Let’s break this out, as it features a common misconception, not just among creationists.
No, I’m dismissing them because they’re wrong. Nobody is an expert in all aspects of biology. It’s not the people who study evolution who are saying there’s no junk DNA, but aren’t those who study the subject the ones you should be paying attention to? Sadly, many molecular biologists aren’t knowledgeable about evolutionary biology. Now, this is a major digression from the subject, but if you want to engage with it you will deal with the points I have already suggested as evidence for junk DNA. Do you remember what they are?
Well, one expert you quoted doesn’t. I don’t think you’ve done an adequate survey. You might ask @Joe_Felsenstein. I can’t myself see why almost all point mutations to junk DNA should not be expected to be 100% neutral. It’s true that the very existence of junk places a slight load on DNA replication, and in that sense insertions aren’t entirely neutral, though they’re clearly close enough to neutral for all practical purposes. And yes, Ne*s<<1 is the criterion for nearly neutral evolution.
No, most non-coding regions are not regulatory. Why would you make that assumption? Why would one species of onion require twice the regulatory DNA as a closely related one? Why would fugu require a tenth the regulatory DNA as closely related fish? Now, some non-coding DNA is in fact regulatory, but that only accounts for a few percent of the human genome. Please don’t confuse non-coding with junk. Junk is only a subset of non-coding DNA, though in humans it’s by far the majority subset. And of course a deleterious mutation can happen even in junk DNA if, for example, it creates a spurious transcription factor binding site. That doesn’t mean that almost all mutations aren’t neutral.
You fail to account for purifying selection. Adaptationists expected that most of the genome would be under selection, as in fact it is in most bacteria. Let’s count history of biology as another thing you aren’t very familiar with.
This. This is the point I was making @PDPrice. And if you read the series I linked to on the other thread you will find tons of sources that back up this claim.
As for the non-existence of truly neutral mutations, @PDPrice offers this quote:
“The first point to make is one of definition; it seems unlikely that any mutation is truly neutral in the sense that it has no effect on fitness. All mutations must have some effect, even if that effect is vanishingly small.”
It comes from from Eyre-Walker A and Keightley PD. 2007. The distributon of fitness effects of new mutations. Nature Reviews Genetics 8:610–618.
This quote has no citation, and the review refers to no evidence supporting the intuition. “It seems unlikely” is the sole support. So much for that.
Ok, I’m willing to discuss this with you if you want. I’d like you to start by defining what you mean when you say “junk DNA”. I am assuming you mean to assert it has no function (thus the name ‘junk’), rather than simply to say its function is unknown.
The term “junk DNA” has been questioned on the grounds that it provokes a strong a priori assumption of total non-functionality and some have recommended using more neutral terminology such as “non-coding DNA” instead.(Wikipedia)
Since you are asserting there is Junk DNA, as opposed my statement that this is now an outdated term, you seem to be asserting the lack of function, rather than unknown function, correct?
It would also seem you are going against the consensus view. That doesn’t make you necessarily wrong, of course, but I’d like you to explain why you think the consensus is wrong about junk DNA.
In January, Francis Collins, the director of the National Institutes of Health, made a comment that revealed just how far the consensus has moved. At a health care conference in San Francisco, an audience member asked him about junk DNA. “We don’t use that term anymore,” Collins replied. “It was pretty much a case of hubris to imagine that we could dispense with any part of the genome — as if we knew enough to say it wasn’t functional.” Most of the DNA that scientists once thought was just taking up space in the genome, Collins said, “turns out to be doing stuff.”
Yes. That’s always been the definition. Unfortunately, many people have got that wrong. Where did you get that quote? “Non-coding DNA” means something quite different, simple DNA that doesn’t code for a protein. There’s plenty of functional non-coding DNA, including RNA genes and regulatory sequences.
You’re quoting a medical researcher, not someone who studies evolution. Collins is quite wrong about that. I’d like to see him back up his assertion that “most of the DNA…turns out to be doing stuff”. Or, since he’s not here, maybe you could. Again, you will at some point have to confront the evidence against that view, which I have already summarized for you.
I won’t interfere much here but junk DNA and non-coding DNA are different things. So that wouldn’t work. That’s one of the biggest misconceptions in this whole debate. Too many people equate junk with non-coding DNA
Non-coding DNA is a term that was proposed after the term ‘junk’ was already in use, and the reason is that the assumption of no function proved to be premature and false.
