445 thoughts on “Evolution Visualized

  1. stcordova: Sheesh Patrick, the mutational load problem was independent of Mendel’s Accountant.Mendel’s Accountant was created to model the mutation load problem, not the other way around.

    Supposedly. Without documentation there’s no way to know.

    Based on historical observations, trusting creationists is foolish. Even if the authors weren’t suspect on those grounds, the lack of details makes any discussion of its results useless. Keep enjoying the smoke and mirrors, though.

  2. JoeCoder: Hey Rumraket!

    redundant failsafe stuff has zero evidence that it correlates with genome size. And with respect to bacteria, it is generally understood that they have pretty much zero junk DNA.

    We know redundancy exists and I gave you evidence for this earlier. How could redundancy NOT increase genome size? I don’t follow your reasoning.

    Oh I see now that I misspoke, I meant to say it does not correlate with discovery of increased proportion of genome that is functional. I would agree of course, that at an intuitive level, the more functions you discover, the bigger the genome would eventually had to be since there’s a limit to how much function you can compress into the same DNA without one function starting to interfere with another.

    Yet even in fraction of the genome we think is functional, it is still a minority of it we know what does. How many of those roughly 20.000 proteins our genome is thought to code for, do we actually know what do? An even tinier fraction still.

    So what I mean is, we have some estimate of what proportion of the genome is functional, and we have some idea about what some of these things do.

    For example in the video, Dr. Noble gives an example with a functional element thought to contribute most of the function of maintaining heart rhythm (confusingly he says it contributes 80% of that function, which he then goes on to contradict by showing that when knocked out, heart rhythm is largely unaffected. Then how come it was thought to contribute 80% of that function? I guess I’m missing something here… ). Anyway, when this element is knocked out, heart rhythm is pretty much still maintained.
    My question is now, why believe this redundancy lies in the areas of the genome we think is mostly junk? Why isn’t this just other pieces of the genome we already know are functional, yet which we don’t know the function of? Or even complex interactions between elements we thought we knew what did? It seems to me there are several more plausible options than it must be in the junk.

    You can’t bring something like this and then just declare it constitutes evidence of additional function in junk. Nothing has been shown that the redundancy examples Noble speaks about lie anywhere but already known to be functional regions of the genome. After all, we know that there’s function in something like 8.5% – 10% of the genome. We have something like 22.000 protein coding genes, another 11.000’ish RNA genes and then there’s a lot of enhancers, promoters and so on. Very very little of all this material which is strongly indicated to be functional, is even understood what specifically does.
    So why do you want to relegate redundancy to areas thought to be junk? Why? That actually seems counterinuitive to me when we have all this stuff we already know codes for proteins that are expressed at high levels, yet we still don’t know what do. It looks like something you’d do if you had a desire to inflate the functional proportion of the genome, rather than something evidence tells you.

    Also, I said “microbes with huge genomes”, not necessarily bacteria.

    Okay, but then it seems a bit too vague to generalize over “microbes” which is not really a technical term. Yes, there are single-celled organisms with very large genomes. They’re eukaryotes and live… strange lives.

    On amoebae for example:

    “amoebae are often cited as the most dramatic example of the lack of correlation between genome size and biological complexity. There are may problems with this conclusion, including a likely variation in ploidy, since some amoeba have hundreds of chromosomes, which may be generally related to cell size, not just in protists but in many different organisms, as well as the presence of significant amounts of contaminating DNA from their prey. The amoeba genome is probably smaller than 20 pg”

    Meh, of course you bring me this John-“dogs ass plot”-Mattick stuff. One doesn’t even know where to begin with this guy.

    How about this: There are still species of single-celled eukaryotes with more precisely measured genome sizes that are larger than the genome sizes for large multicellular eukaryotes, such as humans, which Mattick and colleagues always strangely can’t help but put on top. There are plants with absurd genome sizes much larger than humans too.

