Larry Moran Defends “Junk DNA”

_{Jonathan McLatchie

December 20, 2011

Intelligent Design}

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Earlier, I responded to remarks made by PZ Myers at the recent Skepticon 4 conference. His subject: “Junk DNA.”

On his Sandwalk blog, University of Toronto biochemist Larry Moran has posted a response to my article. Since the post is relatively civil (unusually for Moran, he refrains from calling me an “IDiot”) and offers some scientific criticisms of what I wrote, I will offer a rebuttal.

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Comments

they have little bearing on the 90% of the genome that lacks any known function or the expected signatures of function. PaulMC, And how do you know that we will not continue to find new functions in the 90% of the genome that lacks any known function? It seems to me that the more we research this and biology in general the more we are finding that evidence is trending towards intricate fantastic design that is thousands of years beyond our technological capabilities to recreate and ever further away from the tiny blobs of jello in the "warm little pond" that Darwin initially envisioned.wgbutler_{December 23, 2011
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Understanding the dynamics that allow this to happen in some populations and not in others is what we need. Not analogies. PaulMC, It appears to me as though you are trying to frame the discussion as you, the enlightened materialist simply being on a search for the truth while the ideological and misguided ID proponents are wanting to sweep evidence contrary to their worldview under the rug with broad generalizations and analogies. Are you aware that for decades "enlightened" materialists dismissed "Junk DNA" as useless rubbish and didn't want to waste any time researching it. The ID proponents were the ones saying that this was not so, and as we finally start researching non functional DNA, we are finding out that it does indeed have many functions that are extremely important. I refer you to this link that explains in greater detail the point I am trying to make: http://www.evolutionnews.org/2011/05/has_forbescom_critic_of_read_t046771.html I say lets research all of it. And I'd be willing to bet my life savings that we'll end up finding a TON of new functions that we currently don't know anything about and that are extremely important. But I find it slightly irritating that Darwinists are now trying to rewrite history and act as though they never stated that non-coding DNA was all useless leftover junk from evolution (although some of them are still trying to hold the line and say that this is the case).wgbutler_{December 23, 2011
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The new research referred to here identifies a function in a particular long non-coding RNA. However, long, non-coding RNAs themselves are a class of genomic elements that are not new to science - having been described as a specific class of transcriptional molecules in mice about a decade ago. This class of molecules comprises something like 0.1% of the genome and has already been accounted for in calculations of the functional genome. Like micro RNAs, new lncRNAs will continue to be identified and will contribute to our understanding of gene regulation, but they have little bearing on the 90% of the genome that lacks any known function or the expected signatures of function.paulmc_{December 22, 2011
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"From the post I was replying to." You were replying to my post. Please point to the language that led you to that absurd conclusion, or admit that you pulled it out of thin air and that it didn't come from the post you were replying to.Eric Anderson_{December 21, 2011
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Where in the world did you get that from?
From the post I was replying to.
Materialists: We don’t know what a lot of DNA does; therefore it doesn’t have a function;
You're only making that caricature because you don't know what you're talking about. You can start your education by reading the first comment in this post.
They [parts of DNA] look designed, and meet criteria of design detection, so it is likely they were designed.
Ooh, "Criteria of design detection". That sounds so sciency.lastyearon_{December 21, 2011
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EA:
2- Most everyone agrees that there may well be some junk DNA. Why this would be against design, is unclear. Systems degrade, machines break down, detritus piles up over time in the trunk of my car.
When does the analogy end and the biology start? Stating that you have a messy car gets us nowhere towards understanding junk DNA. In order to be observed as, for example, species-specific differences junk DNA has to spread through populations i.e. either by positive selection or by the escape from purifying selection - genetic drift. Understanding the dynamics that allow this to happen in some populations and not in others is what we need. Not analogies.
Even on the assumption that there is a bunch of truly junk DNA, like so much detritus in the trunk of my car, it doesn’t tell us anything at all about how DNA came about. Indeed, the silly statements by so many materialists about junk DNA being evidence for a natural process and against design is the equivalent of someone seeing all the junk in the trunk of my car and claiming that this proves the car was not designed, but was the result of natural processes. It is absurd.
Why should explaining the population-level retention of junk DNA tell us something about the origins of DNA itself? The point is to describe the processes that affect populations over time, with an aim to explaining the broad structure of the genome. This is actually quite a useful in and of itself, and is not intended as a comment on design. Conversely, junk DNA in large volumes does become a problem for ID, if only because leaders of the movement have made all manner of claims that junk DNA will either not exist or be a small component of the genome.paulmc_{December 21, 2011
