Wednesday, August 01, 2012

Our genome is degenerating, but wait, someone is coming to help us

According to plant geneticist, John Sanford, the human race is degenerating rapidly. It's one of the trade secrets of biology. Every population geneticists knows that it's true.

Sanford has even written a book about this trade secret: Genetic Entropy and the Mystery of the Genome

Now if humans are degenerating at the rate of 1% or so per year then this must mean that they were perfect only a short time ago—like maybe 6000 years?

Are humans doomed just as described in scripture? Yes. Is there any hope for us? Our only hope is Christ.

Interesting. Sanford doesn't exactly say exactly what Christ will do to fix all the mutations in our genome. Will He invert better DNA repair enzymes? What's taking Him so long? And why weren't we better designed to begin with?



[Hat Tip: Uncommon Descent]

63 comments :

  1. The idea that genomes were nearly perfect in the early days following Creation isn't new. I remember apologists using that perfect genome argument to explain why Genesis has Adam and other Biblical patriarchs living for hundreds of years.

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  2. Presumably, the primordial genome was pristine and perfect. But degeneration will inevitably occur due to the accumulation of slightly deleterious mutations that natural selection will not always prevent from fixing.

    What Larry doesn't seem to realize is that some real "junk" exists within exons. For example, some genes have prematurely truncated ends where the C-terminus now resides downstream witin the 3'UTR.

    However, the acquiring of billions of base pairs of useless "junk" is something that natural selection would never have allowed happen given the substantial metabolic and spatial cost involved.

    It is no surprise, therefore, that researchers are continually discovering that more and more of the genome does have some functional role.

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    1. Presumably, the primordial genome was pristine and perfect.

      No, if it were perfect it could not have degenerated by definition.

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    2. Your argument was clearly refuted ever since the existence of selfish DNA (close relative to junk DNA) was suggested.

      I am not surprised that you have not read the proper literature. That would be devastating to your "theories."

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    3. At 1-5% per generation (assuming a 20 year generation, a 6000 year old earth, and a pristine human genome at the starft), that implies that we presently have a maximum of 4.9% ( (1-0.01)^(6000/20) ) of our original DNA.

      This is of course, ludicrous. I believe the actual measurement was on the order of 10 mutations per individual with reference to their parents. The human genome is about 700M worth of data. 10 mutations (each occupying a half-nibble) is about 2.5 bytes. That's not 1%. That's 3.4 parts per billion.

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    4. However, the acquiring of billions of base pairs of useless "junk" is something that natural selection would never have allowed happen given the substantial metabolic and spatial cost involved.

      What's natural selection going to do about it? How much less fit is an organism with (say) an extra 10,000 bases going to be than the rest of the population? Within its descendants, how much less fit will another 10,000 bases make them? Different answers will pertain depending on nutritional limitation, but even with a metabolic cost, gradual accumulations can readily sneak under selection's radar as 'effectively neutral'. It's easier to acquire than get rid of.

      It is no surprise, therefore, that researchers are continually discovering that more and more of the genome does have some functional role.

      No-one is even remotely surprised by that - least of all our host. What would be a surprise would be if (for example) the bulk of intergenic transposons and retroviral debris were found to have a role, and selection 'cared'. There's a good half of the genome for you to go at, just there. It's a percentage game.

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    5. I'll tell you what natural selection would do:

      1. Prevent useless junk from fixing in the population.

      2. Favoring the deletion of any junk by natural processes.

      Larry seems to think that the replication of billions of bp of useless junk, not to mention the subsequent transcription and splicing out of intronic sequences, involves virtually no metabolic cost at all. The nucleus also has to be stretched to accommodate all the chromosomal material. Many polyploid plants have very big cells as a consequence.

      Before Larry can unilaterally declare that 90% of the genome is "junk", he needs to recognize that the discovery of functional transposons etc may not be merely exceptions to the norm, and examples of fortuitous co-option, but part of a more general phenomenon and trend.

      Unfortunately, he isn't prepared to wait until all the research is done and all the data is in. How very immature.

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    6. I'll tell you what natural selection would do:

      1. Prevent useless junk from fixing in the population.

      2. Favoring the deletion of any junk by natural processes.


      Yeah, but .... how? By frowning at it? Growling? The only mechanism available to it - in fact, what it is - is differential reproduction of carriers vs non-carriers. So come up with some figures. What is the metabolic contribution to fitness of:

      a 1-base insertion?
      a ten-base insertion?
      a 100-base insertion?
      a 1000-base ...

      Make up any number you like for the threshold percentage increase that Natural Selection will select against, by increased mortality, and I will give you the range that will be effectively neutral. Iterative accumulation can proceed in that way.

      If selection can't see it, metabolic 'cost', as an evolutionary overhead, is just an illusion. Quantify it, and provide an example of how incremental accumulation by successive fixations cannot proceed through the near-neutral range of selection coefficients, right under selection's radar.

      How much does it really cost a well-fed eukaryote to make and transcribe surplus DNA? How is any notional cost saving converted into the appropriate currency - extra offspring?

