Tuesday, April 29, 2014

Creationists admit that junk DNA may not be a "myth" after all

Creationists in general, and Intelligent Design Creationists in particular, feel very threatened by the idea that most of our genome is junk. We know why they feel threatened: it's because a genome full of junk doesn't seem like something gods would design on purpose. It's pretty hard to reconcile junk DNA with with gods that spend so much effort designing bacterial flagella.

The creationists get very excited whenever a group of scientists publish evidence for function in junk DNA and they could hardly contain themselves when the ENCODE preliminary results were published in 2007 because the ENCODE Consortium said that most of the human genome was functional. You will recall that the creationists fell hook line and sinker for the ENCODE publicity hype in September 2012 when the ENCODE leaders came right out and said that their analysis of the entire genome shows there is almost no junk in the human genome.

The creationists, just like the ENCODE leaders, were very resistant to all of the scientific evidence for junk DNA. Both groups showed a remarkable ignorance of four decades of work leading to the conclusion that our genomes are full of junk DNA [see ENCODE, Junk DNA, and Intelligent Design Creationism ]. Creationists, and even some scientific opponents of junk DNA, quote Jonathan Wells' book The Myth of Junk DNA as an authority of the issue.

Now, I wrote a pretty extensive review of The Myth of Junk DNA showing where mistakes were made and why the evidence still favored lots of junk DNA in our genome [The Myth of Junk DNA by Jonathan Wells]. That was in 2011. Here's how Jonathan Wells responded ... [Jonathan Wells Sends His Regrets].
Oh, one last thing: “paulmc” referred to an online review of my book by University of Toronto professor Larry Moran—a review that “paulmc” called both extensive and thorough. Well, saturation bombing is extensive and thorough, too. Although “paulmc” admitted to not having read more than the Preface to The Myth of Junk DNA, I have read Mr. Moran’s review, which is so driven by confused thinking and malicious misrepresentations of my work—not to mention personal insults—that addressing it would be like trying to reason with a lynch mob.
The ENCODE Consortium has decided that it had better backtrack a little on the subject of junk DNA. Their recent PNAS article (Kellis et al., 2014) pretends that the publicity hype of September 2012 never exisisted and, even if it did, they may have been right to conclude that 80% of our genome is functional. It all depends on how you define function. Apparently they have just discovered that lots of scientists define it in a way that the ENCODE Consortium overlooked in September 2012.

Now they just want to make sure that everyone knows they have done their homework and they acknowledge that there's a wee bit of a controversy—but they weren't wrong! They just have a different way of defining function.

This puts some of the creationists in a difficult position. Some of them are actually willing to conceded that there's a lot of junk DNA in our genome while other are only willing to concede that the case for function may not be quite as rock solid as they thought.

Here's how an anonymous creationist explains the backtracking of the ENCODE Consortium on Evolution News & Views (sic): Defining "Functional": The Latest from ENCODE.

He/she starts off with the obligatory snipe at "Darwinists" and the obligatory misrepresentation of the case for junk DNA. He/she is referring to the Kellis et al. paper ...
First, the paper is a remarkably restrained and balanced response to some of the rather intemperate criticisms of ENCODE from hard-core Darwinists who insist that (a) ONLY an evolutionary approach yields valid information about functionality, (b) evolutionary theory necessarily implies that most of our DNA is junk, and (c) junk DNA provides evidence that Darwinian evolution is a fact. In other words this paper is a model of rational and civil scientific discourse, in contrast to what we have come to expect from some hard-core Darwinists.
(See the quote above from Jonathan Wells for an example of "a model of rational and civil scientific discourse.")

The Evolution News & Views post concludes with ...
The authors conclude that all three approaches must be taken into account, though a simple intersection of the three (which would include only DNA sequences that meet the test of functionality for all three approaches) would be far too restrictive. Unfortunately, the authors do not specify exactly how the three approaches could be integrated to yield a single reliable estimate of the percentage of functional DNA.

So the debate continues.
Believe it or not, that last sentence ("So the debate continues") is pretty remarkable considering that the creationists have steadfastly refused to admit that there is a scientific debate. Over the past decade, they have consistently claimed that the evidence is in and it shows that gods did it after all most of our genome is functional.

Maybe I'm being overly optimistic but it looks to me like some creationists are actually disagreeing with Jonathan Wells. Stay tuned.


Kellis, M. et al. (2014) Defining functional DNA elements in the human genome. Proc. Natl. Acad. Sci. (USA) April 24, 2014 published online [doi: 10.1073/pnas.1318948111 ]

145 comments:

  1. Replies
    1. Too late. I've been hoping for 25 years. If I ever give up, I'll have to stop trying to educate the IDiots.

      Delete
  2. Besides the biological function or assay noise problem (from Kellis et al., 2014):
    "ENCODE maps of polyadenylated and total RNA cover in total more than 75% of the genome but a significant portion of these are of low abundance [for poly-A RNA] 70% of the documented coverage is below approximately one transcript per cell", this data may not even reflect normal biology.

    Look at the cell types in the Encode project:
    http://www.genome.gov/26524238
    .....cancers, immortalized cell lines. Even normal ES cells are marked by a profound lack of silencing markers. So are we debating biology or pathology here? How many of the "less than one transcript per cell" findings map to HELA cells?


    ReplyDelete
    Replies
    1. You will most likely get the same result if you substitute the cancer cells with normal cell types. I would not pick on this

      Delete
  3. The creationist approach seems to be, if creation can't explain the big things, lets look at the small things.

    If man is the zenith of God's creation, why are there so many poorly designed parts? Why did he put all of the eye's connective tissue, nerves, etc. in front of the light sensing equipment, and then run a big nerve through the centre of the retina, resulting in a blind spot? Why did he design an abdominal wall that is not well suited for standing upright? Why did he create a spine that is also not well designed for standing upright? Why did he provide us with a barely functioning appendics that has a propensity to rupture? And my favourite, why did he place our testicles outside of the body, where they are prone to injury?

    Explain how these design flaws were created by an omnipotent God, and I might listen to some of their other arguments.

    ReplyDelete
    Replies
    1. And why did he he route my urethra through my ever expanding prostate gland ?

      Delete
    2. And if he is the only God, why did he make Muslims, Jews, Hindus, and the plethora of other beliefs? Is this just so Christians can feel superior in the belief that they are all going to hell?

      Delete
    3. problem is acartia, you have no way to know if it is bad design unless of course you have testing it against an alternative.

      So what's your proposed alternative to the human eye, which by the way seems to have served humanity well for the last say cuppa thousand years.

      Anyway, curious to see your alternative that solves the blind spot problem, without of cousr impairing other functional areas of the eye.

      Delete
    4. 'Explain how these design flaws were created by an omnipotent God, and I might listen to some of their other arguments.'

      Bad theology is endemic. Not only among the atheists, which you could understand; but also among Christians. The idea that God created a world without death goes against a thorough understanding of the bible. To make a long explanation short God created a world with death so that many generations of people/souls would go to heaven. Jesus explains that God' has many dwelling places for all of us. That is more than just the two for Adam and Eve if they were meant to be living forever in the garden of Eden.There is a lot of biblical evidence for God creating death/suffering. Most people are not capable of coming to grips with that reality though.

      Delete
    5. And why did he he route my urethra through my ever expanding prostate gland ?

      Because you don't believe in him. What were you expecting, that you would go to hell?

      Delete
    6. Bad theology is endemic

      You mean there is any other type ?

      There is a lot of biblical evidence for God creating death/suffering

      In the same sense that comic books provide evidence for the paternity of Superman. Or the Harry Potter books provide evidence for an extra platform at London King's Cross railway station.

      Seriously, you should be ashamed of yourself for getting your jollies from goat herder snuff porn.

      Most people are not capable of coming to grips with that reality

      The projection is strong in this one.

      Delete
    7. @Steve said "So what's your proposed alternative to the human eye..."

      Let's see. How about the squid or octopus eye. They have all the connective material behind the light sensitive cells. No blind spot. But who am I to say that this is s better design? A first year engineering student could see the benefit s of one over the other.

      Delete
    8. To make a long explanation short God created a world with death so that many generations of people/souls would go to heaven.

      One might wonder why god wouldn't just skip this messy (and quite vexing, judging by accounts in the OT) earth interlude and create only heaven in the first place. Come to think of it, by bother with any of it all. Is the universe god's hobby? I wonder what his day job is.

      Delete
    9. There is a lot of biblical evidence for God creating death/suffering.

      Just as there is indisputable Biblical evidence of God prescribing animal sacrifice. These are arguments in favor of God/religion?

      Delete
    10. Steve: So what's your proposed alternative to the human eye...

      Please, please, God, may I have the mantis shrimp's eyes?

      Delete
    11. Please, please, God, may I have the mantis shrimp's eyes?

      Rather incongruously, after that Wikipedia article gets done extolling the wonders of the shrimp's eyes, it segues into how good they are deep fried with garlic and chili peppers.

      Delete
    12. To quote Lewis Carroll, "Such is Human Perversity."

