Over at the ID The Future podcast, Casey Luskin has been doing a series on “the top 10 problems with biological and chemical evolution.” Some of the problems he discusses will no doubt be of more interest to certain listeners than to others. However, the segment on junk DNA is particularly worth hearing (about 13 minutes).
For those who have been following the debate closely there may not be much new in the segment, but it provides a relatively up-to-date review of some of the recent research, with multiple citations that are useful when talking with a friend or colleague who may still be stuck in the naive and outdated idea that the genome is awash in junk. Better yet, ask your friend if they have 15 minutes and an open mind, and then let them have a listen.
It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins. Even with the proliferation of functions for non-coding DNA, we still hear regular pronouncements from the purveyors of the materialist creation myth that “yes, there may be some function for non-coding DNA, but most of it is still junk.”
The whole idea of pervasive junk in our DNA is so naive and absurd as to boggle the mind. Thankfully, the trajectory of the evidence is clearly trending toward a more rational and complete assessment of DNA. Yes, hindsight is 20/20, and soon enough every biologist worth her salt will claim that she “always knew” that most DNA had function. But let us not forget that there were a few lone voices, including prominent ID proponents, long arguing for pervasive function — in the face of ridicule and the stifling, science-limiting attitude of the Darwin establishment about their beloved icon of “junk” DNA.
But surely there’s no selective advantage to all that junk. Can’t we prove that it’s junk by showing that it’s not under selection?
Junk DNA is as anti-science as you can get. Intelligent design always results in a hierarchical organization: big parts are made of small parts. It follows that the design of the genome must be a hierarchy, i.e., a genetic tree. Protein coding genes are at the bottom of the hierarchy. Layered on top are the regulatory or control genes. Just recently they found the master regulator, the one way at the top: nFGFR1.
It might be, if it were true.
EA: Meaning what? Are you claiming that the fact that large swaths of DNA do not code for proteins has not been used by evolutionary proponents to bolster the claim that such DNA is “junk”? This has been an extremely common and pervasive tactic of Darwinist proponents for decades. Embarrassingly, some are still using this tactic today in the face of contrary evidence.
And now that even many Darwinists are reluctantly admitting that “some” non-coding DNA might have function, whence the continuing and repeated claims that most DNA is still junk? Why on earth would any rational person make such a claim? It is a classic argument from ignorance: “We don’t know what it does, therefore it must not do anything. Oh, and by the way, our theory predicts that there should be lots of junk, so evolution is true.” Evolution-of-the-gaps thinking.
OT: Epigenetics on steroids
Here’s a challenge @907:
http://www.uncommondescent.com.....ent-564761
(see the post @908 in that same thread).
Podcast: A Bonus 11th Problem – “The Top 10 Problems with Darwinian Evolution”: – Casey Luskin
In this segment, Casey discusses a bonus eleventh problem: that humans display many behavioral and cognitive ability that offer no apparent survival advantage.
http://www.discovery.org/multi.....h-problem/
“It is truly remarkable, an embarrassment to the stifling nature of evolutionary thinking, that anyone ever entertained the idea that the only DNA worth talking about was DNA that coded for proteins.”
Can we get a reference of a prominent scientist stating that the only DNA worth talking about codes for proteins?
Your statement is laughable.
Mung@1 gets dangerously close to undermining the post. Keep thinking, and you’ll get yourself in trouble around here.
Mapou@2: “Protein coding genes are at the bottom of the hierarchy. Layered on top are the regulatory or control genes. Just recently they found the master regulator, the one way at the top: nFGFR1”
…..nGFR1 is a protein, FYI.
I think my comment is pretty clear: the thing you claimed to be true is not. People didn’t say the only DNA worth looking at was protein coding.
You make several more mistakes in your follow up comments, you should probably learn a little bit about junk DNA before you comment on it further.
No knowledgeable scientist ever said that all noncoding DNA was junk or that it was uninteresting. Back in 1968 every knowledgeable scientist was familiar with functional noncoding DNA so they would have been laughed out of the room if they ever made such a silly statement.