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    7. Joe Bozorgmehr (Atheistoclast) says,

      Larry seems to think that the replication of billions of bp of useless junk, not to mention the subsequent transcription and splicing out of intronic sequences, involves virtually no metabolic cost at all.

      I never said any such thing. You are lying.

      Before Larry can unilaterally declare that 90% of the genome is "junk", he needs to recognize that the discovery of functional transposons etc may not be merely exceptions to the norm, and examples of fortuitous co-option, but part of a more general phenomenon and trend.

      I have discussed that speculation on many occasions and dismissed it because: (a) it makes no sense, and (b) there is plenty of evidence that most defective transposons are junk.

      Unfortunately, he isn't prepared to wait until all the research is done and all the data is in. How very immature.

      I'm basing my conclusions on all the evidence that's available to us today. You, on the other hand, are ignoring that evidence and praying that some future evidence will support your speculation and refute the current evidence.

      And you accuse me of being immature?

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    8. Alan, perhaps you should ask Larry to quantify the metabolic cost of carrying so much extra and unnecessary baggage. It would also be useful if his acolyte in Joe Felsenstein would give us the cost to reproductive fitness also. When they care to do so, they will realize just how flawed their thinking really is.

      You have to accept that in multicellular organisms, consisting of tens of trillions of cells, the energetic cost of maintaining any "junk" becomes very significant indeed. As the function of living organisms is to acquire energy to survive and reproduce, such an accumulation could not have occurred without conferring some benefits.

      Larry only seems to be able to offer us an argument from personal incredulity ("it makes no sense") in order to dismiss the fact that many inactive transposons are in fact contributing some benefit and the majority likely are also.

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    9. Alan, perhaps you should ask Larry to quantify the metabolic cost of carrying so much extra and unnecessary baggage. It would also be useful if his acolyte in Joe Felsenstein would give us the cost to reproductive fitness also. When they care to do so, they will realize just how flawed their thinking really is.

      Way to illustrate a point! If someone else did some calculations that you haven't done yourself (or have, but choose not to present), they would soon see the error of their ways!

      You are the one insisting that selection must act against extra DNA that does not earn its place by function. So it is you who needs to back up that assertion with some figures, rather than waving this 'very significant' non-figure in the air.

      As a proportion of the energy and material cost of large somas, there will be an increment of DNA which is negligible in its fitness cost - the most important decider. Fitness is relative to the current population, not absolute in terms of some 'optimal' organism that does not presently exist. Unless the selectively-visible extension threshold is zero, extensions of the genome of some length will not be weeded out by selection, however much you may wish it were otherwise. Once that argument is swallowed, it merely becomes a question of realising that, once an increment is fixed, there is nothing to stop a further increment from fixing by the same reasoning - a ratchet.

      If a 200-million-base-pair organism became a 3-billion-base-pair organism overnight, perhaps it would be uncompetitive due to metabolic cost. But if the transition were through increments, each effectively neutral, then there is nothing for selection to act against at any given time, for all increment sizes below the 'selective threshold'.

      So, at what increment of DNA extension in a eukaryote genome of your choice does selection start to act? You are allowed to say 'zero', but I think you'd struggle to support that.

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    10. You miss the point. I don't need to put a figure on the metabolic cost. I just need to indicate that it exists.

      Just as any junk could be added through incrementation, so it could also be deleted in a decremental way. Those individuals with less junk would be at an advantage over those with more junk. Hence, differential viability!

      The inactivation of many retrotransposons actually shows that I am right and Larry is wrong. Had they remained active, the genome would be at risk of proliferating exponentially as they would continue to copy themselves. But it is likely that selection favored their inactivation once their insertion produced some adaptive effect.

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    11. You miss the point. I don't need to put a figure on the metabolic and fitness cost. I just need to indicate that it exists and multiply it by the number of cells in the body.

      You forget that any incremental increase in "junk" would also be contrasted against a decremental decrease due to natural deletion. Those individuals with less junk would be at a slight advantage over those with more: Hence, differential viability and natural selection.

      The inactivation of most retrotransposons is hardly accidental as Larry seems to think. In fact, selection has favored this development to prevent the genome from proliferating in size exponentially since these elements will copy and re-insert themselves.

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    12. You miss the point. I don't need to put a figure on the metabolic cost. I just need to indicate that it exists.

      You need to demonstrate that it exists in a sufficient degree, for any increment, to have a selective effect. "It exists" is insufficient.

      The effectiveness of selection depends on the selection coefficient s and the effective population size Ne. There is a threshold for the product Nes above which selection is effective, and below which it is not. So even if you declare "the metabolic cost! see! it exists!", if a particular increment produces a value of s such that the product Nes is below the threshold, selection does not come into it.

      Although decrements will be subject to the same logic, they are less likely to arise, since there are fewer mechanisms producing them. There are no 'anti-transposons', for example. And deletions are more likely to damage genes.

      The inactivation of many retrotransposons actually shows that I am right and Larry is wrong.

