up by another- if the main board failed it automatically switched to the other. AND each board was also redundant- each side a mirror image of the other, both running and checking each other to make sure they had the same 1s and 0s. We could have removed 75% of the system and it still would have functioned, ie 75% was dispensable junk by Nick’s “logic”.
However far from being dispensable junk redundancy is a design feature with those systems.
Also there is another feature of genomes that Nick’s position doesn’t even consider-> that it also serves as a data storage device just as hard drives, flash drives, PROMS, etc do. Meaning there is actual software directing gene expression & alternative gene splicing and determining final form. The DNA just helps in carrying out the instructions it contains.
See also the onion test answered
Applying Nick’s “logic” to soda- Coke cannot taste good because Moxie tastes like crap.
Here are a few points for you to chew on Nick as you defiantly cling to your colossal error of junk DNA:
“Junk DNA” is found to have 100% purpose in an astonishing way in this following paper:
virtual 100% functionality for DNA was established by another method here:
Moreover this study suggests that the simplistic definition of a gene is gone bye-bye:
This following video is a bit more clear as to exactly why the term ‘gene’ is far too simplistic
As well this study found that the 3-Dimensional structure of the genome is found to play a important role:
Related ’3-Dimensional’ notes
Moreover, very unexpectedly from the atheistic Darwinian mindset, the 3-D arrangement of DNA is found to determine ‘the form of the endogenous electric field’
Here is a ‘jaw dropping’ video of a 3 dimensional ‘electric field’ in action:
Moreover, as if the preceding was not bad enough for dogmatic neo-Darwinists like Matzke and Moran who refuse to admit they are wrong on Junk DNA, body plans are not even encoded solely by the DNA code in the first place (as is required in the genetic reductionism model of neo-Darwinism). This inability of body plans to be reduced directly to the DNA code is clearly shown by Cortical Inheritance and ‘epigenetic’ studies.
Besides this mysterious epigenetic information, there is also now found to be ‘non-local quantum information’ along the entirety of the DNA molecule which we really have no clue as to what it is doing:
As well, besides the quantum information/entanglement in DNA that no one really has a firm clue as to exactly what it is doing, there are hints of another whole level of information hidden within the genome that, as well, no one has a clue what it is doing:
Of related interest is this very recent breakthrough which stored 700 terrabytes of functional information on just one gram of DNA!
Notes of interest:
Barry @14, you are being disingenuous in your response to Nick. The definition of function used by ENCODE is paramount to the discussion.
paulmc- so is the definition of dispensable junk.
Here is a particularly good read from Sean Eddy on ENCODE’s findings. You’ll see that junk DNA is functional because of ENCODE’s definition.
paulmc accuses Mr Arrington of being disingenuous:
Really paulmc??? Disingenuous paulmc??? that’s funny because the reality of the situation is that it is neo-Darwinists who are the ones who have been completely disingenuous towards the evidence for functionality in DNA. This ‘disingenuousness’ is especially surprising since the initial 2007 ENCODE findings came out urging a more ‘neutral’ view of non-coding regions. If science were to have operated as it should, this warning should have put severe dampers on Darwinian claims. But it did not, which goes to show, once again, that it is not about the science with Darwinists!!!:
i.e.
Did neo-Darwinists listen to these words of caution paulmc? No of course not! Despite the fact that researchers are dealing with complexity that is orders of magnitude greater than anything ever built by man in computer programs,,,
,,,the Darwinists are, for purely philosophical/religious reasons as far as I can tell, dead set against ever admitting to any hints of Design in life whatsoever. In fact, it is held in some quarters that this irrational stance (indeed unscientific stance) by Darwinists has severely hindered scientific progress:
and this irrational stance of Darwinists can even be argued to have hindered medical progress:
No paulmc, IDists may not be perfect, no human is for that matter, but neo-Darwinists take the cake on being disingenuous towards the evidence for finding functionality in DNA!
further note:
Perhaps you should have read the link in @21 before posting? “Functional” is defined so broadly that junk is subsumed within it.
paulmc, actually Darwinists have junk defined so broadly that functionality is subsumed within it.
About the C-Value paradox
I remember reading a paper from Lynch that 1-50bp deletions in humans were 3 times as likely as insertions. Could lungfish, salamanders, and onions have some process in the replication that has gone wrong, causing them to accumulate extra nucleotides over time? (and therefore it would be junk).
I suppose this is the same as the Darwinian explanation, and also perfectly compatible with ID, esp. given degeneration?
Junk DNA has no bearing on phenotype. Functional DNA for most people would be everything else, rather than just everything that has a degree of biological activity. As Eddy points out – and others have too – you would expect random generated sequences inserted into a genome to qualify as functional under ENCODE.
Therefore it is the definition of function and not of junk that is too broad here.
paulmc:
True, but that does NOT mean that all the DNA that has no bearing on phenotype is junk.
paulmc:
Hang on. Just want to make sure I caught this. Are you saying that some 90% of our DNA (the “junk” figure, plus or minus a couple of percentage points) has no bearing on phenotype?
Eric,
no, not quite – I’d say that 90% of the genome shows no evidence of conservation, and while much of it is likely to be junk, it is not possible to firmly conclude it is *all* junk without a stronger basis. With that said, there is also much that we do know, which allows us to put upper and lower limits on junk.
Firstly, the ENCODE extrapolation suggests a final figure might be 20% functional (by traditional definitions) and 80% junk. Secondly, in the past I have referred repeatedly to Larry Moran’s quantitative account of genome composition as being a good guide – the junk component there being estimated as between 65% to 90%.
The majority of the human genome is junk by any of these definitions.
Really??? That’s a pretty radical claim paulmc! Indeed:
Thus if:
As paulmc claims then Junk DNA would have to be perfectly neutral biochemically and place no unnecessary energetic burden on the cell affecting its normal, healthy, functioning. But that belief in perfect biochemical neutrality is preposterous!
Evolution Vs Genetic Entropy – Andy McIntosh – video
http://www.metacafe.com/watch/4028086
For the cell would have to expend energy replicating totally useless DNA and, according to this new research by ENCODE, transcribing it into massive amounts of RNA, where, according to Darwinists, it does absolutely nothing useful, but is just a unnecessary energetic burden on the cell???,,,
…And so goes the completely insane swamp land of evolutionary apologetics.
notes:
I wonder if ENCODE did a graph comparing the Transcription Regulation in humans to a Call Graph of a computer operating system as the following video does for e-coli:
It would certainly be very interesting to see the comparative differences between the e-coli and Human Transcription Regulation networks since humans have a vastly more expansive regulatory network than e-coli does
Related notes:
per crev.info
Can someone explain to me why scientists use the words functional and junk interchangeably…An answer from you Paul would be nice.
