Sunday, January 18, 2015

Francis Collins rejects junk DNA

Francis Collins is the Director of the National Institutes of Health (NIH) in the USA. He spoke recently at the 33rd Annual J.P. Morgan Healthcare Conference in San Francisco (Jan. 12-15, 2015). His talk was late in the afternoon on Tuesday, January 13, 2015. You can listen to the podcast on the conference website [J.P. Morgan Healthcare Conference].

The important bit is at the 30 minute mark where he comments on a question about junk DNA. This is what Francis Collins said last week ...
I would say, in terms of junk DNA, we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu's, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that's where the epigenome gets involved, and is teaching us a lot.
What seems like "hubris" to Francis Collins looks a lot like scientific evidence to me. We know enough to say, with a high degree of confidence, that most (~90%) of our genome is junk. And we know a great deal about the data that Collins is probably referring to (ENCODE)—enough to conclude that it is NOT saying what he thinks it says.

It would be bad enough if this were just another confused scientist who doesn't understand the data [see Five Things You Should Know if You Want to Participate in the Junk DNA Debate] but he's not just any scientist. He's a powerful man who talks to politicians all the time and deals with the leaders of large corporations (e.g. the J.P. Morgan Conference). If Francis Collins doesn't understand the fundamentals of genome science then he could mislead a lot of people.

Collins has many colleagues surrounding him at NIH and other agencies in Washington. These scientists also make important decisions about American science. I'm assuming that he reflects their opinion as well. If not, then why aren't they educating Francis Collins?


Hat Tip: Ryan Gregory

225 comments :

  1. I was not in favor of Obama's decision to appoint Francis Collins back in 2009. I didn't oppose Collins because he was an evangelical Christian but because he is an outspoken defender of the idea that science and religion are complementary [NIH and Francis Collins]. He wrote a book called "The Language of God" where he promotes the idea that science provides evidence that god(s) exist. Some of that "evidence" is humans, who are special creations according to Francis Collins.

    I was worried that his religious views could affect his interpretation of the natural world. Now, I'm not sure if that's the case here, but I do know that most evangelical Christians have a hard time believing that their gods would have made humans with a genome full of junk. Many of them think that it would be extremely arrogant (i.e. hubris) of us to claim that the gods could have been so sloppy.

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    1. The one thing the postmodernists got right is that science does not exist in isolation from the rest of society and it's not done following a pure and abstract method. It exists in the context of the overall worldviews of the people doing it and is influenced by those.

      Of course, from that it does not mean that epistemological relativism follows, or that there are no such thing as scientific facts and knowledge and epistemological standards we should strive to always meet.

      What does follow though is that it is far from certain that everyone who holds certain religious views will be able to successfully compartmentalize those from his interpretation of scientific data (of course, this is the general statistical trend and does not say anything definitively about each individual in particular). Even less so in an era when philosophy is no longer part of the standard curriculum a scientists goes through during his training, which means that people often aren't even aware of these biases.

      Now, of course, someone will say "But the same applies to your atheism". And I will readily agree, but that's mostly irrelevant because provisional atheism is the most scientifically consistent position on the issue of whether there is a god or not thus if some bias is unavoidable it better be that than something else.

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    2. Larry, I don't suspect his reasons are religious. Collins doesn't have a history of trying to twist the science to fit his preferred beliefs.

      He also headed up an organisation (biologos.org) whose goal it was to convince Christians that evolution is true. One of the authors there (Dennis Venema) is a proponent of junk DNA and has written about it numerous times.

      http://biologos.org/blog/encode-and-junk-dna-part-1

      http://biologos.org/blog/encode-and-junk-dna-part-2

      http://biologos.org/blog/series/understanding-evolution-is-there-junk-in-your-genome

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    3. Collins doesn't have a history of trying to twist the science to fit his preferred beliefs.

      Yes he does. One of his favorite arguments is the existence of a universal Moral Law that points to the presence of gods(s). That's a scientific argument even though it's based on a false understanding of the evidence (a universal Moral Law).

      Another favorite of his is the fine-tuning argument where he argues on scientific grounds that the universe is so fine-tuned for life that you must conclude that there's a designer who planned it that way.

      He also claims that there's scientific evidence showing that humans are special in a way that can't be explained by natural evolution. He says that his god chose evolution as a way of creating special creatures who would worship the god. That's another way of twisting the science to fit his belief in god(s). He refers to his belief as "theistic evolution" and states that, "This view is entirely compatible with everything that science teaches us about the natural world" (Language of God p. 201).

      Many would disagree that this is what science shows.

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    4. One of his favourite arguments is the existence of a universal Moral Law that points to the presence of gods(s). That's a scientific argument even though it's based on a false understanding of the evidence (a universal Moral Law).

      Larry, surely you can see the difference between:

      - An apologetic argument based on a philosophical point of view that is still debated (whether there are such things as objective moral values)

      - Intentionally disregarding the overwhelming evidence in favour of junk DNA while cherry picking the papers which favour a genome which is largely functional.

      Keep in mind that his organisation (biologos) go out of their way to critique the intelligent design movement. It hardly seems feasible that he would be opposed to intelligent design (when it comes to biology) but in favour of this particular design argument.

      I realise that the fine-tuning argument is a design argument, but it isn't a biological design argument (it doesn't require us to believe that God had to meddle with genes in order to bring us to this point)

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    5. I Bought Francis Collins's Book The Language Of God When I Was In Jail In 2006, But I Never Read It (I Had More Interesting Material To Read, Playboy). I Think I'm Going To Try To Read It This Year!

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  2. Hasn't Collins admitted here (with his statement about Alus, etc.) that around 50% of the human genome is junk? So it isn't that he rejects junk DNA entirely. That's something.

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    1. I don't think that if Collins confessed that he thought that the earth was 6,000 years old (which would not surprise me) rather than 4.5 billion years old that we would be saying that "that's something".

      Or if he claimed that while humans evolved from an ape like ancestor his invisible friend infused a mating pair of them with an immaterial god shaped essence (which he does say in the most turgid prose imaginable) that we would be saying that "that's something".

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    2. If Francis Collins really believes that 50% of the human genome is junk because of Alu's then why does he say "we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional."?

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    3. Collins appears to be self-contradictory here. You would have to ask him, but I merely note that part of what he says is an explicit statement that much of the genome is junk, even if he doesn't like the word.

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    4. Steve Oberski:

      You would if you had originally claimed he thought the world was created last Tuesday or Eve was created out of Adam's rib. Progress is relative.

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    5. Laurence A. Moran Sunday, January 18, 2015 10:50:00 AM:

      If Francis Collins really believes that 50% of the human genome is junk because of Alu's then why does he say “we don't use that term any more”

      Possibly because he’s intimately familiar with the prevalent theories in the field of genome biology, such as nucleokeletal and nucleotypic theories, which “describe genome size variation as the outcome of selection via the intermediate of cell size” (1), and because he agrees with Ford Doolitle (2) that by building a larger theoretical framework on genome biology “Much that we now call junk could then become functional” (2).

      (1) Gregory TR. 2004. Insertion-deletion biases and the evolution of genome size. Gene, 324:15-34 ( http://www.ncbi.nlm.nih.gov/pubmed/14693368)

      (2) Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA., 110:5294-300 ( http://www.ncbi.nlm.nih.gov/pubmed/23479647):

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    6. Possibly because he’s intimately familiar with the prevalent theories in the field of genome biology, such as nucleokeletal and nucleotypic theories

      Those are definitely hypotheses that have been proposed but it's not correct to refer to them as "prevalent theories." Most of us don't believe they are correct.

      Besides, Francis Collins tells us why he doesn't use the term "junk" any more. It's because he believes that all that extra DNA is mostly for regulation. I doubt very much that he's familiar with bulk DNA hypotheses since they've been around for 40 years and he only recently changed his mind.

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    7. Laurence A. Moran, Monday, January 19, 2015 10:50:00 AM:

      ”Those are definitely hypotheses that have been proposed but it's not correct to refer to them as "prevalent theories." Most of us don't believe they are correct.”

      I don’t know who “Most of us” are. I know that I, indeed, argued that the nucleokeletal and nucleotypic theories are questionable (1). However, I don’t remember to have seen an explanation from you on the reasons you are questioning these hypotheses.

      My reference to the nucleokeletal and nucleotypic hypotheses as “prevalent” is based on the vast literature on these hypotheses written over the last few decades, and on the recent synthesis of the knowledge on genome biology and biological function by Ford Doolitle (2), who built his theoretical framework based on these hypotheses, particularly on the “nucleotypic function” (2).

      Why is Doolitle’s embracement of the “nucleotypic function” highly relevant? Because for decades he has promoted the notion of ‘parasitic’ or ‘selfish DNA’ (3), only to change his perspective under the presumed influence of Ryan Gregory, who he regards as “the principal C-value theorist” (2) and who has sharply dismissed Doolittle’s old view:

      “Although some researchers continue to characterize much variation in genome size as a mere by-product of an intragenomic selfish DNA "free-for-all" there is increasing evidence for the primacy of selection in molding genome sizes via impacts on cell size and division rates” (4)

      References

      1. Bandea CI. 2013. On the concept of biological function, junk DNA and the gospels of ENCODE and Graur et al. bioRxiv doi: 10.1101/000588; ( http://biorxiv.org/content/early/2013/11/18/000588)

      2. Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA., 110:5294-300. Doolittle WF, 2013; ( http://www.ncbi.nlm.nih.gov/pubmed/23479647)

      3. Doolittle WF, Sapienza C. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature. 284(5757):601-3. Doolittle WF, 1980; ( http://www.ncbi.nlm.nih.gov/pubmed/6245369)

      4. Gregory TR, Hebert PD. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res; 9(4):317-24). ( http://www.ncbi.nlm.nih.gov/pubmed/10207154)

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    8. Why is Doolitle’s embracement of the “nucleotypic function” highly relevant?

      He did not "embrace" the idea that excess DNA could have a nucleoskeletal or nucleotypic role. He simply pointed out that these are possible roles that cannot be dismissed simply on the grounds of lack of sequence conservation. I will do that too if I ever publish my review.

      Doolittle points out that selection for bulk DNA operates at a different level and this should be taken into account when talking about "function."

      He says,
      ... some might suggest, as I will below, that true junk might better be defined as DNA not currently held to account for selection for any sort of role operating at any level of the biological hierarchy. However, junk advocates have to date generally considered that even DNA fulfilling bulk structural roles remains, in terms of encoded information, just junk. Cell biology may require a certain C-value, but most of the stretches of noncoding DNA that go to satisfying that requirement are junk (or worse, selfish),

      I agree with Ford. We need to consider bulk DNA hypotheses even if it's only to dismiss them for lack of supporting evidence.

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    9. I contacted Professor Doolittle on this question a while back in response to a talk he gave at UNBSJ. Here are the relevant bits which I hope clarify matters:

      Doolittle I attach my PNAS article on this, which is pretty much what the UNBSJ talk covered. I am perfectly willing to re-define "junk'. The problem with ENCODE is that they used one operational definition of "function" to refute a claim (that most DNA is junk) which is grounded in a quite different (etiological) definition. One can define "function" however one wants, but this sort of conflation (semi-deliberate on their part)is disingenuous.

      I then asked Professor Doolittle if my own interpretation was guilty of being similarly disingenuous.

      Consider how we are discussing the defined and decidely non-random orientation of a chromosome during interphase. That is mind-boggling. And exactly how does the X chromosome achieve this remarkable “architecture”? I am suggesting it must have something to do with all that bric-a-brac-DNA. Clearly this architecture is there for a reason and must be important; something to do with the function of DNA - i.e. something to do with gene expression. If correct, could we not predict that Birds and Bladderworts have floppier DNA architecture and avail themselves of many, but not all gene-regulatory mechanisms found in Chimps and Humans?

      Professor Doolittle’s patient and indulgent response:

      Doolittle Well no, not disingenuous, but perhaps not new. That "excess" DNA(that 40x as much that lungfish have compared to us, for instance)might play a structural role or determine other cellular parameters under selection has long been accepted, even by us "junk" supporters.

      To my mind, it's like the "clean fill" you see signs for along the
      highway. There may be a need for that much DNA but it doesn't matter what it is, as long as it doesn't contain deleterious sequences. You are also suggesting, I think, that larger-genomed organisms might be regulating the same amount of function as smaller-genomed organisms, just in more (and possibly unnecessarily?) elaborate ways. I agree, as
      spelled out in the paper.