      It shows that you skipped over one feature of transposition, that the act of jumping frequently causes inactivation of the pasted sequence on landing.

      Better yet, claiming victory on cost-driven inactivation forces a concession on 'junk'. Take your pick. If the metabolic cost selects for inactivation of transposons, it hardly helps your claim that they are useful to the organism where they are.

      Still, I do not deny that there is countervailing selection against wild proliferation. Such activity effectively causes total extension to rise above the 'selective threshold', while a class of leaner conspecifics still exists to compete. But if a population moves by incremental fixations below the selective threshold, this issue does not arise.

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    13. I was referring to the deletion of "junk", not functional genes. If there is even a slight fitness benefit to removing any junk, or preventing its fixation, then natural selection can work. I would add that any sneaky incremental accumulation of junk, as you suggest, will eventually lead to a saturation point whereby the amount of junk becomes very cumbersome to bear. After that saturation point is reached, the benefit to removing junk becomes a lot more pronounced. If 90% of the genome was junk, and had no benefit as well as cost, it would have withered away by now.

      The inactivation of retrotransposons by mutation and selection prevents the genome accumulating an excessive amount of mobile elements. But that is not to say that the inactivated retrotransposons are themselves junk. Their insertion could well be functional in some way. But we don't want them proliferating and re-inserting themselves all over the genome. We need some controls in place.

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    14. Atheistoclast,

      How can you claim to be a PhD student (or whatever you say you are) if you don't take your own "scientific" claims seriously? You cannot just indicate that a metabolic cost exists (if you were my student I would kick your imbecilic ass out of my lab after reading what you said), you have to calculate it and compare it against other metabolic costs to figure out its metabolic contribution. Only then you can calculate if such cost would be subject to natural selection or not. Then you have to start taking into account other factors, such as the processes that can increment both selfish and junk DNA, besides the possible mechanisms to get rid of it, if there's any. Your speculations, as plausible as they might sound, are nothing unless carefully investigated. Metabolic costs and selection fitness have been calculated many times by many scientists working in the area. Yet, here comes this Atheistoclast pretentious ass-hole, ignoring all the pertinent literature, thinking that he is the first to propose any of it. What a sad joke.

      Now go truly and seriously study. Otherwise go fuck yourself.

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    15. This comment has been removed by the author.

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    16. It is pretty obvious to anyone with a modicum of intelligence that a significant metabolic cost exists. The art of quantifying it is something I will leave to others as it is not my field. To claim that I don't read the relevant literature is absolutely ridiculous. I have cited numerous papers in support of my contentions many times over.

      But let's get this straight: Larry has repeatedly used images of "junk dna" being binned on this blog. There are natural mechanisms that can delete junk so why haven't they? Why have retrotransposons been inactivated but not deleted? I have asked him this before and he replied by telling me that the rate of junk accumulation exceeds that of junk removal. He provided no evidence for this assertion whatsoever.

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    17. It is pretty obvious to anyone with a modicum of intelligence that a significant metabolic cost exists. The art of quantifying it is something I will leave to others as it is not my field.

      It's my field, biochemistry. The cost is trivial and cannot be seen by natural selection.

      Why have retrotransposons been inactivated but not deleted? I have asked him this before and he replied by telling me that the rate of junk accumulation exceeds that of junk removal. He provided no evidence for this assertion whatsoever.

      The evidence tells us that our genome is full of junk DNA. What is the mechanism behind the accumulation of junk DNA? There are several possibilities. Insertion of new transposons and their subsequent inactivation is one.

      Just because you think that junk DNA should be eliminated by deletion doesn't prove that the DNA isn't junk.

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    18. Atheistoclast,

      Anyone with a modicum of intelligence could realize that junk DNA would have a metabolic cost. What is beyond modicum intelligences, like yours, is that there being a metabolic cost does not mean that the cost is significant. Here is where the scientist, unlike you the ass-hole, comes into the room and actually does some calculations. Not only that, lots of calculations have been published, yet you claim to have read the literature and still can't answer such simple questions. Your field or not, if you are going to claim something, and declare that you are a scientist, then you better check. Your new excuse ("this is not my field"), confirms the precedent. Your imbecilic ass should be fired from whichever lab you are working on. You will be a spectacular embarrassment for that poor lab. If you are going to discuss scientific ideas, you better be scientific about them. Otherwise, as I said before, just go fuck yourself.

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    19. atheistoclast said:

      "Unfortunately, he isn't prepared to wait until all the research is done and all the data is in. How very immature."

      Do you think that when "all the research is done and all the data is in" that it will prove that your chosen god-did-it? If not that, then what? And have you waited until "all the research is done and all the data is in" before making up your mind about believing in your chosen designer/god?

      atheistoclast also said:

      "Larry only seems to be able to offer us an argument from personal incredulity ("it makes no sense") in order to dismiss the fact that many inactive transposons are in fact contributing some benefit and the majority likely are also."

      Therefor jesus?

      What if all DNA is found to be functional, and what if "many inactive transposons are in fact contributing some benefit and the majority likely are also"? So what? What's your point? Do you think that that would prove the existence of your chosen god?

