Mung, to petrushka, elsewhere:
Everyone does not understand “genetic load” and those that do claim to understand are probably wrong. Why don’t you start an OP on genetic load and the genetic load argument? That would be interesting. Betting you won’t.
This is such an OP. I believe the genetic load argument*** was initially proposed by Susumu Ohno in 1972, whose paper also introduced the then-scare-quoted term “junk”. It’s brief, accessible, and worth a read for anyone who wishes to offer an opinion/understand (not necessarily in that order).
The short version: sequence-related function must be subject to deleterious mutations. Long genomes (such as those of most eukaryotes) contain too many bases for the entire genome to be considered functional in that way, given known mutation rates. The bulk of such genomes must either have functions that are not related to sequence, or no function at all.
Interestingly, the paper is hosted on the site of an anti-junk-er, Andras Pellionisz, a self-promoting double-PhD’d … er … maverick. Also of interest is that, contrary to some ID narratives, the idea was initially resisted by ‘Darwinists’, if that term is understood not as people who simply accept evolution, but as people who place most emphasis on Natural Selection. Perfectionism is not the sole preserve of Creationists.
More recent work has characterised the nonfunctional fraction, and this lends considerable empirical support to Ohno’s contentions.
[eta: link to comment]
***[eta: in relation to genome size, not the first time anyone, ever, discussed genetic load!]
People may think that my calculation above is off by a factor of two. But it isn’t, because that is taken care of by the factor of 2 in the mutational load being
in a stretch of genome that has mutation rate 
.
Besides, a factor of two is not enough to make much of a difference here.
Additional quibble. The reduction in fitness is not really a reduction in viability because some of it is a reduction in fertility instead, Still, such considerations are not enough to escape the disastrous calculation.
I’m sure that IDists could counter this argument if any of them were qualified in mathematics.
Joe Felsenstein has already explained the population genetics version of genetic load and pointed out that the argument was developed long before Ohno’s 1972 paper.
However, for the record, it’s interesting to see what Susumu Ohno actually wrote back in 1972 in his famous “So much ‘junk’ in our genome” paper.
Knowledgeable scientists knew about this estimate of 30,000 genes. It was in line with estimates of the number of mRNAs from experiments done around the same time (1968-1974). This is why knowledgeable scientists were not surprised when these predictions were confirmed by the sequence of the human genome in 2001.
Larry Moran,
Welcome to TSZ, Professor Moran.
Have “stickied” this post as we have new commenters joining in.
Look! Look! A squirrel!
That didn’t take long.
Joe Felsenstein,
At what point of inaccuracy would you consider this problematic. 10x? 100x?
Are we possibly missing something in the junk DNA discussion by not paying attention to the amount of genome sequences dedicated to embryo development?
Can you cite anyone who isn’t paying attention to development?
OK, I’m embarrassed. Rereading my comments I am off by a factor of 2. I used
instead of 
, so the reduction of fitness by mutational load should be twofold larger than the value I gave. This of course makes the impact of mutational load greater than I calculated.
colewd:
10x fewer mutations would still be too many. 100x lower rate of mutation would start to make it questionable whether the mutational load is a serious matter.
No. We are paying attention to all the DNA whose sequence is conserved in evolution, and that of course would include any that is involved in development of embryos.
The point I made in the other thread and which seems to have been rejected by mung and colewd is that if the sequence isn’t conserved, and any sequence seems to be as viable as any other, than maybe the sequence has no function.
There are more rigorous arguments than this, but it’s a starting point for discussion.
colewd,
Why would we need to be so fixated on animals, more specifically some species from among the ‘higher primates’? There is junk in plants, single-celled protists … one could try and construct a hypothesis that only applied to one area of the phylogenetic tree. But if the same elements appear throughout it, how would one deal with that?
In invoking the mutational load argument we are “paying attention to” all the DNA. We conclude that there is too much of it for all, or even most, of it to be subject to deleterious mutations.