      I may be missing something here, but to my reading – this puts a whole new spin on the C-value paradox. Doolittle’s interpretation is somewhat nuanced and a more subtle consideration of “bulk DNA” is not necessarily so easily “dismissible”... unless of course I am missing something again.

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    10. To clarify two things:

      The problem with ENCODE is that they used one operational definition of "function" to refute a claim (that most DNA is junk) which is grounded in a quite different (etiological) definition.

      I know nobody cares about that distinction but ENCODE has not tried to refute junk DNA within the scientific literature. There is no mention of the word "junk" in the scientific papers from the consortium, with the exception of the PNAS one where it had to be discussed.

      Well no, not disingenuous, but perhaps not new. That "excess" DNA(that 40x as much that lungfish have compared to us, for instance)might play a structural role or determine other cellular parameters under selection has long been accepted, even by us "junk" supporters.

      I myself actually still have a problem with that. I don't see how it can get selected - the way the genome grows/shrinks is by individual insertions/deletions of DNA, but even if there is selection for increase/decrease in genome size, individually each of those insertions/deletions is quite small in a big genome, this it's contribution to whatever cellular parameter that is being optimized is minuscule (in fact, very close to zero, because the relationship is probably not linear and there is a threshold above which these things can actually have a detectable effect). So how do they get selected for?

      I can see how large genome size can play a causal role, but I have hard time seeing it as a selected effect.

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    11. Hi Georgi
      Re I can see how large genome size can play a causal role, but I have hard time seeing it as a selected effect.

      A few decades ago, I attended some seminars on the non-random orientation of chromosomes in vivo – a chromosomal architecture as it were, that was cell-type specific even. To my mind – this represented yet another level of gene regulation I had hitherto never considered.

      Imagine my delight to stumble across Peter Fraser’s work 30 years later.

      http://www.insight.mrc.ac.uk/2013/09/26/what-does-a-chromosome-really-look-like/

      My exchange with Professor Doolittle was somewhat lengthy and I neglected to include my reference to Peter Fraser’s work.

      Here is the relevant bit:

      PF: “…we found that active regions — containing genes that are used frequently — tend to be located on the outside of chromosomes for easy access by the cell machinery responsible for gene expression.

      Using these 3D models, we have begun to unravel the basic principles of chromosome structure and its role in how our genome functions.


      That is why I naïvely suggested a “functional” role for that excess DNA in some organisms that IMHO as being too facilely dismissed as "junk".

      Dolittle You are also suggesting, I think, that larger-genomed organisms might be regulating the same amount of function as smaller-genomed organisms, just in more (and possibly unnecessarily?) elaborate ways.

      That is exactly what I was suggesting! I really must be missing something here and I am beginning to wonder if we are quibbling over semantics, Doolittle’s earlier accusation of “disingenuous” aside.

      Larry suggested on an earlier occasion that:

      If having junk DNA were a clear advantage for future evolution then the genomes of all extant lineages should have lots of junk DNA and should make lots of lncRNAs.

      I most vehemently must disagree. (cf Doolittle's remarks immediately above) (cf as well the following link)

      http://sandwalk.blogspot.ca/2014/09/are-lncrnas-really-mrnas-in-waiting.html?showComment=1411503256562#c8272973904331213297

      If Peter Fraser’s work is to be at all credited, then the repercussions for the c-value paradox are inescapable: that the bulk of DNA of larger-genomed organisms may indeed have some version of functionality but not necessarily along the lines perhaps, originally envisaged by ENCODE and/or perhaps maybe not necessarily along the lines that ENCODE’s detractors reckon ENCODE originally intended; but nonetheless are real, causal and selected.

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    12. Laurence A. Moran, Monday, January 19, 2015 4:22:00 PM:

      “I agree with Ford. We need to consider bulk DNA hypotheses even if it's only to dismiss them for lack of supporting evidence.”

      Apparently, Doolittle is of different opinion (many thanks to Tom for keeping Larry’s unsupported interpretation of Doolittle’s views in check):

      "Doolittle: That "excess" DNA (that 40x as much that lungfish have compared to us, for instance) might play a structural role or determine other cellular parameters under selection has long been accepted, even by us "junk" supporters.”

      “…has long been accepted, even by us "junk" supporters.”. Does this resonate with you Larry, or you are a “junk” supporter of a different breed?

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    13. Georgi Marinov, Tuesday, January 20, 2015 11:34:00 AM:
      “I know nobody cares about that distinction but ENCODE has not tried to refute junk DNA within the scientific literature. There is no mention of the word "junk" in the scientific papers from the consortium, with the exception of the PNAS one where it had to be discussed.”

      That is correct. And, as mentioned here and elsewhere (see my comments at: http://www.ncbi.nlm.nih.gov/pubmed/23479647), the ENCODE scientists went out of their way not to bring forward the fundamental knowledge in the field of genome biology (see my comments in this post), as this knowledge was in conflict with some of their study objectives and raises inconvenient questions about the relevance of their study and results.

      In light of these facts, Doolittle (1) had no choice but to build the premise for his criticism of ENCODE using secondary sources offered by various science writers (2-4), which is a strong departure from conventional academic standards and sets up a hasty precedent for the scientific literature.

      (1) Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA., 110:5294-300.
      (2) Kolata G. 2012 (September 5). Bits of mystery DNA, far from ‘junk’, play crucial role. The New York Times, Section A, p. 1.
      (3) Anonymous, 2012. Cracking ENCODE. Lancet, 380:950.
      (4) Pennisi E. 2012. Genomics. ENCODE project writes eulogy for junk DNA. Science, 337:1159–1161.

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    14. @Claudiu Bandea

      I am a jnuk DNA supporter and, like Ford Doolittle, I have long accepted that there MIGHT be functions for that extra DNA that might not be under selection for specific sequences. Ford recognized this back in 1979.

      You seem to be terribly confused about this. I can understand why Tom is confused but you should know better. Ford Doolittle cannot be a junk DNA supporter if he believes that most of the genome has a bulk DNA function. He's merely acknowledging that you can't rely exclusively on lack of sequence conservation as proof that the DNA has no function.

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    15. Laurence A. Moran, Thursday, January 22, 2015 10:14:00 PM:

      “You seem to be terribly confused about this… Ford Doolittle cannot be a junk DNA supporter if he believes that most of the genome has a bulk DNA function"

      Yes he can, and here is what he wrote in his PNAS paper ( http://www.ncbi.nlm.nih.gov/pubmed/23479647):

      “junk advocates have to date generally considered that even DNA fulfilling bulk structural roles remains, in terms of encoded information, just junk”

      Does this resonate with you or you are “terribly confused” about it?

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    16. So here we have:

      1) quote mining
      2) appeal to authority

      Well known logical fallacies.

      You have spent way too much time trying to show that such and such famous scientist supports your views. And very little time defending those views with arguments and data. That's not a good sign

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    17. In my comment above, I made the point that Ford Doolittle build the premise for his highly relevant PNAS paper (1) based on secondary sources offered by various science writers (2-4), rather than on the articles published by the ENCODE scientists.

      Is this an acceptable practice?

      (1) Doolittle WF. 2013. Is junk DNA bunk? A critique of ENCODE. Proc Natl Acad Sci USA., 110:5294-300.
      (2) Kolata G. 2012 (September 5). Bits of mystery DNA, far from ‘junk’, play crucial role. The New York Times, Section A, p. 1.
      (3) Anonymous, 2012. Cracking ENCODE. Lancet, 380:950.
      (4) Pennisi E. 2012. Genomics. ENCODE project writes eulogy for junk DNA. Science, 337:1159–1161.

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    18. Laurence A. Moran, Monday, January 19, 2015 4:22:00 PM:
      “I agree with Ford. We need to consider bulk DNA hypotheses even if it's only to dismiss them for lack of supporting evidence.”

      As discussed above, I don't think Ford (Doolitle) dismisses the nucleotypic theory; on the contrary, he embraces it. However, it’s unlikely that Doolitle will step down from his distinguished academic podium and interact with us here at Sandwalk, so it is unlike that we can reach a consensus on his view.

      On the other hand, Larry is our host here as Sandwalk, and if he cannot clearly and specifically articulate the tenets of nucleotypic theory and the reasons he dismisses them, then, me might well question Sandwalk as a serious forum for addressing scientific issues. This is how the nucleotypic theory was presented (1):

      “Although some researchers continue to characterize much variation in genome size as a mere by-product of an intragenomic selfish DNA "free-for-all" there is increasing evidence for the primacy of selection in molding genome sizes via impacts on cell size and division rates” (1)

      Larry, can you specifically discuss this “increasing evidence” and the reasons you believe it does not support the nucleotypic theory?

      Reference

      1 Gregory TR, Hebert PD. 1999. The modulation of DNA content: proximate causes and ultimate consequences. Genome Res; 9(4):317-24). ( http://www.ncbi.nlm.nih.gov/pubmed/10207154)

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  3. I think it’s non-sense to say that Francis Collins and other leading scientists studying genomes and gene expression are not aware of the basic knowledge in the field, such as (i) C-value paradox, (ii) mutational load, (iii) limited sequence conservation among related species, (iv) evolutionary origin of most genomic sequences from transposable elements, (v) essential requirement for some ‘structural’ or ‘spacing’ DNA sequences, and that this knowledge clearly precludes informational functions for most human genomic sequences.

    On the contrary, I think they understand this fundamental knowledge very well, and that’s why the ENCODE scientists, for example, went out of their way not to bring this fundamental knowledge forward in their publications (see my comments at: http://www.ncbi.nlm.nih.gov/pubmed/23479647).

    My theory is that these scientists are ‘victims’ of the current science enterprise, which in order stay at the forefront of public (and political) attention has little choice but to deviate into using deceiving strategies and approaches, such as hyping. Of course there are some reckless scientists who take advantage of this disarray in order to promote their careers, but that’s inevitable, and of course they will do anything to maintain this situation in which they can flourish. But again, ultimately, they are also ‘victims,’ as one day they might be looking into the mirror and be disappointed in what they see.

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    1. Once again you display you lack of understanding of how science is done. The higher you are in the administrative hierarchy, the less time you have about actual science. You get digested and filtered reports of things, and the higher up you are, the more hands those have passed through. The most reliable sources of information are:

      1) Senior people without a lot of such responsibilities who know the deep history of the field and have the proper perspective in which new data is to be interpreted

      2) The people who work directly and closely with the data, because they know all the warts.

      There is some small overlap between these two groups in production and analysis labs but they are mostly complementary to each other.

      The heads of funding agencies, however, are fairly certain not to belong to either, as they are often very far removed from the science.

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    2. @Giorgi,

      You are a young, promising scientist, which is great. Thinking, however, that senior scientists in high administrative positions, such as Francis Collins, are “very far removed from the science” or are not familiar with the fundamental knowledge in a field that they helped establish is foolish, to put it nicely.

      In any case, you might want to consider the advice you just received on the other post (http://sandwalk.blogspot.com/2015/01/functional-rnas.html):

      John Harshman, Saturday, January 17, 2015 8:53:00 PM:

      “Georgi. I'm afraid that this too looks like weaseling to me and, I suspect again, to other readers. I also suspect that everyone would be interested in your answers to the questions, and the fact that people keep asking them should suggest to you that they think you haven't answered them. Now if you don't care that people think you're being a weasel, no problem."

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    3. So you think Francis Collins has been sitting on ENCODE phone calls, thinking about ChIP-seq calling algorithms, RNA-seq transcript assembly. and other problems of the sort? It's possible, but unlikely, I definitely haven't heard him and haven't seen him during meetings.

      And remember that that's just one project within NHGRI (which has several other big projects, some even bigger than ENCODE), which is just one of ~30 institutes within NIH.

      There are only 24 hours in a day...

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    4. It is hard to believe that the scientists working on genome biology are not intimately familiar with the fundamental knowledge in the field. This knowledge is as clear as it can be, and most of it has been around for decades and discussed in all textbooks of biology and genetics:

      (i) C-value paradox or enigma;
      (ii) Mutational load;
      (iii) Evolutionary origin of most genomic sequences from transposable elements;
      (iv) Essential requirement for ‘structural’ or ‘spacing’ DNA sequences in gene expression and genome architecture;
      (v) Limited sequence conservation in most genomic regions between evolutionary related species;

      Again, this is the most elementary knowledge in the field of genome biology, and saying that the scientists working in this and associated fields are clueless about it should be considered highly offensive.