      Delete
    13. What an impressive collection of morons. Not the number of morons, but the shear stupidity of Moran's morons. Actually calling evolutionists morons is an insult to morons. Evolutionists are more like zombies. They can't think. They have no soul. They are the living dead, wondering around caring only about satisfying their based instincts. ugh ugh ugh. Yes, that best describes the twelve zombies that regularly frequent this site.

      Say, what created the eye, random chance they say. What created the brain and the nervous system, random chance of course. What created vast intertwined ecosystems, random chance. No brains here. Some morons realize how stupid this sounds so they invented new buzz words neutral drift. But how did that created complex life? Random forces of course, but we don't call it that anymore. We just don't use the word random anymore.

      hahahahha. Only a zombie could think like this. Moran and his twelve zombies. u r all so stupid u r frightening

      Delete
    14. Why can't we get a better class of creationists on this site?

      Delete
    15. That's sheer stupidity if you don't mind.

      Delete
    16. Mr. Roberts, if you are going to comment about evolution, maybe s grade level of the subject might help.


      Could you point me to any evolutionary biologist, who has published a paper suggesting that evolution is random? I only need one. Are you having a problem finding one? Maybe it is because evolution is not a random process.


      But I should know better than to try to educate the dense.

      Delete
    17. Worst argument ever. Evolution is a stochastic process. Could you find one publication claiming it's not? Arguably describing evolution as a random process was the single greatest insight Darwin had - because it didn't merely revolutionize biology, but Physics and Chemistry along with it. On the strength of evidence for evolution, Boltzmann decided to look at what consequences a stochastic universe would have. The result was statistical mechanics. And you take two more steps (Wien, working out the predicted spectrum of a black body, which didn't quite match observations and Plancks fixing by introducing h) to get to quantum mechanics.

      And within evolution, you don't get anything resembling what we observe if you treat it as deterministic. Molecular phylogenies only make sense given transition probabilities for bases and test of neutrality. The same holds for molecular clocks. There are even very basic issues that arise from individual fitness only being able to take values that are integer multiples of 0.5, rather than being able to take any non-negative value.

      The reason Mr. Roberts is wrong is not the claim that evolution is random. It's the idea that this would prevent it from working. That however is an issue with him not understanding how random processes work.

      Delete
    18. John Harshman asks,

      Why can't we get a better class of creationists on this site?

      You're kidding, right? I'm proud of the fact that Sandwalk attracts the very best and the brightest creationists. Have you not looked at the quality of people who comment on the creationists websites? What we're seeing is the best they have to offer. It's the cream of the crop! :-)

      Delete
    19. Pooh. I remember the great days of talk.origins. We had giants in those days: Karl Crawford, Ted Holden. Why, they could put together entire coherent paragraphs.

      Delete
    20. Simon says (sorry, couldn't resist): "Arguably describing evolution as a random process was the single greatest insight Darwin had..."

      Could you point me towards any statement by Darwin where he says that evolution is random. Darwin's entire theory involves the non-random selection of one trait over another.

      Yes, certain things in evolution tend to function in a manner that approaches randomness. Genetic drift is an example. But genetic drift, by definition, is observed when there is no adaptive value of the change (positive or negative). If the altered gene has an adaptive value, then selection pressures come into play, and are therefore not random.

      Delete
    21. Darwin 1859. "On The Origin Of Species". First Edition. P.5:
      "As many more individuals of each species are born than can possibly survive; and as, consequently, there is a frequently recurring struggle for existence, it follows that any being, if it vary however slightly in any manner profitable to itself, under the complex and sometimes varying conditions of life, will have a better chance of surviving, and thus be naturally selected."

      Note the "better chance". That's the first time Darwin defines selection in print and he defines it as population resampling (which in modern parlance tends to get broken up into selection and drift).

      During the synthesis this was made explicit, with the Fisher-Wright process (polynomial resampling), and later on the Moran model and the diffusion approximation were added to the basic stochastic processes we can use to describe evolution.

      Now, the first generation of the synthesis also introduced law of large number approximations. You can split any random variable X into a constant E(X) and a centered random variable X-E(X). In a LLN approximation the centered variable goes to 0. This can be useful (it often is), but in many cases you cant ignore the centered component. Selection was used less for the resampling process and more for the expected change E(X), drift was introduced as a term for the centered component. At some point people who didn't pay that much attention to the maths came to think of these as separate processes. That was a profoundly bad idea...

      To illustrate that, consider a simple random variable: It takes the values 1,2,3,4,5 and 6 each with a probability of 1/6. I.e. we are looking at a fair die roll. Now we can split that up in the same way and get a constant 3.5 and a centered component that takes the values -2.5,-1.5,-0.5,0.5,1.5 and 2.5 each with a probability of 1/6. Add the two and you have the same thing. But when you start thinking of die rolls of the product of two separate processes, one of which always comes out 3.5 and one of which takes these values, you are not actually getting a better idea of how a die roll works. If you split up population resampling into selection and drift and apply this to individuals, you end up stating things like: That lion has 2.37 offspring through selection and -0.37 offspring through drift for a total of 2 offspring.

      To make matters worse, I don't think anybody has ever made any use of the drift term. Either the law of large number approximation is good and you can ignore it, or it isn't and you use the complete model. The only case in which one could argue that it sees some use is the neutral case and there the complete model is identical to the drift term. For what it's worth, the drift term is not even statistically independent from s.

      Delete

    22. As to the statement that the process stops being random as soon as selection comes into play. Consider a very simple model of evolution (basically a Moran model with a couple of simplification). We are looking at an allele in a haploid population and as time steps choose birth death pairs (i.e. we look at the change that occurs when 1 more individual has been added and 1 has been removed). We also ignore any steps in which both are carriers or both are non-carriers. The change is 0 when the allele has a frequency equal to 0 or 1, otherwise it's 1/N with a probability of 1/(1+e^(-s)) and -1/N with a probability of 1/(1+e^(s)). N is the population size, s is the selection coefficient s=ln(mean fitness of carriers/mean fitness of non-carriers).

      Now this model is basically a model of biased coin flips. The degree of bias depends on s. For s=0 it's a fair coin. For - say - s=10^-5 the probability of going down is 0.49999750. That's not a particularly huge bias (but it qualifies as strong selection in a population of 50,000). You need a lot of these coin tosses to find an observable effect of this bias. And we have a lot of loci, a lot of individuals and a lot of generations to work with. But this idea that it goes from coin toss to something "not random" seems very far off from biological reality.

      Delete
    23. Simon, I think that we are essentially saying the same thing but with slightly different semantics. Yes, with a perfectly weighted die, the probability of obtaining a five will be 1/6 with every roll. Of course, you may get three twos in a row, or take ten rolls to obtain the first five. But the probability is still 1/6 and we would call it completely random.

      However, if we remove a bit of plastic from the face containing five dimples, the probability of rolling a five is no longer 1/6. The probability may have changed so little that it is almost unmeasurable, but it has still changed. It is stochastic in that it can be described statistically, but it is no longer random.

      Whether the shift in allele frequencies in a population is due to drift or due to "active" selection is almost impossible to determine conclusively. For example, we would all agree that the development of antibiotic resistance in a bacterial strain is due to selective pressure and not drift. It did not dominate the population through random events. But assuming that the resistance wasn't imparted by a recent mutation, why was the non-resistant phenotype dominant in the original population? Was it due to random factors (possible) or was it due to small selective pressures (e.g., slightly slower division rates than the non-resistant version)?

      Delete
    24. "It is stochastic in that it can be described statistically, but it is no longer random."

      If you restrict your usage of random to uniform distributions, then it's not clear what this applies to. A random variable is a variable that can take multiple values, with a probability distribution describing how likely particular vaules or ranges of values are. Uniform distributions are special cases.

      It's worth noting that the neutral case has non-uniform increments in all the classical models. In the simplified version of the Moran model I used above the increments are uniform, but that's not something general. And we can rewrite any random variable as a function of a uniformly distributed random variable on [0,1] (and for some time that was used to define random variables - today it's something very useful if you ever run simulations, because you only need random numbers that are uniformly distributed on [0,1] and can use them to transform them into any random variable you might need). I.e. if you want to you can always find the uniform one and conclude it's random under that stipulation, or write it as another probability distribution and claim it's not. At that point the word becomes useless.

      Delete
    25. "Whether the shift in allele frequencies in a population is due to drift or due to "active" selection is almost impossible to determine conclusively."

      I don't like statements like this at all. As I noted above, I think it is silly to treat selection and drift as separate processes. For this reason I find it unhelpful to think in terms of their relative importance. The correct way to frame the neutralist-selectionist debate is "What is the distribution of values for s?", not "How important is drift compared to selection?"

      Now, the "determine conclusively" part is central to near neutral theory. Given a particular value of s and the population size, can we reject the null hypothesis s=0? For some range of s, we can't reject the null and thus we have a near neutral range. But again, that's something pertaining to the distribution of values for s.

      Delete
    26. Hahaha, it is well know that zombies travel in packs. It is true here with the evo-zombies. Birds of a feather I suppose.


      This just in: Human brain microchip is 9,000 times faster than a PC
      from Fox News today: http://www.foxnews.com/tech/2014/05/05/human-brain-microchip-is-000-times-faster-than-pc/?intcmp=obnetwork.