      What exactly is it that you're trying to prove by arguing against junk DNA or anything else that you argue against?

      Do you have any testable, demonstrable, positive evidence of your chosen designer/god, or do you only have bald assertions and immature attacks on science and scientists?

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    20. Here's another question. What's the metabolic cost of producing enzymes that detect and delete junk DNA? And would it be "worth it" to have such a mechanism turned on, all the time?

      It seems "obvious" to me that if there's an accumulation of junk merely as a by-product of mistakes happening during replication, transcription and so on, eventual compensating mechanisms will always be lagging behind so to speak.

      There'll always be junk that haven't been "detected yet", even assuming a considerable metabolic cost of having said junk around.
      It takes no effort at all to evolve more junk, but it probably takes a long time to evolve complicated detecting and deleting machinery that can distinguish between junk and not-junk. It makes perfect sense to say that junk wins every time.

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    21. Evidently, Larry thinks that the metabolic cost of DNA replication, transcription and splicing is but a "trivial" one since 90% of the genome is junk in his view. What's 2.7 billion extra base pairs? Why not 27 or 270 billion? The more the merrier! Introns also make up 30% of the genome, and these will be transcribed before being spliced out. We should remember that this process occurs in *tens of trillions of cells* in an organism like a human being.

      Larry is also wrong to assume that any cost, however small, which adversely affects fitness, won't be "seen" by natural selection: where on earth does he come up with beliefs like this from? Those individuals in a population with less junk would be at a reproductive advantage over those with more.

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    22. Atheistoclast,

      Evidently Larry has looked at those numbers you refuse to see or calculate for yourself. The proportion of junk DNA might be huge compared to other DNA, that still does not mean that its metabolic cost amounts to anything significant over the whole picture. How much energy do you think that your brain uses? (Yes, even yours uses energy.) How do you think that compares to the no-longer replicating neurone DNA in their nuclei? How do you think that compares to intron transcription? Do you really think that every intron is transcribed in every cell you ass-hole? How efficiently do you think such metabolic costs, as reflected over the whole picture, would be eliminated and under what numbers of effective populations?

      Nobody is assuming that costs that adversely affect fitness will not be seen by natural selection. The question is whether there is a metabolic cost enough for its fitness effect to be seen by natural selection. Your obvious misrepresentation of what others say and think for mere rhetorical effect shows that you think that science is about rhetorics and data don't matter. I hope that your supervisor notices this before its too late for him/her to get rid of you. That supposing that you really are in a PhD program. What a waste.

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    23. This seems really straightforward to me- yes there is a cost and yes there will be a positive impact on the fitness of individuals that don't have to pay that cost. It is of utmost importance that we recognize the size of that cost though, as trivial costs wouldn't see much selective force in their favor (more important genetic advantages would drown them out, as selecting for a gene that improves your fitness by 2% while also decreasing your fitness -by way of increased base pairs- by .01% will obviously be a net gain.)

      Now, when I want to look at the impact of a lot of junk DNA I obviously think to compare similar organisms with genomes that vary in this regard. Some polyploid plants were already mentioned but those offer multiple copies of genes that actually do something so the ratio of junk isn't changing much (not important I know, but I'm trying to be as favorable to this costly DNA view as I can.) Instead I would offer that we can look at some animals that happen to have just the kind of genetic situation I described.

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    24. It turns out that animals that fly have greatly reduced genomes. The parts that aren't so important are trimmed WAY down in birds, or even flying squirrels. And so we've solved the first hurdle of finding example species to look at. Instead of pretending these are things I came up with on my own any longer I can skip to the major current conclusion of scientists: trimming down the DNA like this seems to lead to smaller cells which is a good thing for quickly altering a body plan to improve the ability to fly. Species that quit flying seem to bloat their nucleus right back up to the familiar proportions and likewise grow larger cells.

      Now when I hear that the amount of DNA determines cell size I am struck a bit by how ludicrous that sounds. It doesn't much matter though- the data shows all the correlation you could ever ask for. Rather than continue to resist these facts I take a subtle turn down the path of wanting to know how this happens. As of now the best hint at this I've seen is that the nucleus is bigger with more DNA, and this little detail sets my mind racing to think of ways that could echo out into the rest of the structure of a cell. If I eventually decide to devote my time to these matters perhaps I will come up with and implement tests to see how well these mechanisms can match observation, but for now I can't answer that.

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    25. Getting back on topic though, there is a detail that biologists have known about for quite some time (I think it was old news to even the oldest of my professors but I've always been a bit bad about exact historic timing.) That fact is simply this: large complex organisms are inefficient. The earliest bit of this puzzle must have been troubling to those natural philosophers that viewed the diversity of life as a ladder with man at the top. Even straightforward situations like the sperm, eggs, and offspring counts show that we throw away a small ocean of sperm and a majority of our eggs while something like a fish fertilizes every single egg and the wasted sperm can be explained by the nature of the race in which they compete- aside from the outright defects the inferior sperm were simply too slow to arrive at one of the much more limited eggs.