    20pg is about 20 billion base pairs. I doubt all of that is functional. But them also having a high number of ploidy is redundancy by definition.

    Would that not equally affect both deleterious and beneficial mutations?
    It would, but doubling the effective selection coefficient makes selection stronger for both beneficial mutations and deleterious mutations. It’s better at promoting beneficials and removing deleterious mutations. Or it’s possible I’ve made an error myself here.

    Okay fair enough.

    JoeCoder seems to suggest the reason real populations don’t melt down is because god is intervening.

    I think there is no evidence that God is intervening (at present) to prevent populations from melting down. If you disagree, find me a microbe that persists in nature and has a deleterious (not total) mutation rate close to that of humans.

    Not sure how to parse this. Are you saying God is no longer intervening, but did so in the past, and that this is the explanation for common descent being indicated by comparative genetics, but contradicted by genetic load simulations?

    Which would be funny if it wasn’t so ridiculous.

    I apologize that I don’t have a way for both atheism and evolution be true. Let me know if you figure something out though.

    Is it possible you’re incorrect about MA and/or the fraction of the genome that is functional? I’m just putting it out there.

    If it predicts meltdown for a 20% functional human genome, how much would have to be junk for no meltdown to happen? 10%? 5%?

    On a previous page I showed you a simulation in Mendel with 0.5% being functional, and the fitness declined at first but by 3000 to 5000 generations it looked like it was starting to level out. If you want to run a simulation longer than that to see for sure, go for it and post some screenshots. Maybe slightly higher values could also work?

    But that’s what I’m asking. What is the limit according to MA? I can’t get the program to run with realistic values for population size, mutation rate and so on without getting some sort of integer overflow error.

    Rumraket, the part I don’t understand is why you think Mendel is suspect for showing fitness decline when mutation rates are high? That this decline happens in response to a high del. rate has been widely predicted in population genetics for the past several decades. See my comment #26 on page 7 of the comments, for details.

    I see now I was conflating two differen things. You were speaking about the effect of mutation on human evolution (or generally, evolution of sexually reproducing organisms with large genomes), and I was talking about the LTEE. I agree we can’t conflate those two. I’d be interested in seeing MA model the LTEE though as a way of “testing” the program against an actual experiment. That’s another thing I can’t seem to get to run without it requiring supercomputer-like amounts of memory.

  3. JoeCoder: I think we can agree on much more than you may think.

    Maybe so, but I have to say, I don’t really understand your last post. You write:

    I think it would be ridiculous to try to argue evolution is evidence of God.

    The thing is, you also wrote this:

    I apologize that I don’t have a way for both atheism and evolution be true.

    Where I come from, if

    No God entails no evolution.

    then

    Evolution entails God.

    I admit, however, I don’t really get the rest of your post. I take it you mean that what’s “helping” nature might not be God or might not be a traditional version of God or something. I think it’s much more likely that what you’re calling “nature” is too restrictive.

  4. What do you ID guys (stcordova, JoeCoder) think of a guy like James Shapiro and his “Natural genetic engineering”?

    I think there is some, and even if wrong, it’s a better theory than Darwinian theory. I think genomes have some capacity for computational intelligence and self-evolution and self-learning. Furthermore, I think the information processing is not restricted to the genome but resides also in the glycome.

    If I weren’t a creationist, I’d probably be siding with Shapiro.

    I also don’t think mutation is random. The evidence of that are nucleotide biases in the genomes. I wrote about that here:
    http://theskepticalzone.com/wp/chargaff-parity-rule-2-biasednon-random-mutations/

  5. stcordova: If I weren’t a creationist, I’d probably be siding with Shapiro.

    Strange thing to say in a way. Are you somehow saying that you’re putting your creationism above the science someone like Shapiro is doing, or are you saying the “science creationists are doing”(lol) is even better than Shapiro’s, which in turn is better than that of evolutionists?

