Darwin’s defender PZ Myers remains unhappy with the ENCODE findings

_{Denyse O'Leary

March 27, 2015

'Junk DNA', Intelligent Design, News}

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Not much “junk DNA.” From him:

Dan Graur has snarled at the authors of a paper defending ENCODE. How could I then resist? I read the offending paper, and I have to say something that will weaken my own reputation as a snarling attack dog myself: it does make a few good points. But it’s mostly using some valid criticisms to defend an indefensible position.

The world yawns and marches on.

Friends point out that we do not know anywhere near enough to know what is or is not junk in the geonme, but that under those circumstances, it is wise to assume that any given component is doing something useful.

One friend kindly writes to say that the term “junk DNA” was coined by Ohno in 1972, to identify the residue of nature’s failed experiments, comparable to extinct species. He assumed we’d find lots of that. So the concept started out as failed genes.

Now the story is something else, but no matter what happens, they’ll never really give up.

See also: Jonathan Wells on Junk DNA and science and The Myth of Junk DNA

Note: “Useful” doesn’t mean “critical.” Redundancy is part of any well-designed system. Indeed, any system in a time-directed universe would have some obsolete features, however well-designed. See, for example, Who’ll give a buck for junk?:

If design is real, must all DNA be functional? I don’t see why that should necessarily be so. A designed system may accumulate junk. A well-designed system accumulates much less junk. So if design is real, we should see a system with only a small amount of junk, and the reason for it is inevitability.

By the way, Myers features at Skeptical about Skeptics.

