Inter-lineage selection versus "just in case".

I still want to grant the benefit of the doubt to my fellow biologists who recently have made statements about non-coding DNA being potentially useful in the future. Natural selection does not work this way, because it is simply the differential survival and reproduction of entities based on heritable differences. In the most common case, this means individual organisms within populations leaving more or fewer offspring and/or surviving or dying under given conditions in a non-random manner due to heritable trait differences. However, the general principle of natural selection is not restricted to this level, and is a logical consequence in any circumstance in which there is differential survival and reproduction based on inherited variation. There can be selection within the genome among transposons, for example, and some authors also argue that selection can take place among species (as differential speciation and extinction).

The most straightforward way of thinking about natural selection is to imagine that a certain genetic trait is either beneficial or detrimental to an organism, such that it is passed on either more or less commonly to subsequent generations. However, there can be higher-order selection as well, in which some lineages persist longer or branch off to form additional daughter lineages more often than others for non-random reasons. This is not why those traits originated nor why they are maintained from one generation to the next, but it could explain why lineages with those traits are more common or last longer than others.

As an example, consider sex. Sexual reproduction involves the recombination of genes which has two important effects: 1) it allows beneficial mutations to spread more easily in a population, and 2) it prevents the ratchet-like accumulation of deleterious mutations at multiple loci. What this means is that sexual lineages can be expected to evolve more quickly and to last longer than asexual lineages. So, when we look around, we expect to see more sexual lineages than asexual ones, and indeed that is what we see (at least in animals). Sex did not evolve so that lineages would have greater evolutionary potential or would survive for a longer time, but that is nevertheless a significant effect when considering the distribution of biological diversity. However, there is still an issue that sexual reproduction is costly: you only pass on half your genes, you produce “wasteful” males, you have to find a mate, and so on, so we also need to consider immediate benefits that keep the trait around long enough for us to even notice the higher-order effects.

Now back to “junk DNA”. It may be that over the long term, lineages with more non-coding DNA are more flexible and can diverge more often, or that they are more resilient to environmental change and will last longer than those with less DNA. If this is so, then this might explain why we see lineages with lots of non-coding DNA — because those lineages persisted while others disappeared. We would still have to explain the origin of the non-coding DNA and the reason it persists over the shorter term though. There are several possibilities. One, non-coding DNA is beneficial to the organism in some way. Lots of ideas have been proposed for this over the last half century. Two, non-coding DNA could be neutral and is simply not eliminated by selection. Three, non-coding DNA is slightly detrimental, but selection has been too weak (e.g., if populations are small) or mutation too strong (e.g., continual transposable element insertions) for it to be deleted. In any of these situations, it could be possible for non-coding DNA to persist long enough to be co-opted (by chance mutations and subsequent selection) or to have impacts on lineage diversification and/or lifespan.

The problem with this is that species with small genomes are much more common than ones with large genomes and large-genomed species seem to be more sensitive to environmental challenges. So, the most likely scenario is that mutational mechanisms affect DNA amount from the bottom up, while selection comes into play from the top down in terms of effects on cell size and also selection against disruptions of genes. On balance, some lineages end up with large amounts of non-coding DNA, and in some cases this is co-opted into functions like regulation or structure.

It certainly could be that some people are thinking about this from a reasonable perspective based on multiple levels of selection and time scales and are just being sloppy in their descriptions of the net processes. Or maybe they really do think that “junk DNA” is kept because it might become useful. Either way, we need to steer clear of simplified soundbites that obfuscate more than enlighten.

6 thoughts on “Inter-lineage selection versus "just in case".

  1. Its funny that you do not have any information on Dr. Sanfords book, “Genetic Entropy & the Mystery of the Genome “. And also any information on “Haldane’s dilemma”.

    For a fellow that has a PHD, you do not “refute” Dr. Sanfords claim, that he basically refuted the NDE claim that a rock can turn into an Biologist.

    THe silence says it all.

    Have a nice day

  2. Linker, do you honestly expect every PhD biologist to carefully scrutinize every crank’s book that comes out with yet another shattering “disproof” of the theory of evolution?

    I searched for Dr. Sanford’s book on Amazon, and found it, with a publisher’s description that makes me not want to waste any more time (and certainly no money) on the book – “In addition to showing compelling theoretical evidence that whole genomes can not evolve upward, Dr. Sanford presents strong evidence that higher genomes must in fact degenerate over time.” That’s supposed to be compelling? There’s so much wrong with that sentence…

    And then, I saw the “customers who bought this also bought:” list.

    The anti-evolution publishing industry is certainly alive and well, in robust good health. Do you expect me to read all of those books, and respond to each one in detail? Without reading any of those books, I am very confident that none of them have anything new to say beyond “I don’t like my misunderstanding of evolution!”. We usually call this argument from incredulity. It’s a logical fallacy.

    If Dr. Sanford wishes to publish EVIDENCE and DATA in a peer-reviewed, scientific journal, then people like myself, who have a working definition of the word “random”, will read his stuff. My opinions can be changed by application of evidence and reasoning, neither of which appears to be forthcoming. If he merely publishes non-peer-reviewed books for the general public, why should I pay any attention?