      And, based on this knowledge, it is as clear as it can be that in species with high C-value, such as humans, most genomic sequences (possibly over 99% in humans) CANNOT have informational functions.

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    5. It is hard to believe that the scientists working on genome biology are not intimately familiar with the fundamental knowledge in the field.

      It may be hard to believe but the evidence is clear.

      saying that the scientists working in this and associated fields are clueless about it should be considered highly offensive

      I don't speak for Georgi but when I say that those scientist are clueless I mean it to be offensive.

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    6. I don’t think the scientists working on genome biology are clueless. Any high school student with genuine interest in genome biology is capable to comprehend the elementary knowledge I listed above (isn’t that true Tom?).

      And, I don’t think that the ENCODE scientists are “badly trained technicians” as suggested by Dan Graur ((isn’t that true Georgi?); Graur D et al., 2013. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol., 5:578-90).

      As suggested here and elsewhere (see my notes at: http://www.ncbi.nlm.nih.gov/pubmed/23479647), I think we are dealing here with a different ‘animal’ that has unfortunately taken over many fields in the science enterprise.

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    7. @ Claudiu Bandea

      Any high school student with genuine interest in genome biology is capable to comprehend the elementary knowledge I listed above (isn’t that true Tom?).

      i.e. from above

      This knowledge is as clear as it can be, and most of it has been around for decades and discussed in all textbooks of biology and genetics:

      (i) C-value paradox or enigma;
      (ii) Mutational load;
      (iii) Evolutionary origin of most genomic sequences from transposable elements;
      (iv) Essential requirement for ‘structural’ or ‘spacing’ DNA sequences in gene expression and genome architecture;
      (v) Limited sequence conservation in most genomic regions between evolutionary related species;


      I am flattered you would solicit my opinion

      I wish I could agree with you but I alarmed by the dawning realization that Larry may be all too correct as far as Highschool and Freshman Biology is concerned:

      http://sandwalk.blogspot.ca/2014/02/on-difference-between-neutral-theory.html?showComment=1392748873040#c1376247254883111461

      None of those 5 points you mention above are properly represented in any entry-level text or curriculum I am aware of, with the possible exception of (iii)

      The HHMI Biointeractive resources may manage to address some of what you mention, but that means a very small minority of AP students end up being exposed to some of what you list above.

      As you can tell from my most recent post – I myself am experiencing great difficulty (not to mention embarrassment) in playing catch-up.

      http://sandwalk.blogspot.ca/2015/01/looking-for-spandrels.html?showComment=1421698329330#c455952041151147298

      Part of the problem lies in fundamental misunderstanding when teaching Genetics that P Z Myers identifies as “Beanbag Genetics”

      http://freethoughtblogs.com/pharyngula/2011/12/19/steve-pinkers-hair-and-the-muscles-of-worms/

      Failure to properly understand Genetics renders a proper understanding of Population Genetics much less Evolution impossible. For example, any mention of epistasis and pleiotropy is explicitly banned from the AP curriculum.

      While I am at it... I want to again express my thanks to one and all for their patience and indulgence in my efforts to come up to speed.

      Delete
    8. Thanks for responding Tom, but I was contemplating that idea that “any high school student with genuine interest in genome biology *is capable* (intellectually) to comprehend the elementary knowledge I listed above”, not necessary that they have this knowledge.

      There is no reason for students at that stage of their education to be necessarily familiar with this knowledge, but this knowledge is elementary for anyone working in the field of genome biology. Don’t you think so?

      Delete
    9. George, I Display My Lack Of Understanding Of Genetics On My Blog

      Delete
    10. Hi Claudiu

      re I was contemplating that idea that “any high school student with genuine interest in genome biology *is capable* (intellectually) to comprehend the elementary knowledge I listed above”, not necessary that they have this knowledge.

      I apologize for the misunderstanding. I was reacting to

      This knowledge is as clear as it can be, and most of it has been around for decades and discussed in all textbooks of biology and genetics

      Many of the bullets you listed above are in fact not discussed in many introductory textbooks that I am familiar with.

      re ...this knowledge is elementary for anyone working in the field of genome biology. Don’t you think so?

      Following the discussion on this board - I have to wonder... I would say that your ongoing disagreement with Georgi would belie that contention.

      Meanwhile, my own obvious difficulties to wrap my head around much of what is happening would suggest this is not so "elementary" (I hope!)

      P Z Myers just recently posted astute insights regarding striking psychological antipathy to random stochastic processes as a driving force in Biology.
      http://sandwalk.blogspot.ca/2015/01/evolutionary-biochemistry-and.html?showComment=1420828923894#c1066253717208367771

      For example, Francis Collins would seem (from my cursory reading of excerpts from his book) to be a paradigm of P Z Myers' contention that the human brain is apparently hardwired to seek patterns where patterns do not exist and reject outright the absence of patterns when in fact they do not exist. (I stole that idea from Neil deGrasse Tyson of Cosmos fame)

      I hope I am not reading too much into P Z Myers and putting words into his mouth.

      Delete
    11. Collins says that the DNA is not junk but is involved in "regulation". Probably he isn't going to take the time to join us in a long philosophical and evolutionary discussion that would clarify precisely what he means by this, but we know pretty much the way that word is used by molecular biologists across the planet. If A affects B, then A "regulates" B. If X % of sequences are transcribed into RNAs that bind to other stuff, then the way that Joe Molecular Biologist describes this is to say that there is a network of regulatory interactions involving X % of sequences.

      In other words, this is just the same ENCODE fiasco all over again.

      The problem isn't that the human brain is hardwired to see patterns. Junk DNA is potentially a pattern too. The problem is that the human brain is hard-wired to attribute essentialist meanings to things-- to imagine that things are imbued with a deeper truth or value that comes from their history or origins or significance. See anything recently by Paul Bloom.

      Based on all we know about how evolution works, we are not justified in making this essentialist assumption, the assumption that biological features have essences or functions that signify a deeper truth about what the feature *really is* or *really does*. Yet that is how most of biology is understood by most of us, most of the time (even by myself, in spite of years of trying not to). We understand wings by saying that they are for flight. I'm not confident that "junk DNA" is free from this same essentialist baggage. I think it is another form of essentialist valuation-- saying that the DNA has no value.

      I think we can't expect Collins and other non-experts to get these things right until we have developed a new way of thinking about biology, and we are able to convey that clearly.

      Delete
    12. Arlin,Tuesday, January 20, 2015 9:51:00 AM: “I think we can't expect Collins and other non-experts to get these things right until we have developed a new way of thinking about biology, and we are able to convey that clearly"

      Arlin,

      What do you think “the new way of thinking about biology” should aspire to, and what are the ways to “convey that clearly”?

      When it comes to understanding the genome biology and the so called ‘junk DNA’ (jDNA) in species with high C-value such as humans, I think that the current knowledge on

      (i) C-value paradox or enigma,
      (ii) mutational load,
      (iii) evolutionary origin of most genomic sequences from transposable elements,
      (iv) essential requirement for ‘structural’ or ‘spacing’ DNA sequences in gene expression and genome architecture, and
      (v) limited sequence conservation in most genomic regions between evolutionary related species,

      preclude genuine ‘informational functions’ for most genomic DNA sequences.

      Do you think this is fair and clear description of the fundamental knowledge in the field?

      Delete
    13. The list is incomplete - there is zero population genetics in it. When you add that, you also preclude selected-effect functions.

      Delete
    14. @Georgi,

      Why don’t you present your list of the fundamental knowledge in the field of genome biology and elaborate on the point you are trying to make. Does your putative ‘list’ support ‘informational functions’ for most human genomic DNA sequences, as some of your ENCODE colleagues have tried to promote?

      Delete
    15. As I said, once you take population genetics into account, the viability of those ``functions'' (as selected effects) evaporates.

      All of those proposals are based on the idea that extra DNA serves some function by its mere presence. However, that also means that the selective advantage/disadvantage of insertions/deletions, which are the means through which genomes grow/shrink, is proportional to the size of those insertions/deletions, and its absolute magnitude is unlikely to be greater than the ratio between their size and the size of the genome. Unfortunately for you, that ratio is minuscule for organisms with large genomes, and it is also orders of magnitude smaller than what it would have to be to overcome the drift/selection barrier and become visible to selection.

      In fact it's probably even worse, because the selective advantage/disadvantage is probably not a linear function of insertion size. If I add an 8kb transposon to the genome, most likely the size of the nucleus and other such things don't change at all as it can still comfortably fit within the existing volume. If I add 200 megabases, it's a different story, but genomes do not grow through 200 megabase insertions, they do so through insertions at most the size of the largest transposons, usually significantly less than that.

      P.S. I have explained that to you in at least three other threads, apparently to no avail

      Delete
    16. I this particular blog post, I brought forward the fact that the fundamental knowledge in the field of genome biology (e.g. C-value paradox, mutational load) excludes ‘informational functions’ for most human genomic DNA sequences. Again, this is a fact, and the only relevant question remaining is whether most of the so called jDNA has non-informational functions, or not.

      However, for whatever reason, you want to discuss a subject that we have previously addressed in detail in previous posts; apparently, you forgot the results of those exchanges. Here are some of my statements that questioned your fixation with the idea that in order to be functional the genomic sequences must be a product of natural selection. Have you heard of genetic drift and neutral evolution?

      ”Whether jDNA has been evolutionary maintained simply because of a mutational imbalance, favoring amplification of parasitic DNA versus deletion, or because jDNA is under host positive selection (whatever this selection might be), the protective function of jDNA in humans and other eukaryal organisms against insertional mutagenesis by endogenous and exogenous mobile genetic elements, such as retroviruses, is a bona fide fact.” ( http://biorxiv.org/content/early/2013/11/18/000588)

      Selection is not essential for my theory that jDNA provides a protective function against insertion mutagenesis by endogenous and exogenous mobile genetic elements, such as retroviruses.

      So, if we consider that jDNA is the product of genetic drift and neutral evolution, why can’t it provide a protective biological function against deleterious insertional mutagenesis?

      Delete
  4. I am not a molecular biologist or a geneticist, but from my own field (analytical chemistry), I can confirm that the term used to describe something can be seriously misleading if the wrong word is used. In my field, and in most fields of science, "measurement uncertainty" is a critical aspect of any measurement. And this term works fine in any field where the data is being used by other scientists. But in analytical chemistry, the data is often used by non-scientists (eg, regulators). And, unfortunately, lawyers. When you give a lawyer a result that is being used to levy charges against someone, even the mention of "uncertainty" makes them see $$$.

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  5. I vaguely recall that Collins somewhat recently was influenced by some meeting he was at, and/or article he read, that spread the it's-all-functional line. Maybe it was the ENCODE project announcements themselves. His older statements were pretty reasonable. I think it's perfectly possible that he is very very aware of the huge amount of repetitive DNA in the genome -- seeing as he led the sequencing effort -- but he is not particularly aware of the genetic load argument, the details of the wide distribution of genome sizes, and it's especially probable that he hasn't been made aware of the critiques of ENCODE. He's not currently an active scientist, he's an administrator of a huge institution, I doubt he has time to keep up on the literature in any serious way. He will likely hear about the "big stuff" and not much else.

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  6. Professor Moran is it possible that your atheist view might influence your outlook on the natural world? You seem to be objective and I haven't seen you use your scientific knowledge to recruit atheists. If we are honest though Collins suggests that God and science can go hand in hand, atheists insist science and atheism must go hand in hand. Which is more damaging and demands the evidence for God that atheists long for must be concealed?

    ReplyDelete
    Replies
    1. Excuse my punctuation, I hope you can still make sense of my comment

      Delete
    2. Try removing the vowels next time.

      It can only help.

      Delete
    3. People who believe in supernatural beings (gods) tend to interpret the natural world in light of their beliefs. I don't believe in supernatural beings so I don't accept ANY of the stories that believers think are true about their gods. That's the way my lack of belief influences my outlook on the natural world.

      My lack of belief in astrology and homeopathy also influence my view of the natural world in a simillar way.

      A typical believer rejects all the stories about creator gods except for the ones that refer to their own gods. It's difficult to reconcile such a position with scientific thinking. It's also difficult to reconcile belief in astrology and homeopathy with science. Science and atheism go hand in hand in the same sense as science and lack of belief in astrology go hand in hand.

      Delete
    4. Science and atheism go hand in hand in the same sense as science and lack of belief in astrology go hand in hand.

      LOL

      Interesting - Francis Collins never hit my radar before… some google-whacking was in order.

      He clearly sees himself as a critic of intelligent design and young earth creationism. That's gotta count for something!