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Comments

Sorry it took me almost a week to respond--I've been busy myself!
the space of functional sequences is much larger than many IDers admit and randomaly changing proteins isn’t all that destructive
Hold on a minute--70% to 80% of amino-acid altering mutations being deleterious isn't "much larger than many IDers admit". For context let's compare to ID proponent Doug Axe's "one in 10^77" paper that ID proponents so commonly cite. There Axe writes, "about one in four random single-residue changes are functionally neutral." So Axe's estimate of 75% falls neatly between the 70 to 80% estimates linked above. Also as an interesting aside, In salmonella bacteria we see that: "most mutations (120 out of 126) are weakly deleterious and the remaining ones are potentially neutral. The DFEs for synonymous and nonsynonymous substitutions are similar, suggesting that in some genes, strong fitness constraints are present at the level of the messenger RNA." Granted, I would expect ribosomal proteins to be more sequence-specific than most, but what's interesting is that the rates of synonymous vs nonsynonymous deleterious mutations are about equal. I also wrote and you responded:
Many of the losses do affect fitness, but are not life-critical.
there is little evidence for this if changes in somewhere near half the genome have no descernable effect on their host then either quite a lot of the genome doesn’t contribute to a phenotype in any meaningful way, or lots of biological sequences are functional (how else could it be that randomly changing so many bases doesn’t lead to any difference).
You're not considering just how redundant genomes are :). Dennis Noble cites a study in Yeast where 80% of gene knockouts were silent because they were buffered by redundancy. I remember reading other studies where 90 to 95% of genes in various microbes are knocked out and the organism can still survive, but at greatly reduced fitness. I doubt it can be that high in humans. Finally, it takes multiple mutations to knockout a gene, with each having a greater impact on fitness: "Because most mutations are deleterious, the probability that a variant retains its fold and function declines exponentially with the number of random substitutions"
This sort of argument can might for a YEC, but not for others.
I think the universe and earth are old, but I'm actually agnostic on the age of much of the fossil record. In favor of an age less than 50 to 100 thousand years is too much carbon-14 and in-tact biomolecules throughout the phanerozoic. An unbearable and increasing mutational load adds a third argument. But all those pesky rocks above and below the fossils date to tens of millions of years. So I honestly don't know. So "because it supports YEC" is not an argument I accept against having unbearable mutational load. But how long until extinction? Suppose we divide a 3 billion base pair genome into 3 million "genes" of 1000 bases, and it takes on average 10 random mutations to destroy each. On average, in 2 million years (80 thousand generations, 100 mutations per generation) a 1000 base gene will accumulate: 100 / 6 billion * 1000 * 80 thousand = 1.3 mutations. And at least one in 20 genes will be lost completely because they get stop codons. So the genetic entropy argument seems compatible even with OEC timelines, but please check my terms, my math, and my reasoning. ------------ Also, I've been told you're an evolutionary biologist? If so I appreciate your feedback all the more. I'm just a humble programmer with a bachelor's degree who spends too much time reading science journals.JoeCoder_{April 7, 2015
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Hi JoeC, I'm busy today, so these answers will be brief, but I probably won't get to them at all if I leave it, so hope this is better than nothing.
1. We are diploids, and in most cases you must be homozygous for a deleterious allele to affect fitness. This buffers the effect.
Being diploid does buffer these effects, but not as much as might think. Most variants are not classically "dominant" or "recessive", but incompletely dominant, with at least some effect with only one allele. The fact many disease-causing alleles are recessive is partly due to the fact selection has a hard time removing deleterious recessives. In any case, specific load arguments are conditioned on humans being diploid and there being some normal level of dominance. And the load arguments also look at effect mutation-selection balance of many generations.
We have lots of redundant genes serving as backups,
So mutation should be removing those back ups, until we are left with none. This sort of argument can might for a YEC, but not for others.
3. Many of the losses do affect fitness, but are not life-critical.
(a) there is little evidence for this and (b) if we are getting tens small hits every generation we are in trouble in the future!
While something like 70 to 80% of amino-acid altering mutations are deleterious, it typically takes multiple mutations to completely knock out a gene, instead of just reducing its activity. I would assume non-coding functional RNAs are similar.
Indeed -- the space of functional sequences is much larger than many IDers admit and randomaly changing proteins isn't all that destructive :) Again, a YEC might be able to hold that our genome is rotting from some perfect past version (though there is little evidence fo rthis, it's at least a consistant position), it's hard to see how someone who accepts the history of life could do so.
Some nucleotide positions truly are neutral–such as four-fould degeneracy sites. I don’t know how many are, but for the sake of having a position to argue, I’ll take the position that less than 50% of the human genome is truly neutral.
Ok... if changes in somewhere near half the genome have no descernable effect on their host then either quite a lot of the genome doesn't contribute to a phenotype in any meaningful way, or lots of biological sequences are functional (how else could it be that randomly changing so many bases doesn't lead to any difference). I've got to get back to work now. Will try and make time for your second batch later.wd400_{April 1, 2015
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@WD400 at 13. Hello again. I greatly enjoy reading your posts here, even though I'm technically on ID side :) You articulate well and always stick to the data. But I do want to disagree with you about junk DNA. At 13 you wrote:
The best arguments include genetic load, lack of conservation within and between populations, the variability if genome size among similar organisms