      So then why would we waste resources like this? Well, let's put that question another way: why would we invest more energy than the bare minimum required to accomplish a task? Looking again at animals we can see a lot of relevant answers. The antelopes that do high jumps as they run away from predators, the flamboyant tail on peacocks, the way that males of so many species compete with each other in view of females- quite simply all of these say "I'm so successful/fit that I can afford to waste huge volumes of energy."

      So there we have it. Multi-cellular species can afford to carry around a lot of DNA that doesn't do much. Not even for the showboating reasons in those examples above but simply because it isn't worth the effort to pluck it out- that is unless you want to fly, at which point the selective forces quite rapidly prune the contents within the nuclear envelope down exactly the way atheistoclast demands they should.

      And so I think I have thoroughly answered the question here. Where I have not given complete details I have at least taken the question out of the realm of speculation and pointed the most daft individuals straight to data that will have to be confronted for any intellectually honest complaints.

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  3. This is why there are no mice, no flies, no hamsters, no bacteria, no many other living things any more. Their rapid generation times and genomic entropy have completely obliterated their genomes ...

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    1. God started them out more perfect than humans so they would still be around at the time of the rapture.

      He blew it with dinosaurs and trilobites.

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  4. What a load of bs. Sanford should be ashamed of himself.

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    1. You would think. Perhaps he's more likely to feel embarrassed in some other countries?

      Is it okay to say he's stupid?

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    2. Maybe he's not stupid, maybe he's just lying, knowing that the stupid will believe it.

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    3. I almost recoiled when they didn't say anything about recombination. That we can shuffle the DNA around to stick good mutations together and filter out the slightly bad ones is one of the major explanations of why prokaryotes bother with sexual reproduction and I can't imagine being very learned in biology while completely avoiding that topic.

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  5. My favourite quote:

    "If those stats are even close to being correct, if you project backwards, that means the human race is a lot younger than we've been led to believe it is."

    Logic Fail.

    Here's Lynch's paper for those who are interested:
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824313/?tool=pubmed

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    1. Thanks for posting the link to Lynch's paper.

      For those who don't time to read it, here's the bottom line. Lynch is worried about the recent effect of removing selection (negative selection) on the germ lines of people in industrialized nations. Here's what he says ...

      The motivation for this concern is the enormous change in the selective environment that human behavior has induced during approximately the last century. Innovations spawned by agriculture, architecture, industrialization, and most notably a sophisticated health care industry have led to a dramatic relaxation in selection against mildly deleterious mutations, and modern medical intervention is increasingly successful in ensuring a productive lifespan even in individuals with major morphological, metabolic, and behavioral defects.

      What this means is that a thousand years from now the meek and the poor will inherit the Earth. Does that sound like anything the Bible predicts? :-)

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    2. Keeping people out of the grasp of death in their mid thirties and beyond is generally not relevant as they'll have already had all the children they are ever going to and those maladies that so greatly shortened the duration of life, like muscular dystrophy, aren't anything we've so thoroughly conquered as to give those children much chance at raising their own children.

      Once upon a time I thought the people declaring that medicine had put a stop to evolution must all be thoroughly uneducated...

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  6. If Sanford is correct that the human genome is degenerating at such a rapid rate then this should be reflected in the the sequence of old genomes. If we sequence an archaic human - say someone who loved five or six thousand years ago - we should see a genome with much less mutations than current genomes, shouldn't we?
    Well we've begun doing this - I think the Iceman Ötzi, who lived 5300 years ago, was sequenced in the last year. Strangely enough his genome didn't look like a clean, undegenerated version of the modern human genome. Doesn't this falsify Sanfords theory? (Unless, of course, Ötzi was put there by the devil to fool us!)

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    1. They will just claim that it's an incorrectly dated modern human. Come on - these people actually believe everything was created 6000 years ago. Facts are clearly the least of their worries.

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    2. Yeah they'll just deny the date of the individual. Remember their doctrinal state of allegiance: If a conflict should arise between the bullshit in my old book and evidence from the real world, then old-book-bullshit takes precedence. This really is their modus operandi. I know it sounds absurd, but I'm not being funny or making a caricature here. It is litterally what they do and believe. Don't believe me? Check out the doctrinal statements on the AIG or ICR websites.

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  7. More interesting than jokers like Sanford is this related (well sort of) paper by Michael Lynch. Bit speculative but worth a read:

    Lynch, M. (2010) Rate, molecular spectrum, and consequences of spontaneous mutations in man. PNAS, 107, 961-968.

    can check it out here:

    http://www.pnas.org/content/107/3/961.full

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    1. Oh, just seen this paper has already been mentioned. Apologies.

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  8. Leaving the profound ignorance of his statements aside, I was really struck by their doom and gloom outlook. All this stuff about the personal tragedy of death because of mutations (wrong) and the tragedy of passing mutations to your children... by golly! these people are seriously depressed and need to see a psychiatrist right away! Obviously believing in their 'savior' is not helpful for their psyche.