Back then, we knew about centromeres, origins of replication, regulatory regions, and various genes for functional RNAs.
We have been patiently explaining this to ID folk for two decades. If they continue to repeat this untrue statement then they are either lying or incredibly stupid … or possibly both.
Five Things You Should Know if You Want to Participate in the Junk DNA Debate
Stop Using the Term “Noncoding DNA:” It Doesn’t Mean What You Think It Means
Dr. Sternberg was mentioned in Casey’s talk. Here is a fairly recent talk that Dr. Sternberg gave on the human genome that overturns the Darwinian claim that most of the human genome must be junk:
Here is a video along the same line:
Here is the paper:
After ENCODE came out a guy named Dan Graur about had a cow. Here is an analysis of the Dan Graur incident:
Basically, the Darwinian critics of the ENCODE study, which found widespread functionality for supposed ‘junk’ DNA, said that biochemical functionality does not really determine if a sequence is actually functional, only ‘conservation of sequence’ determines what is functional.
With that self-serving definition for functionality, a self-serving definition in which common ancestry is presupposed in the definition of functionality, they arrived at 8.2% functionality:
So basically, only if Darwinian evolution is assumed as true from the outset will Darwinists be willing to accept that a given sequence of ‘junk’ DNA may be functional!,, That is called ‘assuming your conclusion into your premise’ and is absolutely a horrible way to practice science!
Needless to say, science itself does not presuppose common ancestry in the answers for functionality that it gives us, and thus, as should be obvious, functionality does not follow the presupposed ‘conserved’ pattern as Darwinists imagined it would:
Let’s not bother with empirical findings.
And by all means, let’s not use genome size as a marker of relatedness. Can’t you just imagine what the tree of life would look like then? Yech!
Ever since it became apparent that the only causally adequate explanation for the contents of the protein coding regions of DNA memory was intelligent agency, it was entirely reasonable to expect that much of the rest of DNA memory would turn out to be functional. It always seemed to me to be reasonable to expect that some of the rest of it was currently unused but might have been left in a state that would reveal something about prior functionality that no longer exists, but would remain functional in the sense that it was available for use by new functionality. If that sounds like that is how a computer programmer would look at it, that is because it is, at least for this one. ;o)
How do we, in understanding the rest of DNA memory, get to where we are in understanding the protein coding regions of DNA? As a computer programmer who has worked at the level of CPU machine instructions, having written applications in assembler language, and written applications to simulate the instruction set of a CPU for diagnostic purposes, let me explain from my perspective of the utilization of digital information, why understanding the rest of it will probably be much more difficult.
There is a direct correspondence between the bit pattern of an executable instruction in memory and one of the machine instructions from the set of those of which the CPU is capable. Repeated observations of how the bit patterns read in from executable memory caused the CPU to respond as programs execute would soon reveal the complete instruction set of the CPU. Understanding the correspondence between the bit patterns in executable memory locations and the instruction set of the CPU is not the same as understanding that a given range of such memory locations comprise, say, a word processor. Understanding that correspondence would do nothing to help one understand that another range of memory addresses contained ASCII encoded characters, or a JPEG image, or some other kind binary data.
My point is simply that what we understood first, unsurprisingly, was that which was most easily detected by observation. Where functionality is not revealed by a direct and observable correspondence between the contents of digital memory and some activity, such as the assembly of protein machines, does not mean that there is no functionality, but only that the functionality may be much more indirectly associated with the contents of digital memory.
wd400 and Larry Moran,
Quiz – 12 points
1. Who popularized the term “junk DNA”?
2. What was the exact title of the paper that first proposed an evolutionary reason for junk DNA?
3. What was the proposed reason in the paper for so much junk?
4. Why was it considered strong evidence for evolution?
-Q
Querius, you’re making a potentially unjustified assumption in your last question. What makes you think that any knowledgeable biologists ever considered the mere existence of junk DNA to be evidence of evolution?