Also, Maybe it’s time for a redefining of terms in the case of the word “Functional” in evolutionary science. Scientists, I feel, want to use the “junk DNA” words because they think it hurts the idea of an IDer. I agree, it does, but if there was never any real USELESS junk in the genome, and scientists have know that for a while, than I accuse scientists of a half-truth, if not lying for years!
Functional, nonfunctional, junk…it’s all conflated now, especially if you are right Paulmc. The question I would like answered is…do these non-coding sequences have(serve) a purpose in our genome? (the importance of its usage is besides the point)…if yes than ID would predict that…if no than it hurts ID. I don’t claim to know the answer just yet.
paulmc:
Hang on. Weren’t we being told that we share 95%, 98&, 99% (pick the favorite number) of our DNA with chimps? Now you’re suggesting that there is no evidence of conservation of 90% of our DNA. So either our DNA has conserved the vast majority (and thus remains very similar to our common chimp ancestor), or there isn’t any conservation (and thus the idea of DNA similar to the common chimp ancestor has to be questioned).
So you’re accusing these scientists of being illogical?
Eric, conservation = purifying selection.
Mung, I’m sure their logic is just fine. Their definitions not so much.
As I explained in the first ENCODE thread here, and others have explained all over the internet (including Ewan Birney, ENCODE coordinator) – ‘functional’ under ENCODE means something very broad. The definition subsumes what most of us would call junk. They effectively redefine ‘functional’ as ‘biologically active’. In Birney’s words:
So, for a start, functional is defined to automatically include every intronic base in the genome (60% of the genome already) on account of those bases being transcribed. ENCODE effectively redefine junk as anything that doesn’t meet the criteria Birney describes above(i.e. very little).
They argue the purpose of this is to give a precise definition of functional, yet other definitions are possible. The other definitions wouldn’t have made such punchy headlines.
The assumption that Darwinists will change their story suggests finding errors in a theory is somehow a bad thing. This is illogical, as it conflicts with our current, best explanation for the growth of knowledge. Namely, all theories contain errors of varying degree and that finding them is how knowledge grows. It also assumes some ultimate explanation can be found.
For example, even when found to be in error as a whole, as it was in this case, a theory that only roughly 2% of the genome has a specific purpose is better than the vague claim that 100% of the genome “should be functional”. This is because it encompasses the theory that roughly 2% of the genome a specific function, rather than some other specific function, which can be found in error.
Merely assuming the entire genome “should be functional” does not stick its neck out in a way that allows itself to be criticized. Furthermore, if we do not conjecture a specific theory of what specific function they do perform, then we do not know what tests to run. And without tests, we do not know what observations to make. So, merely saying “all genes should be functional” doesn’t tell us where we should look or what we should look for.
In addition, a replicators, we know that genes to serve a purpose. They play a casual role in getting copied. So, of course, they “do something”. The question is, what hard to vary role do they play in adaptations of biological organisms.
IOW, proposing the remaining 98% of the genome did not play a role in building biological adaptations means that the 2% should play the entire role. That’s a testable prediction that can be criticized.
Surviving criticism and *not* surviving criticized is a win win situation, which doesn’t represent a blow to human intellect. In fact, it’s just the opposite. Our ability to devise specific tests that would falsify one theory, but not the other, is an example of human intellect. This is what allows us to make progress.
Furthermore human designers regularly make things that are merely cosmetic or inadvertently end up creating things that serve no purpose. In addition, a designer could make genes non functional in an attempt to obscure its role in the process. IOW, it’s not clear why you would expect an abstract designer with no defined limitations to make all genes functional.
paulmc,
But no so broad as to include all DNA.
IOW, even under ENCODE there is still room for “non-functional” DNA, aka “junk”. True?
But not all of what most of you would consider junk. And that, sir, is the point, isn’t it?
The definition subsumes some of what most of you would call junk, and perhaps even most of what most of you would call junk.
So let’s not pretend like ENCODE has done away with “junk DNA.” There’s still some hope for most of you.
ok. But I think the real issue is purpose. Does it serve any purpose? Is that still an open question in your mind? Or are you still convinced that it serves no purpose?
I have to wonder why they would call it functional if it serves no purpose. Why not just call it biologically active?
As far as I am concerned, “junk DNA” didn’t mean “biological inert DNA,” but rather “purposeless DNA.”
Am I wrong?
here
Just bad science reporting?
paulmc you state:
Unfortunately for you, the neo-Darwinian, atheistic/materialistic, foundation for logic is far from fine on this particular matter, or for any other subject in science for that matter, since atheistic materialism winds up in abject epistemological failure (A.Plantinga, Boltzmann’s Brain).
Indeed, Modern Science was born in the matrix of Christian Theism by presupposing the world was intelligible to the human mind because we are made in the image of the Creator Who made the universe and all life in it. Indeed science was born by presupposing that ‘functionality’ would be discovered in the universe and in life before any functionality was even known to exist in the world or in life. Atheistic materialism, which undergirds neo-Darwinian thought, with its demand for unguided randomness at its foundational base, is simply completely at odds with that very fruitful heuristic that was born out of Judeo-Christian presuppositions. Indeed Neo-Darwinian evolution with its demand for ‘non-functionality’, i.e. for junk, vestigial, etc.., is simply a complete hindrance to science properly done! This undo hindrance that atheistic materialism places on science is already self evident in this new area of investigation of ‘Junk DNA:
I could list many more areas where atheistic materialism has hindered science in such a way. Thus paulmc however reasonable you may think your arguments to be for presupposing ‘non-functionality (I personally find your arguments baseless), the fact is that you are in fact very unreasonable in trying to advance your position!
Non-functional but biologically active sites involved in regulating gene activity? Still “junk”?
http://www.amazon.com/dp/0199550018
http://www.amazon.com/dp/0199594937
NickMatzke_UD:
Really? That’s the best you can do? What does the “onion test” have to do with the human genome, which is, after all, the subject of the OP?
ok, Nick.
Why is there something, rather than nothing?
Answer it or you don’t have an argument.
Off Topic
Here is a free course on
wishfulthinkinggenetics and evolutionhttps://www.coursera.org/course/geneticsevolution
Mung — I’ll run a couple of your posts together and respond to the lot. Firstly:
Actually, Birney suspects that by the end of ENCODE (another 5 years) the figure will be 100% under their definition.