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lastyearon: "ID proponents: The presence of Junk DNA in the genome testifies to a designer." Where in the world did you get that from? Besides, you have completely misrepresented the debate. This is how it has gone: Materialists: We don't know what a lot of DNA does; therefore it doesn't have a function; therefore it testifies against design; indeed, this shows that the whole idea of design is false, nothing in biology was designed; further, this proves that there is no God, no free will, no purpose in the universe . . . ID proponents: But a lot of the DNA you thought didn't have function has turned out to have a function. Further, there are lots of other parts of DNA that are known to have a function, and very sophisticated function at that. They look designed, and meet criteria of design detection, so it is likely they were designed. Materialists: But there is some other DNA that we still don't know what it does; further, there is some stuff in DNA that looks kind of strange; further, some organisms have similar DNA sequences; therefore, DNA was not designed, there is no design in life, yada, yada, yada . . .Eric Anderson_{December 21, 2011
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Darwin: "The number of intermediate varieties, which have formerly existed on the earth, must be truly enormous." Gould: "The extreme rarity of transitional forms in the fossil record persist as the trade secret of paleontology … We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study." Skeptioc: "Micro-evolution is obsvered, while macro-evolution is not, and neither of them tell us how we got here" Dawkins: "Thanks to Darwin, we now understand why we are here and why we are the way we are."Upright BiPed_{December 21, 2011
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Interestingly enough, I stumbled upon a new article discussing a new finding that has relevance for the "Junk DNA" argument: http://www.evolutionnews.org/2011/12/long_non-coding054291.html I'd be interested in reading what the atheists here think about this new research.wgbutler_{December 21, 2011
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No worries just thought I'd mention it.Stu7_{December 21, 2011
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ID proponents: The absence of Junk DNA in the genome testifies to a designer. Evolutionary Biologists: But there's plenty of Junk DNA in the genome. ID proponents: The presence of Junk DNA in the genome testifies to a designer.lastyearon_{December 21, 2011
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Funny that Moran refers to "creationist" arguments in The Myth of Junk DNA. I'm quite sure I didn't find any religious arguments in that book, nor any scriptures used to support the idea that more DNA is functional than materialists often claim. We can argue about the particular portions of DNA that are functional and those that are not. And indeed, those are important discussions I look forward to as we learn more about DNA. However, let's not lose the big picture on the issue of "junk DNA." 1- More DNA is being found to have function all the time. We know that there are many thousands of functions that occur in biology, for which functions have not yet been found. The information for those functions must reside somewhere in the cell. Hanging one's hat on the idea of pervasive junk DNA, as with almost all alleged examples of "non-function" that have come before in biology, is standing on the losing side of the equation. It is, with perhaps a few exceptions, an argument from ignorance. 2- Most everyone agrees that there may well be some junk DNA. Why this would be against design, is unclear. Systems degrade, machines break down, detritus piles up over time in the trunk of my car. 3- Even on the assumption that there is a bunch of truly junk DNA, like so much detritus in the trunk of my car, it doesn't tell us anything at all about how DNA came about. Indeed, the silly statements by so many materialists about junk DNA being evidence for a natural process and against design is the equivalent of someone seeing all the junk in the trunk of my car and claiming that this proves the car was not designed, but was the result of natural processes. It is absurd. There is not one thing about the alleged non-functioning DNA that would lead us to conclude that the highly sophisticated, complex, functionally specified portions of DNA came about through the same process -- quite the opposite, it should lead us to believe that those functional portions didn't come about through the same process, if we are going to let clear thinking reign.Eric Anderson_{December 21, 2011
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Yes I know, but I have seen jim respond to comments on here before and I was hoping he would this time too. It appears to me, as someone who supports ID, that Paulmc has made some valid points, and I was merely hoping to hear what he had to say about them.PeterJ_{December 21, 2011
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Well Jonathan M posted the original article over on the Evolution News and Views site. UD linked to that article.Stu7_{December 21, 2011
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I think we are getting confused by terminology. You are using “modern synthesis” to mean “the assemblage of different evolutionary mechanisms that most modern evolutionary theorists employ”, whereas when most ID people speak of “modern synthesis”, they mean “The Modern Synthesis”, i.e., the “neo-Darwinism” of Mayr, Dobzhansky, and Gaylord Simpson, which was the ruling view in evolutionary theory for decades. Its formula was random mutation plus natural selection.
I think you'll find you are using the term incorrectly. You talk about the modern synthesis in the past tense, and you characterise it with a decades-old formulation. Sure, the modern synthesis has its roots in the 1930s and was hardened into what you refer to in the 1950s, but is generally considered to be alive and much more pluralistic than what you describe. Yes, people will debate what exactly is 'included' in the MS, but it is generally accepted as the current paradigm of evolutionary biology and includes neutral drift. In any case, one only needs to look at how the term 'Darwinist' is used on this website to see that it is used to describe all kinds of contemporary evolutionary biologists, not simply those wedded to the past. It is a misleading and inaccurate term.