The genetic load argument is an argument I frequently use against evolutionary theory. Per Larry Moran, "if the deleterious mutation rate is too high, the species will go extinct... It should be no more than 1 or 2 deleterious mutations per generation." Even the mammal conservation studies report 5-10% or even higher, which implies they are nucleotide specific--what I call "strictly" functional. So I don't see how we can reject that fitness can only decline in higher animals? But why would 60 to 100 deleterious mutations kill us after only one generation? 1. We are diploids, and in most cases you must be homozygous for a deleterious allele to affect fitness. This buffers the effect. 2. We have lots of redundant genes serving as backups, often built in completely different ways than the primary systems (a solid engineering principle for reliability). Per ENCODE 2012, "Loss-of-function tests can also be buffered by functional redundancy, such that double or triple disruptions are required for a phenotypic consequence." 3. Many of the losses do affect fitness, but are not life-critical. 4. While something like 70 to 80% of amino-acid altering mutations are deleterious, it typically takes multiple mutations to completely knock out a gene, instead of just reducing its activity. I would assume non-coding functional RNAs are similar. 5. Some nucleotide positions truly are neutral--such as four-fould degeneracy sites. I don't know how many are, but for the sake of having a position to argue, I'll take the position that less than 50% of the human genome is truly neutral. As you know wd400, lack of conservation presupposed unguided common descent to begin with, so it's circular to use that as an argument for junk DNA. Conversely, if all mammal genomes were >90% similar would you then take it as an argument for design? That wouldn't follow. So that leaves us with the c-value enigma. But I think there are several good reasons for varying C-values: 1. On a very large scale, genome size is correlated with number of cell types. See figure 2B from this paper by T. Ryan Gregory. More cell types would generally require more information. Although note that they only plot protostomia and deuterostomia animals as two points and we can't see differences between individual clades. 2. Take a look at this composite image I put together from this angiosperm paper and also a paper from T. Ryan Gregory in 2001. There seems to be a good correlation between cell size and genome size. The idea being that larger cells require more RNA's. One textbook makes an analogy: "The situation is like that of a car factory aiming for a steady output of cars: engines, wheels and doors must be made at the same rate; if overall output is to be increased the number of each must be increased by the same proportion. Moreover, if each robot, machine tool, and operative is already working at maximal rates, one can increase output only by increasing the number of assembly lines." Although I doubt it's that simple since there aren't necessarily more protein coding genes. 3. Genome size differences may represent tradeoffs between different forms of data storage. One ENCODE researcher commented on reddit: "Organism introduce genetic variation in different ways. For instance, in Drosophila, a 100 kilobase gene (DSCAM) encode thousands of different proteins through a complex alternate splicing mechanism. One could envision copying each of these transcripts - without the alternate splicing - into the genome thus increasing the size of the genome by 10 million bases, or roughly 10%, but not changing the complexity at all." This is similar to how our own compression algorithms operate--frequently used sequences are stored only once and re-referenced, as opposed to the same information being stored multiple times, at perhaps higher fidelity. A png image is not 90% junk just because it's 10 times larger than an equivalent lossy jpeg. 4. Finally, some taxonomically restricted cases of varying c-values (like onions) may be legitimate cases of junk through runaway transposon duplication. But I don't think these can be used to then argue that most genomes in most organisms are junk. Let me know what you think about this, and if I'm wrong on anything :) Depending on where we go with this, I'd also like to test some arguments against junk DNA on you. But one thing at a time.JoeCoder_{March 30, 2015
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Is that it on the vestigial nonsense then?Joe_{March 29, 2015
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Aurelio:
I want you to ask yourself the following question and think deeply before you answer. Can ostriches fly?
No, but that doesn't mean the original function of their wings was flight. You would have to show that they evolved from flying birds and you can't do that.Joe_{March 28, 2015
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Mung: wd400: A designer could do anything. And unknown designer with unknown capabilities and unknown goals , ie the designer of ID can do anything yet you cannot do anything. Wd400 can do some things as witnessed by your response ergo, you are not a designer. Ergo,learn the difference between " a designer" and "all designers"velikovskys_{March 28, 2015
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Zachriel is talking out of its arse, again. Please show that ostrich wings are vestigial.Joe_{March 28, 2015
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DATCG: Assumption 1 = degraded – conjecture, unknown The history is derived from common descent. DATCG: Assumption 2 = present useless condition – failure As already pointed out, Darwin was aware that vestigial structures may have secondary functions. Ostrich wings are vestigial, even though they are used for balance during running. DATCG: Assumption 3 = record of former state of “function” – conjecture, unknown Again, the history is derived from common descent.Zachriel_{March 28, 2015
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wd400: A designer could do anything. yet you cannot do anything. ergo, you are not a designer.Mung_{March 27, 2015
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Darwin's Origins of Species, chapter 14... Assumptions based upon ignorance of organ function, not scientific research...
Finally, as rudimentary organs, by whatever steps they may have been degraded into their present useless condition, are the record of a former state of things, and have been retained solely through the power of inheritance--we can understand, on the genealogical view of classification, how it is that systematists, in placing organisms in their proper places in the natural system, have often found rudimentary parts as useful as, or even sometimes more useful than, parts of high physiological importance.
Assumption 1 = degraded - conjecture, unknown Assumption 2 = present useless condition - failure Assumption 3 = record of former state of "function" - conjecture, unknown So, organs "degraded into their present useless condition" USELESS CONDITION - how did he know organs degraded into useless conditions? He did not. He was clueless to "degradation" as much as he was clueless to organ origins. Clueless ruminations not based upon scientific research, but assumptions. More usage of "useless" in Chapter 14 by Darwin...