That’s exactly what they have done. ENCODE has effectively defined away junk DNA, as I have explicitly outlined. Again, the expected figure of functional DNA in the human genome by the end of ENCODE is 100%, once the project is complete. This is not because it’s all contributing to phenotypes, but because it has binding sites or gets transcribed, etc.
Again, consider what happens when there is a random insertion into the genome – say 30 random bp inserted in the middle of an intron. The intron is still removed in the production of the mature mRNA molecule, and there is no appreciable effect on the organism. I would say that there has been an increase in the junk content of the genome, ENCODE would literally claim that there has been a functional expansion of the genome.
To be clear — if you randomly generate a sequence and insert in the genome it would be “functional” under the definition used by ENCODE. Surely, this is not a standard that an ID advocate would accept as functional.
Nope, you’re not wrong. I wouldn’t use the word purpose, but I know what you mean and you are right as far as I am concerned. This is the heart of the matter and why so many scientists are unhappy with ENCODE’s characterisation.
No, I wouldn’t say so. Sites involved in gene regulation are not junk, even though many of the interactions might be of little significance (as we expect many interactions to arise by chance). Michael Eisen has an excellent discussion of this from his own work. The point is not that the human genome is complex — of course, it is — the point is that beyond the four million switches are large swathes of DNA that have arisen by retrotransposon duplication and mutated to non-function, by traditional definitions. ENCODE still considers them functional by definition.
as to:
nothing like presupposing your conclusion for non-functionality into the very question being asked for functionality is there paulmc??? Like I said before atheistic materialism is a hindrance to science and certainly does not provide a fruitful heuristic for discovery!
Mung:
It has a lot to do with it. If we want to make the positive case that the majority of non-coding DNA in humans is functional in the traditional sense — i.e., it is necessary to regulate the genome — then we need to have a functional explanation of genome size that can explain a few things:
1) What is so complex about an onion, compared to a human, that it needs substantially more non-coding DNA than we do?
Now, it is possible that we simply don’t understand the complexity of the onion, and perhaps it really is much more complex than we are. There is no evidence for this, but even if we accept this:
2) Why does one species of onion need 4x as much non-coding DNA as another biologically and ecologically similar species of onion (both in the genus Allium)?
This is not to say that there is no possible explanation for the differences in these two onion species. However, there is no clear functional explanation, yet we need one before we would conclude that the enormous variation in genome size is actually necessary DNA. Lacking such an explanation, we fall back to the far simpler explanation — that much of the excess non-coding DNA is not biologically necessary. This is our null position, because we understand the processes that cause the accumulation of DNA well and can see these processes operate.
However, if we accept that this is possible for onions, we should also be open to the possibility that not all of the non-coding DNA in humans is necessary either. For example, within the vertebrates there is much genome size variation. Why is the fugu genome only 400Mb when ours is about 9x larger? Is it because we need that much additional regulation? Or, like the onions, is this more likely to represent an excess of non-coding DNA?
paulmc:
Perhaps I’m misunderstanding your terminology. I understand purifying selection to refer to natural selection acting to eliminate deleterious characteristics. (We could quibble a long time about the whole concept of ‘selection,’ let’s set that aside for now.)
So if I’m understanding your reference to genome “conservation,” what you’re suggesting is that all the junk DNA (65%, 80%, 90%, whatever% of DNA) shows no evidence of elimination of deleterious characteristics?
I just want to make sure I’m understanding your point.
paulmc:
No, they haven’t. As I have explicitly outlined, lol.
Now you’re just making things up.
WHY would Encode claim there has been a “functional expansion” of the genome?
According to your own admission the insertion would not change anything. It would still be removed. So Encode would discern no difference at all.
Why?
If you randomly generate a sequence and insert it into the genome, what are the possible scenarios?
Surely one of the possible scenarios includes changing a formerly “functional” sequence into a “non-functional” sequence.
If not, why not?
I am not sure why any scientist would object. It’s there for a reason has to trump it’s there for no reason at all.
But for me, the jury is still out. The issue is not “functional” DNA but rather “purposeful” DNA.
paulmc,
Get back to me when you have a species of human that “needs” 4x as much non-coding DNA as another biologically and ecologically similar species of human.
Eric – yes, that’s right. In fact, it is not possible for the majority of the bases in our genome to be subject to purifying selection at the current mutation rate.
Mung:
But this is their definition Mung – and is the main point! A stretch of DNA is called ‘functional’ in ENCODE simply if is transcribed. Because introns are transcribed — even though they are removed in the production of the mature mRNA from which a protein is translated — they are considered functional, even if they are entirely biologically inert in every other sense.
ENCODE does discern a difference here because it is annotating this section of the genome as being intronic. Therefore an expansion in this region contributes to the functional component of the genome under ENCODE.
Absolutely, one of the possibilities is mutating something functional. If a chunk of random sequence falls in an exon, for example, it is almost certainly going to be deleterious. These mutations are removed quickly by purifying selection – often they won’t produce a viable organism. Many, many other insertions do not have this effect because they occur in areas of the genome that are not subject to purifying selection – e.g. in the middle of a typical intron.
Mung:
The point stands that if we can observe such enormous variations in genome sizes, they warrant explanation. The variation suggests the tendency towards accumulating non-coding DNA that lacks any evidence of function, and there is no biological sense in treating humans separately here. This is a phenomenon that occurs across the eukaryotes.
Paulmc…what does it mean for the genome to have non-functional DNA? Or useless DNA? What is it?
paulmc:
Absolutely. We agree. But the fact that we do not yet have an explanation for x (the genome size of various species of onion) does not mitigate against the facts that we do have at hand concerning the human genome.
Please explain how onion genomes affect the human genome.
What was the most recent common ancestor?
paulmc:
So what?
The darwinian view is that transcription of ‘functionless’ DNA is a waste of energy and therefore should be selected against.
Mung:
It should be fairly clear that it is not a case of the onion genome “affecting” the human genome. The challenge is to explain genomic variation broadly. You haven’t offered any reason to doubt that the variation in genome sizes between different onion species is due to anything other than junk.
The point we learn from onions is that non-coding DNA cannot be assumed to be functional (in the traditional sense). We know that half of any typical mammalian genome comprises old, degenerate retrotransposons – sequences that accumulate by their mutational pressure. Such a volume of non-coding DNA is lacking in some other vertebrates like fugu as I mentioned before – this is the multicellular end of the c-value enigma: there are no patterns of differences in complexity between these organisms, only massive variation in their non-coding, nuclear DNA.