As for your first three questions, Moran has already answered them in this article:
http://sandwalk.blogspot.com/2.....-case.html
REC:
Well, it goes without saying that control/regulatory/noncoding genes cannot perform their tasks directly. They must be using actual proteins to do their bidding in various locations within the organism. I could be wrong but I do not think that nFGFR1 is the actual master regulatory gene. I strongly suspect that it is but a slave gene used by other non-coding master genes. I suspect that every level of the genomic hierarchy uses one or more of these slave genes/proteins. I am only basing my hypothesis on what an intelligent designer would do.
PS. Regardless of the final understanding, there is no question that the genome is organized like a tree, which is consistent with intelligent design.
Nullifidian,
My post was addressed to wd400 and Larry Moran, not you. They made their assertions here on this UD topic, not Sandwalk.
Presumably they can speak for themselves.
-Q
http://www.nature.com/news/200.....018-7.html
“Mice do fine without ‘junk DNA'”
“Mice born without large portions of their ‘junk DNA’ seem to survive normally. The result contradicts the beliefs of many scientists who have sought to uncover the function of these parts of the genome.”
‘Nuff said. Non-ID, non-YEC scientists were hypothesizing and finding function in ‘junk DNA’ a decade or more before the Discovery Institute existed (see, for example, Zuckerkandl, E. 1981A general function of noncoding polynucleotide sequences. Mass binding of transconformational proteins Mol. Biol. Rep. 7149–158.).
Regarding selective advantages – well, all of evolution is not about selection. If you folks were actually as well read as you like to present yourselves, you would have known this.
The following study highlights the inherent fallacy in gene deletion/knockout experiments that have led many scientists astray in the past as to underestimating what the minimal genome for life should actually be:
Genetic Redundancy is incompatible with Darwinism:
Nullifidian @17:
Fair enough. It was only the unknowledgeable biologists, as well as the myriad pushers of the materialist creation story who claimed that the existence of junk DNA was evidence for unguided evolution. Sadly, we don’t even need to look back several decades for many examples. The “lots of DNA is junk, which shows evolution is true” is still being put forth by claimants today.
@20
Knowles cautions that the study doesn’t prove that non-coding DNA has no function. “Those mice were alive, that’s what we know about them,” she says. “We don’t know if they have abnormalities that we don’t test for.
… But he also believes that non-coding regions may have an effect too subtle to be picked up in the tests to far.
“Survival in the laboratory for a generation or two is not the same as successful competition in the wild for millions of years,” he argues. “Darwinian selection is a tougher test.”
Q,
I’m not going to play some silly game with these questions
You are presumably referring to Ohno’s paper where he explicitly includes non-coding DNA in the non-junk portion of the genome and articulates one of the positive arguments for junk DNA.
…all of evolution is not about selection. If you folks were actually as well read as you like to present yourselves, you would have known this.
LoL!
Quierus @ #19:
“My post was addressed to wd400 and Larry Moran, not you. They made their assertions here on this UD topic, not Sandwalk.”
Yes, and I was pointing out that three of your questions already had readily ascertainable answers, if you were to use just a little bit of initiative. I don’t see what difference it makes if these facts are pointed out here or at another link, nor do I see that there is some sort of magic force field around your comments that prevents other people from adding their two cents.
Eric Anderson @ #22:
“Fair enough. It was only the unknowledgeable biologists, as well as the myriad pushers of the materialist creation story who claimed that the existence of junk DNA was evidence for unguided evolution.”
Well, if you concede that only unknowledgeable people are making the argument, then whether the majority of most eukaryotes’ genomes are junk or not has nothing to do with the theory of evolution as it is actually formulated, does it? After all, bacteria are acknowledged to have very little if any junk DNA, but mainstream biologists don’t think that’s because they don’t evolve.
“Sadly, we don’t even need to look back several decades for many examples. The ‘lots of DNA is junk, which shows evolution is true’ is still being put forth by claimants today.”