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    1. Yeah, speaking of depressed and doom and gloom, think of how negative all the religious crap is. Everything and everyone is dying, degenerating, fallen, sinful, evil, wasting away, mutating into oblivion, the sky is falling, everything is falling and failing, the end is near, we're all gonna die, repent now!

      Religion is obviously a MASSIVE downer.

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  9. In the vid, Sanford advances a mutational theory of ageing that seems non-standard. And then claims that some of that 'ageing' is passed on to offspring who - despite this load - appear to cling doggedly to the tradition of being born young.

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  10. Sanford a trained horticulturalist. Doesn't mean his opinions are invalid but his training is not in genetics, molecular biology, evolution, or other relevant field.

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    1. Lysenko was a trained agronomist, a closely related field. His view of inheritance of acquired traits was no better then Sanford's view of aging.

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  11. As usual Bozorgmehr has to outright lie and misrepresent his interlocutors to prop up his iron-age mythology. It's happened many times before. He's been suspended on several occations from rationalskepticism.org for misrepresenting me and outright insulting me (for my nationality among other things) when I took his creotard bullshit to task. Standard creationism, nothing new under the sun.

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  12. Atheistoclast: I was referring to the deletion of "junk", not functional genes.

    There's one reason you may be misleading yourself, right there. Nothing in the genome has a clue what's functional and what isn't, just by 'looking' at a stretch of DNA. You have to run the program. Transcription finds the genes, bound factors find the sites they regulate, but it's all just one big mess to deletion mechanisms. Unless you know different.

    Imagine a computer program with a million accidental copies of a line "let x=x". The program would be more efficient without. How does any 'deletion' process, presented with the raw bit-sequence of the code, target the lines that need to go? All it can do is blindly slice out chunks, and see if it gets away with it. The bigger the deletion - ie the more chance of achieving the notional benefit of stripping out the dead wood - the more likely you will remove something functional along with it. Insertion lacks that constraint. Assuming you find a safe place to insert, big insertions will do little more damage than small ones. This produces an asymmetry in the prevalence of various plus-or-minus-changes of various sizes in the population, even if +n and -n were equally likely at source. I agree, the relation to fitness is not indefinitely linear - eventually, as function gets more and more widely spaced, the balance shifts, and other forces gain in strength.

    Why have retrotransposons been inactivated but not deleted?

    Different mechanisms, different constraints.

    Inactivation of a transposon does no harm to the cell, and may benefit it. Deletion involves a different mechanism, with no connection to the first, and is not 'surgical'. But even if a genome presents itself to selection with a neatly excised transposon, selection will look at the 300 base pairs removed and say "big, fat, hairy deal".

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    1. Hahaha, Allan Miller I had to re-read your post 3 times. I mistook your name for Atheistoclast which is right below yours and I just couldn't believe he'd write something that made sense. *facepalm*

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    2. I think both you and Rumraket are seriously confused about natural mechanisms involved in the deletion of genetic material. I am referring to purely *random* deletions made in the replication process, and during recombination - these can be just a few base pairs or even much larger. I am not referring to any sophisticated mechanism involving enzymes that selectively removes junk alone. If an inactive transposon really were just a waste of space, as Larry supposes, deleting mutations would have whittled it away by now.

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    3. I think both you and Rumraket are seriously confused about natural mechanisms involved in the deletion of genetic material. I am referring to purely *random* deletions made in the replication process, and during recombination - these can be just a few base pairs or even much larger.

      Bong! Such purely random deletions are precisely what I was talking about.

      They can't tell what they are deleting - and nor could a more active mechanism. There are several mechanistic bases for a bias favouring insertions over deletions, inflating the genome and keeping it inflated, which I had a stab at illustrating. You haven't addressed one word of it - just restated your original supposition as to what 'would' have happened, without any mechanistic support - an argumentum ad I-reckonum.

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    4. It doesn't matter if mutations can't tell what they are deleting. If they delete actual junk, selection will favor this development whereas if they delete functional stuff it won't. That's elementary evolutionary theory, Alan!

      Yes, the genome has a natural tendency to become bigger, but this is more due to duplication events rather than to the insertion of individual base pairs or to retrotransposition. And, again, it is *selection* that decides whether any of this is retained. It is clear that, for instance, aneuploidy or polyploidy in plants does confer adaptive benefits. Larry seems to think natural selection has no role at all in determining genomic size.

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    5. It doesn't matter if mutations can't tell what they are deleting. If they delete actual junk, selection will favor this development whereas if they delete functional stuff it won't. That's elementary evolutionary theory, Alan!

      I refer you to the elementary evolutionary theory posted above.

      1) If the product Nes is below a threshold, s might as well be zero. Only if it is above the threshold will selection favour an incidental deletion of junk over the status quo. And this cannot stand independent of the fact that:

      2) deletion damages 'real' genes more often than insertion, and in asymmetrically increasing proportion wrt no of base pairs involved. This means that selection acts against deletions more often than insertions, distorting frequencies in an upward direction (up to a point).