However, variation in genome size broadly correlates to population size, as laid out finely in the Lynch et al. review paper I linked to above. And this ties closely into your next point:
The accumulations of non-coding DNA occurs incrementally. Each addition does not waste much energy, and in small populations, selection is too weak to remove such variation.
While it is true that the ultradarwinist view would not allow to such accumulation, this view doesn’t represent mainstream evolutionary biology, and hasn’t for decades. A more pluralistic approach will accept that the well-established limits of selection in small populations, and the population-genomic consequences. Lynch lays all of this out in a quantitative framework, with thresholds for junk accumulation.
paulmc:
OK, just to make sure I understand what you are saying.
1. Are you saying that because the mutation rate is too high (compared with our reproductive cycle), most of the mutations cannot be eliminated through purifying selection?
2. If so, are you then further saying that because those mutations haven’t caused any identifiable problems then we can infer that those sequences were/are non-functional?
paulmc:
Sorry to butt in, but that sentence jumped out at me. So what we’re being told to believe is the following:
1. In small populations with long lifecycles (like humans) selection is so strong and so effective that it was able to fix in the population numerous miniscule changes over a relatively short time period of a few million years that add up to huge differences between us and chimp ancestors.
2. In small populations with long lifecycles (like humans) selection is so weak and so ineffective that it is unable to purge a massive quantity of junk that, even under the highly questionable assumption that such junk would not cause problems for cellular function, the junk at the very least: (i) utilizes the majority of the copying resources every cell division, (ii) utilizes a meaningful portion of the transcription resources on an ongoing basis, and (iii) produces nonsense RNA strands that have to be located, recognized and broken down, over and over, minute by minute, day after day, for generations.
Sounds more like a convenient story than a coherent story.
Why are none of my questions being answered!?!? I want to know what non-function DNA is! I also want to know why any scientist would label DNA as junk if it has a purpose. Can we get an illustration here also preferably applying this same kind of idea to vestigial organs?
In software engineering, the concept of “coupling” is used to describe the the way that software modules interact with each other in accomplishing the overall function of a computer system. This concept was pioneered by Larry Constantine and Ed Yourdon in developing the Structured Design approach (Structured Design: Fundamentals of a Discipline of Computer Program and System Design, Prentice-Hall, 1979).
They describe the differences between “loosely coupled” and “tightly coupled” systems (Wikipedia provides a good summary of the ideas involved).
A tightly coupled module is difficult to modify or swap out for a superior alternative without a detailed knowledge of the way that related modules do their job. Tightly coupled systems have greater interdependency between their parts, require more coordination between parts, and require greater information flow to maintain function. Tightly coupled modules may even rely on modifying the functions of related modules. Loosely coupled systems have the opposite characteristics.
In systems design, “loose coupling” is to be preferred to “tight coupling”.
Loosely coupled systems evince good design (clear forethought about module functions, inter-module communications and the likely need to modify or enhance functionality in the future – all good teleological attributes.
Tightly coupled systems, on the other hand, evince a lack of forethought, an ad-hoc approach to making things work, and a tendency to develop spaghetti code. In other words, tightly coupled systems tend to develop “organically” (designers and programmers modify the current structure in small ways to overcome the next immediate difficulty), rather than reflecting a long-term view of the function, development and maintainability of the overall system.
The genetic control systems of cellular function are clearly “tightly coupled” in the sense used by Constantine and Yourdon. The expression of a protein from a gene template is mediated by a complex parallel set of genetically encoded transcription and timing controls, each of which is specific to the particular expression pathway, and has the ad-hoc characteristic of tight coupling.
Hence, if design in natural biology is to be inferred by analogy to human-designed templates (we recognise design in non-human nature because it is analogous to examples of human design), then we are forced to the inference that biological systems are poorly designed. And worse yet – the more complex the cellular functions happen to be, the worse the design.
Or to put it differently, if the complexity of cellular control systems demands that deliberate design is a superior explanation for their origin (compared to mutation plus natural selection, or neutral drift following by functional co-option), then we are also paradoxically forced to the conclusion that the actual deliberate design is inadequate to the long-term survival of the system.
[In the interests of full disclosure, I should say that I have shamelessly plagiarised this idea from a more loosely coupled organism than I am.]
It is so interesting watching Darwinists make ad hoc and ex post facto pronouncements.
When pseudogenes are found to have function, thus undercutting their “junk DNA” argument, they say: “Oh, what’s the big deal. No one ever said that there was ‘junk-DNA’.”
Then you have this study that shows that 80% of the genome is transcribed, and has some, minimal, “chemical” function, and they say: “See, under this definition, anything can be termed ‘functional.’ We all know that there’s all this ‘junk’ in the genome. Just look at the onion.”
So, which way is it, boys? Have you never said there was junk, or are you saying there’s all kinds of junk?
As usual, your answer will be whatever you perceive is needed to prop up a failed theory. Let’s hear it for Ptolemy.
In the meantime, thanks for the entertainment.
You know what I’d like to see?
I’d like to see these guys who claim there is so much junk in the genome to “practice what they preach”!
Wouldn’t it be nice if there was a way for them to delete whatever part of the genome they think is junk in the cells of their own children?
Not that I would wish that on their kids, but I’d love for there to be a way for them to put their faith into practice and then we would be able to see what they really believe.
How many of these guys would have been willing to delete 98% of the genome they claimed was junk in their own cells or in their kid’s cells? None, I’m sure, and that makes me question whether or not they really believe that.
It’s like the tightrope walker asking people if they think he could take a guy piggy back across the falls. They all say yes and then he said “Who will volunteer?”
Needless to say, there were no volunteers. It’s easy to claim you believe something – but when the rubber meets the road, the truth comes out.
timothya @62, that is one of the most absurd things I have read in a long time. Neither you nor anyone else has the slightest clue about how biological systems could be better designed. Your failed analogy (setting aside for the moment your very questionable interpretation of tightly/loosely coupled module design) is just another in the long history of pathetic attempts to say “no designer worth his salt would have done it this way.” Never is a detailed analysis done; never is a better method put forward with enough detail to ever determine whether the vague assertions about ‘it could have been better’ are true. And lastly, as I think you mention, even if it is poorly designed, it doesn’t mean it wasn’t designed.