Then perhaps you could provide a representative sample of cites to these “many examples” of people saying that the mere existence of junk is evidence of evolution? I’m quite curious to see what their reasoning is, and, alas, I’ve not been as fortunate as you are to see this argument mooted by any biologist I’ve ever come across in print or in person.
And as long as we’re talking about it, you claimed above that “It is a classic argument from ignorance: ‘We don’t know what it does, therefore it must not do anything. Oh, and by the way, our theory predicts that there should be lots of junk, so evolution is true.’” Now, if it really is the case that biologists use an argument from ignorance to conclude that the majority of, to take a specific example, the human genome is junk, then it must follow that the majority of the human genome is unidentified. So, do you think that the majority of the human genome consists of unidentified genetic elements?
1. Who popularized the term “junk DNA”?
I can’t read your mind, but I assume you’re referring to the 1972 paper by Susumu Ohno.
2. What was the exact title of the paper that first proposed an evolutionary reason for junk DNA?
The title of Ohno’s paper was “So much ‘junk’ in our genome.” His main argument was based on genetic load. Does that count in your mind as a “evolutionary reason”? I can’t read the minds of IDiots so I have no idea what you mean by “evolutionary reason.”
Or are you referring to the King & Jukes paper of 1968?
3. What was the proposed reason in the paper for so much junk?
Humans could not tolerate the number of deleterious mutations that would arise if most of our genome were functional.
4. Why was it considered strong evidence for evolution?
It wasn’t.
HTH HAND
Moran:
Of course it was and you gave us the answer yourself while feigning that it wasn’t. The author (Ohno) assumed that a high number of mutations are needed to drive man’s evolution. He assumed that, given the required mutation rate, if most of our genes were functional, we would become extinct because the number of deleterious mutations would be too high. This is typical evolutionist crappy reasoning. Why deny it? Buy yourselves some huevos and admit that you people predicted something that turned out to be 100% wrong.
Evolution is trial and error. There are ‘experiments that fail’. Just look at fossil remains of extinct species. They’re Junk Species – evolution’s failed experiments.
Since evolution experiments and sometimes succeeds and sometimes fails, is it any wonder that our genome too is filled with remains of extinct genes?
… no argument here that Junk DNA is evidence supporting evolution?
A Short History Of The Junk DNA Argument Of Darwinists
A graph featuring ‘Kimura’s Distribution’ being ‘properly used’ is shown in the following video:
The following video provides a detailed refutation of Fisher’s work, from the 1930’s, in population genetics:
At the 2:45 minute mark of the following video, the mathematical roots of the junk DNA argument, that is still used by many Darwinists, can be traced through Haldane, Kimura, and Ohno’s work in the late 1950’s, 60’s through the early 70’s:
Sternberg traces how the junk DNA argument developed through the mid 1970’s to the early 80’s and beyond in the following article:
Dr. Wells gives some historical background as to why some neo-Darwinists are doing everything they can to discredit the recent (Sept. 2012) ENCODE findings:
Amazingly, many leading evolutionists as of 2010-11 (Ayala in 2010; Francis Collins in 2010) still insist that most of the genome, which does not directly code for proteins, is useless ‘Junk DNA’.
In 2011, PZ Myers argues for well over 50% junk DNA in the following video:
The reason why many Darwinists are now trying to distance themselves from the fact that leading Darwinists use to claim up to 90% of the DNA was junk is nicely summed up in the following excerpt:
Let’s face it, if we have literally only just discovered and started to understand clever and sophisticated parts of prokaryotic genomes such as palindromic sequences and related sequences due to CRISPR/Cas systems, how arrogant are we to then say we can happily and confidently label 90% of the human genome as “junk”?
Just shows the faith-led system of materialism.
Darwinists might have a lot better chance convincing ordinary people that DNA was not designed if DNA did not overwhelmingly appear to be designed:
At the 10:30 minute mark of the following video, Dr. Trifonov states that the idea of the selfish gene ‘inflicted an immense damage to biological sciences’, for over 30 years:
In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, “Reading only one message, one gets three more, practically GRATIS!”. And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint, although the writing was too small for me to read.