The argument does not depend on assigning some particular function to any part of the DNA. It does not ignore any part of the DNA that is able to have deleterious mutations. That would include parts that function in development.
Conservation of sequence is, as petrushka noted, a somewhat separate argument. We expect that only a small minority of mammalian DNA can be subject to deleterious mutations, and that part should also show some conservation of sequence in evolution. There is a small fraction of the sequence that is conserved, and that confirms the conclusions from the mutational load argument.
I read colewd as hinting at a view that development is linked to what-is-thought-to-be-junk in some way. It must be in a non-sequence-dependent way though.
I have to assume he thinks the Larry Moran percentage of functional DNA is not sufficient to account for development. That’s not silly as a conjecture, but it’s also not original and not unexplored.
If anyone thinks Moran et al are wrong, let’s see the data.
I misspoke in my earlier post. I should have written cost of substitution.
Does that change your answer?
It’s not about junk DNA. It’s about genetic load and what everyone knows [or does not know] about genetic load.
It appears to have been a six part discussion of junk DNA, not “a six part discussion on Sandwalk of genetic load.”
I didn’t reject anything. My interest was in your claim about the genetic load argument and your desire to skip past it.
There are different kinds of “genetic load”. Mutational load is used in the argument about junk DNA.
Substitutional load (or the “cost of natural selection”) is relevant to arguments by Walter Remine, who thinks that it poses a barrier to explaining the evolution of humans.
I debated with Remine for years on sci.bio.evolution. I also wrote a paper in 1971 on this kind of load that I think clears up a lot about it.
I assume by now you have been freed from any mental chains imposed by my memory lapses and are able tho think clearly again.
Mung,
What was the question?
Joe Felsenstein,
So are you saying one should not equate genetic load with cost of selection?
Just to supplement: I don’t quite grasp how a genetic load which is due to fitness differentials could be anything other than a ‘cost of selection’.
Semantics aside, the two loads arise in different cases. In the mutational load case, the deleterious alleles arise by mutation, and are continually being eliminated by natural selection.
In the case of substitutional load, the environment changes, and a previously common “normal” allele is now deleterious and is eliminated, while a previously rare allele is now non-deleterious and replaces it.
In Remine’s argument, there is no actual ‘load” — it is an argument that there are insufficient fitness differences to explain the postulated changes of gene frequency (say, in a scenario for the evolution of humans). His “cost” is supposed to also apply when the alleles that substitute are new beneficial alleles.
So Mung, have I guessed correctly as to what case of “genetic load” you are intending be discussed?
Or is this another case where you aren’t revealing that?
Joe Felsenstein,
Thanks, I had not appreciated that distinction.
Not every thread her is productive in the sense of revealing an important new truth.
I think we should all show appreciation to mung for revealing a new biological truth.
And that is, if Petrushka says Larry Moran had a six part series on genetic load, and it was actually more general, about junk DNA, then mainstream biology is wrong, ID wins, and there is no junk DNA.
In the meantime, perhaps mung will grace us with his dissertation on why the genetic load argument for junk is not valid.
I think he should stick to revealing why I am wrong. That seems to be a more successful line for him.
Everything is relative I suppose 😛
Buy shares in the DI if it ever has an IPO.
Glen Davidson
I’m not interested in arguing about junk DNA. Perhaps if junk DNA somehow threatened things I believe, but it doesn’t. I don’t believe humans were created 6,000 years ago. I am wondering though when we are going to enter the “seventh day” of creation. Shouldn’t we be there by now?
Yes, you’ve got it.
When I saw petrushka’s comment it brought to mind Walter ReMine’s arguments. I got the sense from ReMine that everyone does not understand genetic load, but it’s been awhile since I have revisited that subject.
I probably don’t even have his papers on this computer.