PaV, I think you make an astute observation. There appear to be two trends in evolutionary thought right now in regards to junk DNA. The first, which we are starting to hear occasionally, is “What junk? We never really meant it was junk.” The second, championed by wd400 and paulmc here, is to dig in the heels and battle tooth and nail against every additional finding that suggests there might be more function than previously thought. The former approach will eventually become more common as more and more function (the only possible way the evidence can trend) is discovered. But it will be painful for the latter group, and I suspect we’ll see plenty more defintional/rhetorical battles waged by them in the next few years before they finally throw in the towel.
paulmc:
Then why are you so narrowly focused on one species of onion?
timothya @62, you have a lot of assumptions built into that argument that may or may not hold even for software systems, much less for an attempt to apply principles of software design to biological organisms.
One could just as easily argue that what you have described are not separate modules that “ought” to be loosely coupled, but rather a single module that “ought” to be tightly coupled according to the software principle of encapsulation.
Nice try though. Perhaps if you developed the argument further.
I’m interested in the extent to which software design principles are present in biological systems. Biological Design Patterns anyone?
Nah Eric, it’s like this.
No one ever said every non-coding sequence was junk. Ohno, in the first papers about the idea was quite explicit about this. So finding this or that pseudo-gene now drives expression of some thing or other doesn’t disprove junk DNA.
On the other hand, the ENCODE result includes every nucleotide of every intron in its definition of “function”. I don’t think any sane person could think every nucleotide of every intron was actually require for proper functioning of the cell (and to believe that, and that Fugu can get by fine with many times smaller introns in a real stretch), so clearly the ENCODE total is too high.
(BTW, this is one of those topics that exposes how the verbal tic of calling evolutionary biologists “Darwinists” is really misleading – only ultra-Darwinian biologists would think the genome was full of functions. So, the people arguing for junky genomes are actually talking about non-Darwinian theories of genome evolution)
wd400:
That’s one way to set up a straw-man.
But has the question “why introns” even been answered yet?
To what extent are introns found in non-Eukaryotes?
http://en.wikipedia.org/wiki/Intron
Mung: I was not proposing human software design as template for understanding the structure and functioning of biological systems. In fact, I think digital computing is a particularly poor analogy of how biological systems work. I need to say this upfront, just so Eric doesn’t bark himself into a lather up the wrong tree again.
I will include one partial response to Eric’s comment that:
This would be news to generations of plant and animal breeders, developers of genetically modified organisms, developers of gene therapy solutions, stem cell researchers etc etc, all of whom by different pathways are “investigating how biological systems could be better designed” (that is, better fit to human health and requirements). I used to do it for a living, so actually I do have a clue. Enough said.
My point (and probably not a particularly important one) is this. Simply asserting designedness in non-human systems on the basis of prior knowledge about how humans design things is insufficient. If, in fact, undesigned, natural processes can create complexity, then you have simply fallen prey to an illusion.
We need to look at how the complexity of human designs is materialised, and pay particular attention to how human designers typically achieve desirable features – functional fitness, sustainability, upgradability, adaptability. Software design is a reasonable example of how human designers go about achieving these attributes.
Any computer program (that “works”) will be at least as complex as is required to deal with the processing problem at hand. The designer essentially has two canonical approaches to creating the necessary complexity.
Either follow the structured design approach, in which individual functional modules are robustly designed to perform a “class” of function, and the overall program control module contains all of the complexity required to deal with the full range of potential processing inputs – deciding which functional module to call on the basis of the input case, assembling its input data, handling its output etc etc.
Alternatively, the designer can embed all of the control switching capabilities into each functional module (or, as you point out, dump all control and processing functionality into one bag of code), so it can autonomously handle all possible input combinations.
We would expect to see very different abstract structural characteristics of two programs written to solve a problem using the two approaches. The first would have a single, complex control structure with a minimal set of “functional” modules. The second would either have as many functional modules as there are input possibilities, or one undifferentiated processing structure with processing code, control code and variable definitions studded throughout like plums in a pudding.
Now. When faced with a new input case, the designer of the first type will typically add a switch to the control module. The designer of the second type will typically modify an existing functional module to handle the new case, or even create a new module to deal with the new eventuality.
Both approaches can, in principle, deliver the functional fitness attribute, but the structured design approach requires significantly less effort to deliver sustainability, upgradability and adaptability.
The structure of cellular control in biological systems appears to be one of ad-hoc modification of existing processes to meet new input cases (of dazzling intricateness). It clearly exhibits the “one control system per function” model. This, in itself, is counter-evidence to the argument that there is a long-run intention for sustainability and adaptiveness behind the processes of biological systems, irrespective of whether they were designed in the first place.
I happen to believe that the ad-hoc model of modifying existing systems is precisely what one would expect if the functional changes arise from random mutations in the genetic code, followed by selection under environmental pressure on the resulting phenotype. I would not expect to see a consolidated unitary control system. And it appears that reality confirms this prediction.
Mung, it’s not a strawman, it’s ENCODE’s definition!
And no, it’s not clear why intron’s exist, but it’s worth repeating evolutionary biology doesn’t require something to have a purpose in order to exist. Michael Lynch and his crew might well argue introns are non-adaptively complex
wd400,
Introns exist to make alternative gene splicing possible. And your position cannot explain alternative gene splicing.
And we await your experiments in which you remove all introns and get a viable organism.
Loljoe, even if that is true, most genes don’t make alternative products. so, why so many introns? And why so big?
Joe. I didn’t say all introns are junk, Just that encode calling every nucleotide of every one if them functional is a bit of a joke.
wd400-
Your entire position is a joke because you cannot explain functional DNA and you cannot explain alternative gene splicing.
And again FUTURE FUNCTIONS- ie theb reason not all genes make alternative products- why so big (introns)? Because they also house software.
As I said eliminate them and see what you get.
wd400:
No-one ever said anyone said that every non-coding sequence was junk. We’re talking about a broader concept here. paulmc and I are discussing selection and what evidence may or may not exist about selection’s action in the genome.
I’m not so interested in the ENCODE definition in what I am discussing, other than the fact of pervasive transcription and the implications of that. I realize you and others on the thread are focusing on the ENCODE definition. paulmc and I are talking about other aspects. However, in response to your comment I would note that you cannot assume that the ENCODE total is too high. You may end up being right that the definition is too broad and that some portions of some introns are not necessary for funcion. However, we will find more functions in the future, and we also know that some portions of DNA are important due to their placement, transcription timing ‘pause’ elements, and there is even multi-layered information in some elements. So it is not at all clear that 80% will be too high at the end of the day.
