Skip to comments.Jumping 'Junk' DNA May Fuel Mammalian Evolution ('Junk' DNA not junk at all...ID Vindicated Again)
Posted on 06/21/2007 5:55:18 PM PDT by GodGunsGuts
Tiny, jumping bits of DNA are looking less like genomic junk and more like significant players in mammalian evolution, according to a new analysis...
(Excerpt) Read more at sciam.com ...
Dembski on ID Vindication:
AiG Creationists nailed this a long time ago:
I don’t follow this stuff closely, but I must say, the concept of “junk” DNA, just because we couldn’t immediately figure out its function, seriously flunked the smell test.
From the getgo, I had problems with so-called scientists researching DNA biology and announcing that there were so many "useless" segments of DNA:
Translation - if I can't understand it, it must serve no positive dunction.
What sort of science is that?
Even the popular name, 'junk DNA' gives the game away.
Didn’t pass the smell test indeed!
More from National Geographic:
First Decoded Marsupial Genome Reveals “Junk DNA” Surprise (but not for ID/Creation scientists!):
==Funny how AiG and Dembski arent the ones who researched this, it was them durn evilutionists who figured this out!
Wrong...see links in post #2
The Darwiniacs have been fooled over and over by their own paradigm. This is just the latest episode where they got egg all over their face. See links in post #2 to see how IDers/Creation scientists predicted this turn of eventsâGGG
“Putting thousands of animals aboard the Ark could have had a dual purpose. Not only did it preserve their lives, but also it would probably allow transfer of genetic material and/or activation of latent genes simultaneously in all land animals. Under the relatively crowded Ark conditions, transfer of genetic material from one species to another through broad host range viruses, parasitic mites or fleas would be facilitated. This might have produced a distribution of AGEs in species in such a way as to defy evolutionary phylogeny, as is seen for the Tc1/mariner family and in the gypsy family of retrotransposons.”
That isn’t science...
It’s called speculation. They nevertheless predicted that Junk DNA would turn out to be functional DNA, as did the IDers.
re: “Junk” DNA
Church of Darwin 0
My main point is that it is sorry science to even contemplate a concept such as 'junk DNA'.
On the eternal shouting match level, my attitude is a pox on both their houses!
And if it flunks a buzzard's smell test...
==My main point is that it is sorry science to even contemplate a concept such as ‘junk DNA’.
Actually, it makes perfect sense from the Darwinian perspective. The problem is, science has once again proved them wrong.
Did it (smell bad enough to) knock him off the wagon?
They also believe the Earth is 6,000 - 10,000 years old...
No, it’s not science. It’s total rubbish.
Anyone who thinks genetic material is transmitted by fleas should consider the dog.
==They also believe the Earth is 6,000 - 10,000 years old...
And your point is????
Goes to the scientific knowledge, or lack their of, of one of your sources.
==Goes to the scientific knowledge, or lack their of, of one of your sources.
They understand the science as good as any. In the case of creationists, they simply believe that if the Bible is true, then the science will back it up, while simultaneously frustrating Darwinian materialism. Whether you believe IDers (mostly old earthers) or creationists (mostly young earthers), their respective paradigms predicted that “junk” DNA would turn out to be functional. Thus ID/Creation science 1, Darwinists ZERO when it comes to the specific issue of “junk” DNA.
And good for them for doing so...
Now let's see if their talk and their research directions don't change just a tad away from absolutism.
(Over time of course, evolvution and all that.)
Wrong. While some non-coding DNA is functional -- and this has been known by evolutionary biologists for many many years now -- there is very strong evidence (based on, among other things, exactly the same kind of analysis as the current study which you're jumping all over) that the bulk if it is, indeed, non-functional and superfluous. "Junk" if you will.
And this hardly "vindicates 'ID'" in the least, because a) it's perfectly consistent with standard evolutionary biology, b) what is already known about such DNA strongly falsifies a number of clueless "ID" claims, and c) the fact that some non-coding DNA is functional in no way helps support the unsupported "ID" dogma that it was therefore "designed" by some unnamed "designer(s)". Sorry, but epistemology just doesn't work that way.