Allan Miller,
I don’t have an argument here. I am just wondering to what extent this has been explored. I read a paper on placenta development that identified about 750 micro RNA’s involved in placenta construction. This in itself is not going to move the junk needle except if it is the tip of the iceberg.
colewd,
micro RNAs are 20-odd nucleotides long, so even 750 are not even going to scratch the surface. If they are the tip of an iceberg, you still have to think about the genetic load argument. And, they must come from the 30% or so of the genome that is neither transposon nor intron. 70% is still a lot of ‘junk’.
When I usd the word everyone, I was thinking about the people who post here, all of whom should know Joe F’s argument, and all of whom are on notice that Sandwalk a vigorous defence of junk DNA.
So that should be the baseline for discussion. If you think Larry or Joe are wrong, say so and defend yourself. But please don’t repeat argument that ignore them. State their argument and explain where they are wrong. Trying to pretend they haven’t covered the bases is just silly.
I don’t believe i have had anything to say in this thread (or the previous thread) about junk DNA other than to say I’m not arguing about junk DNA. Perhaps you should save your concern that I might repeat an argument and ignore what Joe and Larry have written when I actually do so. Until then I’ll just go on pretending they haven’t covered the bases. Silly me.
Perhaps the honest thing to do, if you think that ID doesn’t predict junk DNA (although your motivation for not getting involved in the debate is that it doesn’t threaten any of your beliefs… awkward) is to actively confront those in the ID camp who claim it does. ID doesn’t predict anything whatsoever, so it shouldn’t be too much of a challenge
dazz,
I agree with you here and so does Mike Behe. Design in an inference based on an aggregation of evidence. It does not have a mathematical model that can be used to make predictions.
You don’t need a mathematical model to make predictions, just some theoretical framework with some explanatory power. And I don’t see Behe challenging those who keep touting ENCODE as evidence for ID. Behe is in the profit making side of ID. He is a con artist and a dishonest POS.
And ID is not based on any valid inference. It’s ironical that all your arguments are inspired by your obsession with Darwin. Darwin’s mentioned inference to the BEST EXPLANATION. Since by your own admission ID lacks any kind of explanatory power, ID is not a valid scientific inference. Period
dazz,
I don’t agree with your extreme statement. Also your criticism of Mike Behe is very naive. If you want to live in a world of polarized ignorance thats up to you. Do you have an example of a theoretical frame work that is not mathematical that makes predictions outside the TOE?
Mendeleev’s periodic table; the various eka-elements.
Plate tectonics
Neuron theory, linguistic theories.
Some mathematics may be involved with both, but that’s also true of evolutionary theory.
Biology has a number of theories not primarily mathematical in nature.
Glen Davidson
I remember your mention of jDNA and all that nonsense about mathematical models in this video:
Behe’s response? “Yeah, yeah, yeah, right, yeah, well… on second thought… yeah, right”
Oh, the irony
Is it time yet for cole to declare victory?
That clarifies, finally, what you meant by “genetic load” and that it is not the mutational load argument about junk DNA. But everyone here, including me, and including Alan’s OP, misunderstood that as being the issue Mung was raising.
Now that so much ink has been spilled here, I think it might be best to do that in a new thread. I am busy with other matters and will leave that to someone else, but in that thread I will defend my position that Remine has not found a way to put an upper bound on the rate of substitution.
And that argument has nothing to do with whether or not there is junk DNA, since Remine thinks that his “cost” calculation also puts a bound on the rate of neutral substitution, so would apply to junk DNA too.
Joe Felsenstein,
Well, hang on, this is the timeline I was following:
So, I did precisely that! Granted that Mung appears to have been talking about something else entirely, I can only go on the words used.
It’s a shame there is no trace of discussions that occurred at ARN (and to some extent at ISCID) as I recall Remine still posting there when I first became aware of ID as a movement.
I did find this Creationwiki page.
I also came across an article by Ian Musgrave at Panda’s Thumb where he writes:
In another PT post, Pim van Meurs cites a paper (PDF) by Leonard Nunney who writes:
(I also came across this 😉 )