It appears you are willing to concede that not all of the formerly-called “junk DNA” (the non-coding region) is actually junk. But you insist that nonetheless, this term should be used. Why is that? What percent of the non-coding region do you assert is actually junk?
That is a bizarre claim. @swamidass, would you agree that Francis Collins is unqualified to talk about evolution, as he appears to be saying here? Or unqualified to make the statement that he is quoted as having made?
As I’ve explained countless times before (and I have no doubt you will disagree), “evolution” is not operational science, it’s a philosophy of history. There is no conflict between being an expert in medicine and understanding the philosophy of evolution well enough to meaningfully comment. I don’t find your hairsplitting to be legitimate here. Especially since the question of junk DNA is a medical question. Whether DNA has function is not a question of evolution (history) but a question of operational, medical science (how the human body works).
But you are also making an assertion, and since you are taking issue with the above statement, I can only conclude you mean to assert most (or at least 50%) of the non-coding region has no function and is “junk”. What is your reason for making that claim? I’d like to understand your logic.
That’s nonsense. It isn’t true. We’ve known about functional non-coding DNA since long before the term “junk DNA” was invented. You are making this up.
No; that’s not what “junk” means, and it’s never been what “junk” means. This is false history.
Approximately 90% of your genome is junk.
Of course. But there is also no reason to suppose that an expert in medicine must understand evolution. It’s neither a drawback nor a qualification.
That’s only one of several approaches to identifying junk DNA. How much of the genome do you think has been shown by experiment to be functional? What’s your evidence?
Then you should actually read my posts rather than ignoring the bulk of their content.
In other words, close relatives have wildly varying genome sizes. I have also mentioned that the pattern of fixations in most of the genome matches the mutation rate and is spread evenly over the sequences, i.e. no evidence of conservation, that mutational load arguments (which you like) preclude functionality for most of the genome, that much of the genome consists of broken retroelements. Do you remember seeing any of that?
A good education can be had by reading Larry Moran’s blog articles, as @Rumraket has mentioned.
Yes, that is your personal assertion not accepted by virtually anyone in the scientific community.
Humans aren’t the only species on the planet. Perhaps you aren’t aware that all species on the Earth have varying amounts of junk DNA in their genomes?
Doubtless, you will say it countless times in the future. But that won’t make you correct.
Yes, some people might view evolution as mostly about natural history. Others, self included, consider it more a science of observed ongoing processes of change in the biosphere.
But that makes this discussion a puzzle. If you only see evolution as a philosophy of history, why would you even care about junk DNA? The junk DNA is relevant to ongoing processes of change, but knowing about junk DNA is unlikely to tell you much about history.
What I am trying to convey is that, regardless of when the term ‘noncoding DNA’ was first used, the term ‘junk DNA’ rose to prominence as a description of the entire noncoding region, and has subsequently been mostly rejected as such. Many are now calling for the use of the neutral term ‘noncoding DNA’ instead. That is not something I’ve made up. Take for example this letter to the editor in the Journal of Forensic Sciences, written by Jennifer K. Wagner, J.D., Ph.D. Center for the Integration of Genetic Healthcare Technologies,University of Pennsylvania:
What started as a clever talk title by Susumu Ohno (1) to
describe non-protein-coding DNA (ncDNA) quickly became a
ubiquitous phrase (“junk DNA”) causing substantial confusion
and distraction from a more sophisticated and accurate appreciation of the majority of the human genome that does not encode for proteins … The scientific community, should it
choose to do so, can relegate the “junk DNA” phraseology to the
history books and forge ahead to a more nuanced understanding
of genomics and the central dogma.
To quote once again from the Wikipedia page,
According to T. Ryan Gregory, the nature of junk DNA was first discussed explicitly in 1972 by a genomic biologist, David Comings, who applied the term to all non-coding DNA.[39]
I have just shown you that it has been what it meant, though today that understanding is being continually revised as new functions are discovered.
Please explain how you know that. As I have shown you, that is certainly not the consensus (if there is one). Please provide a justification for making this claim, rather than simply asserting it.
I do read them, and thus far you have been making unjustified assertions.