      Try this for size. I am 6ft 2. My 'metabolic cost' is significantly greater than that of someone who is only 5ft. I've got loads more DNA than he has, and plenty other overheads besides.

      Apart from the fact that I could steal his lunch, why aren't we shrinking as a race due to the saving of 'metabolic cost' in making shorter people? In fact, the entire eukaryote multicellular clade ought to deflate, wibbling like a pricked balloon into single cells with lean economic genomes replicating as fast and cheaply as possible. Kind of like ... hmmm. You think there may be some other factors at play, here? You can think of one - it's all absolutely essential: selection is pumping the tyres like a mad bastard. You seem unwilling to consider any others.

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    6. 1. If N is large, selection is very effective.

      2. Genes make up less than 4% of the genome. Hence, any deletions would tend to affect non-genic regions.

      And, yes, as a taller person you should have an advantage in collecting food and securing a mate compared to someone a foot shorter than you. However, there are clearly limits to human height. Only freaks are more than 7 feet. Likewise, there are limits as to how much junk a genome can contain.

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    7. 1. If N is large, selection is very effective.

      So, N is always large, then? Consider population sizes in the typical eukaryote, the clade with the most bloated genomes.

      2. Genes make up less than 4% of the genome. Hence, any deletions would tend to affect non-genic regions.

      I'm talking about functional regions, not specifically protein-coding genic ones. In a function-packed genome, most deletions of any length would be deleterious. Insertions would not suffer the same load. As the genome inflates, the balance shifts.

      And, yes, as a taller person you should have an advantage in collecting food and securing a mate compared to someone a foot shorter than you.

      You're just making stuff up. Organisms at the larger end of their 'normal' size range always have a nutritional advantage over those towards the lower? If all get sufficient for their needs, neither has the advantage on that score. Likewise, if compact-genome and flabby-genome races are equally well-fed, the flabby one suffers no disadvantage, and there is no selection on 'metabolic cost'.

      However, there are clearly limits to human height. Only freaks are more than 7 feet. Likewise, there are limits as to how much junk a genome can contain.

      Not saying there aren't. But you have simply scuttled to the opposite end of the continuum. Wherever feels safest.

      It does not solve the general question of "where is eukaryote x on the junk scale"? Obviously, none have passed a limit beyond which they burst like Mr Creosote. Counterbalancing selective forces undoubtedly play a part in restricting genome size. But you are applying this 'metabolic cost' argument across the scale, and it does not apply with constant force throughout.

      You seem to think that our genomes cannot be 'junky' because this 'metabolic cost selection' would favour shrinkage, absent positive 'earn-your-keep' selection. But in such a function-rich genome, deletions would be strongly selected against, because of the damage they do to functional DNA. An occasional one may succeed in paring off a little junk, but only infrequently. Meantime, insertions would suffer nothing like that same pressure. They happen more often anyway, and each one would provide a 'safe' inter-function region where further insertions could accumulate comparatively harmlessly. As such regions grow, the pressure against deletion loses its force - but this does not predict an oscillation back to the 'all-lean' state.

      At the leanest end of the continuum, insertions are more likely to fix than deletions. Your mythical all-function genome is unstable, and more likely to expand, following the move away from prokaryotic nutritional limitations. Transposons exploit this headroom.

      Numerous lines of evidence argue against pervasive function.

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  13. Larry said, “this must mean that they were perfect only a short time ago.” – How so? The constant laws of physics would indicate that entropy and electromagnetism have always been at work in the universe, and therefore the universe has been breaking down ever since its beginning.

    Larry said, “Sanford doesn't exactly say exactly what Christ will do to fix all the mutations in our genome.” – Why should Christ fix anything in our genome or anything physical, since the universe looks like it was designed to self-destruct? Your question reveals a limited view of reality, which includes the spiritual. It should be obvious that the physical universe wasn’t made to last forever, which, of course, naturalistic scientists are confirming every day.

    Larry said, “Will He invert better DNA repair enzymes?” – Even though the human body has natural repair mechanisms, it should be obvious to anyone who’s ever seen death and destruction, or knows that the universe’s supply of hydrogen is gradually depleting, that nothing in the physical universe is designed to last forever. You use the term “better.” If this is simply negative innuendo toward creationists, fine. Otherwise, in the big picture of how the universe appears to work, what is your definition of “better,” and what would be the point to “better?” (P.S. Thank you for capitalizing the pronoun He, as a sign of deity and respect.)

    Larry said, “What's taking Him so long?” –How long is long? Compared to what? What do you think was supposed to have happened and how long was it supposed to have taken?

    Larry said, “And why weren't we better designed to begin with?” – What were you expecting, Larry? Again, exactly what would your “better” ‘design’ look like (which really wouldn’t be designed), and what would be the purpose and objective of that “better” design, from an atheistic point of view?

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    1. "It should be obvious that the physical universe wasn’t made to last forever"

      Ok, why wasn't it made to last forever?

      "How long is long? Compared to what?"