      Apparently the human brain that has evolved by some unspecified process is 9000 times faster than a pc. It used to be random mutation. Now it is aimless drift, whatever that means because nobody seems to know.

      That's not all - PC''s use 40,000 times more power than a human brain. Isn't that amazing. And this is supposed to have happened by some designerless process, Hahaha. I just can't stop laughing. I know it's rude. But evolution is so damn ridiculous. Only a zombie could put all their brain power behind it. And just think (if you can). The pc is the height of human scientific accomplishment. We us quantum mechanics, nano technology and aimless natural forces are 40,000 times more efficient.

      Absolutely incredible.

      Oh, and there was a previous post about is there knowledge beyond scieence, and all the evo-zombies were stumped. Well the obvious answer is LOVE! Proof again that only evo-zombies dwell here, ugh, ugh..

      Delete
    27. Ahhh. The "human science can't do it so God must exist" argument. But wait. Hot off the 2011 press; The K computer from Fujitsu is four times faster and stores ten times the data of a human brain (20 times faster and 1000 times the data that can be stored by yours). But don't fret. You can now argue that the K computer was designed, which is further proof of ID.

      Delete
  4. Just a small point. Your first line is a little misleading

    "Creationists in general, and Intelligent Design Creationists in particular..."


    They are both the same thing. Hypothetically, what do you think their response would be if it was proven, beyond doubt, that life on earth was created by an advanced life form living on Alpha Centauri? Logic would suggest that the ID camp would do cartwheels, be ecstatic that they have been proven right. Dies anybody seriously think this would be their reaction? Of course not. It would run counter to the motivation behind their "theory", that man was created by a God. But not just any God, the Christian God.

    ReplyDelete
    Replies
    1. This in addition that many creationists, particularly of the young earth variety steadfastly contend that there is no life elsewhere in the universe. Even this is goalpost moving from their previous position that there were no other planetary systems in the universe.

      Delete
    2. As far as I know, the Theistic Evolution Creationists don't have a big problem with junk DNA. That's why I phrased the statement the way I did.

      Delete
    3. @Arcatia Tonsa: Why do you think that non-Christian types would be immune to creationism? Or have I misread you.

      Delete
    4. Sorry, "Acartia Tonsa", not Arcatia Tonsa.

      Delete
    5. @Joe: I didn't say that non-Christians were immune from creationism, but it is safe to say that the main push to have ID taught as a science (or evolution removed from the education) in North America comes from the Christian community.

      Delete
  5. Honestly I don't see the problem here. Can't they simply say that "the designer" designed us with junk DNA to reduce genetic load?

    ReplyDelete
    Replies
    1. Why do that - he could just reduce the mutation rate. It's not as if it can't be done - ours is quite high compared to other species

      Delete
    2. Can't they simply say that "the designer" designed us with junk DNA to reduce genetic load?

      ?? For a particular per-base mutation rate, you do the same amount of damage regardless of how (or if) genes are spaced.

      Delete
    3. Georgi Marinov,

      I am not saying that there has to be any logic that would convince you or me. Rather I remember certain people arguing that theism is so mutable, undefined and goalpost moving that we can never hope to refute it with science (and so we have to call a philosopher to the rescue, as if a scientist could not spot goalpost moving). As a prime example, it is often said that ID is untestable because literally everything can be rationalized into evidence of design.

      So why the inflexibility on the rather minor point of junk DNA?

      Allan Miller,

      I am not an expert on this, but I have a hunch that while it would not reduce polymerase errors that are indeed per-base, having a lot of unimportant sequence around might perhaps cushion against some other mutagens, such as radiation or radicals?

      Also, to invoke somebody who knows more about that particular topic than I do: http://sandwalk.blogspot.com.au/2009/11/genetic-load-neutral-theory-and-junk.html

      Delete
    4. I'm waiting for the argument that only god could have the audacity to include junk DNA, whereas the cut-throat business of Darwinian evolution would eliminate it quickly. They will be able to find quotes in the scientific literature to support this new contention.

      Delete
    5. I am not an expert on this, but I have a hunch that while it would not reduce polymerase errors that are indeed per-base, having a lot of unimportant sequence around might perhaps cushion against some other mutagens, such as radiation or radicals?

      How is the expansion of DNA going to be selected for under this mechanism? Other than large duplications (and excluding WGD events, which do not change the fraction of the genome that is noncoding anyway), the largest incremental increases in genome size are due to the insertion of transposable elements. The largest of those in mammals are L1 repeats, at 6.4Kb. So let's, for the sake of the argument, assume that expansion of noncoding and nonregulatory DNA has a beneficial effect by buffering against mutations, and let's imagine a mammalian genome that is 2GB in size, and has 300Mb of functional sequence (working from 10% functional sequence in the current human genome). So we're adding 6.4kb to 1.7GB of noncoding and nonregulatory DNA, and by doing that, we're increasing the buffering capacity by 6.4 x 10^3 / 1.7 x 10^9 = 3.7 x 10^(-6) and decreasing the probability of harmful mutations (we assume all 300Mb to be vital, which is unrealistic - of course you have degenerate codon positions, positions in transcription factors binding sites, plenty of unconstrained sequence in UTRs, etc., but for the sake of the argument we assume that) from 0.15 (= 300 x 10^6 / 2 x 10^9) to 0.14999952 (= 300 x 10^6 / (2 x 10^9 + 6.4 x 10^3)). or by 4.8 x 10^(-7).

      Let's assume that's the selective coefficient. This is an overestimate, first, it need not be as large as the decrease in the probability of harmful mutation, and second, we are discarding all the negative effects that such an insertion might have, but for the sake of the argument we take it to be that number. The effective population size of that mammal is probably on the order of 10^5 at most. How is that going to be selected for? With all the unrealistic assumptions in favor of the hypothesis, we still get 1/4N_e = 1/(4*10^5) = 2.5 x 10^(-6) > s = 4.8 x 10^(-7), i.e. that beneficial selective effect is invisible to selection.

      Sure, a large genome full of junk DNA does buffer against mutations. But this need not be a selected effect and in all likelihood it isn't.

      Delete
    6. I did not say that it was necessarily selected for. It could have happened partly accidentally, partly through parasitic DNA, but thus facilitating the evolution of something more complicated than fast-growing, low-DNA-content bacterial cells.

      Gene duplication events are not immediately selected for either, in fact they merely constitute waste. But they allow the subsequent specialization of the two copies and thus facilitate the acquisition of new functionality.

      Delete
    7. When people bring these things up, they usually do so with the goal of providing a causal explanation for why all that DNA exists - and this is what I replied to.

      Delete
    8. I don't see how this line of reasoning makes sense. Its like proposing to put trailer parks on the outskirts of town so that the tornadoes don't do as much damage to the more well-to-do homes in the interior. The energetic photon (or the peroxide radical) that is headed toward base-pair # 1734389 in your genome does not care whether it is the start codon of a gene or it is one of million bases in a vast expanse of junk. Neither do your repair enzymes. If base-pair # 1734389 is within a start codon for beta-tubulin, you want your repair enzymes to get to base-pair # 1734389 right away and fix the problem. You don't want your repair enzymes busy fixing the damage to a 20-fold excess of junk.

      Delete
    9. In all likelihood, junk DNA, and the expansion of the genome, is not selected for. It simply isn't selected against. We get hung up on things like blind cave fish that have lost their eyes. But what must be remembered is that there is a large cost (metabolically) in developing and maintaing eyes. It is easy to see how they would be selected against when they provide no value.

      But what is the metabolic cost of maintaining non-functional DNA? Not being a biochemist, I don't know this answer, but I suspect that it is low. I am sure that there is an upper limit, but whether or not we have achieved it is anyone's guess.

      Delete
    10. That is, of course, correct with respect to certain kinds of mutations, But there are also others that do occur in limited numbers (like transposable element insertions themselves), for which it would superficially make sense. It still does not make sense in general, of course.

      Delete
    11. @Arlin,

      Your point makes sense. However, as you well know, mutagenesis comes in many flavors. You might want to take a look at a radically different rationale and model on the protective function of junk DNA (jDNA) and the evolution of genome size: http://biorxiv.org/content/early/2013/11/18/000588

      Delete
    12. acartia -- You wrote, "In all likelihood, junk DNA, and the expansion of the genome, is not selected for. It simply isn't selected against.. . . But what is the metabolic cost of maintaining non-functional DNA?. . . I suspect that it is low."

      I agree that junk DNA isn't selected for, just not selected against. However, the cost of replicating all that unneeded DNA is fairly high, when multiplied by all those cells. If we could get rid of it all at once, we'd free up a lot of energy to accomplish things -- or, in my case, to expand with stored fat the way balloons expand with air. :-)

      The problem is, how would junk DNA be selected against? If there were a cellular process that could remove a lot of DNA, it wouldn't "know" the valuable DNA to leave it undisturbed. Bits of junk DNA here or there can be -- are -- lost to mutations, but compared to the whole expanse of the genome, that's just a tiny fraction. At least for many multicellular organisms, including humans, conspecific individuals differing in a few bits of junk DNA are so similar in their energy use that the difference can't be selected for (compared to all the other things subject to selection). And so the junk DNA grows.