The "ID" folks keep doing silly stuff like this -- they engage in circular reasoning, which of course is a major fallacy and "proves" nothing. In this case, their "successful predictions" are vacuous because they boil down to, "if life was designed, then it will have functional elements, and this study found functional elements, therefore we were right when we say that life was designed!" Excuse me while I roll my eyes. What they overlook, of course, is the obvious -- evolutionary origins predict functional elements as well. Therefore it's idiotic to claim that finding functional elements "vindicates" ID over evolution. It's nonsense. This is how children "reason". It's like, "physics is all wrong, because my Pink Unicorn theory predicts that the Earth will have gravity, and by gosh it does!"
Please try to learn some actual science before you attempt to critique it.
Both of your links in post #2 make the same elementary fallacies you do. They, too, need to learn how science actually works, and stop misrepresenting results in order to flog their favorite religious beliefs. That's not science, that's apologetics, and it's dishonest to try to disguise it as an actual scientific validation when it's not.
In order to have a *useful* prediction, which actually helps "validate" ID in some way, they would have to make their predictions much more specific, and predict in advance what *kind* of functional elements will be found in the genome, in what *amounts*, what *properties* those functional elements will have (in both a qualitative and quantitative way), wha *kinds* and *amounts* of similarities will be found among similar species, *and* what *kinds* and *amounts* of differences will be found among similar and not-so-similar species. *This* is the kind of scientific prediction (based rigorously on actual features of the specific theory) which allow a scientific theory to be validated or falsified by subsequent findings. EVOLUTIONARY BIOLOGY MAKES THOUSANDS OF SUCH DETAILED PREDICTIONS, and HAS SUCCESSFULLY PASSED THEM ALL. This is why evolutionary biology is real science, and accepted by the vast overwhelming majority of biological scientists and educators. "ID" does *not* make even a single testable quantitative prediction, much less the vast number that evolutionary biology does, which is why "ID" is *not* science, it's a crank hypothesis in search of suckers to buy books and pay for lecture fees.
Do feel free to notify me whenever the "ID" folks get off their butts and make an attempt at doing science as it actually needs to be done, instead of just declaring victory any time they think they can spin some real scientists' findings in a way that the "ID fans" will be gullible enough to swallow.
What's *really* hilarious is that you folks don't even realize that by accepting the results of this latest scientific study, you're *accepting* the common descent of all mammals (including man) that many of you strive mightily to try to deny. Because the study's findings stem from a comparison of how much different sections of DNA have changed SINCE THE LAST COMMON ANCESTOR, and the conclusions of the study only hold if indeed all mammal species are descended from a common ancestor. Thanks for admitting evolutionary common descent, we appreciate it.
It sure does, which is why the actual biologists didn't use that goofy method in order to arrive at the concept of junk DNA.
Thanks for playing, though -- come on back when you've taken a few beginner's biology classes and have the very start of what it takes to be able to critique the subject.
Then perhaps you can tell us what, if anything, is wrong with the actual methods used to conclude that large sections of most vertebrate DNA is non-functional. For example, from prior posts of mine:
Another example was in an editorial I read recently:
Also be prepared to point out that contrary to bone-headed (and unsupported) claims that "it probably never was 'junk'", the fact remains that even though rare cases have been found of specific pieces of "junk DNA" (i.e. non-coding DNA) having some use, only an idiot would leap from that to the conclusion that "it probably never was 'junk'" on the whole, because a) the vast majority of "junk DNA" is non-conserved (e.g. "Comparative genomics has revealed that approximately 5% of the mammalian genome is under purifying selection.", leaving 95% of the genome "inconsequential" from a survival standpoint), a clear indication that it is, indeed, not used in the genome, among many other lines of general evidence supporting the same conclusion (is your correspondent ignorant of these, or just dishonest?), and b) specific tests of "junk DNA" have shown that if it's used at all, the use is extremely rare or subtle, because giant whacking swatches of it can be removed entirely without any kind of obvious harm to the animal.