Concluding powerpoint of the lecture (at the 1 hour mark):
Verse:
here is a neat quote to go with Shapiro’s ‘poem’ metaphor for DNA:
Larry Moran @ 27 replied,
First of all, thank you for being straightforward and answering my “quiz.” I will respond in kind. The reason that I posed the questions was to try to bring the discussion into a historical context with the assumption that this would facilitate an intelligent exchange.
Yes, I was referring to Ohno’s paper, which I read repeatedly as a result of previous arguments here.
Yes, that’s the title and no, I’m unaware of a 1968 King & Jukes paper. Are you thinking of Kimura? What I appreciated near the end of Dr. Ohno’s paper were his creative proposals including the idea that “junk DNA” was the genetic remnants of evolution. If I remember correctly, he thought it might be analogous to the fossil record, and suggested that investigating it as such might provide valuable insights into the evolutionary history of humans.
That was the other evolutionary reason he proposed (maybe I should have termed it a “rationale”). It seemed to me that both of these possibilities were very insightful, reasonable, and testable.
That surprises me to hear from you for the reasons mentioned in 2 and 3. Were Ohno’s proposed reasons for so much junk DNA not widely accepted at the time, or is there another reason why you believe it was not strong evidence for evolution?
Thanks,
-Q
The Response to Kimura (1968) and King and Jukes (1969)
King and Jukes chose the provocative title of “Non-Darwinian Evolution” for their paper, and the name stuck to the hypothesis until the early 1970’s when it was redubbed the neutral theory of molecular evolution. Kimura was not fond of the “non-Darwinian” label and asked King and Jukes to change it to emphasize molecular evolution, instead of evolution in general. King and Jukes had choosen their title with the intention of provoking the evolutionary establishment. Although both reviewers rejected their article, it was published upon appeal and the blasphemous title remained unchanged.
Thanks to everyone for the comments.
There seem to be several individuals who are all caught up by my statement in the third paragraph that many evolutionists in past years have displayed an attitude that: “. . . the only DNA worth talking about was DNA that coded for proteins.”
To be sure, this is a generalization about the attitude that has been pervasive. I did not intend to say that no-one ever thought otherwise. Indeed, in my fourth paragraph I specifically stated: “But let us not forget that there were a few lone voices . . . long arguing for pervasive function . . .”
I certainly acknowledge that there have been some careful individuals who have long argued for broader function in DNA beyond protein-coding sequences. But the existence of those careful voices does not change, indeed it underscores, the fact that the popular representation, the oft-made assertion, is that most DNA is junk. And why would anyone think that? Well, first of all because it doesn’t code for proteins. And second, because we haven’t yet found any other function either. That is the attitude that has long characterized the debate over junk DNA as it relates to evolution. This is hardly controversial. Nearly all of the major proponents of evolutionary theory in recent decades have trotted out some form of the junk DNA argument as evidence for the materialistic evolution story. Worse yet, that argument is still being made by some evolutionary proponents.
It will not do, it does not refute the broader issue, to point out that some biologists here and there were aware of other functions for some small percentage of DNA and were valiantly toiling away to tease out those functions. In the context of the evolution debate, which, it hardly bears reminding, is the context of this discussion, junk DNA has absolutely been touted as evidence for evolution, with the fact that most DNA does not code for proteins being a key piece of “evidence” for such a position.
All that said, yes, I could have limited my sentence in paragraph 3 up front, rather than making the poor reader wait until the following paragraph. So I acknowledge the error of my ways and hereby rephrase the offending sentence as follows: “. . . almost the only DNA worth talking about was DNA that coded for proteins.”
There. That addresses the majority of the objections to what I wrote.
—–
The great irony in so many of the discussions about junk DNA is that so often the very individuals who take great umbrage to anyone pointing out that evolutionists have long argued that most DNA is junk — claiming with indignation that such an observation is a perversion of history — in the same breath turn around and continue to argue that most DNA is junk. A remarkable example of cognitive dissonance.