      He also clearly sees himself as a “born-again” Christian. Now this represents a remarkable constellation of credentials.

      advocatus diaboli ON

      Francis Collins perhaps poses a greater threat to the Weltbild of QUEST, mreagnor and their ilk than anybody on this forum could ever hope to manage. Collins doesn't number amoung the easy-to-dismiss-and disregard "enemy".

      It lies within the realm of possibility that individuals such as Francis Collins could effect a significant sea change of current North American lumpenproletariat arc-reflex hostility to anything and everything evolutionary to an eventual and general public grudging acceptance of Evolution as both accepted fact and theory.

      advocatus diaboli OFF

      Scroll down to paragraph 2 in chapter 6:

      http://tinyurl.com/oo6q9nm

      Delete
    5. I checked this pages on my cellphone last night and I noticed last night that Quest's response to my post above was indignant outrage and has been since deleted.

      Too bad!

      Quest was rambling on about agreeing with Larry for once and denigrating Collins for "buttering his bread on both sides"...

      Quest's response constituted the best confirmation possible that my devil's advocacy had merit!

      Now if only mreagnor would dogpile on to confirm my thesis!

      ;-)

      Delete
    6. Quest, I am outraged that Professor Moran's too-obvious contempt for the sacred principle of Freedom of Speech has led him to ban you from his blog! I can't tell you how happy I am that you posted on Professor Moran's blog to tell us all that Professor Moran has banned you from his blog. Had you not posted this very important information on Professor Moran's blog, I'm sure that the evidence of Professor Moran's speech-suppressing perfidy would never have come to light. God bless you and God bless your heart, Quest!

      Delete
    7. I begin to believe that it is actually true I could swear I so Quest's comment today. Is it possible Byers is just Quest's sockpuppet?

      Delete
  7. Never mind punctuation, it doesn't make good sense anyway.

    ReplyDelete
  8. It seems to me that the hubris is on you, Dr. Moran, for blithely calling an expert in the field a liar or worse.
    As far as your motive-mongering is concerned:
    Your 'objectivity' is just as skewed as anyone else's. How can YOU claim to be the one who is objective?
    Do you deny that you believe there is no creator?
    How do you think that belief affects your interpretation of data?
    When you are confronted with an expert in a field with an interpretation that you disagree with, your role is to sit down, listen, and learn.
    Just like the rest of us.
    As for your 5 'rules' that I'm supposed to believe before being qualified to speak on the subject:
    Are you aware that most or all of them are based on atheistic assumptions?
    No, of course you don't, because you've imbibed these assumptions as fact, and that's evidence that you are not qualified to comment objectively on the topic.

    ReplyDelete
    Replies
    1. Ed, rather than blithely finger-pointing, perhaps you should explain what issues you have with the 5 'things'? Also, go read some of Austin Hughes' (evangelical Christian) work on neutral theory before you start claiming anything about what is atheistic and what is not.

      Delete
    2. Ed Reynolds asks ...

      Do you deny that you believe there is no creator?

      I have not been convinced by any argument claiming that a supernatural being exists. This includes arguments for ALL of the god(s). I assume that you have also failed to be convinced by almost all of those arguments except for those supporting one particular god?

      How do you think that belief affects your interpretation of data?

      People who believe in creator god(s) tend to interpret data far differently than I do.

      When you are confronted with an expert in a field with an interpretation that you disagree with, your role is to sit down, listen, and learn.

      I think that I am more of an expert on this topic than Francis Collins. I wish he would sit down, listen, and learn from me or from any of several other scientists who know what they are talking about.

      As for your 5 'rules' that I'm supposed to believe before being qualified to speak on the subject: Are you aware that most or all of them are based on atheistic assumptions?

      No, I wasn't aware of that. Thanks for pointing it out. I also don't believe in Santa Claus or fairies. Are the five things also based on assumptions about the nonexistence of Santa Clause and the tooth fairy?

      Delete
    3. "I think that I am more of an expert on this topic than Francis Collins. I wish he would sit down, listen, and learn from me or from any of several other scientists who know what they are talking about."

      Do you think Dr. Collins is ignorant of some important research results that you and your colleagues can help him out with?

      About your 5 points, I'll start with the first one:
      "Genetic Load
      Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk."

      Oh, now I see why you have such a visceral distain for Dr. Noble - he points out that many epigenetic systems are at play to compensate for genetic errors.
      Your assumption that "they must be junk" as the only explanation is a bit simple-minded and outdated, don't you think?
      C'mon, Doc, try to keep up - science marches on.

      Delete
    4. Are you aware that most or all of them are based on atheistic assumptions?

      Just too damned many atheistic assumptions around these days. Why, its gotten to the point that every time an airplane crashes, no one blames an angry god anymore. Instead the crash investigators muddle about with their danged atheistic assumptions.

      Delete
    5. @Ed Reynolds

      I'm not familiar with the work of Dr. Noble. Could you supply references where he/she shows how epigenetic systems can compensate for newly arisen deleterious mutations?

      Delete
    6. Professor Moran,

      I think Ed is referring to Dr. Danis Noble whose video you posted here several weeks ago. I think he is referencing this article:
      Physiology is rocking the foundations of evolutionary biology by Denis Noble

      Delete
    7. @Johnny

      Thanks. I had completely forgotten about that very forgettable video. However, I don't think it explains why epigenetics can prevent deleterious mutations.

      Delete
    8. I don't know if deleterious mutations can be prevented by epigenetics. I'm not a biochemist. It appears to me Ed was making the point that epigenetics can somehow compensate for the inevitable deleterious mutations. I haven't read Dr. Noble's paper, so I don't know whether it explains it how epigenetics is supposed to do that.

      Delete
    9. Thank you, Johnny, that is correct. Now for thing number 2:

      "C-Value Paradox
      A comparison of genomes from closely related species shows that genome size can vary by a factor of ten or more. The only reasonable explanation is that most of the DNA in the larger genomes is junk."

      Pure speculation. You forgot another reasonable explanation:
      You don't know enough about the genome to make such self-important proclamations.
      It's called an 'enigma', yet you treat it as if you fully understand it.

      Delete
    10. Thing number 3:
      "Modern Evolutionary Theory
      Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome."

      A sweeping, self-serving generalization that says nothing about how you claim junk DNA, except that it doesn't fit your model.

      Delete
    11. Thing number 4:
      "Pseudogenes and broken genes are junk
      More than half of our genomes consists of pseudogenes, including broken transposons and bits and pieces of transposons. A few may have secondarily acquired a function but, to a first approximation, broken genes are junk."

      Pure rhetorical question-begging:
      Call certain genes "broken", and POOF! They're junk!

      Delete
    12. Thing number 5:
      "Most of the genome is not conserved
      Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can't rule out some unknown function that doesn't depend on sequence."

      First, your assumption of "conserved" genes is based on your assumption that all life evolved from a single form, which has not been verified.

      Second: at least you admit that you may not know something.
      There may be hope for you yet.

      Delete
    13. Second: at least you admit that you may not know something.
      There may be hope for you yet.


      Anyone got a replacement irony meter?

      Delete
    14. Ed Reynolds@ "Pure rhetorical question-begging:
      Call certain genes "broken", and POOF! They're junk!"


      No. When you find a car with no wheels, an engine block that has cracked in half due to an explosion, an empty gas tank, the steering wheel disconnected and the gearbox rusted away, would you agree the car no longer works?

      Same thing with pseudogenes. They're broken. We know what makes a gene work, which is why we know pseudogenes don't. They're broken.

      I know this is unwelcome news to some one who thinks he was divinely created, but you should get over it and just deal with the facts instead of keeping up this religion-motivated delusion that a gene missing important transcription factor binding sites, is missing several key exons, has multiple premature stop-codons and nonsense frameshifts, is somehow still a functional gene. It isn't, it's broken. Stop trying to rationalize it away, just deal with it as it is. Like an adult. Like you would the broken car.

      Your response will prove whether you are prepared to discuss this subject rationally or not.

      Delete
    15. Not, I think.

      Meyer mentions KNOCKOUT EXPERIMENTS which seem, on the face of it, to powerfully demonstrate irreducible complexity in the case of the flagellum.

      The movie "EXPELLED" is condemned for being actually "against science" because it blows the whistle on corrupt, anti-science practices of the Darwinist establishment.
      This is one of Genie's favorite tricks; to equate the Darwinist establishment with "science".
      Sorry, Genie, but to beg the question just isn't good enough anymore.
      You have to defend the validity of the 'scientific' fairy tales told by the Darwinist establishment to the public. They are under attack.
      By scientists.

      Delete
    16. Humans have mastery over the workings of a car, because we built them ourselves.
      We have no such mastery over the genome.
      The ENCODE project, though far from the final word, has found 80% of the human genome to have known functions.

      Don't get me wrong, I don't believe the human genome is "pristine", all functioning how it is supposed to. Of course there are mutations that have occurred since we were created. But you assume that humans inherited a genome full of junk from some ape-like ancestor. Swallowing that theory wholesale skews your objectivity.

      You MUST find overwhelming amounts of junk in the DNA to support your religiously motivated belief, so you immediately start attacking ENCODE instead of sitting down, listening, and learning from it, like an adult.

      Delete
    17. Ed Reynolds says,

      ... you immediately start attacking ENCODE instead of sitting down, listening, and learning from it, like an adult.

      This guy has to be a troll. A real, sincere, person could not say that with a straight face.

      Delete
    18. She grins like a cheshire cat when she can 'imperialize' over a lay person.
      She doesn't do so well when facing the pro's.


      Hey Ed, do you some sort of conflicted love/hate thing going on for Eugenie Scott ?

      Delete
    19. Ed,

      I have a few question for you I hope you don’t mind?
      1. Does Dr. Noble’s paper or video explain how epigenetics compensate for the deleterious mutations? I’m sorry for putting you on the spot but I haven’t had a chance neither to read the paper nor to watch the video due to the lack of time. Pardon me please.

      Delete
    20. I have many questions for many bloggers on this forum so don't feel intimidated please It's my inquiring nature Sorry for that

      Delete
    21. Johnny,

      He didn't go into any known mechanisms in his paper, as this is such a new area of research. I picked what I thought was the most relevant piece of the paper that may help you look into it further:

      "Epigenetic effects can even be transmitted independently of the germ line. Weaver and co-workers showed this phenomenon in rat colonies, where stroking and licking behaviour by adults towards their young results in epigenetic marking of the relevant genes in the hippocampus that predispose the young to showing the same behaviour when they become adults (Weaver et al. 2004; Weaver, 2009). (This field is growing so rapidly that there is not space in this review to cover it. A more extensive bibliography can be found at http://shapiro.bsd.uchicago.edu/Transgenerational_Epigenetic_Effects.html.)"

      Hope this helps :)

      Delete
    22. Ed, you have made a number of false assertions in a very short time. In addition you have attempted to cover for them by invoking the conservative appeal to motive fallacy. We are not interested in your psychoanalyzing us and making your bullshit psychoanalysis as to why we know vastly, vastly more than you about genomics and why we have presented mountains of evidence that your genome is 93% junk.

      If Christians were such good judges people's motivations and psychology, they wouldn't constantly be putting rapists, child molesters, sexual harrassers grifters, con men, pyramid schemers, etc. etc. etc. behind the pulpit as priest, pastor (or worse, "youth pastor"), bishop, archbishop, cardinal-- not to mention congressmen.

      Please submit your bullshit psychoanalysis to the Journal of Bullshit Armchair Psychoanalysis by Right-wing @$$h0!e$, although they will probably not publish it, because you have so much competition-- so many right-wingers proclaim themselves expert in that field nowadays.

      Ed: "Your 'objectivity' is just as skewed as anyone else's."

      Appeal to motive, appeal to motive, and must be dismissed as such. This assertion by you is not supported by evidence. This assertion itself is a product of your religious bias, and should be dismissed as such. You have not presented evidence that more than 8% of the genome has a function which constrains sequence and contributes to the fitness of the host organism.

      Ed: How can YOU claim to be the one who is objective?

      He didn't, and we don't care if Larry is objective. We care if his facts are accurate and relevant. His are; your aren't.

      If Larry was molested by a priest as a kid and therefore hates religion, and fights it by presenting accurate facts, why should we care about Larry's motivation? He presents accurate facts; you're a robot who copies from conservative anti-scientists without double-checking his allegations. Your "facts" are not accurate nor relevant, and thus the issues you raise are ones of abnormal psychology (yours) and should be addressed by psychoanalysts.