  6. . Are you somehow saying that you’re putting your creationism above the science someone like Shapiro is doing, or are you saying the “science creationists are doing”(lol) is even better than Shapiro’s, which in turn is better than that of evolutionists?

    No. I’m saying if I rejected as a matter of principle highly exceptional events as a mechanism for biological complexity (you can call them black swans if you’re an atheist, or miracles if you’re a creationist), one would have to believe in some sort of intelligent like entity, and in Shapiro’s case that’s the organism itself. In principle, it seems appealing, but I don’t think a bacteria can re-engineer itself into a Eukaryote!

    I think exceptional events are a better explanation. Whether one attaches theological aspects to exceptional events is a separate question, but it seems an exceptional event (something out of the ordinary, probably not repeatable in a testube) was responsible for certain features of life. Hoyle (an atheist/agnostic) argue the Universe itself was intelligent. It was in his book Intelligent Universe that he used the phrase “intelligent design”.

  7. Hello Rumraket,

    I think you are on the right track now to argue about the amount of functional DNA. You are correct to presume that we don’t know even what most of that 20% is doing. I find the three evidences I listed (exons+protein binding, conservation, GWAS) to be compelling, even if we don’t have functions assigned to them yet. I think a fourth case can be built by realizing that most differentially-transcriped transcripts we study end up being functional, and extrapolating to the rest:

    “the vast majority of the mammalian genome is differentially transcribed in precise cell-specific patterns to produce large numbers of intergenic, interlacing, antisense and intronic non-protein-coding RNAs, which show dynamic regulation in embryonal development, tissue differentiation and disease, with even regions superficially described as ‘gene deserts’ expressing specific transcripts in particular cells… where tested, these noncoding RNAs usually show evidence of biological function in different developmental and disease contexts, with, by our estimate, hundreds of validated cases already published and many more en route, which is a big enough subset to draw broader conclusions about the likely functionality of the rest”

    It’s hard to get an exact percentage of function (subject to deleterious mutations) from this. And it’s unlikely that every nucleotide of these is subject to deleterious mutations. But it seems very difficult that it could be as low as the perhaps 1-2% needed to alleviate the problem of deleterious accumulation.

    Redundancy… heartbeat.. Then how come it was thought to contribute 80% of that function? I guess I’m missing something here

    I expect they find out what’s functional by knocking out a gene as well as other genes that kick in if the first fails. As I quoted like 10 thousand comments ago: “loss-of-function tests can also be buffered by functional redundancy, such that double or triple disruptions are required for a phenotypic consequence”

    So why do you want to relegate redundancy to areas thought to be junk? Why?

    I’m not. Maybe I communicated poorly somewhere. I expect redundancy is in both the parts of the genome assumed to be functional as well as those that are non-coding and with no known function. I don’t even have a good way of knowing how much is where.

    My original reason for bringing up redundancy was because some here have argued that a high del. rate would make us dead after just a few generations. That would likely be true if we were haploids with no redundancy. But redundancy greatly buffers this effect and lets us last far longer.

    There are still species of single-celled eukaryotes with more precisely measured genome sizes that are larger than the genome sizes for large multicellular eukaryotes, such as humans

    I think most of the DNA in those large single celled eukaryotes is probably junk. Perhaps transposons ran amok and greatly inflated their genome sizes. But I don’t have enough information to rule out redundancy, or even other purposes: It’s up to you whether you consider this relevant or not, but in my own experience in computer science, the number of bytes usually indicates very little about how much function there is. In a simple example, a png can be 10 times smaller than a bmp of the same image, and a jpeg can be 10 times smaller than the png. But the bmp is optimized for fast encoding/decoding speed, the png is slowest but loses no information, and the jpeg is smallest but has a loss of fidelity.

    Likewise in a genome I would think you could have 1 thousand transcripts that are each specialized for a specific variant of a particular job, or one transcript that can do all of those jobs at perhaps 90% efficiency.