It is understandable that the population geneticists are a bit irritated that “evolution” will no longer be their private playground, where they don’t have to answer to anyone.
I would be happy to end our conversation here if you believe that accurately characterises the state of affairs. I find it hard to believe you can have a rounded knowledge of contemporary literature in evolutionary biology (as I've seen you claim) while genuinely believing that population geneticists have owned 'evolution' as their own 'private playground' without having 'to answer to anyone'. Firstly, evolutionary biology encompasses a broad range of disciplines, of which population genetics is but one. Secondly, the arguments between disciplines have been extraordinarily fierce - e.g. biologists vs molecular geneticists on the neutral theory of molecular evolution. Thirdly, there have been massive arguments within population genetics that aren't well reflected by the image of a playground with no one to answer to. What you describe is a fiction.paulmc_{December 21, 2011
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paulmc (4.1.1.3.8): I think we are getting confused by terminology. You are using "modern synthesis" to mean "the assemblage of different evolutionary mechanisms that most modern evolutionary theorists employ", whereas when most ID people speak of "modern synthesis", they mean "The Modern Synthesis", i.e., the "neo-Darwinism" of Mayr, Dobzhansky, and Gaylord Simpson, which was the ruling view in evolutionary theory for decades. Its formula was random mutation plus natural selection. You are right, however, to say that ID people also criticize some other proposed evolutionary mechanisms which postdate The Modern Synthesis. The reason for that is that none of those mechanisms, e.g., "drift", seem capable of actually building any new biological form. For that matter, not even all critics of neo-Darwinism have anything much better to offer. Lynn Margulis's mechanism of combining genomes has some application at the level of microorganisms, but beyond that level it seems a chancy and erratic mechanism to generate macroevolutionary change. What is needed is something that transcends freak mutations, freak genome combinations, and the endless shufflings of population genetics. What is needed is something that can explain apparent evolutionary tendencies toward useful form. In various ways, Conway Morris, Denton, Shapiro, Sternberg and others are all working towards an explanation of novel form that does not depend, ultimately, on blind searches. But of course the old guard, whom you apparently represent -- whether neo-Darwinian or not -- are going to defend the fortress on which their careers were built, until they leave the scene. Thus, no new ideas are going to come from Dawkins, Coyne, Lewontin, Eugenie Scott, Ken Miller, Francis Collins, etc. The future of evolutionary theory will not be dominated by population genetics, as it was in most of the 20th century. It will be increasingly shaped by input from fields traditionally distinct from biology: physics, engineering, computer science, information theory, pure mathematics. It is understandable that the population geneticists are a bit irritated that "evolution" will no longer be their private playground, where they don't have to answer to anyone. They probably think that all these new "immigrants" to biology will lower the property values. But for ID people the future of biology is looking brighter than it has looked at any time since 1859, provided that the younger voices are not strangled in the crib by their jealous elders. T.Timaeus_{December 21, 2011
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I've been looking forward to a response from Jonatahn M to Paulmc. Thankfully I didn't rustle up some popcorn as it doesn't appear to be very forthcoming. Please Jonathan, what is your take on the points raised by Paulmc?PeterJ_{December 21, 2011
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If you wish to cite the cases of functional Alu copies, for the sake of balance it is worth discussing the other side of the accumulation of of transposable elements in the genome. Lynch et al. (2011) make a compelling population genetics argument:
As genome sizes increase from?1Mb in the smallest eukaryotes to >10 Gb in the largest, the most pronounced change is a progressive increase in the contribution of noncoding DNA. This pattern is common to all forms of noncoding sequence, from the three main classes of mobile elements to introns to pseudogene associated sequences ... This general syndrome of genomic bloating, operating in parallel across eukaryotic lineages, is thought to be a consequence of the reduced efficiency of selection opposing the accumulation of excess DNA in taxa with reduced Ne and a mutational bias toward insertions of large segments of DNA. The underlying premise of this hypothesis is that essentially all forms of excess DNA are mutationally hazardous.
They go on to argue:
One of the primary predictions of the mutational-hazard hypothesis is that the susceptibility of a genome to the accumulation of excess DNA is a function of the ratio of the power of mutation to drift ... One of the more dramatic sources of support for this point derives from observations on organelle evolution. Although the nuclear genomes of land plants and animals have independently arrived at quite similar architectural states, these lineages have evolved enormous differences in the structure of organelle genomes—those in land plants are bloated with intergenic DNA and introns, whereas those in animals are extremely compact, to the point that the translation-initiation and translation-termination codons of adjacent genes often overlap. These dramatic disparities can be explained by the fact that mutation rates in plant organelles are typically ?100 times lower than those in animal organelles, whereas the nuclear mutation rates and average values of Ne are roughly comparable across both lineages.
Citations and references to figures removed. Thus the accumulation of junk is best currently explained through slightly deleterious mutations passing under the radar of purifying selection in species with small population sizes, as the strength of selection against such insertions are the result of a composite mutation-rate--effective-population-size variable.paulmc_{December 20, 2011
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