      How do you think that belief affects your interpretation of data?

      Appeal to motive again. Larry presented accurate facts; so we don't care what his motivation is.

      Your "facts" are laughably inaccurate. We're laughing at you. Since you've insulted a blog full of real scientists, you've made a big mistake. Now I'm going to diogenize you.

      Delete
    23. Ed says: "When you are confronted with an expert in a field with an interpretation that you disagree with, your role is to sit down, listen, and learn.
      Just like the rest of us."


      Wow, you're ignorant-- you didn't know you blundered into a blog full of real scientists! Now we're the experts, so "your role is to sit down, listen, and learn."

      Yes, sit down, shut the $%^& up, and listen.

      Ed: "The ENCODE project, though far from the final word, has found 80% of the human genome to have known functions."

      Bullshit! The ENCODE project found no such thing, as was admitted by Ewan Birney himself, and by many other ENCODE scientists -- Birney admitted on his blog, and in media interviews, that the fraction of the genome that's actually functional is (he guesses, optimistically) 20 % (quote below). That's 20% Ed, not 80%-- and 20% is optimistic.

      What's worse for you, Ed, is that we know ENCODE scientists and/or they contribute to this blog, and indeed, to this very thread!

      Look up, Ed. Loop right up in this thread. Do you see this comment right above your head? It's the Sword of Damocles!

      Georgi Marinov, ENCODE SCIENTIST, wrote on THIS thread: "...ENCODE has not tried to refute junk DNA within the scientific literature. There is no mention of the word "junk" in the scientific papers from the consortium, with the exception of the PNAS one where it had to be discussed." [Upthread comment by Georgi Marinov that Ed Reynolds didn't bother to read]

      Do you realize how stupid that makes you look, Ed? Now sit down, shut the $%^% up, and listen to the experts. US.

      (Note: the PNAS paper was written later, in which the ENCODE leaders walk back their claim that 80% of the genome is functional, and try to claim they didn't mean what they meant.)

      Now here is ENCODE poster boy, Ewan Birney, the guy who made the "80% functional" claim, writing at this blog:

      Ewan Birney: ... using very strict, classical definitions of “functional” like bound motifs and DNaseI footprints; places where we are very confident that there is a specific DNA:protein contact... we see a cumulative occupation of 8% of the genome. With the exons (which most people would always classify as “functional” by intuition) that number goes up to 9%. Given what most people thought earlier this decade, that the regulatory elements might account for perhaps a similar amount of bases as exons...

      ...We estimated how well we have sampled, and our most generous view of our sampling is that we’ve seen around 50% of the elements. There are lots of reasons to think we have sampled less than this...A conservative estimate of our expected coverage of exons + specific DNA:protein contacts gives us 18%, easily further justified (given our sampling) to 20%.

      We use the bigger number [80%] because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.
      [Ewan Birney at his blog admits only 20% of the genome is functional]

      Biological activity, Ed. Activity-- not biological function.

      In fact, ENCODE performed NO assays for biological function! OOPS!

      Now you sit down and shut the $%^& up because we've only gotten started, Ed Reynolds.

      Delete
    24. Ed writes: [quoting Larry] "Thing number 5:
      "Most of the genome is not conserved
      Most of the DNA sequences in large genomes is not conserved. These sequences diverge at a rate consistent with fixation of neutral alleles by random genetic drift. This strongly suggests that it does not have a function although one can't rule out some unknown function that doesn't depend on sequence."


      [Back to Ed] First, your assumption of "conserved" genes is based on your assumption that all life evolved from a single form, which has not been verified."

      NO ED, it is NOT. You're shit-ignorant of genetics if you think this assumes all life evolved from a single form.

      You better go back to "appeal to motive" because your shit-ignorance of genetics is disgusting to put on display.

      Consider this recent paper (January 19) published in Nature Genetics. They conclude that 7% of the human genome is functional and the other 93% is JUNK.

      "A method for calculating probabilities of fitness consequences for point mutations across the human genome" Brad Gulko, Melissa Hubisz, Ilan Gronau, and Adam Siepel. Nature Genetics January 19, 2015. dx.doi.org/10.1038/ng.3196

      And how do they do that, Ed Reynolds? Certainly not by assuming all life comes from a human ancestor-- rather, by assuming all humans come from a single ancestor.

      Yes Ed, we now have enough sequenced individual human genomes to compute sequence conservation within the human species. There is too much variation within the human species for 100% or 80% or even 50% of the human genome to be functional. Not possible.

      And we're sequencing more individual human genomes all the time. More and more data, Ed. You creationists are SCREWED.

      Ed, will you retract your ignorant blurt: "First, your assumption of "conserved" genes is based on your assumption that all life evolved from a single form, which has not been verified."

      Retract. You have no choice. We won't forget this, we won't let you change the subject, and appeal to motive don't work on us. You cannot change the subject, you cannot Gish gallop. I know how you lying conservative weasels operate: right now you're strategizing how to change the subject with non sequiturs. Won't work with us. You're screwed.

      Delete
    25. Diogenes:

      What are you, an idiot?
      Saying that all life came from a common ancestor necessarily entails the fact that all HUMANS came from a common ancestor.

      Besides, you are a disingenuous idiot if you say you do not believe all life came from a single form.

      Delete
    26. Ed, you did exactly as I predicted: you attempted to change the subject. You did not originally claim: "Saying that all life came from a common ancestor necessarily entails the fact that all HUMANS came from a common ancestor." That was NOT your claim, so you're lying and trying to rewrite your own words.

      Copy and paste your original statement, Ed. Here it is:

      ""First, your assumption of "conserved" genes is based on your assumption that all life evolved from a single form, which has not been verified."

      This statement is false and the paper I cited proved it. Instead, you change the subject to a new claim:

      "Saying that all life came from a common ancestor necessarily entails the fact that all HUMANS came from a common ancestor."

      Duh. You originally claimed:

      Conservation requires assuming X.

      I cited a paper which computed conservation WITHOUT assuming X, but did assume Y.

      Now you idiotically blurt:

      X entails Y.

      This is a moronic counter-argument, because it has to be the other way around. You must prove that Y ENTAILS X, you must not assume X ENTAILS Y. THEY ARE NOT THE SAME THING.

      Consider

      1. X entails Y.

      2. Y entails X.

      Are these the same, Ed?

      Now consider:

      1. Universal common descent entails common descent of all humans.

      2. Common descent of all humans entails universal common descent.


      They're not the same. Now we're the experts here, so you follow your own advice, sit down, shut the $%^# up and listen to the experts.

      Delete
    27. Ed, you wrote: Thing number 3: "Modern Evolutionary Theory Nothing in biology makes sense except in the light of population genetics.” but number iii on the list of things to know before talking about junk DNA was the “evolutionary origin of most genomic sequences from transposable elements.” One might quibble about the “most,” but basically this is the observation (not assumption) that a great many DNA sequences match or nearly match known transposable elements. You’re not giving me great confidence that you know what you’re talking about.

      Delete
    28. bwilson:
      You're absolutely right, I don't have any specialized knowledge in biology. I'm just a slob with half a brain who knows how to read. I rely on professionals to translate the important points for me; all the rest I don't have a clue what you guys are talking about.
      Oh, I'll look up a term from time to time, and I just bought a current university biology textbook (Campbell), so I can keep up if you dumb down the language a bit.

      So, you're challenging me on whether I am conversant on "transposable elements".
      You win! I could look it up right now, but I won't even do that, because it has no relevance to the argument I'm making.
      Suffice it to say that there are plenty pro's just like you that don't swallow this "junk DNA" bullshit like you do.

      Delete
    29. Ed ReynoldsTuesday, January 27, 2015 1:38:00 PM
      Thing number 3:
      "Modern Evolutionary Theory
      Nothing in biology makes sense except in the light of population genetics. The modern understanding of evolution is perfectly consistent with the presence of large amounts of junk DNA in a genome."

      A sweeping, self-serving generalization that says nothing about how you claim junk DNA, except that it doesn't fit your model.


      We've gone over this one countless times but apparently it has not been sufficient so let's do it again.

      The favorite target of creationists is Darwin, because that's all they know. And that's key because it reveals the nature of one of their biggest misunderstandings of evolution (if they understood it, they would be attacking Fisher, Wright, etc. but they are not, and we all know why). Darwin did two main things:

      1) Provided tons of evidence that evolution happened though he was by no means the first person to come up with the idea of evolution
      2) Provided one mechanism for how it occurs - natural selection

      But that was in a context of almost complete absence of knowledge about how inheritance works and you cannot understand evolution without a good understanding of inheritance.

      People (re)discovered the basics of inheritance in the first half of the 20th century and as a result population genetics was born, and in the second half of the 20th century things moved to the molecular level, which triggered further important theoretical developments. As a result now we have a reasonably complete theory of evolution on the molecular level.

      The critical thing to understand about it is that it starts with knowledge about how inheritance works and after that it is all math and the conclusions follow in the same inevitable manner that they do when one is developing mathematical theory. There are no "self-serving generalizations" there - as long as our understanding of inheritance is correct and the measurements of the relevant parameters are correct, we can be reasonably certain in our conclusions based on the theory.

      In the case of the human genome, the critical parameters for the question we're discussing here (genome size and mutation rate) were first measured way back in the 1950s, and from that people were able to estimate the number of genes and the fraction of the genome that is under constraint with remarkable accuracy given how long ago it was and how primitive the tools they had at their disposal were from our modern perspective.

      Read Ohno's junk DNA paper if you do not believe me:

      http://www.junkdna.com/ohno.html

      Estimate of the number of genes: 30,000
      Estimate of the fraction of the genome under sequence constraint: 6%

      Based on a few very simple principles and essentially back-of-the-envelope calculations.

      Real number of genes: 20,000 protein coding genes + a few hundred miRNAs + a few thousand lincRNAs (many of which, however, are not that highly conserved)
      Real fraction of the genome under constraint; 5-10% depending on how you calculate it.

      I call that a remarkable success.

      Delete
    30. And Georgi is an ENCODE scientist, and Ed cited ENCODE as his authority above. But when Georgi proves Ed wrong, will Ed follow his own advice: "When you are confronted with an expert in a field with an interpretation that you disagree with, your role is to sit down, listen, and learn."

      Is it not true, Ed, that you have been "confronted with an expert in a field with an interpretation that you disagree with"?

      No matter; certainly Ed is a hypocrite who will not follow his own advice and acknowledge that his "role is to sit down, listen, and learn."

      Delete
    31. Quest: "... you are just a liar like your gods Darwin and Satan."

      Now that's discriminatory language. It's now fair to be prejudiced against us just because we worship the Prince of Darkness.

      At any rate, Satan's death toll in the Bible is enormously smaller than God's. He's clearly the least psychotic, least murderous of the Bible's many deities.

      Delete
    32. "The critical thing to understand about it is that it starts with knowledge about how inheritance works..."

      You mean it starts with ASSUMPTIONS about how inheritance works...

      Delete
    33. As expected, Ed can't defend his false assertions that "your assumption of "conserved" genes is based on your assumption that all life evolved from a single form", nor his false assertion that "The ENCODE project...has found 80% of the human genome to have known functions.", nor can he defend his appeal to motive "Your 'objectivity' is just as skewed as anyone else's", nor his moronic claim that "most or all of [Larry's evidence for junk DNA] are based on atheistic assumptions." Actually, Ed never demonstrated that ANY of Larry's evidence was based on "atheistic assumptions." So what's the next of Ed's piles of ignorant bullshit?

      [quoting Larry] "Genetic Load
      Every newborn human baby has about 100 mutations not found in either parent. If most of our genome contained functional sequence information, then this would be an intolerable genetic load. Only a small percentage of our genome can contain important sequence information suggesting strongly that most of our genome is junk."


      [Back to Ed: Oh, now I see why you have such a visceral distain for Dr. Noble - he points out that many epigenetic systems are at play to compensate for genetic errors.

      Once again, as above, Ed has confused a presupposition which he needs, with its converse. Ed needs to prove his presupposition:

      1. If it's a deleterious mutation, then epigenetic factors will compensate for it.

      This is what he needs to refute Larry's argument. Instead, Ed claims, citing the authority of Noble, that

      2. If it's an epigenetic factor, then it will compensate for deleterious mutations.

      1 and 2 are different; in fact, 2 is the converse of 1; the truth of 2 does not entail the truth of 1, but Ed doesn't understand logic. So Ed above claimed that "Dr. Noble... points out that many epigenetic systems are at play to compensate for genetic errors", thus alleging 2, but that is not what he needs to refute the evidence from genetic load. Ed actually needs 1, which is not entailed by the truth of 2.