For example: Megabase deletions of gene deserts result in viable mice. In short, the researchers snipped over 2.3 *million* basepairs of apparently "junk DNA" out of mouse DNA, then produced offspring mice which were entirely missing that DNA. The resulting mice were normal in all respects. As a press release states:Another specific piece of evidence is that the genome of the fugu fish (as well as other fish in the blowfish family) is remarkably "clean" compared to that of other fish (or other vertebrates), even other fish which are rather closely related. It's *missing* most of the DNA that other fish (and vertebrates) have that are collectively known as "junk DNA", and as a result has a genome that is nearly "pure" genes (i.e. coding regions) stripped of most non-coding regions. And the fugu gets along just *fine* without them. How and why its genome got "streamlined" by "cleaning house" of most of its "junk DNA" is a fascinating question which is being looked into, but the fact remains that if this "junk DNA" is all that critical and "actually" used for something after all, on the whole, then how does the fugu do so swimmingly (sorry, bad pun) without it at all?
"In these studies, we were looking particularly for sequences that might not be essential," said Eddy Rubin, Director of the JGI, where the work was conducted. "Nonetheless we were surprised, given the magnitude of the information being deleted from the genome, by the complete lack of impact noted. From our results, it would seem that some non-coding sequences may indeed have minimal if any function."
A total of 2.3 million letters of DNA code from the 2.7-billion-base-pair mouse genome were deleted. To do this, embryonic cells were genetically engineered to contain the newly compact mouse genome. Mice were subsequently generated from these stem cells. The research team then compared the resulting mice with the abridged genome to mice with the full-length version. A variety of features were analysed, ranging from viability, growth and longevity to numerous other biochemical and molecular features. Despite the researchers' efforts to detect differences in the mice with the abridged genome, none were found.
So I repeat -- there are very good reasons, based on testing and on the evidence, that "junk DNA" on the whole really is "junk". And that doesn't change even if a *few* specific non-coding regions end up being involved in gene expression or whatnot. Finding a few discarded items of value in the city dump doesn't magically change the whole thing into a mountain of pearls.
"Even the most hard-core junkologists admit that a significant portion of human DNA is probably dispensable. For instance, Ohno, now semi-retired from City of Hope, points out several reported cases of people born with millions of bases missing from their X chromosome. And yet, these people lead perfectly healthy lives, an indication that the lost bases probably add nothing to human life."That said, however, there has been a trend to rename such DNA to something other than "junk", since that is a somewhat misleading term, given how active some (repeat *some*) of it is, and the role it often plays in evolutionary novelty. Instead some have suggested the "genomic scrapyard" or some similar more evocative term.
A complicating factor is that evolution is adept at making use of, and building upon, things that start out as "random junk". For example, from Perspective: transposable elements, parasitic DNA, and genome evolution: "Of particular interest are transposable element traits that early evolve neutrally at the host level but at a later stage of evolution are co-opted for new host functions."
Furthermore, it's clear that the noncoding DNA has not been "designed" as such, because the evolutionary origins of most kinds of noncoding DNA are understood, and their evolutionary histories can be traced through cross-species genome comparisons. For example: A detailed look at 7 million years of genome evolution in a 439 kb contiguous sequence at the barley Hv-eIF4E locus: recombination, rearrangements and repeats .
Going to the core of the issue, however, there *are* features in the genome which actually assist in increasing the efficiency of mutational improvements in the genome, but they hardly rise to the level of "thinking" or "designing", they just do things like raise mutation rates in response to environmental stress (e.g. times when the species might need to genetically adapt or die), or keeping redundant or obsolete copies of genes around as grist for the mill of recombination. All these methods of boosting the effectiveness of evolution are themselves well within the realm of features that could themselves have evolved, they don't look at all "designed" or "preplanned" or "irreducibly complex" or whatever.