Well, there may be better terms. Your classic ultra-Darwinist Dawkins, however, loves to proclaim how much junk DNA there is, so I’m not sure you’ve got your categories quite right either.
And Darwinian evolution includes two general principles: variation plus selection. It seems the first aspect is pretty broad and picks up just about everything. Whether selection is acting or hasn’t acted yet, or is only slowly acting, is of course an open question. I understand your point, however, that there may be other specific stories about how certain features came about that one could view as less Darwinian. Most of which are just variations on the overall evolutionary ‘explanation’ that “stuff happens.”
timothya,
The structured approach has been replaced by the object-oriented approach. And before the structured approach there was some other “best” way to develop software.
It’s probably not a good idea to just take one of them when seeking to find comparisons in biology. And as you can see, human understanding changes.
wd400:
Introns do not exist in all organisms. (I’m not trying to imply that you don’t know that, I’m sure you do.)
So did they just magically appear in numerous lineages independently?
Or have they been inherited from a common ancestor?
When the first intron appeared, how did it spread throughout the population? Drift?
I would think that one would assume that there was some initial selective advantage.
So I don’t think it’s at all unreasonable to think that they had some purpose, at least in the beginning.
Something new appears on the scene that gives the carrier and it’s descendants a reproductive advantage, by which means it is then spread through the population. Wash Rinse Repeat. Much less likely to happen if if serves no purpose.
Mung,
Introns evolved once, there used to be a debate about whether they were excised by prokaryotes or invented by eukaryotes, don’t know where we stand on that one today. Even if they are a eukaryote invention, it’s worth remembering that there are models of non-adaptive complexity (read the link in my earlier comment).
Eric.
OK, only about 10% of the genome is subject to purifying selection. Done?
wd400:
1. What is the evidence that introns evolved?
2. Why did introns evolve at all?
3. Why did introns evolve only once?
Your link doesn’t work.
But what I’m looking for are the models of non-adaptive junk, not models of non-adaptive complexity.
I don’t really know why this is relevant, but the evidence for a single origin of introns is that fact they are limited to a single calde – Eukaryotes.
Their orign is unclear – perhaps they started out as selfish elements, perhaps the splicisome etc is a relic from and RNA world that prokaryotes, with their much more efficient genomes, could remove. I’m not sure why it matters? I still think you’d have to be mad to think every nucleotide of every intron was functional.
The non-adaptive origin of complexity paper is this one:
http://www.ncbi.nlm.nih.gov/pm.....MC3121905/
and all models of junk DNA are non-adaptive, that’s sort of the point.
Well, I just think introns are very interesting and remain an unsolved puzzle for biology. I just have to decide I guess how much they can be explored in a blog.
Perhaps one of the first things to reflect on is the fact that introns don’t exist in isolation. Would we even recognize an intron as an intron if there were not some biochemical process that excised them? But why would such a system as that arise, absent any introns in the first place? Yet another classic beef and egg problem?
http://en.wikipedia.org/wiki/Intron
http://en.wikipedia.org/wiki/RNA_splicing
The existence of introns is certainly interesting, and a challenge to the panglossian view of the genome that some engineering-types have. But no matter the origin of introns, do really think every single nucleotide of every single intron is “functional” is a bit strange, which is one reason to discount ENCODE’s 80% number.
wd400:
Straw-Man
Take Threonine for example:
As that final nucleotide in the codon “junk” because it can be any of the four and still result in the production of threonine? What ‘function’ does it have?
It can’t be a strawman, because it is ENCODE’s definition!
And no, the degenerate nature of the genetic code is not “junk” anymore than the fact you could change most residues in a protein and not alter the functions make most positions in proteins “junk”.
wd400:
The problem is not that “every single nucleotide… is “functional” “. The problem is if introns and other non coding sites are globally functional, and what functions they do have.
As Mung has very correctly mentioned, not even in protein coding genes “every single nucleotide is “functional” “. That’s why we have a lot of neutral mutations. Even deletions of aminoacids can in some cases be irrelevant to the function of a protein.
So, the function issue has to be judged on proper terms, and not at the single nucleotide level.
Chop out a nucleotide in a protein coding gene and see how it works. Do the same to an intron…
There was a discussion above about purifying selection (selection against deleterious mutations). One result from population genetics is that purifying selection isn’t very effective in small populations, so mildly deleterious mutations can be fixed in the population. (Humans have a small effective population size, historically, so this applies to us to some degree. It’s probably why transoposon insertions, which are probably only mildly deleterious, can be fixed in mammals) The result is that in very small isolated populations, deleterious alleles can build up quickly, increasing the mutation load severely. As it happens there is a paper in this week’s PNAS on such a case. ttp://www.pnas.org/content/109/37/E2496.abstract
@NickMatzke_UD #6
Hi Nick. About the onion test. It reads:
I suppose one hypothesis, within an ID worldview, would be that there could be some nutritional value in the onion for other species. Pumping up the DNA size might simply pump up the nutrional content or variety of benefits.
Example:DNA is Not Destiny article from Discover magazine (excerpt):
(bold emphasis mine)
So, an ID-ist might persue the discovery of overlapping genetic benefits between speices (e.g. humans and onions). This is a possible prediction that could not be made faithfully within the Darwinist view because it would apparently presume a feature of an organism (the onion) the exclusively serves the good of another organism(humans or other onion eaters).
JGuy
I think I used a bad example (methyl donors), but the hypothetical premise seems to hold potetial.
The remarkable story of eukaryotic introns
Eugene V. Koonin, The Logic of Chance: The Nature and Origin of Biological Evolution
Mung-
If it defies imagination then they will either not want to discuss it, take LSD to help their imagination, or give the rest of us LSD to help ours.
It may seem that the ID community celebrated too early on this. According to Jay Wile’s blog, a vast majority of pseudogenes are non-functional. And yes, I did leave a nasty note on there.
http://blog.drwile.com/?p=8766
Larry Moran’s blog says that the PR people screwed up the story and that Junk DNA is still alive.
@ JLA Shapiro also weighs in;
http://www.huffingtonpost.com/.....73935.html
And
http://www.huffingtonpost.com/.....81788.html
But are the pseudogenes really completely non-functional or are they a design feature that provides redundancy if a primary pathway is broken???
Either way Darwinism loses, i.e. if pseudogenes are a design feature of some type, such as providing redundancy, or some other design feature that hasn’t been looked for yet (given the extreme overlapping complexity of the coding in DNA), then the purported pseudogenes overtly support ID, and if the vast majority of pseudogenes really are broken genes, as Darwinists prematurely presuppose (think vestigial organ arguments that have now been overturned), then they provide further proof that Darwinian processes are excellent at breaking things but are powerless to create things!