      No creationist has ever made a serious attempt to address the evidence from genetic load.

      So let's hammer it home. Every human baby, every single human being, all 6 billion of us, have about ~130 more new mutations that its parents didn't have (depending on how you measure), which means ~260 more new mutations that its grandparents didn't have, and ~390 more new mutations that its great-grandparents didn't have, ad infinitum. That's a lot of mutations.

      Problem: creationists say that the whole human genome is functional, 100% of it, and creationists say that all mutations are "catastrophic." So if creationism is true, that means that every single human being, all 6 billion of us, have about ~130 more "catastrophes" that our parents didn't have, 260 more "catastrophes" that our grandparents didn't have, ~390 more "catastrophes" that our great-grandparents didn't have, and so on ad infinitum. That's a lot of catastrophes, yet 6 billion humans survived.

      So creationists are screwed, right? Right, but they can always lie.

      Now Ed's lie (and it's a new one) is basically to contradict every creationist for the last 100 years and say so sorry, mutations are NOT catastrophic after all!

      Oh you assholes figured that out now, did you? Let's be clear what you need to prove: you need to prove that of those ~130 new mutations in every baby born anywhere are almost all compensated for, every one, by epigenetic factors.

      If epigenetic factors can only compensate for, let's say, 50% of all mutations, then the genetic load argument stands: most of the human genome is still junk. You did not prove that epigenetic factors compensate for at least 90% (being generous) of all new mutations in every baby born everywhere. Not even close.

      Delete
    34. Something else I forgot to mention regarding population genetics, this time more philosophical in nature. Again, it's something I've posted about in the past, but it's worth revisiting:

      We need to keep in mind the distinction between the fact of evolution and the theory of evolution. I am not really interested in discussing the fact of evolution even though there are tons of creationists who deny that too. That is a fact, as uncontroversial as any other in science. The more interesting question concerns the theory and the various versions of ID/theistic evolution that keep God in the picture.

      Here, creationists (of the ID/TE sort) once again miss the substantial point by a wide margin. It is true that it makes no sense for the genome to be mostly junk if it was designed. But it makes no sense from our own perspective and who we are to say that a deity would operate according to the same principles?

      Here is where the fact that population genetics works, and makes valid predictions (such as the one I outlined above about the content of the human genome) actually has very important implications. It is entirely possible to construct a theistic theory of evolution - that's what ID (in its common-descent, no-special-creation versions) is, that's what the various TE proposals are. All of those imply that population genetics is false - because all the equations of population genetics are based on assumptions of "randomness" (random, if biased mutations, random sampling of alleles and gamettes, etc.), and if the process was/is in fact directed by a deity (by whatever means) that means those equations are false because the random-sampling assumption does not hold (this is why theistic evolution is not a reconciliation of theism with the theory of evolution, but a rejection of it, except in a vary narrow special version of it that almost nobody believes in). Thus the more successful population genetics is, the more our confidence in its assumptions increases. Not that the above is a primary reason to reject theism but it does lower our current prior on it being true to an even smaller value than the 10^(-n) where n is a rather large number that it already was.

      Delete
    35. Mr Reynolds writes:
      ""The critical thing to understand about it is that it starts with knowledge about how inheritance works..."

      You mean it starts with ASSUMPTIONS about how inheritance works..."

      Yes, but assumptions combined with evidence (as expert Marinov shows you) leads to facts.
      Mr. Reynolds you forgot to add the other and also important bit of Georgi's comment "and after that it is all math and the conclusions follow in the same inevitable manner that they do when one is developing mathematical theory."

      Thus we can conclude that, Mr. Reynolds, you're (accidently?) ignoring your own advice: When you are confronted with an expert in a field with an interpretation that you disagree with, your role is to sit down, listen, and learn.

      I assume you're sitting down, it should be really easy to follow the two next steps, yes?? Go up a few comments and re-read Georgi's comment , then try again to listen and perhaps, you might even learn something.

      Good luck.

      Delete
    36. Ed,
      Nope, sorry, but that's about the only thing he said worth replying to.
      Think about it: If you base your work on the wrong assumption, it doesn't matter how good your work is, you'll still get "garbage out".

      Delete
    37. So according to you we are completely wrong about how inheritance works?

      Given that it is a natural requirement for grandiose claims to be backed up by equally impressive arguments to be taken seriously, can you please enlighten us on how exactly we have it wrong and how that invalidates the relevant results we're debating?

      Delete
    38. All I can tell you with full proof is that Darwinian common descent is an unverified assumption initially made by Darwin, based mainly on the fact that "it sounds good and it makes sense".
      Darwin didn't even attempt to verify this; he left that up to his posterity, as the evidence became available.
      Problem is, nobody got around to verifying Darwin's central thesis that a naturalistic mechanism has caused life to morph from a single cell into all the kinds we have, and have had, on this planet.
      -See 'Darwin's Black Box', chapter 8: PUBLISH OR PERISH.

      Delete
    39. So you're basically avoiding the question.

      Regarding common ancestry:

      1) Common ancestry has been tested to the extent that it can be (see PMID: 20463738), and common ancestry between the three major groups of organisms of the planet comes out as the overwhelmingly more likely possibility.

      2) The rejection of common ancestry does not imply theism. It could be that life arose multiple times independently (this is what was tested in the paper I linked to). That does not mean it was created independently. However, as I said, common ancestry is overwhelmingly more likely when it comes to the deepest divisions in life today - archaea (plus eukaryotes) vs bacteria. Which is a split that happened billions of years before the common ancestry that creationists care about (the relationship between humans and the rest of life on the planet) and the only one that could possibly be in doubt given the totality of the evidence.

      P.S. "Publish or perish" conspiracy arguments are completely irrelevant when it comes to things established long before WWII. It is only after WWII that the modern scientific system was established and even more recently that competition for scarce resources got so desperate that this started to influence what science is done and how. Ironically (and sadly), the dominance of creationism (as part of a broader anti-scientific attitude within society) is a significant contributing factor towards why science finds itself in such a sorry state. So you have no idea how infuriating it is to read such comments.

      Delete
    40. Mr. Reynolds, from your comment above it clearly looks like you ASSUME Darwin didn't provide any evidence for natural selection. Perhaps you should actually read Darwin's work.

      Rather amusing though, you cite Georgi's ENCODE project as expert first, but when Georgi's proves you wrong, you move the goalposts and now your expert is Behe?

      Delete
    41. "why science finds itself in such a sorry state"

      Which is why academics and researchers from all over the world are a major import product in the US.
      For some weird reason private funds, like the Dutch and American Cancer Societies, won't fund research based on 'goddidit' but ask for facts and evidence. Perhaps prof. Behe should apply for a grant there?

      Delete
    42. @Ed Reynolds

      Ed, reject the existence of pseudogenes it seems. Why? What is this rejection based on?

      Why do you think a gene missing important transcription factor binding sites, is missing several key exons, has multiple premature stop-codons and nonsense frameshifts, is somehow still a functional gene?

      Delete
    43. Ed is impermeable to facts. He has posted a lot of misinformed bullshit, and when corrected, he obviously can't understand what the explanations mean. He said so himself. He does not know what a transposon is, he does not know how we know that a gene is broken, etc. He works under the assumption that whatever you explain comes from preconceptions, because he cannot understand one iota of these explanations. This is why he can post and post and post quotes from whatever you say "corrected" to whatever he prefers you had said, given his commitment to creationist propaganda.

      I doubt that he would be willing to follow an explanation. He seems to scan quickly to find something that he can quote to continue blaming everybody here of being biased, and such shit, but attempts at understanding are out of the question for him.

      It's a waste of time because Ed has no idea, and doesn't care. He is convinced that we are wrong and biased, not because he understands anything, but because he has heard said so by his favourite creationists.

      Delete
    44. Why do you think a gene missing important transcription factor binding sites, is missing several key exons, has multiple premature stop-codons and nonsense frameshifts, is somehow still a functional gene?

      Because he doesn't know what a transcription factor binding site is, he doesn't know what frameshift means, let alone a nonsense one, he doesn't know what premature stop codons are, he doesn't know what an exon is, let alone a key one (or how we would know that the exon is key). All he knows is that "we don't know everything about how genes work, therefore God."

      Hey, if he can mistake "epigenetic modification of gene expression" for "protection from mutation," he must be way off his element. And he still thinks that he can come and teach us something! That incompetence at self-awareness explains quite a lot about his comments. He's simply too much of an idiot.

      Delete
    45. I predicted Mr. Reynolds would follow the creationist Gish gallop script of making numerous factually false statements, and then, when their factuality is refuted, he would change the subject to something completely different. And so it is; he has not attempted to defend any of his false statements about Junk DNA (which I listed above)-- but tried to change the subject to new false statements about universal common descent. Gish gallop and red herring.

      In order to prove that universal common descent was merely Darwin's "assumption" never tested in 155 years, Mr. Reynolds cites as his authority Michael Behe. Michael Behe accepts common descent and has described it as "trivial", that is, given the evidence, proving that common descent happened is trivially easy, according to Behe.

      "Trivial." Creationists do not challenge Behe on this assertion, because they don't want to undermine his authority as their science expert. They would be furious if an evolutionist said the same thing-- "Trivial!"-- but when Behe says "TRIVIAL", the creationists fall silent, stare at their shoes, and mumble something about Darwin = Hitler.

      Mr. Reynolds keeps citing authorities who say the opposite of what he says they said. It happened with ENCODE and now it happened with Michael Behe. Before citing an authority as his evidence, Mr. Reynolds should first know what that authority has said, written, or proven-- and (we may wish) how, by what experimental means, the authority "proved" it. Mr. Reynolds tells us to sit down and listen to the experts, yet he does not sit down and listen to the experts he himself is citing.

      Delete
    46. Re Ed Reynolds

      One has to get a good laugh out of Reynolds' citing Michael Behe as being dubious about common descent. I suggest that Reynolds read Behe's testimony at the Dover trial where, in response to a question from the defendant's attorney, he specifically responded that he accepted common descent. In Darwin's Black Box, Behe cited the claim that whales evolved from a land animal as something that was lacked evidence of intermediate forms. Since that book was published, a dozen such intermediates have been found (Basilosaurus, Ambulocetus, Pakicetus, etc. anyone).

      Delete
    47. "Trivial." Creationists do not challenge Behe on this assertion, because they don't want to undermine his authority as their science expert. They would be furious if an evolutionist said the same thing-- "Trivial!"-- but when Behe says "TRIVIAL", the creationists fall silent, stare at their shoes, and mumble something about Darwin = Hitler.

      Yes, it's one of the curious things about the Intelligent Design movement, that they don't appear to see any importance in resolving some of these differences between advocates of their "theory". How did the "intelligent designer" create all life forms? Did he do it thru specially creating each individual "kind", or thru common descent? Why aren't they trying to settle this controversy? When ID proponents claim to have found evidence refuting common descent, why do they only say this disproves evolution, and never that it also disproves Behe's theory of Intelligent Design?

      When William Dembki comes out and says that the story of Noah's flood is factual, do all his fellow ID proponents agree with this? If not, why don't they correct him?

      We can see from this very post how evolutionists like Larry Moran will openly disagree with and dispute claims made by fellow evolutionists like Francis Collins. That's how science is supposed to work, thru open disagreement and discussion of the evidence supporting both sides. Why don't we see this happening within ID? It's almost as if they're not acting like scientists, but rather like some kind of religious cult, in which dissent and disagreement cannot even be acknowledged.

      Delete
    48. Colnago, Behe made his claim about the alleged absence of transitional fossils leading to whales prior to Darwin's Black Box. I don't think that claim is in the book. Of course, even at the time that Behe made this ill-fated claim-- "Where are they [transitional fossils]?"-- we already knew back then about some transitional fossils like Dorudon and Basilosaurus. Behe has repeatedly misrepresented the scientific literature, pretending to have encyclopedic knowledge of the literature, claiming it contains no information, no answers, no evidence when in fact the actual evidence was almost always ALREADY in the literature, and well known to experts, before Behe made his false claims. Behe has never followed Ed Reynolds' dictum of sitting down, shutting up, and listening to the experts.