    Are you saying God is no longer intervening, but did so in the past, and that this is the explanation for common descent being indicated by comparative genetics, but contradicted by genetic load simulations?

    I actually reject common descent, and I disagree that comparative genetics lends evidence to it. But that’s at least as big of a topic as genetic load so I’m trying to keep us focused. If you want my view about how or when God did this or that, I don’t have any good answers.

    I can’t get the program to run with realistic values for population size, mutation rate and so on without getting some sort of integer overflow error.

    Population size is the most frustrating limit to Mendel. Pay attention to the blue bar at the top before you start the simulation. As you change parameters it tells you how much memory you’ll need. The reason I simulated populations of only 1000 is because of those limitations, and the time needed. The Mendel authors report:

    “With a population size of 5,000, the rate of mutation accumulation was 89.38%. Doubling the population size to 10,000 resulted in 89.05% accumulation, and doubling the population size again to 20,000 resulted in no further improvement (89.05% accumulation)”WAS) to be compelling, even if we don’t have functions assigned to them yet. I think a fourth case can be built by realizing that most differentially-transcriped transcripts we study end up being functional, and extrapolating to the rest:

  8. Rumraket, I enjoy reading articles by Shapiro but I haven’t yet had a chance to read his book. So I’m probably not educated enough to comment there. And like stcordova I would probably favor it over neodarwinism.

  9. Hey walto, you wrote:

    Where I come from, if No God entails no evolution.

    then Evolution entails God.

    I believe that’s a form of the fallacy of affirming the consequent. God can exist AND there be no evolution. My point was that if you want evolution, I don’t see a way for it to happen without some kind of help.

  10. JoeCoder: Where I come from, if No God entails no evolution.

    then Evolution entails God.

    I believe that’s a form of the fallacy of affirming the consequent. God can exist AND there be no evolution.

    Yes, but you have it reversed there, he didn’t commit the fallacy. He would have, had he started with “If No evolution entails no God”.

    If it is true to say that “if there is no God then there is no evolution”, that means the only way there’d be evolution is if there’s a God. So in so far as you discover there to be evolution, it’d entail God(because you just said there wouldn’t be any evolution without a God).

  11. JoeCoder,

    So you retract this statement, correct?

    I apologize that I don’t have a way for both atheism and evolution be true.

  12. walto: My own sense is that that claim simply must be wrong, that smart people plus computers could put together a reasonably representative model.

    I think this is a very valuable comment.

    I would disagree and our disagreement is perhaps the seed of a testable hypothesis. What needs to be done is to clarify what we mean by “a reasonably representative model”.

    I would say that a “reasonably representative model” is one where people couldn’t distinguish a difference between data from the model and data from nature if presented in the same format.

    Would you agree with this clarification? If not why not?

    peace

  13. kieths, I don’t retract that statement. I would need a way to solve this mutational load problem, among other issues.

  14. Heh. This is funny stuff.

    If there’s a process of some kind that somehow manages to produce otherwise rare beneficial mutations that “could not have happened by normal means”, would that have to be thought of as an eternally omniscient, omnipotent and perfectly good but bodyless person? Somehow that just seems stretched to me, can’t put my finger on it 🙂

    Ironically, someone like James Shapiro would relegate that to a variation on his “natural genetic engineering” stuff.
    From wikipedia:

    Shapiro points out that multiple cellular systems can affect DNA in response to specific environmental stimuli. These “directed” changes stand in contrast to both the undirected mutations in the modern synthesis and (in Shapiro’s interpretation) the ban on information flowing from the environment into the genome.

    In other words, that there’s a kind of environmental feedback going on that produces beneficial mutations beyond the frequencies you’d expect by the mere chance accumulation of mutations, separate from environmental input.

    Weren’t you sort of pro Shapiro? But we need God now?

  15. So as walto pointed out, JoeCoder is asserting that

    I apologize that I don’t have a way for both atheism and evolution be true.