Of related interest form ENCODE, and shattering to the foundational Darwinian precept of the “Central Dogma’ i.e. DNA makes RNA makes Proteins, is the fact that ENCODE found that a ‘gene’ is not a gene anymore:
BA77
So if there are pseudogenes then ID is correct. If there are no pseudogenes then ID is correct. Isn’t this the type of reasoning Darwinists use? This sounds like a just-so story that they are always being blamed for. According to Jay’s blog, ID and creationism predicted the presence of pseudogenes but we all know that’s not right. Junk DNA is not a myth as previously thought and it kills one of ID’s best arguments. It might be time to go where the evidence leads…Darwin was right.
But darwinism cannot explain the existence of genes…
JLAfan2001, you are missing the entire point of experimental (empirical) science. Even Einstein’s theories (special and general relativity) were considered nothing more than conjecture until experimental proof was brought forth confirming time dilation for special relativity (now confirmed by multiple lines of experiment) and the experimental proof of the warping of 4-D space-time (i.e. bending of starlight during a eclipse) confirmed general relativity. In other words, why should Darwinism even be given the time of day, a free pass as far as Darwinists are concerned, as to explaining how genes arose when Darwinism has NEVER EVER been observed to create even a single functional gene and/or a functional protein in the first place??? whereas intelligence has been observed to create as such???
JLAfan2001 it is simply beyond ludicrous, indeed insane, for you to presuppose Darwinism as true for all of biology with no empirical basis to support your position that Darwinism can create functional complexity. Moreover for you to point to broken (vestigial) genes, which I grant Darwinism processes would be more than excellent at achieving, as proof that Darwinism is true simply because you can’t envision a Designer (God) allowing such genetic entropy to occur after He has implemented top-down design, is simply not even in the field of empirical science, and, in reality (not Darwinian fantasy land), such argumentation clearly is theological argumentation that you, and other Darwinists, have been using solely to try to support your empirically bankrupt, and philosophically motivated, theory!
Notes:
Michael Behe talks about the preceding paper on this podcast:
There is no evidence of Darwinian processes ever creating novel genes or proteins in humans whereas the detrimental nature of mutations in humans is overwhelming for scientists have already cited over 100,000 mutational disorders.
I went to the mutation database website cited by John Avise and found:
I really question their use of the word ‘celebrating’. (Of note, apparently someone with a sense of decency has now removed the word ‘celebrating’). Such a high rate of detrimental mutations is further elaborated here by Dr. John Sanford:
This detrimental mutation rate is far higher than what even leading population geneticists agree is acceptable:
A graph featuring ‘Kimura’s Distribution’ for mutations, and how it completely falsifies evolution, is shown in the following video:
Further reflection on the implications of genetic entropy are discussed here:
JLAfan2001, you mentioned following the evidence where it leads, those are wise words indeed. Why don’t you please follow your own advise??
Just up at ENV:
ENCODE Results Separate Science Advocates from Propagandists
David Klinghoffer September 20, 2012
http://www.evolutionnews.org/2.....64491.html
Further Thoughts on the ENCODE/Junk DNA Debates – Jame Shapiro – Sept. 18, 2012
Excerpt: The ENCODE scientists have learned that it is wise to avoid interpreting the data from a fixed view of genome organization. That is why they speak of “DNA Elements” rather than genes or any other artificial categories. They tend to restrict themselves wisely to operationally defined features, such as transcription start sites (TSSs) and splice sites at exon-intron boundaries.
Diogenes and like-minded people argue that we knew enough in the 1970s to understand the basic principles of genome organization. They do not accept that the flood of new information from genome sequencing and the kind of methodologies exemplified by the ENCODE project will fundamentally alter our genetic concepts. While they are certainly entitled to these opinions, I think we have to recognize that they are nothing more than that — simply opinions that fly in the face of scientific history.
http://www.huffingtonpost.com/.....93984.html
BA77 and Joe
My comment was not asking where genes come from or how Darwinism can’t explain the lack of functional genes. I will phrase it in some questions.
Did ID predict that junk DNA would be a myth?
Did ENCODE find junk DNA or non-functioning pseudogenes?
If so, does this undermine the ID argument?
All I want to know is are there or are there not any junk DNA in the genome?
And you are ignoring this glaring, and profound, deficiency of evidence because why exactly????
i.e. Why should I care one iota what you think about the evidence when you are basically reading tea leaves and calling it science whilst you are completely ignoring the elephant standing on your chest in the middle of your living room!?!
Over at ENV:
“The debate thus hinges on whether activity such as transcription, transcription factor association, and histone modification are signs of true function. My own view is that such such activity is suggestive of functionality, but not proof. Therefore I would be cautious about claiming that these results show 80% of the genome to have function in the sense that we normally use that word.”
It seems that even IDists are starting to reel in the reigns on their celebration of no junk DNA. If Jonathan M. is becoming cautious about 80%, why shouldn’t everyone else. Anything more to add, BA77? Keep in mind that this thread is about the issue of junk DNA not origins of life or CSI.
I think the 80% will lower quite a bit in the future becoming a hard blow to ID.
“I think the 80% will lower quite a bit in the future becoming a hard blow to ID.”
Nothing prejudiced there! i.e. Why should I care one iota what you think about the evidence when you are basically reading tea leaves and calling it science whilst you are completely ignoring the elephant standing on your chest in the middle of your living room!?!
as to which way the functionality percentage will go, well I’ll let the evidence speak for itself:
Why can’t you just admit ID and Jonathan Wells were wrong on this? It also seems there is bias on the other side because it very well could be junk which I suspect will be.
“Why can’t you just admit ID and Jonathan Wells were wrong on this?”
They weren’t! On the other hand Why can’t you admit to the overwhelmingly obvious fact that DNA, and the coding in DNA, is unfathomably complex, being several orders of magnitude more complex than anything our best computer engineers or computer programmers have ever built or programmed??? Or is going through life with you head stuck in the sand how you prefer to do science?
notes only 4 grams of DNA can store the entire information content of the entire world:
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:
etc.. etc.. etc..
I never said that I didn’t agree with any of things you mentioned. In fact, I do agree with it very much. I think any biologist out there would too. What I’m trying to find out is if all that complexity came to be after years of trial and error. Perhaps the junk DNA is proof of that.