      Delete
    13. Claudiu, thanks for the interesting link. For a limiting event such as tranposon insertion that iss targeted at DNA (rather than X-rays that continue coming forever and don't care what they hit), when one considers only the first event in isolation, extra DNA can serve as an entropic decoy. I agree with that basic point.

      The problem is that this doesn't capture the dynamics of the whole system. We think we dodged a bullet, but the bullet isn't dead-- what has really happened is that the total number of live bullets in our genome has increased by +1.

      That is, I suspect that this rationale also will fall apart upon further inspection. Let's say that, in order to reduce my chance of getting tuberculosis by breathing tuberculosis spores, I fill my house with bunnies and pigs. After all, we are all breathing the same air, and the more of them, the more likely one of them will breath in and absorb the spores instead of me.

      The problem is that the spores don't necessarily die inside these decoys. They might grow and then re-infect me. Having decoys might actually make the problem worse.

      Likewise, inserting a transposon into junk DNA is not like flushing it down the toilet. It is still there. If we are talking about replicative transposition, then we now have 2 copies in the genome instead of 1. The problem is actually worse than it was before.

      Delete
    14. Arlin,

      Let me expand on your interesting ‘bunnies and pigs’ example. One preferable solution would be that you acquire a few special ‘bunnies and pigs’ that would serve as preferred targets for the M. tuberculosis spores; having only a few ‘bunnies and pigs’ around will also help with the ‘food’ bill (apparently, that’s the approach some highly evolved organisms, such as bacteria, employ to protect themselves from inserting viral elements).

      Another strategy, particularly if you have a big house, dispensable food, and tend to be ‘junky’, is too have a large number ‘friendly pets’ around; the problem with this, as you said, is that they might increase the burden of spores. So, the solution would be to acquire ‘defective bunnies and pigs’ that don’t proliferate the spores but serve as targets for the primary threat which are: the exogenous spores.

      Also, as I strongly emphasized in the paper, the major problem with insertion mutagenesis, and key to understand the associated selective pressure, are not the germ-line or somatic mutations leading to cellular death, but those that cause uncontrolled proliferation of cells, which can lead to neoplastic transformations, or cancer.

      Delete
  6. They do...? Really...? I'm not much into this junk DNA stuff, but there are few, less complex organisms than evolutionists that have none or little junk DNA...
    What makes you think that most of your genome is junk...?

    Actually, I don't care too much about the answer, because the day it is going to become obvious that YOU WERE WRONG, I will be knocking on your doors....

    ReplyDelete
    Replies
    1. It is nice to see that you are keeping an open mind about junk DNA (sarcasm font, in case you are not smarty enough to figure it out). The difference between science and ID is that if it is demonstrated that there is no junk DNA, we will accept it and move on. ID crazies, regardless of the evidence, would never change their opinions (beliefs).

      Delete
    2. Quest's mind is so open that he leaves it unclear what we are all wrong about. But we must be wrong, or so he says. He also has not answered the questions posed to him in the discussion on chimp/human common ancestry.

      Delete
    3. Joe,

      I think that I like you too much to overwhelm you with there fundamentals.... You have never claimed to be an expert on abiogenesis, why should you became now...? You don't seem to care about that.. Well, it just happened thanks to "unreasonable and unexplainable accident that became the fundamental cornerstone of your "science"... Very, very convenient....

      Delete
  7. The ENCODE Consortium has decided that it had better backtrack a little on the subject of junk DNA. Their recent PNAS article (Kellis et al., 2014) pretends that the publicity hype of September 2012 never exisisted and, even if it did, they may have been right to conclude that 80% of our genome is functional. It all depends on how you define function. Apparently they have just discovered that lots of scientists define it in a way that the ENCODE Consortium overlooked in September 2012.

    That's not my reading of it - Figures 2 and 3 show things quite clearly.

    ReplyDelete
    Replies
    1. Are you talking about figures in the Kellis et al paper? If so, I don't see your point. I don't think those figures say anything at all about the proper way to define function,

      Delete
    2. I wasn't talking about that - I was referring to the fraction of the genome that's functional.

      Delete
    3. Sorry. I see now that you are focusing on the fact that they are now using 75% as the fraction of the genome that's transcribed and they don't actually give a number for the fraction of the genome that has "biochemical activity" (i.e. 75% plus the other regions that don't overlap).

      Is that what you meant?

      Delete
    4. BTW, I know that some of the authors stll think that most of our genome is functional. You know some of those authors. What fraction of the genome do they think is functional? Do any of them think that 90% is junk?

      In this paper (Kellis et al. 2014), the authors point out that many of the transcripts are expressed at a level below one copy per cell. They mention that it's very difficult to rule out that these may be non-functional accidental transcripts.

      The authors knew about this possibility back in 2007 when many critics pointed it out after publication of the preliminary study. Do you know why it wasn't prominently brought up in the summaries and conclusions that were published and hyped in September 2012?

      Surely they knew back then that they were dealing with very low abundance transcripts when they talked about the significance of pervasive transcription?

      Delete
    5. Georgi Marinov: That's not my reading of it - Figures 2 and 3 show things quite clearly”

      Apparently, Figures 2 and 3 are as clear as mud:
      http://liorpachter.wordpress.com/2014/04/30/estimating-number-of-transcripts-from-rna-seq-measurements-and-why-i-believe-in-paywall/

      Delete
  8. ENCODE researchers are backed up by the philosophers they deserves Junk or functional DNA? ENCODE and the function controversy. Of course they blame the media for the 80% hype and state

    As we have argued in this paper, the mapping of the biological activity of DNA elements produced by the ENCODE project is indeed a ‘collection’ in that sense, that allows biologists to generate precise hypotheses about the biological role of certain DNA elements.
    Like all maps, the ENCODE is a means of doing—it is meant to foster a particular kind of science, which we tried to describe. In this view, ENCODE’s claim of functionality, understood as a methodological claim about the proportion of the genome relevant for biomedical research, is part of the map. And as we have argued, understood as such it is a debatable, but defensible claim. The real, empirical disagreement is precisely as to the proportion of DNA one could remove (or mutate) from the human genome without noticing a relevant difference—where relevance is ultimately determined not by evolution but by our interests."


    In other words, it doesn't matter if anything in biology makes sense in the light of evolution or as they put it earlier in the text:

    "In light of this analysis, we argued that ENCODE’s controversial claim should be
    interpreted as saying that 80 % of the genome engages in relevant biochemical
    activities and is very likely to have a causal role in phenomena deemed relevant to
    biomedical research. In other words, that most of what has been called junk DNA
    cannot be ignored in biomedical research."


    Seemingly, they assume a difference between biology and biomedical research. I am afraid that we will have to concede that there is some truth in this. However, not in the sense they've put it. IMO we are watching how parts of the biological sciences are taken over by what Dan Graur identified as badly trained technicians.

    ReplyDelete
    Replies
    1. SPARC says,

      IMO we are watching how parts of the biological sciences are taken over by what Dan Graur identified as badly trained technicians.

      I agree.

      Delete
    2. SPARC, you're being unfair.
      First, we're not blaming only the media, but explicitly acknowledging that the consortium at best didn't do anything to avoid the hype and confusion, and most likely fostered it.
      We all agree that there's something wrong with the way the ENCODE consortium dealt with the whole issue, and (once more) as we explicitly wrote we did not want to give a wholesale defense of ENCODE. Instead we wanted to show that the whole criticism treated the "notion of function" issue much too lightly, and the quick dismissal of the disagreement shoved some genuine questions under the rug.
      Second, our "assuming a difference between biology and biomedical research" has nothing outlandish, especially if you think in terms of what they try to explain -- think of Mayr's classical distinction between evolutionary and functional biology. We wrote in the paper why the difference matters: if it's not clear we'll be happy to elaborate, provided you ask genuine questions or provide genuine arguments, instead of just asserting the contrary.

      Delete
  9. Speaking for YEC creationists. Junk DNA is irrelevant to origin issues except in some off broadway idea about how dna should look if this or that was true about origins.
    There is no reason we couldn't have DNA to play with. iN original creation week we were meant to live forever.
    In fact we probably could change our bodies at will.

    ReplyDelete
    Replies
    1. Irrelevant for YECs? Why then did your Co-YEC Paul Giem recently state
      "I have seen some claim, with some plausibility, that LINE elements may have something to do with original sin."
      link

      Delete
    2. Original sin or the fall would of changed the DNA on earth. We would not of had even immune systems up to that point.
      So dysfunction in dna can be seen as from the fall.
      Its really off broadway looking at dNA to settle if God created things.
      Complexity, diversity, its here is the great evidence for a thinking being behind it all.
      Its the first obvious conclusion.
      Critics must go a long way to debunk it.

      Delete
    3. We would not of had even immune systems up to that point.

      Right, 'cause there would have been no bacteria - oh wait, we and all other large life forms need bacteria to live (e.g., nitrogen-fixing bacteria that allow plant life to grow).

      Its the first obvious conclusion.