And your point is????
The point is that they have allowed their religious dogma to override vast and overwhelming mountains of multiply independent cross-confirming lines of evidence that the Earth is, in fact, billions of years old.
And if they can cheerfully trashcan 300+ years of vast amounts of scientific knowledge on as thoroughly settled an issue as the age of the Earth just because they think their reading of the Bible might say otherwise, then how in the heck can we trust them on the more complex stuff like biological origins?
Labeling something *junk* just because you don’t immediately see a use for something isn’t science either.
This thread post 20 and 26.
That's a very impressive statement. I'd be curious what then you make of the following:
"The expectation was that many of the most active DNA sequences in humans would be prevalent in other mammals, too, because evolution tends to save and reuse what works best. But more than half were not found in other creatures..."
". . . But more than half were not found in other creatures which suggests they may not be that important in people, either, said Ewan Birney of the European Bioinformatics Institute in Cambridge, England, a coordinator of the Encode effort."
Imagine that. DNA that is under neutral selection tends to mutate freely.
Why? One can contemplate whatever one likes as long as one goes out and tests it. Initially after we had just discovered genes people understood the ones that coded for protein, but didn’t understand the point of all the rest of the DNA. So scientists went out to look for function, and we’ve found it as expected (some regulatory, some structural, some over time making new genes). However, the majority of noncoding (protein and organized regulatory RNA transcripts) DNA still has no known function.
==And if they can cheerfully trashcan 300+ years of vast amounts of scientific knowledge on as thoroughly settled an issue as the age of the Earth just because they think their reading of the Bible might say otherwise, then how in the heck can we trust them on the more complex stuff like biological origins?
The age of the earth was not settled three hundred years ago, let alone in Darwin’s time.
==Please try to learn some actual science before you attempt to critique it.
Please learn how to shorten your diatribes so people will read them.
Well, I did provide the source, and the article in question has been posted here recently in another thread. Excuse my for assuming certain things....it won't happen again.
The reason I posted that particular quote is because it seems to be in line with the terms laid out in Ichneumon's post....and although the term prediction wasn't used, I would think that "expectations" would be a distinction without a difference when used in context with a scientific theory. I assumed the point I was making was obvious, and I'm a little disappointed that you didn't comment on, or address that, in any way.
It didn’t bother you that the conclusion was entirely different from the conclusion that you wanted us to draw? Was that perhaps why you chose that particular spot to terminate the quotation?
God doesn’t make junk.
Well, was not the conclusion an assumption based on faulty expectations? Instead of trying to defer the conversation to your assumptions of my behavior, why don't you address the primary point I'm trying to make. If you feel it's untenable, then just say so, and why...
No. Evolutionary biology says genes under strong selection will not vary widely in sequence. This has been repeatedly confirmed. These genes are under neutral selection, which is why the sequence varies so. This is the conclusion reached, you tried to make it look like they were completely stumped and befuddled by terminating the quotation early.
I'm not sure why then, their expectation was contrary to the results, but I'll defer to your expertise in these matters...
...you tried to make it look like they were completely stumped and befuddled by terminating the quotation early.
I did nothing of the sort. I was merely making an inquiry. After all, that is the nature of this particular forum, is it not? If you prefer to read something into it that's not there, then so be it, who am I to stop you....
For anyone who didn't actually read the article, it does NOT suggest, or infer, or justify, or provide any evidence regarding any claim that "junk" DNA is functional in general. Or even that MOST of it is functional. Or even that a significant percentage of it is functional. Or even that 10 or 5 or 2 percent of it is functional.
The study discussed found around 10,000 short DNA sequences in the approximately 95 percent of "non-coding" mammalian DNA that were found to be "conserved" across mammalian lineages generally. Conserved means they varied little among diverse mammalian groups. The logic is that if the sequences were preserved by evolution, then they must have some function. If they didn't have a function then evolution wouldn't be able to prevent them changing randomly over time, LIKE MOST OF THE "JUNK" DNA INDEED DOES.