    Also, what is “the NDE claim that a rock can turn into a Biologist”? I have never met that expression before.

  3. thebrummel;

    If you have did your research (maybe 10 minutes on the internet), before you made yourself look foolish, according to “Google Scholar” Dr Standford published 358 in “peer-reviewed, scientific journals” , so you cannot write this person off as a crackpot. He knows his stuff. And if you are honest with yourself I would read what he has to say, and let the evidence lead you where it leads

    Google Scholar search

    “Http:// “

    You said;
    “do you honestly expect every PhD biologist to carefully scrutinize every crank’s book that comes out with yet another shattering “disproof” of the theory of evolution?”

    Well yes, however if an PHd in the field (this fellows blog)has not read the material that another MAJOR PHd in the field (Dr. Sanford) has, that falsifies the “primary axiom” of what he is studying , I find that kinda of strange don’t you?.

    Tell me what I am missing?

  4. Someone has already done this here and here.

    Please feel free to present your reasoned and referenced rebuttal to the statements on that other blog.

  5. Dr Standford published 358 in “peer-reviewed, scientific journals”

    In what field? If I publish 300 papers in metallurgy, does that make me qualified to spout off ridiculous opinions in the field of radio astronomy? From the review of the book linked to by Dr. Gregory, above, it seems that Dr. Sanford describes himself as an “agricultural geneticist”. OK. That’s not too far off – we’re at least in the realm of genetics, if not squarely in evolutionary biology. What were those 358 papers on? Individual genes and alleles of important crop plants, or phylogenetics? I expect the former.

    Well yes, however if an PHd in the field (this fellows blog)has not read the material that another MAJOR PHd in the field (Dr. Sanford) has, that falsifies the “primary axiom” of what he is studying , I find that kinda of strange don’t you?.

    Tell me what I am missing?

    1. What’s the difference between a “MAJOR PHd” and a minor one?

    2. The field. Key phrase. Does Dr. Sanford study the evolution (here meaning merely “change through time”) of genomes? I’m guessing he has studied the effects on plant development of some interesting genes and allelic variants. Not the same thing.

    3. What’s the primary axiom here? That genomes evolve through time under the influence of natural selection, drift, migration, and mutation? Or something else?

    4. You’re mainly missing the current topic of discussion – this post was apparently about the importance of clear statements about how evolution and natural selection work; specifically, that there is no evidence that natural selection plans for the future in any way. You showed up and ran off in a completely different direction with a contemptuous drive-by. Additionally, you seem to be missing the fact that a vast array of nonsensical books are published every year that all have one and the same goal: to find the killer argument that completely refutes all of biology as a scientific discipline since 1859. Nobody has achieved this in nearly 150 years of constant attempts. Why would you expect a working biologist, who has so much else of greater importance to do (we call it “research”) to attempt to keep pace with this deluge of delusion, falsehood, and stupidity? Do you, or Dr. Sanford, as apparent creationists, read every article in every issue of the journals Evolution, Molecular Evolution, Evolutionary Biology, BMC Evolutionary Biology, Development Genes and Evolution, Evolutionary Anthropology, Evolutionary Ecology Research, Journal of Evolutionary Biochemistry and Physiology, Molecular Phylogenetics and Evolution… et cetera, et cetera? Do you prefer only books written for a popular (non-scientist) audience? Have you read and refuted every argument in the recent (and not-so-recent) books by Michael Shermer, Richard Dawkins, Jared Diamond, John Brockman, David Linden, et cetera? Have you read and considered the inherent contradictions, lies, poor analogies and logical fallacies of the recent (and not-so-recent) books of Michael Behe, Jonathan Wells, and William Dembski?

    Have you read anything by Charles Darwin, or the important evolutionary biologists of the 20th century, such as Ernst Mayr, Ronald Fisher, Sewell Wright, or J.B.S. Haldane?

    You accuse me of poor scholarship as I (admittedly) did not search for publications by Dr. Sanford before denigrating his book. How rigorous is your scholarship – I hope more so than is indicated by a “maybe 10 minutes on the internet” google search. My excuse is that I have become desensitized to the cranky claims of topic-shifting blog commenters – what’s your excuse?

    There is a veritable MOUNTAIN of evidence in support of the major hypotheses of the theory of evolution. These hypotheses have been tested again and again, by hundreds of scientists, and the current set of hypotheses have all passed these tests. To repeat Dr. Gregory’s request: where is the evidence in support of Dr. Sanford’s (and your own) assertions? Only in that one book, in a collection of works by him, or in some other published source I have not considered? Can any of this evidence be presented here, or on another website that you could link to?

    Finally, it’s called punctuation. Your arguments would carry more weight if you used some. Undefined abbreviations and acronyms such as “NDE” are similarly unhelpful.

  6. kudos TRG for the thoughtful post on noncoding dna. Not enough folks IMO have pondered the possible role of higher-order selection here and how that might translate (or not) into “evolved for” language.

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