      No immune systems or bacteria is "obvious"? (As well as being less complex and diverse - so both complexity and diversity as well as their opposites all point to God?)

      Delete
    4. "In fact we probably could change our bodies at will"

      What the what?

      Delete
    5. Robert said: "Critics must go a long way to debunk it." Critics don't have to debunk irreducible complexity because it is a non-argument. Using your argument, you cannot debunk the theory that life on earth was accidentally seeded by an intergalactic, trans-dimensional luxury space yacht cleaning out their septic tanks as they tracelled through the solar system.

      Delete
    6. What the what?

      Signs and wonders. There is apparently no limit on the amount of nonsense an otherwise intelligent and reasonable person will accept if it appeals to his or her religious convictions. But present him with the facts of evolution, which if he knows anything about biology he will realize it is inevitable, and suddenly he is all skeptical and discriminating. Religion has to be the most absurd and ridiculous human phenomenon.

      Delete
    7. acartia
      Complexity is the case for a complex origin. So a creator is demanded as nature could not create complexity. its a great point. Historic.
      its up to critics to show complexity is easily the result of chance.
      not prove it is bUT just first show its easily to be seen this way.
      They can't do it!
      In fact even these days they have to figure out great ideas to explain complexity. right or wrong they it still means they are under intellectual pressure to do so.
      This because complexity is too much for chance and so must be a guy's idea.

      Delete
    8. Robert, have you ever seen a crystal grow? It produces very complex forms and is completely natural. The rings of Saturn are very complex, but naturally formed. Haemoglobin is a very complex molecule, but is formed naturally, millions of times every day in every body. Unless, of course, you are arguing that every time a molecule is formed, it is under the direction of a God.

      Delete
    9. Hi acartia - occasionally I too give in to the temptation to respond to Robert, but surely you can gather that for someone who believes we had no immune systems and could change our bodies at will before The Fall (and apparently needs no particular proof other than his "logical" reasoning from a certain book), and thinks God stuck a bunch of dinosaur bones in a 6000-year-old planet, the proposition that crystal growth, Saturnian rings, and hemoglobin formation must all be results of either God's direct intervention or follow rules laid down by him is quite easy to believe.

      Delete
  10. Laurence A. MoranWednesday, April 30, 2014 5:37:00 AM
    Sorry. I see now that you are focusing on the fact that they are now using 75% as the fraction of the genome that's transcribed and they don't actually give a number for the fraction of the genome that has "biochemical activity" (i.e. 75% plus the other regions that don't overlap).

    Is that what you meant?


    If that's how you're reading it, then it is not doing what it's supposed to, which is real unfortunate.

    The results are:

    1) The signal strength distribution follows something like an exponential distribution, with a small fraction of the genome having high-signal and a much larger fraction having a low-level signal

    2) There is a strong correlation between conservation and signal for almost everything you would expect to have it. The exceptions are H3K9me3, which exhibits inverse correlation with conservation, something completely expected as, if anything, H3K9me3 can be thought of as marker of junk DNA (that's, of course, a gross oversimplification, but nevertheless an useful one), and H3K4me1, for which conservation plateaus (that one we don't quite understand).

    These are not unexpected results, but now they are there for everyone to see. The implications are clear.

    There is also a whole paragraph discussing the resolution of the assays.

    But so far nobody who has commented on the paper seems to have actually taken a careful look at the figures and the text. Sure, it is far from perfect, but at least this time the data is shown in much more detail than what was done before.

    ReplyDelete
    Replies
    1. The data is not teling us anything that we didn't know before. It says that a huge fraction of "biochemical activity" is perfectly consistent with junk DNA. The obvious conclusion for many of us is that most of our genome is junk in spite of pervasive transcription and transcription factor binding.

      The obvious conclusion from the data is that "biochemical activity" is a very unreliable way of defining function. What this means is that the September 2012 publications were using a bad definition of function when they declared that most of our genome is functional.

      Do you think that's what the ENVODE Consortium is now admitting in this paper? Is that how they interpret Figures 2 and 3?

      Delete
    2. Where did I say it was something you did not know before?

      One cannot speak for others about how they interpret things, one can speak for himself.

      Delete
    3. I was merely pointing out that the ENCODE leaders seem to have arrived a bit late at the party. I wasn't accusing you of saying something silly.

      As for the opinion of ENCODE leaders, I can understand why do don't want to say in public what they might be thinking. What's clear from their paper is that they are very reluctant to reach the conclusion that's blindingly obvious to many of us; namey, that biochemical activity is a useless way to define function in the absence of other criteria.

      Delete
    4. Actually I don't agree with that statement - Figure 3 shows correlation between the strength of the biochemical signal and conservation. So those two things are not unrelated, meaning that one of them cannot be completely useless.

      But yes, on its own, biochemical activity does not imply function, that is entirely correct. Which is why ENCODE is in principle not in the business of providing an estimate of how much of the human genome is functional, its primary goal is to generate a list of candidate functional elements to be subsequently studied in detail through genetic and other means.

      Delete
    5. I think everyone now agrees that the ENCODE Consortium produced a lot of data that may or may not be useful. (The current consensus says not very useful.)

      In principle, the data could have provided a lot of information on what parts of the genome are functional. That required a bit of critical thinking when the results were announced. Unfortunately, the ENCODE leaders skipped the critical thinking part and proclaimed that the concept of junk DNA was dead.

      Now they're trying to show that they really can think critically about the data. It ain't pretty.

      Delete
    6. Figure 3 shows correlation between the strength of the biochemical signal and conservation.

      As would be expected if there is also transcriptional noise. The higher expressed parts would be highly expressed because they do something, and therefore we'd also expect them to be conserved.

      So those two things are not unrelated, meaning that one of them cannot be completely useless.

      Mere biochemical activity is completely useless, that's the point. We'd need the level of activity and/or degree of conservation to determine whether it is probably a functional stretch of DNA. Again, those would be expected to correlate: Higher degree of conservation implies purifying selection, which implies function, which implies transcription levels well above one copy pr. cell.

      Out of curiosity, is there any known transcript that would only need to exist/does only exist, at one copy pr. cell, and still has some kind of important known function? I can't seem to think of any off the top of my head, but I'm open to being shown wrong.

      Delete
    7. Mere biochemical activity is completely useless, that's the point. We'd need the level of activity and/or degree of conservation to determine whether it is probably a functional stretch of DNA.

      You don't just detect biochemical activity, you measuring its levels is an intrinsic part of the detection with the methods used by ENCODE.

      Out of curiosity, is there any known transcript that would only need to exist/does only exist, at one copy pr. cell, and still has some kind of important known function? I can't seem to think of any off the top of my head, but I'm open to being shown wrong.

      There are no good examples, and I don't think there ever will be for just 1 copy. But there RNAs that play a role in cis -- naturally, one would expect many of those RNAs to be present at fewer copies than RNAs acting in trans (of course, one can argue that things like Xist are acting in cis too, and they are highly abundant, but I am talking about other models). The problem is that we are not at all good at measuring things in terms of copies per cell - you need single-cell measurements for that and all known methods have serious sensitivity and/or resolution problems in that range.

      Delete
    8. P.S. I often get the feeling that the anger towards ENCODE seems for some reason to have transitioned into a wholesale rejection of genomics as a tool. Regardless of one's opinions about ENCODE, this is not at all justified, and is a grave mistake in fact. I don't understand how anyone would seriously make the argument that a qPCR with a few primer pairs is superior to a ChIP-seq or RNA-seq dataset.

      Delete
    9. I think the 'anger' you sense isn't specific to ENCODE and is not a wholesale rejection of genomics as a tool. It, in my opinion, is a rejection of the lack of rigorous thinking that goes into many, not all, of these kinds of experiments. This is not new. When microarrays first came online I sat through an inordinate number of talks where the researcher basically didn't know what to do, decided to do microarrays to hopefully get a handle on the problem (not necessarily a bad thing). Once the data came in, every difference and similarity was promoted as being critically important and insightful and then not pursued further.

      It's the use of the tool inappropriately that is being rejected not the tool itself.

      Delete
    10. The Lorax says,

      I think the 'anger' you sense isn't specific to ENCODE and is not a wholesale rejection of genomics as a tool. It, in my opinion, is a rejection of the lack of rigorous thinking that goes into many, not all, of these kinds of experiments.

      I agree. The main complaint is the interpretation of the data and the absence of critical thinking. The recent paper (Kellis et al. 2014) demonstrates this absence of critical thinking very nicely. In that sense, it reinforces what we suspected was true of the ENCODE leaders.

      The entire field of genomics is going to suffer from collateral damage as a result of the behavior of the ENCODE Consortium leaders. This may seem unfair but if the top, best-funded, researchers in genomics don't understand the evolution of genomes then that's a problem.

      Delete
  11. This comment has been removed by the author.

    ReplyDelete
  12. The comedy never ends at Uncommon Descent; just today they published an article which mentions that "recent studies have shown that species which look very similar and behave similarly can have vastly different genetic structure (notably frogs)," seemingly oblivious to the ID party line (recently put forward by Luskin) that the reason human and chimp genomes are so similar is that there is some sort of functional constraint on the genes and even on codon arrangement and ordering. Truly bizarre - do they even read each other's work or does each author just focus on bashing real science?