‘What I’m trying to find out is if all that complexity came to be after years of trial and error.’
A review of The Edge of Evolution: The Search for the Limits of Darwinism
The numbers of Plasmodium and HIV in the last 50 years greatly exceeds the total number of mammals since their supposed evolutionary origin (several hundred million years ago), yet little has been achieved by evolution. This suggests that mammals could have “invented” little in their time frame. Behe: ‘Our experience with HIV gives good reason to think that Darwinism doesn’t do much—even with billions of years and all the cells in that world at its disposal’ (p. 155).
http://creation.com/review-mic.....-evolution
Michael Behe, The Edge of Evolution, pg. 162 Swine Flu, Viruses, and the Edge of Evolution
“Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell–both ones we’ve discovered so far and ones we haven’t–at best extremely limited benefit, since no such process was able to do much of anything. It’s critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing–neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered–was of much use.”
http://www.evolutionnews.org/2.....20071.html
Where’s the substantiating evidence for neo-Darwinism?
https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit
This raises an interesting question that even Behe brought up. Why would the Intelligent Designer (and we all know who that is even if ID wants to pretend they don’t) design malaria, HIV and E.coli? That would imply that the Intelligent GoDesinger was not all good.
So do you want to argue theology or do you want to focus on the fact that you are empirically bankrupt for your preferred answer of Darwinism? Either way you lose!
i.e. the argument from evil presupposes the existence of a absolute standard of good of the way things ought to be but are not. Exactly where do you derive this standard of good from to enable you to judge by if it did not in fact exist in reality?
Stephen Meyer – Morality Presupposes Theism (1 of 4) – video
http://www.youtube.com/watch?v=uSpdh1b0X_M
Cruel Logic – video
Description; A brilliant serial killer videotapes his debates with college faculty victims. The topic of his debate with his victim: His moral right to kill them.
http://www.youtube.com/watch?v=4qd1LPRJLnI
Albert Einstein and his answer to his Professor ! – video
http://www.youtube.com/watch?v=fLOZDpE1rkA
I admit that I went off in a different direction but it wasn’t because of proof or lack of it. I just thought that would be an interesting question to pose. All the videos that you posted were about moral evil. I was referring to natural evil. Malaria, HIV and E.coli don’t have moral codes but kill humanity because they were seemingly designed to. Why? Why does the design of nature require so much death and survival? This seems to be poor design right from the get go but in falls in line with the idea of natural selection.
First you apologize for making a theological argument and state “it wasn’t because of proof or lack of it”, then instead of presenting any proof that Darwinian processes can produce functional information you go ahead and dig a deeper theological hole by bringing ‘natural’ evil into it, i.e. death. So I ask you again to you “do you want to argue theology or do you want to focus on the fact that you are empirically bankrupt for your preferred answer of Darwinism? Either way you lose!”
The following book has a brief Biblical exegesis the fall of man affecting all of creation even to the point of death preceding the fall:
i.e. God’s view of time is simply not linear, sequential, temporal, as we view time, but is eternal, timeless, knowing the beginning from the end,, thus explaining why when we sinned against almighty God it affected all of creation even in a future effecting the past manner. If you hold that such is not possible, well advances in quantum mechanics begs to differ with what you would prefer to believe
Notes:
It is also very interesting to point out that the ‘light at the end of the tunnel’, reported in many Near Death Experiences(NDEs), is also corroborated by Special Relativity when considering the optical effects for traveling at the speed of light. Please compare the similarity of the optical effect, noted at the 3:22 minute mark of the following video, when the 3-Dimensional world ‘folds and collapses’ into a tunnel shape around the direction of travel as a ‘hypothetical’ observer moves towards the ‘higher dimension’ of the speed of light, with the ‘light at the end of the tunnel’ reported in very many Near Death Experiences: (Of note: This following video was made by two Australian University Physics Professors with a supercomputer.)
Verse and music:
Are you a YEC or OEC? If you are an OEC then natural evil was already in the world prior to the fall. Man’s sin didn’t bring it in. If you think that’s the case, please provide some citations that test the effects of sin on tornadoes, floods, disease etc.
Also, I think I hijacked this thread which I fully admit. I would like to continue this discussion but off thread if you are interested. Despite my tone, I am seeking answers to these questions but I don’t find pat answers satisfying. I’m not saying that’s what you’re giving but that’s what I’m finding.
So instead of focusing on the science, and the complete bankruptcy of Darwinism to explain the complexity we find in life, you decide to go full bore into a theological argument??? Oh well, so much for you being objective,, you ask,,
“Are you a YEC or OEC?”
I hold closely to what Dr. Dembski has laid out here in this book,,,
The End Of Christianity – Finding a Good God in an Evil World
William Dembski PhD. Theology and Mathematics
http://www.designinference.com.....of_xty.pdf
you then state:
“If you are an OEC then natural evil was already in the world prior to the fall.”
That’s not the proper Theological view when taking into account, in the fall of man, that we sinned against almighty God who is timeless, eternal, outside of time spoace matter and energy, knowing the beginning from the end,, etc… etc…, i.e. our sequential, temporal, frame of reference is completely useless as a frame of reference for time in dealing with the issue of our complete separation from God! If you still hold that such ‘retrograde action in time’ for death entering the world is impossible, well I’ve already cited empirical proof from quantum mechanics, as well as noted the ‘eternity’ of special relativity, that shows such retrograde action is not impossible as far as physics is concerned, and that there is, in fact, a higher ‘eternal’ dimension that really is above this 3-D material dimension, just as theism has always resolutely held!
You then go full bore into theological argumentation and state:
‘provide some citations that test the effects of sin on tornadoes, floods, disease etc.’
Incredible Parallels Between Israel and the U.S. Evacuations – Bill Koenig (the precise timing of the Katrina hurricane and America’s actions against Israel)
http://www.watch.org/showart.p.....38;mcat=24
Jonathan Cahn, author of The Harbinger, shares nine omens that spell judgment for America on this edition of Jewish Voice with Jonathan Bernis. – video
http://www.youtube.com/watch?v=H13DPkb6kjQ
you then state:
‘Also, I think I hijacked this thread which I fully admit. I would like to continue this discussion but off thread if you are interested.’
I’m not.
Despite my tone, I am seeking answers to these questions but I don’t find pat answers satisfying. I’m not saying that’s what you’re giving but that’s what I’m finding.
I don’t believe you.
To bring it back to the science, ENV has another article up highlighting the desperate situation Darwinists are in with this entire junk DNA dogma of theirs: