Salvador seems to have successfully hijacked the early embryonic mutations thread and turned it into a discussion of junk DNA. So I thought I’d share my thoughts on the subject of junk DNA. Why care?
Various strains of creationism hold that the earth and life started out perfect, then came the fall, and it all went downhill from there. Both young earth and old earth forms can easily accommodate the presence of junk in DNA. So the presence of junk DNA does not mitigate against the creationist position. But what of it’s absence?
Now perhaps it would appear to be nothing short of miraculous if it turned out that the genomes of organisms were mostly or completely functional or otherwise serve some identifiable purpose. But are we even close to being able to demonstrate that such is the case? Anywhere close at all? I think not. Thus the opportunity for much hot air and no end of people willing to spout it. We are far from having a complete understanding so perhaps a wait and see attitude is appropriate.
So arguments over how much DNA is junk and how much isn’t don’t serve much useful purpose in the debate. People aren’t going to be converted. If we simply must talk about junk DNA wouldn’t it be better just to discuss the implications one way or another? If neither side can make predictions that can be falsified what is the point? Ah. Pointless debate. Of course.
Does evolutionary theory predict junk DNA, and if so how much junk does it predict?
What does a phylogeny of junk DNA look like?
If it turned out that the genomes of organisms were mostly or completely functional or otherwise serve some identifiable purpose would evolutionary theory be falsified? My answer to that question is no, evolution would not be shown to be false.
The debate is mostly a waste of time. The irony. 🙂
Mung asks,
“Does evolutionary theory predict junk DNA, and if so how much junk does it predict?”
No, evolutionary theory does not predict junk DNA. Some parts of evolutionary theory, such as natural selection, suggest that genomes should not contain junk DNA. That’s why Darwinists were opposed to junk DNA from the beginning.
“What does a phylogeny of junk DNA look like?”
The trees have the basically the same topology as all the other trees. The distances are closer to a universal molecular clock since the differences between species are due to fixation of nearly neutral alleles by random genetic drift and the rate of change corresponds to the mutation rate.
“If it turned out that the genomes of organisms were mostly or completely functional or otherwise serve some identifiable purpose would evolutionary theory be falsified?”
Much of evolutionary theory would be called into question if most of mammalian genomes were functional. That’s because the result would conflict with the standard views on genetic load, sequence conservation, C-value comparisons, and the molecular clock. It would also call into question much of biochemistry and molecular biology, especially our understanding of pseudogenes and defective/degenerate transposons. We would have to rethink our view that half of the genome consists of fragments of degenerate transposons that appear to be nonfunctional by any reasonable criterion.
“The debate is mostly a waste of time. The irony.” 🙂
I believe that finding the truth is never a waste of time. I understand why you might have a different viewpoint. 🙂
People aren’t going to be converted
Moar creationist projection.
Larry Moran,
Hi Larry, can you please link to the scientific theory of evolution so we can all read what it really says? It is written down, isn’t it?
Does it say how to test the claim that mammalian genomes are the result of natural selection, drift and other blind, mindless processes, starting from prokaryotic genomes?
The first problem is defining “junk” with respect to DNA without basing it on our ignorance. Companies to engineer redundancies into some of their products. That means you can remove those redundancies and still maintain functionality. But redundant systems are far from junk.
Then there is just the physical nature of DNA. If it is an information storage mechanism then its size is not determined by what parts are required to carry out the instructions, ie the alleged functional part.
I’ve never thought much of the debate about junk DNA. Of course the origins and amounts of junk DNA do matter, but these don’t really touch a whole lot on what I think are more interesting questions of the evolution of functionality.
Junk DNA mostly reinforces the evidence that exists otherwise for evolution anyway. That it agrees with the evidence of evolution with selective pressures presumably is a kind of check on the rest of the evidence, but it hardly changes much.
Anti-junk IDists want a victory over the evilutionists, which is why they’re constantly pushing the idea that there’s little junk DNA. However, if they ever decide that denying junk DNA is a loser for them, they’ll just accommodate it anyway, claiming some metapurpose, with the mysteriousness of the Designer being the excuse of last resort.
Glen Davidson
LoL! Coding DNA makes the case for ID, Glen. That is one reason your position has to start with functioning cells, complete with DNA- it doesn’t have anything to account for it.
I have never understood the arguments over “junk DNA”.
For myself, I just take “junk DNA” to be a technical term. I don’t assume that the particular DNA is literally junk. We can wait for further research on that.
I tend to think of it as something that participates in mutation and recombinant DNA, but is protected from selection pressures. Perhaps that’s important for biological innovation.
Larry Moran,
What evidence is there that these fragments are non functional? Is it a low level of expression?
J-Mac cited this paper previously. What is your opinion of the conclusion?
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003569#pgen-1003569-g001
This states the authors opinion that low levels of expression do not signify non functionality. The paper claims that if a gene can be shown to be regulated then it should be deemed functional. My experience is that expression levels vary depending on the functional condition of the cell. A gene can be dormant most times but very active during cell division.
colewd,
http://sandwalk.blogspot.com.es/2013/07/how-to-make-scientific-argument.html
Yes, that appears to be their opnion. And I stated my opinion that their opinion was based on a couple of non-sequitors, and asked if anyone was willing to defend the authors’ logic.
Result: crickets.
Are you willing to discuss this paper, or is this perhaps yet another hyper-selective appeal to authority?
I absolutely agree with Glen here. Take software development. Over time it’s not uncommon for parts of the code base of an application to serve no useful function yet it’s still maintained. It’s not necessarily good practice but it happens anyways.
Both creationism and ID can accommodate junk DNA. I guess if I was an opponent of ID I’d be clamoring for IDists to put a stake in the ground wrt junk DNA. ID can only lose, and that’s a wager even Salvador could appreciate. 🙂
Moved a comment to guano.
Some history:
Up until about 1972, people tended to assume that all DNA was functional.
1972, Ohno coined the term “junk” (complete with scare quotes). Ohno’s definition, quite a useful one, was ‘DNA that cannot suffer a deleterious mutation’. His idea was initially resisted.
1980, two papers published in the same edition of Nature, by Orgel and Crick and Doolittle and Sapienza, suggested that a significant fraction of the genome was due to the action of ‘selfish’ DNA, whose spread is largely on their own account. The genome forms an environment which they can colonise, much like ‘real’ organisms. They impact upon organismal selection, however, because they add to material and energetic cost, and act much like mutagens when they land in important sequence. These ideas were initially resisted.
A lot of the human genome is made up of such elements. Some have become ‘domesticated’, much as mutations can be beneficial. But these functions cannot be exported to the whole class – Alu sequence in a promoter region is not evidence that all million Alus are there to provide promoter sequence.
Now we enter the Age Of Revisionism. ‘Darwinists’ have always loved the idea that we are junk, ‘cos they are atheists and hate the idea that we might be special. Some brave soldiers are turning back the tide and showing those ‘Darwinists’ what for. That the idea they have held to doggedly since … well, since they stopped resisting it, let’s say 1985 … is now on the verge of total overthrow because … well, 82.5 ‘megabytes’ isn’t nearly enough.
If Salvador or any other Creationist or IDist really wants to discuss junk DNA I’d like to recommend they address the arguments in the following book:
Relics of Eden: The Powerful Evidence of Evolution in Human DNA
This is one of those books that I own but have only browsed, because I could care less if humans and other primates share a common ancestor. I will say though that the claims that this book presents a problem for intelligent design are probably over-rated.
According to this book, evolution means common descent.
Junk DNA can support claims of common ancestry, but would lack of it disprove common ancestry?
If any members have read this book and can readily point me to relevant sections that present arguments against intelligent design I would appreciate it.
Mung,
Are you sure of that?
Well, I admit I’ve been reading the blurbs and assuming the comments about the book were informed by the contents of the book. 🙂
Yeah, ID and creationism can “both” accomodate jDNA… and both can use the same ad-hoc rationalizations based on arguments from analogy. It’s almost as if ID and creationism were one and the same thing!
– My preacher told me we’re now OK with jDNA, because, you know, some software developers suck!
– Intelligent Design theorists agree! Praise Jeebus!
Why not code comments Mung? Those are not “functional” and would make your designer look less of a retard
Mung,
The evidence of common descent is evidence of evolution. They aren’t the same thing though, and I’d be surprised if the contents – or even the blurbs themselves – really said they were.
How are you defining “common descent”?
The book has a glossary. In the glossary evolution is defined as speciation.
So the typical evolutionist equivocation. Hard to be surprised anymore. According to this definition of evolution there is no conflict with Creationism or ID. Even young earth creationists accept evolution in this sense of the word.
Only someone who thinks all species are specially created or that new species share a common ancestral species but not due to genetic differences would disagree with this definition.
If there is some disproof of Creationism or ID in this book it’s probably based on a straw-man.
Unbelievable.
Look, there’s a theoretical framework, and then there’s a huge body of evidence that tells a particular story about how evolution happened and all of it happens to be consistent with the theory. There’s no equivocation whatsoever. How come you still don’t understand those things after so much time discussing these topics with pros in these forums?
No, that’s not correct. Knowledgeable scientists had been discussing junk DNA for many years before that. It comes from the understanding of genetic load or the idea that humans and other species can only tolerate so much functional DNA without going extinct.
Ohno describes it in a review published before the paper you refer to.
Ohno, S. (1972) An argument for the genetic simplicity of man and other mammals. Journal of Human Evolution, 1:651-662. [doi: 10.1016/0047-2484(72)90011-5]
He says in his review of the scientific literature dating back to the 1940s,
There is a finite upper limit to the number of gene loci, which an organism can afford to have. An organism having 3 x 10^6 or so gene loci would exterminate itself from an unbearable mutation load. Yet, the mammalian genome is large enough to accommodate that many gen loci…. At least 90% of the mammalian genomic DNA appears to represent ‘nonsense’ DNA base sequence of varous kinds.
The idea of junk DNA is still actively resisted by many in the scientific community in spite of 40 years of accumulated data.
Those papers were part of the resistance. They advocated a function for the excess DNA; namely, that it was selfish DNA consisting mostly of functional transposons. The idea was rapidly taken up by most scientists who cared to think about it.
Later on, we learned that most of the genome consists of dead transposons and bits and pieces of once active transposons. They are not selfish because they are dead. They are pseudogenes. This is junk DNA. Many scientists either don’t know this or else they postulate some sort of function for this debris.
The vast majority of Alu sequences have mutated so they can no longer be transcribed and are no longer capable of transposition to another locus. They are junk.
The term “Darwinist” refers to someone who thinks natural selection is by far the dominant force in evolution. They actively resisted the idea of junk DNA right from the beginning because there’s no room in their worldview for maintaining DNA with no function. It should be eliminated by negative selection. IDiots have told this lie consistently for almost 30 years in spite of the fact they’ve been corrected hundreds of times.
About 10% of our genome is functional. That’s roughly 320,000,000 base pairs. It’s more than enough to build a human.
Scientists who really understand evolution and have studied biochemistry & molecular biology are the “brave soldiers” who are fighting the junk DNA deniers. They are winning against other scientists. The consensus in 2017 among knowledgeable scientists is that 90% of our genome is junk. We are also convincing some IDiots but that’s much harder.
Various strains of creationism hold that the earth and life started out perfect
Those strains of creationism must be wrong as I recall God called his creation good and not prefect.
Genesis 1:31 ” God saw all that He had made, and behold, it was very good…”
Thanks Larry. Perhaps one of these days we can get to “not enough mutations.”
Another interesting topic and probably more relevant than junk DNA.
Five Things You Should Know if You Want to Participate in the Junk DNA Debate
Larry Moran,
No, evolutionary theory does not predict junk DNA. Some parts of evolutionary theory, such as natural selection, suggest that genomes should not contain junk DNA. That’s why Darwinists were opposed to junk DNA from the beginning.
What evolutionary theory are you talking about Larry? You claim not to be a Darwinist and I can quote more than few evolutionary biologists (which you are not) who would not agree with you… So, what evolutionary theory are you talking about? Your own? Because this would explain why not many evolutionary biologists would agree with you including on the “creative powers” of random genetic drift.
Your confidence is not evidence. It isn’t even an argument.
If science was about bald assertions and pontification Larry’s comment would mean something to science.
But anyway, Larry has a mechanism that can account for the alleged junk DNA. Does he have a mechanism that can account for the coding DNA? If yes please show your work
Not happy with that definition. I would think that any DNA could suffer a deleterious mutation, for example if that mutation created a spurious transcription factor binding site that created a downstream problem.
I don’t appreciate this characterization as VJ Torley said he wanted an open discussion, and the junkDNA issue is partly a response to VJ agreeing to Larry’s view of the epigenome, which I contested vigorously.
Because of Mung referencing my relevant discussion of junkDNA in VJs thread, I’m boycotting this thread other than this comment. I’ll discuss junkDNA elsewhere at TSZ, but not in Mung’s thread.
I’m glad to see Larry offering his views here, and I yield the floor to him and others.
Straw man alert:
What if it is structural as opposed to functional, Larry? If most of our genome were for structural purposes which are not sequence specific, it could handle the changes.
See if you only have the functioning 10% then all mutations would be to it which would cause major problems very quickly. If you overload that 10% with the 90% that can tolerate change then generational mutations have a smaller chance over messing things up. Then if you use that 90% to store immaterial instruction sets for the 10% you have a solution to many issues.
The problem is we have no idea what is really going on inside the cell. We can only watch the molecules and what they do. Yet we haven’t been able to show that living organisms are reducible to physics and chemistry. And if ID is right then DNA is storage for the immaterial information unaccounted for by physics and chemistry
I’m hurt. I am truly hurt Salvador. If I ever accused you of child abuse I take it back. 🙂
DNA_Jock,
Sure. I have been agnostic on the junk DNA discussion but am becoming more skeptical.
stcordova,
Torely seems to be enjoying Larry’s patting on the back… so gradually he will be swaying towards materialism…
Just like my mother who learnt that her church teaching was contradicting the Bible. So initially, she opposed it vigorously. But one day the pastor called on her and said that her voice was like an angel’s voice and the church choir was not the same without her…
Can you guess what happened?
Baby J-Mac?
I thought there were organisms whose genomes were 100% or very nearly 100% functional, without any junk. Viruses, maybe, or some bacteria or protists. So I would not expect evolutionary theory to predict either junk or no junk, since we see both. I can understand the tradeoff between the cost of maintaining nonfunctional DNA, and the cost of weeding it out.
I think the pufferfish has next to none jDNA, or so I’ve read
Mung,
I don’t speak to morons…So guess what comes next…
must…resist…must…resist…
In the preface of the book (approx two pages), the word “evolution” appears eight times. It’s never defined. But there are a few hints.
The appeal to other genome projects, especially the chimpanzee and rhesus macaque projects, and the reference to “literally millions of molecular fossils in DNA.”
These point to the argument for common descent, and thus for the “evidence for evolution” being the evidence for common descent.
Either you are not speaking to me, or I am not a moron. 🙂
I speak to morons though
People who talk to themselves are often misjudged.
dazz,
Why would you want me to abuse the rules of this blog to describe your mind or the lack of ?
Mung,
Who are you talking to then?
Preaching to the choir J-Mac. Preaching to the choir. Have you perused the suggested reading material?
Just remind why you don’t believe in evolution and you believe in common descent at the same time.
BTW: I hold no grudge against people who prove me wrong. You did. So I appreciate it and move on, Thank you!
J-Mac, to Mung:
Mung:
…or J-Mac is wrong about not speaking to morons.
The correct answer is (c).
There’s little room for doubt that “evidence of evolution for humans” refers to common descent.
Humans evolving from other humans? I’m betting that’s not what the evidence shows. LoL.
Evidence of common ancestry = evidence of evolution. That’s a real problem if evolution is common ancestry. Evidence of common ancestry = evidence of common ancestry. Evidence of evolution = evidence of evolution. Well, duh.
Seems to me Larry Moran is pretty open to the idea of a fully functional genome…
Why is he defending the 10% function then?