      Behe is not an expert in paleontology, whale fossils, malaria, antimalarial drug resistance, HIV, the immune system, blood clotting, or protein molecular structure. In every case he has pretended to encyclopedic knowledge in all those fields, falsely stating that the literature in those fields does not contain evidence that was in fact IN the literature AND well-known among experts at the time Behe made the false statements. Thus he has been repeatedly and publicly humiliated when the falsity of his statements becomes well-known among non experts in the fields.

      An incomplete list of Behe's public humiliations:

      1. 1980's: Behe says no whale transitional fossils, "Where are they?"; ignores Dorudon and Basilosaurus already known then; meanwhile, scientists in Pakistan were digging up many more, and appeared in literature soon after

      2. 1996: Darwin's Black Box claims blood clotting system is irreducibly complex; Behe doesn't know whales, chickens etc. have reduced blood clotting system

      3. 2005 Dover: on witness stand Behe claims the literature has no explanation how immune system evolved; attorney for plaintiffs piles up 54 scientific papers about evolution of immune system on witness stand in front of him; Behe says he hadn't read them.

      4. 2010 Edge of Evolution: Behe claims HIV virus never evolved a protein binding site; he is immediately humiliated by grad student "ERV" who points out that HIV protein Vpu recently evolved protein binding site & gated calcium channel.

      5. 2010 again: Behe claims system for building flagellum is "irreducible complexity SQUARED"; Behe immediately humiliated by Nick Matzke who points out organisms with reduced systems for building flagellum.

      6. 2014: Analysis of malaria shows there are multiple pathways to evolving resistance to chloroquine; all paths to CQ resistance involve sequential, non-simultaneous mutations that were beneficial, neutral, or (on some pathways) singly deleterious. Back in 2010 Behe had predicted that EVERY pathway to CQ resistance would require multiple deleterious, and therefore MULTIPLE SIMULTANEOUS, mutations. Behe, having been proven seriously wrong, bizarrely claims victory, and Discovery Institute demands that his opponents apologize for being right and for being proven right by experiment, thus raising serious questions about Behe's mental condition and the DI's sanity.

      Delete
    49. Mikkel:
      Do you agree with wikipedia's definition of a pseudogene:
      "Pseudogenes are dysfunctional relatives of genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell.[1] Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism. Although not protein-coding, the DNA of pseudogenes may be functional,[2] similar to other kinds of non-coding DNA which can have a regulatory role."
      http://en.wikipedia.org/wiki/Pseudogene

      If so, please give your definition of "functional" as used above.

      Delete
    50. Quest: "I would pay a lot of money to be able to see his face in front of the computer sweating bullets and trying to answer this fundamental to his beliefs question"

      How much money? Be specific. I will post a photo or video of myself in front of the computer answering your question and you will donate "a lot of money" to the NCSE in my name, IF your monetary offer is big enough. So make me an offer. I warn you: my time is not cheap. How much money, Quest? Answer a friggin question for once: How much money for a picture or video of me answering your question?

      Delete
    51. Colnago:
      I think you're a little confused, saying that the Basilosaurus was discovered after Behe wrote Darwin's Black Box LOL.

      "Original discovery[edit]

      Caudal vertebra from Owen 1839
      During the early 19th century, Basilosaurus cetoides fossils were so common (and sufficiently large) that they were regularly used as furniture in the American south.[18]"
      http://en.wikipedia.org/wiki/Basilosaurus

      Ya wanna rephrase that?

      Delete
    52. Re: Ed Reynolds

      1. Yes, Basilisaurus was discovered before Behe made any claims. jesuit accused of killing three men and a dog will triumphantly produce the dog, alive.

      2. I believe Mr. Reynolds has ben posting elsewhere under the name "Steady Eddie". He makes about as much sense under either nym.

      Delete
    53. @Quest

      "Even if Behe "...has no particular reason to doubt common descent..." he still says "...the root question remains unanswered: What has caused complex systems to form?..."

      Why..?

      "...ID is not the opposite of evolution. Rather, it is the opposite of Darwinism, which says life evolved by an utterly unguided, undirected mechanism. If God directed the process of evolution, or rigged the universe to produce complex life, then that is not Darwinism - it is intelligent design..."


      How could Behe support common descent and at the same time not agree with Darwinism? It doesn't make any sense to me.

      Delete
    54. @Quest

      "Even if Behe "...has no particular reason to doubt common descent..." he still says "...the root question remains unanswered: What has caused complex systems to form?..."

      Why..?

      "...ID is not the opposite of evolution. Rather, it is the opposite of Darwinism, which says life evolved by an utterly unguided, undirected mechanism. If God directed the process of evolution, or rigged the universe to produce complex life, then that is not Darwinism - it is intelligent design..."


      How could Behe support common descent and at the same time not agree with Darwinism? It doesn't make any sense to me.

      Delete
    55. Re Diogenes

      Correction re Basilosaurus accepted. However, the other 2 I mentioned were found after Behe criticized common descent. In fact, it's even worse then I cited as, apparently, Behe ignored Basilosaurus.

      Relative to ERV (aka Dr. Abbie Smith), she challenged Behe to a debate about the evolution of HIV. He declined on the grounds that she was only a graduate student at the time. Of course the real reason was that she was doing her PhD work on HIV and knew a lot more about the subject matter then he did. Ole Mikie has some chicken feathers where his intestinal fortitude should be.

      Re Ed Reynolds

      Given Behe's Dover trial admission on the witness stand under oath that he accepted common descent, are you still going to cite him as a critic?

      Delete
    56. Well no, Quest, the RNA world hypothesis has never been based on faith, but your belief that evolution is a religion akin to yours is just your religious belief "based on faith", and may be dismissed as such. Moreover, your assertion that "you don't have any answers for the origins because it is all based on faith" is false, I have answers and I've already offered to write them down, and make a video of myself of writing them down, and post my answers and the video on the internet, as long as you donate "a lot of money" for the pictures as you said you would do.

      Quest wrote: "I would pay a lot of money to be able to see his face in front of the computer sweating bullets and trying to answer this fundamental to his beliefs question"

      So you said you "would pay a lot of money". Now you have to pay a lot of money. You can donate it to the NCSE, a non-profit, in my name.

      Now let's negotiate $$, Quest. Cough up real numbers. How much are you willing to pay for both an answer and pictures of me answering, as you said you would pay? Or were you lying? A lying creationist? Oh, shocking.


      Quest: "I would pay a lot of money to be able to see his face in front of the computer sweating bullets and trying to answer this fundamental to his beliefs question"

      Delete
    57. Colnago, my dates are a bit wrong in my list of Behe's public humiliations. The quote on whale transitionals was from 1994; here it is.

      Michael Behe, 1994: "Finally, and most glaringly obvious, if random evolution is true there must have been a large number of transitional forms between the mesonychid and the ancient whale: Where are they?

      [Diogoenes inserts: IN PAKISTAN, in the Sulaiman moutnains, idiot. And what do you mean by “random evolution”? Is that like “random gravity” or “random electromagnetism”?]

      It seems like quite a coincidence that of all the intermediate species that must have existed between the mesonychid and whale, only species that are very similar to the end species have been found. ["Experimental support for regarding functional classes of proteins to be highly isolated from each other." Michael Behe. In Darwinism, Science or Philosophy? Eds. Jon Buell and Virginia Hearn, Foundation for Thought and Ethics: Houston, Texas. 1994. See ARN Michael Behe Files].

      As for other dates I got wrong, Darwin's Black Box was 1996 and Edge of Evolution was 2007.

      Delete
    58. Quest wrote: "I would pay a lot of money to be able to see his face in front of the computer sweating bullets and trying to answer this fundamental to his beliefs question"

      So you said you "would pay a lot of money". Now you have to pay a lot of money. You can donate it to the NCSE, a non-profit, in my name.

      Now let's negotiate $$, Quest. Cough up real numbers. How much are you willing to pay for both an answer and pictures of me answering, as you said you would pay? Or were you lying? A lying creationist? Shocking.

      Delete
    59. It's Jerry Coyne, and the "original" Neo-Darwinian mechanism, if by that you mean natural selection, is sufficient to produce new species, if by new species you mean populations that are reproductively isolated from each other. You want evidence? Jerry (with H. Allen Orr) has a whole book of evidence for you, entitled, conveniently, Speciation. Read it. If you can read.

      Delete
    60. @Ed Reynolds "Do you agree with wikipedia's definition of a pseudogene:"

      Yes I agree with that definition, in it's entirety(As in not just the part that might corroborate my preconceptions). Ed, notice that it says "may have a function" in that description. Not that they DO have a function. Ed, please don't just stop reading once you have found something you think confirms your preconceptions.

      Tell me Ed, what does the L-gulono-gamma-lactone oxidase pseudogene in humans do?

      Delete
    61. Re Rasmussen

      How about Reynolds telling us what the gene for making vitamin C in humans and the great apes does. Being broken, it sure doesn't produce vitamin C.

      Delete
    62. "Quest,"

      Poor evolution... firstly... it breaks a perfectly functioning gene in some mammalian ancestor nobody knows which one... Now our poor ancestor has got to look for food with vitamin c...whatta pain...

      No you imbecile. The gene broke because those ancestors had plenty of vitamin c available in their food, and thus the gene was mostly useless. When something is useless, it does not matter if it breaks idiot, and thus a broken gene can spread in a population with no ill effects.

      Then natural selection can't get rid of third broken gene....so that it gets spread to so many different species... Why does it get preserved since it is no doubt a deleterious mutation...?

      You imbecile, because there's no mechanism to cleanly getting rid of useless DNA. Evolution is not an intelligent being, it's a natural phenomenon.

      Well... so far the only logical explanation is that evolution knew that evolutionists would use it in the future as the only proof for common ancestry and that we have evolved from ape-like ancestor with the same and ONLY genetic defect...

      No imbecile, this is but one of many examples that show that natural phenomena are, ahem, natural phenomena.

      Can't argue with that... LMAO...!!!

      Be careful not to break your ass of so much laughing at your own imbecility.

      Have more stupidity to show off Quest? I bet you do. Go ahead, show what it takes to be a creationist like yourself. You are a great help in keeping children away from your imbecilic beliefs. All we need to do is point and ask them if they really want to grow up to be just like you.

      Delete
    63. "Quest,"

      I think it's time we started being serious about the limitations of the RNA world as a possible explanation for the origin of life.

      I doubt that you have read the pertinent literature. The RNA wold is not about the origin of life, but about a plausible intermediate. Nobody is married to the hypothesis, but the hypothesis is based on several observations that make sense if at some point RNA was more generally working as both catalyst and genetic material.

      It's simply not possible to imagine a scenario where the first catalysts are RNA molecules because that requires a primordial soups full of nucleosides and sugar molecules.

      It's good then that nobody has proposed that RNA were the first catalysts. Such a claim would be both too ignorant and too presumptuous. As I said, you have not read the pertinent literature. I bet you have not gone beyond creationist propaganda, and some press-releases.

      It requires the spontaneous synthesis of nucleotides and their polymerization.

      Which require catalysis! And guess what? There's plenty of demonstrable catalysis in many environments going on that do not involve life forms. And guess what? Some of those catalyzed reactions produce nucleotides!

      "Quest," if only you took your "name" seriously, you would save yourself a lot of embarrassment. But don't worry, your stupidity works as warning against the ill effects of creationist propaganda.

      Delete
    64. The Scientist is not direct literature, but still, guess what "Quest"? It shows that the RNA world hypothesis is not based on faith, and that scientists don't mind challenging it at all. That contradicts your bullshit directly, and you did not notice! You still quoted and quoted unaware that you were refuting your own claims that recognizing the RNA world limitations "ain't gonna happen." You're such an imbecile!

      This is golden! You come here all pretentious and make a claim only to contradict yourself! Go on, laugh your ass off.

      Delete
    65. Quest, As usual you have completely dodged the issue. I read your "paper", which seems never to have been published. It also seems to have nothing to do with speciation, by whatever definition. It's also tedious, as it takes 14 pages just to arrive at anything mentioned in the abstract. It makes a lot of claims, none of which seem to be supported by evidence, or in fact by reality. In particular, he seems to be using mostly taxonomically scattered bacterial genomes, and when he gets to eukaryotes confuses species with higher taxa up to the level of Class (e.g. Cnidaria). I can see why it wasn't published.

      On the other hand, Coyne & Orr's book provides lots of experimental and observational evidence for its claims.

      Delete
    66. Hey Quest!