    …and that

    I think it would be ridiculous to try to argue evolution is evidence of God.

    …without noticing the inconsistency.

  16. colewd: I have read Jame’s book and corresponded with him on email. I think his ideas are the closest to having a shot a being right.

    Then you accept there’s a natural evolutionary process responsible for the diversification and complexification of life.

  17. Rumraket:
    What do you ID guys (stcordova, JoeCoder) think of a guy like James Shapiro and his “Natural genetic engineering”? Do you think he has a good case for it? Is it bullshit?

    Now that they’ve responded, let me raise my worries about Shapiro’s thesis, the little I understand it:

    A. The organisms have got a superb genetic engineering machine in them which produces just the right genomic changes that they need. So …

    B. It must be coded for somewhere. Where is it?

    C. Wherever in the genome it is, it must be maintained functional by natural selection opposing deleterious mutations in it. But …

    D. Those mechanisms that are used only once a million years or so, how are they maintained in the face of mutation constantly disrupting them, if they are put to the test that rarely?

    Shapiro does not seem to address these. Or have I misread him?

  18. JoeCoder:
    Hey walto,you wrote:

    I believe that’s a form of the fallacy of affirming the consequent.God can exist AND there be no evolution.My point was that if you want evolution, I don’t see a way for it to happen without some kind of help.

    Read it again. I denied the consequent.

  19. Joe Felsenstein: A. The organisms have got a superb genetic engineering machine in them which produces just the right genomic changes that they need. So …

    Actually, Shapiro denies that organisms anticipate need or produce just the right kind of mutations.

    What he says is more subtle and moe like evolvability.

    He says that the kinds of mutations — not their content — are optimized to produce a better than random assortment of variants.

  20. petrushka: He says that the kinds of mutations — not their content — are optimized to produce a better than random assortment of variants.

    If so, then he has a more viable hypothesis. But he’d have to have some way a site knows to produce a G rather than a T, etc. In general adaptability can evolve, as some simulations have shown.

    But how fine-tuned you can get it, particularly to respond to infrequent challenges, is to be doubted.

  21. I didn’t see him address g vs t, but i think he would argue that duplications are more useful than say, a randomly placed copy and paste.

  22. petrushka:
    I didn’t see him address g vs t, but i think he would argue that duplications are more useful than say, a randomly placed copy and paste.

    There may be some optimization of those rates. There are two problems remaining:

    A. Any genetic change that influences the mutation spectrum or even the mutation rate gets separated by recombination from the descendant that suffers the consequences, so it is hard for it to be held accountable. (This has troubled population geneticists trying to make models of optimal mutation rates for years — it is discussed in a paper in American Naturalist by Egbert Leigh in 1970).

    B. If a particular type of mutation is needed only once every million generations, will a base change that favors it itself get mutated away more often than it is preserved by that rare selection?

    It seems that a quantitative account is needed, plus some actual locating of the mechanisms in the genome.

  23. Rumraket,

    Then you accept there’s a natural evolutionary process responsible for the diversification and complexification of life.

    Yes, I have always believed this is possible. I just don’t believe the current paradigm is the right answer. I agree with Joe’s challenges to Shapiro’s work. We know that some form of NGE is going on given DNA repair but this is based on information that exists. Formulating the sequences of a new complex protein is a big job.

  24. Joe Felsenstein: petrushka: He says that the kinds of mutations — not their content — are optimized to produce a better than random assortment of variants.

    If so, then he has a more viable hypothesis. But he’d have to have some way a site knows to produce a G rather than a T, etc.

    Yes and that’s also been my issue with these kinds of suggestions before. How is some at bottom “mechanical” feedback system going to “know” what mutations in what locations are beneficial? It doesn’t even seem to be possible to predict a statistical bias in that respect. Nobody as far as I know, has shown that adaptive mutations are generally Transversions, or they’re more likely to be adaptive if they happen in certain loci. It is trivial to imagine a mechanism that has the ability to make certain mutations happen, it’s another thing entirely to show it knows which one to pick and how to mutate it in response to novel environmental changes.