Rudimentary organs may be compared with the letters in a word, still retained in the spelling, but become useless in the pronunciation, but which serve as a clue for its derivation. On the view of descent with modification, we may conclude that the existence of organs in a rudimentary, imperfect, and useless condition,
Assumption 1 = Rudimentary - conjecture, unknown Assumption 2 = can be compared to "useless" letters - fail Assumption 3 = serve as clue for organ's derivation - unknown Assumption 4 = useless condition - fail "serves as a clue for its derivation Only if you make assumptions to start like Darwin. His analogy to letters in words fail since we can actually trace language, have observed evidence of characters and translations between languages. But not so in macro-evolution - it has not been observed, and uses assumptions like Darwin did, lending itself to story telling and ruminations of what-ifs like Darwin, speculating it is a problem for Design. He continues with more assumptions and conclusions as arguments against design and evidence for his original unguided aborted process...
... or quite aborted, far from presenting a strange difficulty, as they assuredly do on the old doctrine of creation, might even have been anticipated in accordance with the views here explained.
He attempts to use this conjecture as evidence against ... old doctrine of creation and for his new doctrine of unguided, gradual creation or "degradation." Functions are found in "vestigial" organs. They qualify as evidence against his faulty assumptions and expose his lack of knowledge at the time. If Darwin himself is claiming "useless" organs as evidence against Design, then finding function is evidence against his anti-design conjectures. Thus erroneous speculation about "useless" organs by Darwin present a "strange difficulty" for those that try to abort history or revise it.DATCG_{March 27, 2015
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A designer could do anything. But 90% of functional sequences remain functional when they are randomly changed it seems that a lot of sequence-space contains biological function. Most non-sequence specific functions seems sort of hacky too -- adding bulk to take up space or noise to slow down transcription, for instance, don't seem like cutting edge desigs. It's not impossible that a designer would do that, but, as I say, it's not the vision of the cell many IDers seem to have.wd400_{March 27, 2015
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wd400 I'm really sorry but I don't get your point. If a designer could introduce flexibility into a genome that would be superior to rigid sequence X = function Y and that is it. You would still have a very well oiled machine of the cell. Anyway, for others interested in learning a "non-junk" view of non-coding DNA and functionality for much of this portion of the genome, this is an interesting read: http://protein.bio.msu.ru/biokhimiya/contents/v79/full/79130039.htmlDr JDD_{March 27, 2015
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That's your opinion. Of course it is based on ignorance.Joe_{March 27, 2015
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Maybe, Joe. But if you end up thinking 90% of the functional DNA in our genome doesn't have sequence-specific function then ID's vision of the cell/genome as a well oiled machine is harder to credit. (It's very hard to credit to start with)wd400_{March 27, 2015
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so all those CSI arguments about hard it is to find biological function in sequence space….
What about them? Just because some functional sequences aren't sequence specific doesn't mean all functional sequences are like thatJoe_{March 27, 2015
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wd400: Thanks for the examples. One thing I would say is that if you were to consider the design inference, it as you say would make no sense for a designer to create something that could be so easily deleterious to the organism. Therefore I think that many of the design advocates would not equate functionality with necessity. And as stated, many design advocates are fine with some degeneration ("junk?!") from an original more optimal design. Further I personally suspect there is a lot that occurs in stem cells and processes related to responses (environmental) that implicate many parts of the genome poorly understood. It will be interesting to see over the coming years how our understanding of these processes deepens...Dr JDD_{March 27, 2015
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so all those CSI arguments about hard it is to find biological function in sequence space....wd400_{March 27, 2015
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Take the load argument, I’ve asked people here plenty of times to tell how you can (a) have a genome made almost entirely of functional sequences and (b) not be dead from the 60 or so new mutations (and plenty of old variants) that you were born with.
The functionality isn't 100% sequence specific.Joe_{March 27, 2015
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The best arguments include genetic load, lack of conservation within and between populations, the variability if genome size among similar organisms, the fact that some of that variation be explained by population genetic or ecological variables. I guess you can dismiss these since some of them overlap with an "evolutionary paradigm". But the arguments are grounded in very simple observations. Take the load argument, I've asked people here plenty of times to tell how you can (a) have a genome made almost entirely of functional sequences and (b) not be dead from the 60 or so new mutations (and plenty of old variants) that you were born with.wd400_{March 27, 2015
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LINEs and SINEs are postulated to have functions don't ya know. What are the good arguments for >50% of the human genome for example being junk? I would be interested in knowing more about the evidence, outside of the evolutionary assumptions and paradigm, to support these areas of the genome as junk.Dr JDD_{March 27, 2015
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JDD, OK, but the arguments for junk are much better than "we don't know what it does". So you major objection to junk DNA seems to be one of these "arguments from ignorance" people keep talking about. ...Implies that the original motif was the repetitive elements H'uh? Most of the genomes is made up of dead LINEs, SINEs and viruses. Even after these stop copying themselves it will take a long time for them to rot away to such a degree we don't' recognize them.wd400_{March 27, 2015