      Matthew 24:34. 2000+ years is long compared to one "generation".

      "exactly what would your “better” ‘design’ look like"

      Maybe not look like, in Sanford's words, "we are a perishing people in a dying world"?? Wouldn't that be a better design?

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    2. David said, “Ok, why wasn't it made to last forever?” – Countless philosophers, scholars and regular Joe’s have struggled with questions like that ever since anthropologists could discern human from hominid evidence. My response can be nothing more than an overly abbreviated expression of my own individual understanding, and what Allan Miller might call, Best Guess. Here goes. God made us to be with Him and enjoy His world with Him – a world which is not limited by gravity, entropy, electromagnetism, and deleterious vs. favorable mutations, etc. It would be a non-natural/supernatural world (existence) absent the things that make our natural worldly life miserable. It would be an existence where we could live lives virtually unrestricted (especially the physical part, which is now severely limited) from all the things we always longed for – an existence where we are allowed to live to the fullest of our capacity, unhindered by our mistakes and the mistakes of others. He wants a true individual loving response to His grace and mercy, grace and mercy which is available and visible in the ‘natural’ – our body, our mind, our heart/spiritual soul, and the sum of our natural surroundings. He knew, in order for our response to be honest and genuine (true love) it must be a free choice (therefore a return of His love), and we would require the option to say no to His invitation to join Him. Otherwise, any response imposed on us by Him, would not be free and loving. One doesn’t need forever to choose. I ‘guess’ He thought that a lifetime would be enough time to choose. I also ‘guess’ that there is a time for all natural things to end and the fullness of all eternal things to begin. That’s what natural evidence says, anyway (things will end). Human historical and biblical scriptural evidence agrees. If my “Best Guess” is correct, then it’s the responsibility of the individual to validate it without bias. If my “Best Guess” wrong, nothing lost – except some money, some time, and some annoyance caused to others by me. I don’t think there’s any in-between. Even multiverse simply brings us back to the same point over and over again.

      David said, “Matthew 24:34. 2000+ years is long compared to one "generation".” – I’m not sure what you mean, in the context of Larry’s question, which I took to mean several thousand years to 14 billion years.

      David said, “we are a perishing people in a dying world.” “Wouldn't that be a better design?” - I don’t get your statement. It sounds very doom and gloom to me, which, at the end of the day, is what I think atheistic evolutionists teach. That’s not what the Bible teaches, especially in the twenty-chapter length passages (predictions of natural phenomena) that can be correlated to today’s scientific evidence.

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    3. Hi Denny,

      [“we are a perishing people in a dying world.” “Wouldn't that be a better design?” - I don’t get your statement. It sounds very doom and gloom to me, which, at the end of the day, is what I think atheistic evolutionists teach.]

      How nice of you to take Sanford's words and blame them on "atheistic evolutionists". Is Sanford, the man in the video above, an "atheistic evolutionist"?
      I don't think we are a perishing people in a dying world. He does. His particular version of your cult does.

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    4. "Here goes. God made us to be with Him and enjoy His world with Him – a world which is not limited by gravity, entropy, electromagnetism, and deleterious vs. favorable mutations, etc."

      Why? Why did God made us to be with Him and enjoy His world?

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  14. Anonymous and The whole truth speak of “doom and gloom.” – There’s only doom and gloom for those who reject the point of the temporary physical life.

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  15. Denny, do you have any actual evidence for any of that religious mumbo jumbo?

    "There’s only doom and gloom for those who reject the point of the temporary physical life."

    Let me guess: The people who "reject the point of the temporary physical life" are rejecting your imaginary god's "invitation to join him" and even though your imaginary god allegedly gives all people a "free and loving" choice as to whether they want to join him or not, if they choose not to they will have plenty of doom and gloom because they will burn in a lake of fire for eternity. Gee, what a nice god you worship and promote. NOT. And what a nice guy you are (NOT) for threatening people with eternal punishment just because they don't share your arrogant religious delusions.

    I'm curious about something. If the only reason for physical life is to have some time to decide whether you want to join your imaginary god or not, and since you have already made up your mind and have decided to accept your imaginary god's invitation, then why don't you kill yourself right now and join him? Aren't you just wasting time and resources by putting off the acceptance of his invitation? Aren't you anxious to join him? Aren't you eager to exist in a world which is not limited by gravity, entropy, electromagnetism, and deleterious vs. favorable mutations, etc.? A world that would be a non-natural/supernatural world (existence) absent the things that make your natural worldly life miserable.? A world that would be an existence where you could live your life virtually unrestricted (especially minus your physical part, which is now severely limited) from all the things you've always longed for – an existence where you are allowed to live to the fullest of your capacity, unhindered by your mistakes and the mistakes of others?

    What are you waiting for? What's the matter, don't you have any faith?

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  16. You wouldn't need to have a junk dna eraser turned on full time, you could for example turn it on only during oogenesis or embriogenesis. That's when most of the cleaning is done. Actually its a nice idea. Anybody up for the task? We have CRISPR-Cas9 now,old geezers

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