    ReplyDelete
    Replies
    1. I am reminded of a creationist I encountered recently who once declared that God designed DNA to resist mutation by giving genomes DNA repair mechanisms, but later declared that the genome is deteriorating due to God cursing us over original sin.

      Delete
    2. Well, credit god for getting with the molecular biological era - global floods are so bronze age.

      Delete
  13. Sorry but I'm a bit puzzled and confused. You have to forgive me. Maybe I'm not used to the style of blogging by professor Moran. I'm just not sure where creationist really admit to what you claim. Just because J. Wells is appalled by the way and style of professor Moran's evaluation of his book, it doesn't mean he agrees with it does it? I'm just not sure what the "energy" of this blog is. I may came across as naïve or a fool just because I have not been following it since the "conflict" I assume.

    ReplyDelete
    Replies
    1. Practice your reading skills and you may do better. The point of quoting Wells is to show that he dismissed Larry's claims without seeing the need to refute them. Not the sort of thing a scientist ought to do.

      It isn't Wells who admits there might be such a thing as junk DNA; it's the anonymous creationist on Evolution News & Views.

      There's a good hint for you in the penultimate sentence of Larry's post. All you have to do is read it: "Maybe I'm being overly optimistic but it looks to me like some creationists are actually disagreeing with Jonathan Wells."

      Delete
  14. The entire ENCODE fiasco is easily summed up.
    They failed to establish a reasonable Null Hypothesis that took into account biochemical noise. Any authentic signature of "function" has to rise above an expected baseline. The expected baseline is not zero. It really can't get more fundamental than that.

    ReplyDelete
    Replies
    1. Well said. John Stamatoyannopoulos (ENCODE leader) recently gave a talk at the University of Toronto. He claims that the onus is on us to prove that the DNA does NOT have a function.

      That's a clear demonstration of the problem. They can't formulate a correct null hypothesis if they don't understand molecular evolution.

      Delete
    2. I guess I'd put their lack of understanding of biochemistry ahead of their lack of understanding of molecular evolution. You know, specific binding sliding off to less specific binding rather than being digital yes/no binding. But it can be hard at times to pick just one type of misunderstanding in those who do it so well.

      Delete
  15. Heh, I was reading Dan Graur's recent blog post on defining function and it struck me just how self-contradictory the ID position on junk DNA is.

    ID creationists like to claim that mutations always and inevitably destroy function and "degrade information", whether that be in DNA, RNA transcripts or amino acid sequences. Yet at the same time, in their insistance that the entire genome must be functional, they have to rationalize that the neutrally evolving portions of the genome all remain functional regardless of how much they mutate. They can't both think that mutations only destroys the perfectly designed biopolymers and simultaneously think that the randomly mutating junk regions are all functional, all the time.

    I wonder how they'd try to squirm out of that one.

    ReplyDelete
    Replies
    1. Excellent point.

      Many would be Young Earth Creationists who say that the genome is deteriorating and that means that the process is recent, and can't go on much longer, and that We Live In Those Last Great Days™.

      Creationists are unclear on how effective natural selection is. As you note, they assume that natural selection is effective (in preventing immediate deterioration of the genome) but that if a mix of a few advantageous, many deleterious, and many more neutral mutations occurs, that natural selection does not favor the advantageous ones enough to improve fitness. Using fixation probability formulas shows otherwise. There can be many more deleterious than advantageous mutations, and still have many more fixations be of the advantageous ones than of the deleterious ones.

      And in the middle of this muddle, they also say that natural selection is tautological and meaningless (but only after having granted it the power to preserve "function").

      Delete
    2. Naturally, none of this matters.
      I just noticed an article on UD about the co-opting of viral or transposon sequences for function relevant to the host. I haven’t read the paper under consideration but one of the first comments:

      “Long live transposons! They are the perfect algorithmic tool with basic random activity that a designer can use to intelligently remodel the genome”.

      Maybe this is meant to counteract the genomic degradation stemming from our original sin... or something. God works in mysterious ways.

      But surely such co-opting would have never been countenanced by IDers at one time because it smacks a little too much of evolution – until such time they think they can use it as a criticism of naturalistic evolution or junk DNA.
      There is no fact, real or imagined, understood or misunderstood, that cannot be purposed as the actions of their Invisible Designer.

      Delete
    3. "...The net fitness consequences of human mutations remain unclear and will likely continue to be a major challenge, but some general arguments allow an order-of-magnitude assessment of the situation. Using rather different approaches, Yampolsky et al. (55) and Eyre-Walker et al. (56) have derived similar estimates of the distribution of fitness effects of new amino acid altering base-substitution mutations: approximately 11% cause fractional reductions in heterozygote fitness with s < 10−5, 12% with 10−5 < s < 10−4, 50% with 10−4 < s < 10−2, and 27% with s > 10−2, with an overall average selective disadvantage of approximately 0.04. Only approximately 1.5% of the human genome consists of coding DNA and approximately 25% of coding sites are silent, so we expect approximately 0.86 novel amino acid altering mutations per newborn. Approximately 5% of such mutations will lead to nonsense mutations, many of which will likely be in the category of s > 10−2, but the remaining 95% will be missense in nature, with deleterious fitness effects averaging approximately 4% or less according to these results. Thus, with a complete relaxation of natural selection, the expected decline in fitness associated with mutations in coding DNA alone appears to be on the order of 1% to 3% per generation...."

      1-3% per generation...?..Hmmm... This could mean that only few thousand years ago human genome could have been almost perfect....

      ....Why didn't we die out thousand times over ever since we diverged from a common ape-like ancestor some 560 million years ago....?

      I'm sure that Joe has a third explanation... a "miracle like power" of evolution... lol

      Evolution and natural selection can perform miracle if they put their "mind" to it.... lol
      ...and Joe will have an undeniable scientific proof for such miracles...lol

      Rate, molecular spectrum, and consequences of human mutation-Michael Lynch

      Delete
    4. Sometime you just can't beat the bible when it comes to an appropriate response to Quest:


      2 Kings 18:27

      27 But Rabshakeh said unto them, Hath my master sent me to thy master, and to thee, to speak these words? hath he not sent me to the men which sit on the wall, that they may eat their own dung, and drink their own piss with you?

      Delete
    5. Quest, You are an extremely rude person, and that is one of the reasons I don't read your posts.You must be a pride of your church. If you had anything valuable to convey you wouldn't have to use force. Your reasoning doesn't work with me.

      Delete
    6. "Thus, with a complete relaxation of natural selection, the expected decline in fitness associated with mutations in coding DNA alone appears to be on the order of 1% to 3% per generation...." (Michael Lynch)

      ....Why didn't we die out thousand times over ever since we diverged from a common ape-like ancestor some 560 million years ago....?

      I'm sure that Joe has a third explanation... a "miracle like power" of evolution... lol

      Evolution and natural selection can perform miracle if they put their "mind" to it.... lol
      ...and Joe will have an undeniable scientific proof for such miracles...lol
      (Quest)

      Now that's funny. We didn't die out, and some of us even developed some reading skills. So we could read Michael Lynch's statement and realize that it holds for the case of "a complete relaxation of natural selection". And that's the answer: natural selection. For Quest's benefit: "complete relaxation" means the absence of natural selection. No miracle, just ordinary natural selection. (There are nice results in theoretical population genetics showing how natural selection will hold these deleterious mutations to a low frequency).

      But some of us never developed enough reading skills. Nor do they answer the questions about common descent proposed to Quest in another thread. From which Quest, like Brave Sir Robin, ran away.

      Delete
    7. Joe,

      There are a lot of math courses on the basics of arithmetics that could possibly help you to calculate the basics of what Lynch has calculated with 1-3% deterioration over a generation... I know that you are an old school moron who has an issue with the basics... Well... try some of the online courses and then if that doesn't help, you might wanna ask some of the morons here... I'm sure that Dino-genes can help you to calculate this very complex arithmetic.... If not, I could be of some help.... though I'm not a mathematician...

      Delete
    8. quest, humans didn't diverge from a common ape-like ancestor some 560 million years ago. Your "arithmetics", among other things, need some work.

      Delete
    9. Quest still doesn't get it what Lynch means by "complete relaxation of natural selection", and why with natural selection possible the rate of deterioration of the genome would be much lower, or nonexistent.

      But that's OK, he made bold and sweeping statements about lack of common ancestry (in a previous thread) and when asked what kind of evidence of common ancestry he would accept, Brave Sir Robin ran away.

      Delete
    10. At least Quest isn't obtuse about it. I can think of a few creationists who hide the bogus argument in long pieces of test. I.e the whole
      1. Most substitutions are nearly neutral
      2. Most novel mutations are nearly neutral.
      3. We can approximate fixation of nearly neutral alleles as neutral.
      4. Therefore the probability of fixation does not depend on s and selection doesn't do anything at all.
      5. Therefore the genome is going downhill.
      thing that creationist like to do and preferably hide well enough so the various fallacies in that argument don't become too obvious to laypeople is shown here in a form that is quite open.