Mung @ 39 noted
LOL. Thanks for the historical context. I’m glad that King and Jukes stuck to their guns on the title because their theory is indeed a significant departure from the RV+NS dogma.
Eric Anderson @ 40 noted
Realize that these are not easy times for Darwinists. It’s stressful to maintain the appearance of an immutable orthodoxy while evolving to a new immutable orthodoxy. Then, with all us IDiots running around making noise, it’s little wonder that alcoholism, domestic strife, and road rage are increasing at an alarming rate among these parts of academia!
-Q
You still don’t seem to understand anything about this topic, EA.
The folks arguing that there were functions in non-coding DNA were not “lone voices”. Everyone who knew the first thing about biology, including Ohno and other proponents of junk DNA, knew about functional RNAs and regulatory sequences. In Ohno’s paper (linked about) he specifically includes some classes on non-coding DNA in the non-junk portion of the genome.
The twin myths that the idea of junk DNA led people to simply dismiss non-coding DNA and that the arguments for junk DNA amount to “We don’t know what it does, therefore it must not do anything.” are both based on ignorance. As I have said, if you want to talk meaninfully about junk DNA you should learn about the topic.
That people as so happy to parade their ignorance about this topic, while blathering about how “naive and absurd” evolution biology is no less, tells you a lot about the ID movement’s connection of reality.
What? Where have I or any other evolutionary biologists taken objection to the claim evolutionary biologists have argued most DNA is junk?
The best evidence still supports the idea that most of the DNA in the human genome is junk. Evolutionary biologists have long held this to be the case, and indeed that’s why evoltutionary biologists did a much better job than did most molecular biologists when they estimated the number of genes in the human genome.
As I’ve said above — what you have wrong is the nature of the argument for junk DNA. If you undestood that you might see how wrong your posts on this topic are.
Eric Anderson,
Umm, is there anyone who ever thought otherwise? I haven’t seen that sentiment.
Yes, that is a common assertion.
That’s part of it, but there’s more to it than that.
I would say that all biologists were/are aware of functions for some non-coding dna.
There’s no irony or dissonance in saying that most dna is junk, and saying that many evolutionists have argued against that position.
How do we measure the “junkiness” of DNA?
Is the DNA of unicellular organisms mostly junk?
Noncoding DNA is not ‘junk’ but a necessity for origin and evolution of biological complexity
Mung asks
You have to understand that “junk” now has a very specific technical meaning among evolutionary biologists.
It essentially means “highly valuable with unknown function worthy of further study.” Of course some of us stupidly assumed that junk meant something without function and of little value.
Shame on us!
-Q
One way to infer widespread functionality in the genome, despite not having knowledge of the precise function the entire genome, is to note that the entire genome, contrary to Darwinian presuppositions, is subject to multiple layers of DNA repair:
In fact, multiple overlapping methods of DNA repair is contradictory to Darwinian presuppositions:
Another way to infer widespread functionality across the entire genome, despite not having knowledge of precise function, is empirically:
Another way to infer widespread functionality across the entire genome, despite lacking knowledge of precise function, is to note the trend in evidence. Every element that Darwinists have insisted to be junk in the past has now been shown to have function of one kind or the other. In other words, there has only been an increase in the amount of the genomic elements known to functional, not a decrease!
Moreover, if the DNA were mostly dead weight, i.e. ‘neutral junk’, as many Darwinists hold, then we certainly should not be seeing the optimal energy efficiency in the metabolic pathways that we see!
I showed the following biochemical pathway (metabolic) chart to a Darwinist once, when he had asked me for ANY evidence of intelligent design in biology.
His response upon seeing the chart was something along the lines of, ‘Just because it is horrendously complex does not prove it was designed.’. ,,, Well maybe so it does not ‘prove’ in the 100%, absolutely impossible, sense, but such ‘horrendous complexity’ certainly does not give any comfort whatsoever to the notion that such ‘horrendous complexity’ can be the accumulation of random genetic accidents either!