Ok, but that is not proof that the DNA is non-functional. You are making an assumption based on your lack of knowledge about how something works (rather than your knowledge that it doesn’t).
This is what I’d like to home in on. Please explain what you mean by this exactly.
I think you should first actually show there is a consensus view, as opposed to a significant controversy among two camps of which you don’t really know the actual sizes.
That was never an assumption, it was always and still is an evidentially derived conclusion researchers were led to time and again, even in the face of their actual hunches that natural selection should get rid of it. If you want to understand the basis for that you should read the references given in the link in my previous post.
Disagree? Then please provide references before the first DNA was sequenced where researchers predicted it should be mostly junk, based on this strange idea you’ve posited that evolutionary biologists said it must follow from the idea that life has evolved through copying errors.
That is what you said, so now it’s come time for you to support that claim with correct historical references:
@T.j_Runyon was kind enough to also provide a link to a series of posts by T. Ryan Gregory where he documents in considerable detail, the reverse of the history you’re claiming here, for example by showing how it was data (as opposed to some sort of evolutionary assumption) that changed the mind of genome researchers.
Again, that just plain isn’t true. You have been grossly misinformed by whatever creationist web site you got that from. The reference to Ohno, if you actually check it out, will show you that you’re wrong, as Ohno mentions several sorts of functional, non-coding DNA. From the very beginning, junk DNA and non-coding DNA were not synonymous. And seriously, a quote from a letter to the editor by a lawyer, in a journal that has nothing to do with evolutionary biology?
Already mentioned, and ignored, several times.
No such thing as proof in science. It’s evidence.
No, no no. That has nothing to do with it. You aren’t reading.
If most of the genome were functional, most mutations would be deleterious. Mutational load would be so great that the human population would rapidly go extinct rather than rapidly expand. This applies even more strongly to species with large populations and short generations. There wouldn’t be a mouse, fly, or paramecium left in the world.
I see you’ve snipped the majority of the arguments for junk DNA.
I’ll leave that to the population geneticists to figure out. @Joe_Felsenstein? It’s the argument I rely on least, though. Lack of conservation is the strongest, if you ask me, including of sequence and size.
So far I’ve quoted Wikipedia (which, in turn, quotes other sources) and I’ve shown you a couple of other quotes as well. Nothing came from a creationist website. You’re just dismissing this history because you don’t like it. I’ve sufficiently backed up what I’ve said at this point.
Here’s an interesting pattern that’s been repeated several times now. I say something and back it up with citations, and then you dismiss my citations because you claim they don’t know what they’re talking about, or they aren’t qualified enough (appeal to authority), etc. etc. What I don’t see is you citing anything that shows I’m wrong. You would need to back up your claim that the term ‘Junk DNA’ has never meant the entirety of the noncoding region. I have already shown you that it indeed has been used in that way, and now people are arguing against using it that way.
No, you’ve made some vague references. I want you to come out and actually back up your very specific claim that 90% of the genome is junk with no function. You cannot merely assert it.
Evidence that is entirely unconclusive. You are arguing there is no function based upon your lack of knowledge about what the function could be. That is fundamentally poor reasoning.
I certainly am. Could you stop with the repeated ad hominem attacks and just answer my questions please?
That’s interesting. Why do you say that?
That is called genetic entropy. It’s exactly what Dr Sanford is arguing is happening. So you’re saying, in essence, if most of the genome is not junk, Dr Sanford would be completely correct. Do I understand you so far?
That’s not correct. Such populations have much lower per-generation germline mutation rates, by virtue of the fact that there is less time for mutations to accumulate. Also, such species have much lower percentages of noncoding DNA, meaning fewer nearly neutral mutations to accumulate. And lastly, such populations have much more purifying selection going on, and higher tolerance for greater amounts of selection. All of these factors put together means that we would not expect such populations to be as susceptible to the problem of increasing genetic load. However, that by no means makes them totally immune over an indefinite period of time.
I have linked an entire series dealing with the history of these terms. @Rumraket has reminded you of it and you still aren’t engaging it. And also showing a few papers or letters to editor isn’t going to provide you any support. You know people are wrong sometimes? And one thing I’ve already said is that one of the biggest misconceptions about the junk DNA debate is that it’s equivalent to non-coding. A mistake that is routinely corrected by experts in the field. This is another example of your selective reading.