  25. Rumraket: It is trivial to imagine a mechanism that has the ability to make certain mutations happen, it’s another thing entirely to show it knows which one to pick and how to mutate it in response to novel environmental changes.

    If there were a single-base substitution that created such a system, then natural selection would most likely favor it, though there is the issue of the resulting adaptive mutations segregating away from that single change before they themselves could be favored. But establishing such a feedback system isn’t that simple.

    In effect, we’re making a Michael Behe edge-of-evolution argument against it!

  26. walto: But that’s not their goal, I don’t think. Rather, it’s simply the claim that what is incontestably going on isn’t the sort of thing that nature could do ON ITS OWN.

    No one knows what nature can do on it’s own. The claim that nature can do things on it’s own may not even make sense. It surely lacks any semblance of being a testable claim.

  27. Patrick: False equivalence.

    It’s true that Dawkins is no creationist. But that’s about as far as the false equivalence goes. And hand-waving isn’t an argument.

  28. JoeCoder: I apologize that I don’t have a way for both atheism and evolution be true. Let me know if you figure something out though.

    I am trying to convince atheists to accept the Many Gods interpretation of evolution.

  29. Mung: It’s true that Dawkins is no creationist. But that’s about as far as the false equivalence goes. And hand-waving isn’t an argument.

    You know, Mung, when you cut out all the context and respond with a non-sequitur, other participants might get the idea that you have nothing to contribute except “a tale old by an idiot, full of sound and fury, signifying nothing.” Surely you want to be taken more seriously than that?

  30. walto: Not sure if anyone else here will agree with me, but I find the ‘Evolution as Proof for the Existence of God’ idea pretty amusing.

    🙂

    Well, it certainly appear to be nothing short of miraculous that search space for evolutionary innovation includes things like eyeballs and brains, and that there is a search program running that has a linear string of characters that can be mutated and a set of apparatus that can translate [decode] those characters into phenotypic traits that just happen to prove beneficial, and when added up, make things like eyeballs and brains

    Or consider the “Many Gods” interpretation of evolution.

  31. stcordova: You want to ignore the mutation load question, that’s up to you, but you can’t use the amount of documentation on Mendel’s Accountant as much of an excuse to ignore the substance of what JoeCoder is saying…

    Sure he can.

  32. Patrick: Surely you want to be taken more seriously than that?

    There are only so many ways of claiming you’re a flaming hypocrite without just coming out and saying it, but I am trying.

    You had no problem, it seems, coding a Weasel program without understanding the underlying model. You even manage to claim that creationists don’t understand Weasel and cumulative selection, implying that you do.

    I’d sure love to see a thread from you explaining it all. Don’t forget to bring the documentation.

  33. Mung: There are only so many ways of claiming you’re a flaming hypocrite without just coming out and saying it, but I am trying.

    You had no problem, it seems, coding a Weasel program without understanding the underlying model. You even manage to claim that creationists don’t understand Weasel and cumulative selection, implying that you do.

    I’d sure love to see a thread from you explaining it all. Don’t forget to bring the documentation.

  34. Based on what mung has posted here, I still think he does not understand GAs.

    He can code one that doesn’t work, but I’ve worked with lots of guys who coded things that didn’t work.

  35. Mung: Well, it certainly appear to be nothing short of miraculous that …

    Is it really certain that it appears miraculous? It doesn’t appear miraculous to me. At all.

  36. Rumraket: Well if it *does something* for you mentally and emotionally, who am I to question that?

    Yup. The power of cumulative selection is subjective and psychological.

  37. Patrick: Based on all the material I’ve read, I remain unconvinced that Mendel’s Accountant models anything other than Sanford’s religious beliefs.

    Yup. We see what you’re about.

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