      In the same way, kudos for not quotemining. It would be so easy to just remove the part of the sentence that makes Lynch contradict what creationists would like to hear and there is a long history of doing just that in the creationist literature.

      I do have some qualms with the Lynch paper, which for that estimate assumes that selection coefficients translate into effects on absolute fitness. There's also not a lot of attention paid to changes in population size. Sure, medical intervention likely reduces |s| for a lot of mutations, but at the same time it's been one of the factors leading to the growth in human population. And of course better medical care, less variation in crop yield and the like by themselves have pretty substantial positive effects on the absolute fitness of humans.

      Delete
    11. Newby,

      What do you want from me...? You wanna know why I lose my patience with some on this blog... or evolutionists in general...?
      You don't want me to use profanities...?
      What's your point...? Spell it out....

      Delete
    12. Joe,

      I totally forgot about the evidence for the common ape-like ancestors that humans and chimps diverged from... Please remind me where the thread was... if you don't mind..?

      I don't remember how far we got, so I'm going to start from the beginning:
      You and many like you claim that humans and chimps had a common ancestor millions of years ago, and that is why our genomes are similar... Right?

      According to you and Larry, only 2% or so of our genome is functional and the rest is just garbage acumulated over millions of years of trail and error of evolution-mutations... Right?

      It follows that out of 2% of our functional genome about 98% of it is similar to chimps... Right? Correct me if I'm wrong...

      Now:

      1. The ape like ancestor for chimps and us is extinct.... Too bad.. Do you have any proof of his existence; his DNA some remain where the DNA could have been preserved?

      2. What makes you think and what's the best evidence you have to prove that we had a common ancestor...?

      3. If more, and more junk DNA will turn out to be functional, will you have a change of mind...?

      4. If most of human genome will turn out to be functional, will that also have any correlation to human chimp ancestry issue...?

      It should be enough for now.... I don't what to raise 100 issue at once....

      Delete
    13. Joe,

      "Long-Term Consequences of Germline Mutations.
      Dating back to Muller (49), considerable thought has been given to the potential for a cumulative buildup of the deleterious-mutation load in the human population (2, 3, 50, 51). The motivation for this concern is the enormous change in the selective environment that human behavior has induced during approximately the past 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 carrying mutations with major morphological, metabolic, and behavioral defects. The statistics are impressive. For example, fetal mortality has declined by approximately 99% in England since the 1500s (52), and just since 1975, the mortality rate per diagnosed cancer has declined by approximately 20% in the United States population (53). Because most complex traits in humans have very high heritabilities (54), the concern then is that unique aspects of human culture, religion, and other social interactions with well intentioned short-term benefits will eventually lead to the long-term genetic deterioration of the human gene pool. Of course, a substantial fraction of the human population still has never visited a doctor of any sort, never eaten processed food, and never used an automobile, computer, or cell phone, so natural selection on unconditionally deleterious mutations certainly has not been completely relaxed in humans. But it is hard to escape the conclusion that we are progressively moving in this direction."

      "Of course, a substantial fraction of the human population still has never visited a doctor of any sort, never eaten processed food, and never used an automobile, computer, or cell phone, so natural selection on unconditionally deleterious mutations certainly has not been completely relaxed in humans. But it is hard to escape the conclusion that we are progressively moving in this direction.

      Delete
    14. Joe,

      Tell us what Lynch means by.."..complete relaxation of natural selection.." and in what context he said it... ;)

      Delete
    15. Quest, your ignorance amazes me. The idea that our common ancestor with the chimp is extinct is simply the wrong way to look at it. By definition, something that is extinct has no descendants. But there are no shortage of humans and chimps, so there has been no extinction here, just change.

      The Dodo is extinct. The great Auk is extinct. The dinosaur is extinct (except for the mall offshoot that led to birds).

      For any organism alive today, there has been no extinction in their lines.

      If you are going to try to argue a subject, at least obtain theist basic understanding if it.

      Delete
    16. It's really a shame "Louise G" and "Pauline" are no longer at Sandwalk. If they teamed up with Quest, between the three of them they might manage to have two functioning neurons to rub together.

      Delete
    17. Quest, aside from everything else (and I do mean everything), your numbers are wrong. It isn't 2% of the genome that Larry thinks is functional, it's around 10%. The functional 2 or 10% isn't what's 98% similar, it's the average over the whole genome; the functional 2-10% is more like 99.5% similar.

      Your more important error is in misinterpreting Lynch, but I'll let Joe explain that if he ever cares to. But there's no real point, as you never understand anything and have no interest in understanding anyway.

      Delete
    18. Quest, In this case. "complete relaxation if natural selection" means that the mutants occur but they do not have their frequencies reduced by natural selection. So each generation more deletrious mutants pile up.

      Without this imagined "relaxation", natural selection would bring the population into an equilibrium state where as new mutants occur, old ones would be tossed out by natural selection against them. In that equilibrium the fitness is not endlessly declining.

      Delete
    19. Quest, I'm so glad you are restraining yourself from asking 100 questions. Because we've been trying, hard, to get you to answer one question.

      It will be found here in the thread "Branko Kozulic responds". I can keep reminding you that you have not answered that question. Sorry you keep forgetting that you were asked it.

      Delete
    20. I asked Pest to tell us how he knows Witton is in prison for tax evasion. I asked that many times. Pest never answers any questions relevant to the topics he himself raises. Does he think we're so dumb we'll forget how weaselly he has been, every hour of every day?

      Delete
    21. Johnny Harsh,

      "Quest, aside from everything else (and I do mean everything), your numbers are wrong. It isn't 2% of the genome that Larry thinks is functional, it's around 10%. The functional 2 or 10% isn't what's 98% similar, it's the average over the whole genome; the functional 2-10% is more like 99.5% similar. Your more important error is in misinterpreting Lynch, but I'll let Joe explain that if he ever cares to. But there's no real point, as you never understand anything and have no interest in understanding anyway."

      Well boys.... You have a marvelous imagination just like Joe thinks of natural selection as his spandex underwear... Well boys.. the only reason why some of you still talk to me is because you have no evidence for your claims... Not only that , you have no evidence for common ancestry... Like Joe just failed to prove it.... So.. I've decided not to mention the "shark killer" because I don't want to deal with suicidal people like Dino-genes, and the rest of the morons who seem to get it but not quite....

      Delete
  16. Someone once compared human genome to a car and "Junk DNA" to the various parts of the car that seem to have no function. Just because they are not being used, like a spare-tire, it doesn't mean they have no function. I have not used my spare-tire ever since I bought my car over 8 years ago. Does it mean it has no function? Same applies to many other parts of the car that may never be used, like airbags, bumpers and such. They may not have a function to someone who is learning about the car, but they definitely had a function to the designer of the car.
    Just because scientists don't know YET what the function of "Junk DNA" is, it doesn't mean it has not function.

    ReplyDelete
    Replies
    1. 1. A genome is not a car.

      2. Yeah, but that is not how scientists came to the conclusion of junk, it's not "we don't know - therefore junk".

      3. It's "we have actually tested most of it and it turns out, yeah - it was junk".

      Vast amounts of our DNA is broken pseudogenes. Tens of thousands of them. Many of these are the same gene (a version of reverse-transcriptase from viruses), copied over and over again thousands of times. DO you get this? The same gene that viruses use to copy their RNA based genome into our DNA based genome(therefore the name, it does reverse transcription). It's a left-over from ancient viral infections. A retrovirus now. But the gene is broken, key parts a missing, what is left has mutated beyond repair. This gene exists in our genome in thousands of copies, broken copies of the same stupid ancient viral gene. It's junk, it shows all the hallmarks of what junk would look like, it simply doesn't work. This is not "oh we don't know lets just call it junk". It's really just junk. It no longer codes for a protein, the start codon is destroyed, or it's missing multiple key exons and so on and so forth. We're not talking spare tires here, we're talking having your car spend too much time in an industrial hydraulic press, turning it into a useless block of crushed metal and plastic.

      What's worse, this is just one kind of junk. There are many different kinds of broken pieces of DNA that no longer function. Broken regulatory regions, broken protein coding genes, broken duplicates, dead transposons with nonsense mutations in them. Pseudogenes with missing exons, premature stop codons bla bla bla.

      It gets tiresome for you IDiots to come here and spew the same ignorant argument over and over again, accusing scientists of engaging in this kind of fallacious "we don't know - therefore junk" reasoning. They actually bothered to find out you know, you should acquaint yourself with some of the history behind the concept.

      Delete
    2. Let's suppose that not only had you never used your spare tire, but nobody had. And in fact on close inspection it turned out that everyone's spare tire was only a papier mache model of a tire. Now would you admit that it was junk?

      We don't think it's junk because we don't know its function. We think it's junk because it accumulates mutations at a rate that would disable any functions it had before long.

      Delete
    3. Johnny Harsh,

      It's a double edge sword....

      If human genome accumulates mutations at a rate that would disable any function, that can very well mean that humans are not evolving, because their genomes are deteriorating...

      You logic can also very well support the view of some religions, which claim that humans were created perfect (with flawless genomes) and now are deteriorating due to imperfection and that is why they accumulate mutations...