IOW the whole logic of this result ASSUMES evolution. So why would you -- an antievolutionist -- be justified in drawing any conclusion (even a false and misleading one) from it?
“the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, in contrast, can easily explain them as nothing more than failed experiments in a random process”
--Ken Miller 1994
“...And theres lots more DNA that doesnt even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, tandem repeats, and other nonsense which may be useful for forensic detectives but which doesnt seem to be used in the body itself. Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA. ... Can we measure the information capacity of that portion of the genome which is actually used? We can at least estimate it. In the case of the human genome it is about 2% - considerably less than the proportion of my hard disc that I have ever used since I bought it.”
--Richard Dawkins 1998
Now let see what Intelligent Design scientists were saying on the subject of “junk” DNA:
“If it is true that a vast amount of DNA in higher organisms is in fact junk, then this would indeed pose a very serous challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary events, when it would not in a strict sense be junk in any case, could the finding be reconciled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. On any teleological model of evolution, most, perhaps all, the DNA in the genomes of higher organisms should have some functions.”
"Finally, Science reports “Hints of a Language in Junk DNA” (25 November, p. 1320). Those supposedly meaningless strands of filler DNA that molecular biologists refer to as “junk” don’t necessarily appear so useless to those of us who have designed and written code for digital controllers. They have always reminded me of strings of NOP (No OPeration) instructions.. . .Perhaps the “junk DNA” puzzle would be solved more rapidly if a few more computer scientists would make the switch to molecular biology."
—Forrest Mims III 1994
“A couple of potential uses that spring to mind as I sit here at my desk include bonding to active hemoglobin genes during DNA replication in order to stabilize the DNA; guiding DNA recombination events; and aligning protein factors relative to active genes.”
—Michael Behe 1996
an ID theorist, reckoning that an intelligent designer would not fill animals’ genomes with DNA that had no use, predicted that much of the “junk” DNA in animals’ genomes — long seen as the detritus of evolutionary processes — will someday be found to have a function.
—John G. West 1998
“But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through along, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how “non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.” Design encourages scientists to look for function where evolution discourages it.”
—William Dembski 1998
Many other ID and Creation Scientists have repeated these predictions, and they now being vindicated. Having said that, I suggest that you read the following CAREFULLY, as it does indeed demonstrate that these New Findings Challenge Established (Darwinian) Views On the Human Genome (while at the same time vindicating the IDers, some of which were mentioned above):
“The new data indicate the genome contains very little unused sequences and, in fact, is a complex, interwoven network. In this network, genes are just one of many types of DNA sequences that have a functional impact. Our perspective of transcription and genes may have to evolve, the researchers state in their Nature paper, noting the network model of the genome poses some interesting mechanistic questions that have yet to be answered."
"Other surprises in the ENCODE data have major implications for our understanding of the evolution of genomes, particularly mammalian genomes. Until recently, researchers had thought that most of the DNA sequences important for biological function would be in areas of the genome most subject to evolutionary constraint that is, most likely to be conserved as species evolve. However, the ENCODE effort found about half of functional elements in the human genome do not appear to have been obviously constrained during evolution, at least when examined by current methods used by computational biologists."
"According to ENCODE researchers, this lack of evolutionary constraint may indicate that many species genomes contain a pool of functional elements, including RNA transcripts, that provide no specific benefits in terms of survival or reproduction.”
Sometimes it takes a little shouting, among other things, to settle an argument. It's called progress. Embrace it or be eaten alive.
That's a settled issue in your mind I can tell; that must make it true then, huh?.
Nearly every test one can think of gives an age of the earth of at least 50,000 years. Most give an age around 4 billion years.
Not one valid scientific test gives a result of 6,000 - 10,000 years. NOT ONE.
All of which did nothing to refute Stultis’ post. Thanks for playing!