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wd400 I think my first point is pretty obvious and needs little explanation. The genome is the only place we term something of unknown function as "junk". Your implication here: "It will take a long long time to completely remove a motif" Implies that the original motif was the repetitive elements. That makes no sense in the paradigms discussed. Considering 65-70% of the human genome is made up if repetitive DNA sequences this is not of insignificance.Dr JDD_{March 27, 2015
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If we identified a new set of proteins or class of lipids present in a particular membrane that we could not find a function for, would we term this “junk protein” or “junk lipid”? Of course not, because that is not the way science works.
OK. What does this have to do with junk DNA?
Yet because we focused so much on the gene-centric view of DNA that we have done this with the genome…and more to the point it was low hanging fruit for “supporting” evolution and be what evolution would “predict” therefore this is why it is termed junk.
Again, I've no idea what this means, or how it relates to junk DNA.
) the very fact it is repetitive suggests it is “conserved” and therefore not a “junk” area so has importance – if it was useless it would be heavily mutated 2) There is growing evidence for roles of repetitive DNA in many aspects we don’t fully understand in the genome, if nothing more at least in structural necessities for example in chromatin packaging and the like. Which is unsurprising that repetitive elements would have structural roles as this is perfectly what you would expect.
The repetitive elements are in fact pretty "heavily mutated" in humans and other groups with mostly dead elements. But the rate at which a single base picks up substitutions is ~1e-9/generation. It will take a long long time to completely remove a motif. Some repeat elements are involved in cellular processes, but any attempt most or all of the repeats to a "functional" class if going to need to deal with the onion test...wd400_{March 27, 2015
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Ome of the reason IDists are so opposed to the term junk DNA is that in no other context would you use this term and it highlights the point I tried to make recently how evolutionists twist things to support their theory despite lack of real evidence. If we identified a new set of proteins or class of lipids present in a particular membrane that we could not find a function for, would we term this "junk protein" or "junk lipid"? Of course not, because that is not the way science works. Yet because we focused so much on the gene-centric view of DNA that we have done this with the genome...and more to the point it was low hanging fruit for "supporting" evolution and be what evolution would "predict" therefore this is why it is termed junk. so that is the primary problem we have with the term junk - it is not how science works, or should work. Further, when we talk about what the "majority" of the genome is being junk, I actually think there is evidence against that. Firstly, when you add up % of known function you may conservatively get 10% (genes, various RNA structures and regulatory RNA etc). However a very large proportion is repetitive DNA. There are 2 things to say about repetitive DNA in a very simplistic sense: 1) the very fact it is repetitive suggests it is "conserved" and therefore not a "junk" area so has importance - if it was useless it would be heavily mutated 2) There is growing evidence for roles of repetitive DNA in many aspects we don't fully understand in the genome, if nothing more at least in structural necessities for example in chromatin packaging and the like. Which is unsurprising that repetitive elements would have structural roles as this is perfectly what you would expect.Dr JDD_{March 27, 2015
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So why are IDers so wedded to the idea there is almost no junk in our genomes?
We like weddings and like American Pickers we find treasure where others see junk. :) :cool:Joe_{March 27, 2015
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REC- Good one- no really. Some or even most IDists don't think there would be too much junk DNA because they don't think that is a good design. I don't know if that is true. Knowing there would be mutations a junk-filled design would minimize the impact as most would hit non-essential sequences. However it is true that we are ignorant, still, but learning so we really don't know what is and isn't junk. It- junk DNA- is a non-argument- it is neither for nor against ID and it is neither for nor against evolutionism. Both can explain its absence and both can explain its presence.Joe_{March 27, 2015
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Darwin defined vestigial as no longer having its original function, not that it has no function.
You would have to know what its original function was. How could we do that?Joe_{March 27, 2015
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I’m not sure where this quote is from, but is something that creationists continually point out. It makes total sense from an ID or creationist point of view. We see systems breaking down, not increasing in function. This is normal and happens all the time.
So why are IDers so wedded to the idea there is almost no junk in our genomes? So much so they'll still say totally ignorant things like this -- which shows they've not taken any time to learn about the good arguments for junk DNA:
At any rate, as was pointed out, simply because we don’t know the function does not mean there is no function. So the junk DNA argument is an argument from ignorance.
wd400_{March 27, 2015
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So the UD position is something like this: 1) We don't know how much junk DNA there really is. 2) The presence of junk DNA is consistent with design. 3) Intelligent design, but not evolution, would predict whatever amount of junk DNA there is or is not.REC_{March 27, 2015
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tjguy: Now they try and disguise the egg on their face by changing the meaning of the term vestigial and claim it doesn’t mean there can be no function. Darwin defined vestigial as no longer having its original function, not that it has no function.
Darwin, Origin of Species: An organ, serving for two purposes, may become rudimentary or utterly aborted for one, even the more important purpose, and remain perfectly efficient for the other... an organ may become rudimentary for its proper purpose, and be used for a distinct one: in certain fishes the swim-bladder seems to be rudimentary for its proper function of giving buoyancy, but has become converted into a nascent breathing organ or lung. Many similar instances could be given.
Zachriel_{March 27, 2015
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