      Delete
    4. If human genome accumulates mutations at a rate that would disable any function, that can very well mean that humans are not evolving, because their genomes are deteriorating...

      No it doesn't. You still don't understand the difference between the parts which are really junk (and therefore have no effect when it mutates), and the parts that aren't junk but have important functions (and is therefore less tolerable to mutation).

      You logic can also very well support the view of some religions, which claim that humans were created perfect (with flawless genomes) and now are deteriorating due to imperfection and that is why they accumulate mutations...

      No it can't, because purifying selection prevents the accumulation of too many mutations in regions that are functional, because individuals with too many deleterious mutations simply die or reproduce less. That's selection in operation.
      That's why the junk is mutating a lot over generations and why the rest isn't.

      As usual creationists have got it all wrong.

      Delete
    5. Re the spare tire analogy. although a stretch, this analogy is not completely wrong (just almost completely). There is a cost to having and keeping a spare tire in the trunk. Not only is there the cost of the tire itself, but the cost of fuel required to move it around.

      Does it have a function? Of course. But can I envision a time when the cost of having one far outweighs the risk of not having one? Again, the answer is yes. n fat, I am old enough to remember a time when the spare tire was a full size spare tire. As the quality of tires improved (steel belts, no tubes, better rubber), the quality of roads improved, the frequency of flats dramatically decreased. The car companies responded by replacing the full size spare with the mini spare. Cost to produce and move around was reduced without increasing risk. Selection at its' finest.

      Delete
    6. Quest, I can't speak for Rum, but if your comments were directed at me they wouldn't offend me at all. The only people who can offend me are those who's opinions I respect.

      Delete
    7. @quest "You logic can also very well support the view of some religions, which claim that humans were created perfect (with flawless genomes) and now are deteriorating due to imperfection and that is why they accumulate mutations...". Your hypotheses would require us to discard the foundations of biology, archeology, paleontology, geology and cosmology. You would need to drag the whole of science back to the 17th century. I doubt if a few dentists, engineers, vets and preachers from the bible belt will manage that.

      Delete
    8. I always like to use language analogies. We know what functional sources some of the "junk" came from (i.e., we know it once said "tire" and now says "tgre"). And we can see it, as Mikkel says, repeated over and over again ("tgretgretgretgretgretgretgretgre"). So we know we once had "tire" - perfectly understandable and functional as a word in the English language - and there is now only "tgretgretgretgretgretgretgretgre," repetitive non-functional nonsense.

      Scientists really do know a great deal about how genes and the relevant biochemistry work, so when a working structure loses an essential piece it's just as plain as a screwdriver with its handle broken off.

      Delete
    9. Larry has removed most of my comments... Why...? So.. if something doesn't fit... ask Larry....

      Delete
    10. Quest, if Zlarry has been removing your comments (which I doubt) it is probably to prevent you from making a bigger fool of yourself than you already have.

      Delete
  17. Newbie's comment is typical of pelople maybe well-meaning but sorely lacking in knowledge and understanding of biology in general and evolutionary biology in particular.

    I don't want to demean Newbie in any way, he may be the sweetest and most honest guy in the world, but he need more knowledge about this stuff. I have spent a lifetime of keen interest in evolution but I am not a scientist. It all started with a curiosity about or own origins: where did man come from? So Newbie, I can only recommend you spend thousands of hours reading scientific literature aimed at the general public with a sincere desire to learn and understand what science has to offer. Scientists are not idiots, they are people like you and me, I presume, but I wouldn't be surprised if they generally may be smarter than you and me.

    ReplyDelete
    Replies
    1. Ralf, Thank you for your kind words. I'm learning. I'm not a scientist and I'm not going to pretend to be one on this blog. I don't think it is possible. I'm a medical doctor who, unfortunately turned out to be a layman in the eyes of his kids. What can I do? Go back to school at 45?

      Delete
    2. The Talk Origins Archive is a good starting place for the creation / evolution issues.

      Delete
    3. Yes, start with Theobald's excellent "29+ Evidences for Macroevolution" at TO.

      Delete
    4. Theobald and Talk Origins is hocus pocus nonsense, a site that has a page on how to debate with creationists can hardly be called scientific.....

      Evolution, materialist style is just another religion!

      Delete
    5. Thank your for stating your unsupported opinions on matters which you've repeatedly demonstrated you have zero understanding of.

      Delete
  18. sez quest: Joe,

    I totally forgot about the evidence for the common ape-like ancestors that humans and chimps diverged from... Please remind me where the thread was... if you don't mind..?

    What do you think such evidence would be, Quest? What sort of data do you think would support the proposition that both humans and chimps are descended from an ancestor that the two groups (humans and chimps) share in common? Some people think that there are some detailed similarities between the genetics of the two groups which count as evidence that humans and chimps share a common ancestor; do you agree that detailed similarities between the genetics of humans and chimps would constitute evidence to support the proposition that humans and chimps share a common ancestor? If you don't agree with that, what sort of data would, in your view, constitute evidence to support the proposition that humans and chimps share a common ancestor?

    ReplyDelete
    Replies
    1. Cubist, unfortunately the only evidence that Quest (a misnomer if I ever saw one) would accept is evidence that was contained in a book starting with "in the beginning..."

      Delete
    2. sez acartia tonsa: Cubist, unfortunately the only evidence that Quest (a misnomer if I ever saw one) would accept is evidence that was contained in a book starting with "in the beginning..."
      I suspect you're right. But as long as Quest insists on reviving his hoary old where's-the-evidence schtick, it will be useful to continue reminding him that he hasn't displayed any indication of what he thinks 'evidence' should be. Which, in turn, will go a long way towards demonstrating to readers whether Quest's objections are based on comprehension of the relevant issues and data, or, instead, whether Quest is just mindlessly shouting "Nuh-uh!" like a tape recorder.

      Delete
    3. Cubist, I am new to the Sandwalk but it didn't take me more than two days to figure out that Quest was a knuckledragging moron.

      Now, if Quest could present a cogent argument for anything, I would be willing to change my opinion.

      Delete
  19. Newbie, no, you don't have to go back to school. But at 45 - I'd just barely begun to really trying to get answers tosome of the questions about evolution that I had. At 84, I still remember clearly how I wondered about how for instance the giraffe got it's long neck. By and by, I realized the power of the mechanism of natural selection, and what I only "recently" have realized finds it's expression in "differential reproductive success within populations". That, it seemes to me, must be a fact of life no matter what idological bias one is bearing.

    A mechanism like that explains why and how life has been able not only to survive through the wildly shifting conditions on our planet over millions of years, but also to adapt and thrive in the most improbable environments.

    I find the evidence overwhelming. The alternatives have a lot to explain – which they understandably never do.

    No, I don't think it would demand more of you than just taking an interest in getting some of the questions sorted out like I have done. Buy some entertaining, good reads like Carroll's "Endless Forms Most Beautiful", Neil Shubin’s "Your Inner Fish", Richard Fortey's "Life, An Unauthorized Biography". “The Riddled Chain” by Jeffrey K. McKee deserves mention as well. I prefer books where the author is present instead of the dry, object oriented kind that might as well be written by a robot, like books written for school use.

    What got me started on this interest of mine was at 13 reading about fossils, particularly human ones, I have found “The First Chimpanzee” by John Gribbin and Jeremy Cherfas especially interesting. I think you might enjoy reading it. It covers many subject details one doesn’t often find in books on human origins research.

    Right now I am re-reading “Supercontinent” by Ted Nield. He offers a quote from Thomas Henry Huxley: “

    Sit down before fact as a little child, be prepared to give up every conceived notion … or you will learn nothing.”

    That’s what I’ve done all my life. From the very beginning my approach was to go where the evidence would lead withot any desire for any particular outcome: Were the origins of species a result of natural forces at work, or did religious scriptures have a more credible explanation?


    ReplyDelete
  20. Home Work For All The Wise,

    I have been thinking about the origins of life and what I would do, if I were NOT TO RECREATE LIFE at which science has failed miserably... but about creating a new form of life.... We have some very smart guys who believe that life, as we know it, has originated by natural processes, so creating another form of life by intelligent products on natural processes should be a piece of cake... For not particular reason this has not been accomplished by any; and I repeat. Any human designer... What is wrong...? What is wrong with intelligence that can't overcome mindless nature...?

    ReplyDelete
    Replies
    1. Quest, Quest, Quest. You are criticizing us for not being fast enough for you? Nature had a couple billion years. It seems oy fair that you would give us a small fraction of that. A million or two years would be a relative blink of an eye. I know it's not the six days that God took but, after all, he was God.

      But if the news tomorrow was that a scientist created life from scratch, your response would be that this was proof of ID. After all, it took human intelligence to do it.

      Delete
    2. Pest writes: "We have some very smart guys who believe that life, as we know it, has originated by natural processes, so creating another form of life by intelligent products on natural processes should be a piece of cake... For not particular reason this has not been accomplished by any; and I repeat. Any human designer"

      Creationist logic: we have never observed a living cell being designed by an intelligence, life cannot be designed by an intelligence, therefore life was designed by an intelligence.

      He'll write that shit 1,000 times but never acknowledge how moronic I the logic is.

      Delete