      If RNA World hypothesis is not good enough for you to explain the origins why don't you finally tell us how the Designer did it. You've been ranting about how the ID set up quantum mechanics to produce life. Why don't you tell us how he did it? I've never seen anyone making such a claim so prove me wrong you are not mad. If you do it nicely maybe even professor Moran will show you mercy and not remove your comment. I personally think professor Moran tolerated you and your vulgar language too, too long.
      Yes, he uses strong language when he is upset or frustrated with some IDiests, but this is his blog and he lives in the country that cherishes freedom of speech and religion. Nothing campers to USA. I've lived here for most of my life and I know.

      Delete
  9. The five things one should know about before saying talking about junk DNA aren't "rules." They're facts -- observations or (in the case of ii) calculations about facts. These aren't based on religious or atheistic assumptions. (To be sure we avoid assumptions, we might rephrase iii as "Many genomic sequences were inserted by transposable elements.)

    I'm an expert in certain aspects of plant taxonomy. When I talk about them, people should pay attention and learn. However, I have sometimes confidently proclaimed things that turned out to be wrong. I've had to apologize and change. I am sure Frank Collins can make mistakes too. And so can Dr. Moran, though on the junk DNA topic his ideas seem well thought out (they takes into consideration all 5 listed facts and more) and they look right to me.

    ReplyDelete
  10. By the way, bwilson295 = Barbara who has been posting here sometimes. I'm not trying to create sockpuppets, not that there's be any point in that for me. I'm just incompetent dealing with the fact that my e-mail account changed.

    ReplyDelete
  11. Barbara,
    You said "The five things one should know about before saying talking about junk DNA aren't "rules." They're facts -- observations..."

    That's not correct.
    As I demonstrated in my posts about the things, they are based on inferences, not observations.
    Of course you know, this is a huge difference to a scientists, because inferences (or assumptions) should never be used as an evidential foundation for a theory or interpretation.

    ReplyDelete
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    1. As you wouldn't know, never having met any actual scientists, observations are just very strongly supported inferences. Inferences and assumptions, on the other hand, are quite different things. Inference is the essential tool of science.

      So, yes. Those five things are inferences, observations, and facts.

      Delete
    2. Ed Reynolds: As I demonstrated in my posts about the things, they are based on inferences, not observations.

      You demonstrated no such thing. Every one of your substantive points had been shown by us to be factually incorrect. When the factualuty of your false claims was refuted above, rather than defend them, you changed the subject to other false claims, which have also been refuted.

      For example, you assert that sequence conservation assumes universal common descent from one life form. When presented with a paper demonstrating that only 7% of the genome is functional, but which only assumes all HUMANS descend from a common ancestor, you emit nonsensical blurts.

      You cite ENCODE scientists as your authorities for how much of the genome is proven functional, but your own authorities dispute your claims.

      You cite Michael Behe as your authority for claiming common descent is merely an "assumption" never tested in 155 years, not knowing that Behe accepts common descent and even considers it "trivial", though Behe posits that the mechanism of generating mutations was supernatural in the past-- a "puff of smoke" as he called it.

      You have made no points which were not factually incorrect and refuted as such. You just change the subject when proven wrong.

      Delete
    3. It's not even necessary to invoke any kind of common descent to estimate the fraction of the genome that is constrained. The classical argument is based on the mutation rate and would be just as valid if multiple human lineages were independently created. The creationist assertion that the whole genome has to be functional is a metaphysical, "God don't make no junk" assumption about the nature of the deity.

      Delete
    4. Ed Reynolds, I keep hoping that people blundering around here writing really ignorant things are just awkward, ignorant people who would like learn more about evolution. And once again, I am disappointed.

      For one thing, it’s hard to believe you could reach a stage of being able to write grammatical, correctly spelled sentences and not know that we do not start with “ASSUMPTIONS about how inheritance works” but with a good basic understanding about how inheritance works.

      As to the specifics of the list:

      (i) C-value paradox or enigma – Observation: organisms that we think are simple (e.g. onions) sometimes have a lot more DNA and a lot more genes that organisms we think are complex (e.g. humans). Sometimes organisms that are very similar in structure and appearance differ by a factor of 12 or more in the amount of DNA they have. (This is called a paradox or enigma because we expected that complexity and DNA content would be correlated, and observations didn’t meet our expectations.)

      (ii) mutational load – observation of about 100 (70? 150? – I forget) mutations per newborn human plus calculations about effects of that many mutations if all DNA is functional leads to the conclusion (certainly not an assumption) that that many mutations would kill off so many embryos that humans would go extinct unless each of us produced thousands of offspring.

      (iii) evolutionary origin of most genomic sequences from transposable elements – Observation: many DNA sequences in diverse organisms match or approximately match DNA sequences of transposons. (I can’t confirm that “most” do, but many do.) We understand that and much about how transposons jump around the genome propagating themselves and can get stuck some places, slowly mutating to oblivion (conclusion from interesting observations and experiments). Combine the first observation with our knowledge of transposons, and conclude (don’t assume) that many DNA sequences in diverse organisms originated from transposons doing their own thing.

      (iv) essential requirement for ‘structural’ or ‘spacing’ DNA sequences in gene expression and genome architecture -- a summary of observations and thought; some DNA is used for other useful things, not for making useful proteins, not for making useful RNA, and not for regulating DNA. Just for providing necessary attachment points or shapes. You should actually like this one – is explains that some non-coding DNA is essential, not junk.

      (v) limited sequence conservation in most genomic regions between evolutionary related species, -- Observation: if you compare DNA sequences of species we think (on morphological grounds) are related, you find that some parts of the DNA have the same or very similar sequences (are conserved). Further research shows that most of these similar sequences code for proteins or for useful RNA’s such as the parts of ribosomes. In many other parts of the DNA – in most parts of the DNA – corresponding sequences are somewhat to very different (not conserved). Oh, and if you want to compare sequences from random species, just to get rid of that level of thought about relatedness, most sequences won't match and aren't conserved.

      The idea that much DNA is “junk” or useless or unnecessary results from observations such as (i), (iii), and (v) and pseudogenes, and both results from and explains (iii).

      Delete
    5. Georgi Marinov:

      The creationist assertion that the whole genome has to be functional is a metaphysical, "God don't make no junk" assumption about the nature of the deity.

      We should add that their argument is a "good design" argument.

      But if you make a "bad design" argument about some adaptation, creationists react in horror. We can't make assumptions about the mind of the Creator, they cry. What makes you think that you can know what kind of design the Creator wanted?

      They are totally, utterly, wildly inconsistent in all this, rejecting good/bad design arguments in general, and then using them for the case of Junk DNA.

      Delete
    6. Barbara:
      Biologists have done much valuable research, and I don't mean to devalue it.
      On the other hand, the Darwinistic rhetorical framework is imposed upon all students who want to partake in this research. Dr. Moron is a prime example, publishing a textbook that neatly weaves Darwinian assumptions into real science. For students and researchers to break free of this racket, they need to be able to separate the Darwinian assumptions from the good science.
      Unfortunately, this causes no little embarrassment to the Morons who occupy the Ivory Tower, for their irresponsible Darwinian assertions are finally being challenged at the molecular level, and revealed for the atheistic dogma that they are.

      Delete
    7. Dr. Moron is a prime example, publishing a textbook that neatly weaves Darwinian assumptions into real science.

      Thank-you for buying a copy of my book.

      ... their irresponsible Darwinian assertions are finally being challenged at the molecular level,

      I'm a biochemist so I can make some claim to being an expert on what happens at the molecular level. Read, listen, and learn from the expert.

      Delete
    8. Dr. Moron,
      Okay, so as a biochemist, you are familiar with all the attempts to defend Darwin's challenge on the molecular level?
      I'm referring to this challenge, implicit in Darwin's admission:

      “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case.”
      ― Charles Darwin, The Origin of Species

      Here, Darwin is much more genuine in his challenge than many Morons to follow - he implicitly challenges his opponents to produce an example of a complex structure that putatively cannot be arrived at by numerous, successive, slight modifications (notice, though, that Charly still doesn't have the balls to include "beneficial" in his modifications, even though he knows full well that all his steps must be beneficial or they simply won't happen. Also, he uses the term "impossible", which is meaningless in science, so his progenitors must demonstrate something that is plausible, not just possible.)

      Well, thanks to all of biochemistry, many scientists have recognized scores of ready examples, putatively of just the type to which Darwin was referring.

      The challenge implied by Darwin is no less than:
      "Bring it on, IDiots: show me a complex structure and I'll show you how it could be formed by slight modifications"

      And it's been coming on. For decades now. The decades-old term "irreducible complexity" was picked up and dusted off by Michael Behe, for instance, after he read Michael Denton's book "Evolution - A Theory In Crisis".
      Behe, who had up until that time been spoon-fed by Charlie's Morons, realized that there's no empirical reason to accept that the neoDarwinian mechanism of chance mutations along with ANY naturalistic cause, is true.

      So Doctor, in your experience, what have YOU done or seen done that has demonstrated that even the very FIRST example, the bacterial flagellum, can be explained the way Darwin claimed?

      Delete
    9. Ed says: "Dr. Moron is a prime example"

      That's Professor Moron to you, Ed.

      Seriously, with a name like "Ed" you're doctoring other people's names? You want us to doctor yours? Think a minute: what could we do with "Ed" if we wanted to? Three guesses. You want us to treat you like you treat Prof. Moron? It can be done.

      Why does every anti-evolutionist who comes here make false statements, get proven wrong & humiliated, and then call Prof. Moran "Moron"? You're the 99th antiscientist we've had come through here and do that. Same arguments: "Atheism is a religion, you're biased but I need no evidence, your observations I'm going to call atheist assumptioons..." Ken Ham's robotic cool aid drinkers.

      Delete
    10. Oh, Ed R. You blithely disregard several items as "assumptions." I go on at too-great length explaining that these are observations, not assumptions, a distinction that is rather important. You dismiss all this with, "Biologists have done much valuable research, and I don't mean to devalue it. On the other hand . . .," apparently not noticing that the point is that you'd made a major classification error.

      Then, you go on to say that Darwin "knows full well that all his steps must be beneficial or they simply won't happen" although, as has been explained repeatedly at this site, steps in evolutionary change can be neutral or even somewhat harmful.

      You're just playing with words, words you don't even understand. You don't know about patterns of biodiversity; you don't know about biochemistry; you don't seem to understand how to reason from evidence to theories (partly because you don't recognize the evidence -- observations -- for what it is); you don't seem to understand evolution (what "Charly" might have thought is much less important in 2015 than you think); and you don't know about how science works as a social phenomenon.

      If you took the time and effort to learn some of what you're missing, you might have interesting things to say. I won't hold my breath.

      Delete
    11. Ed Reynolds,

      You're an ignorant imbecile with delusions of grandeur. Stop trying to pass your ignorance for knowledge. You present the stuff with malice and misunderstanding only proper of propagandists. You're not doing yourself or your beliefs any favours. Imbecility and arrogance don't work well together. You should renounce at least one of them.

      You're "citing" Darwin without having actually read the book. Don't be ignorant on purpose, go ahead and actually read it. Then come back and tell us if Darwin talked about molecules, and genetic material, and mutations at all. Situate Darwin in time, situate Mendel, molecular biology, and please explain to us how you think that Darwin was thinking of mutations.

      Also, make sure that Darwin "omitted" the word "beneficial" with the malice that you imply, you ignorant fool. He repeatedly used such wording as "useful to its possessor" and other words that obviously implied "beneficial." Read the book idiot! Pay attention to it! It doesn't work to come back with quotes taken out of context. It doesn't work if you go hunting for misquotes in creationist propaganda. You have to read the book for comprehension.

      Not only that, then prove that Larry, and everybody else here who does not share your imbecilic beliefs, believes that Darwin had it all figured out and that only beneficial and useful changes can make it into evolutionary events. After all, you think that we all were indoctrinated into Darwin (what an ironic, ignorant, nonsensical, arrogant, claim, as if those who decide to work in science did so just in order to let themselves be indoctrinated, you're too much of an idiot!). OK, show that we unquestionably follow Darwin.

      If this was up to me, I would ban you and then use your comments to demonstrate the creationist-propaganda-sucking mentality that keeps arrogant imbeciles like you in creationism (good riddance, I would not want an idiot like you on my side).

      Delete
  12. Dear Morons,

    Being called names isn't pleasant, is it?
    Why don't you tell that to the Grand Moron? I'm only giving him a dose of his own medicine. I'm sure he can take it.

    Anyhow, rather than nit-picking at my choice of words, why not face the elephant in the room:
    The challenge that biochemistry poses to the Darwinian claim - The irreducible complexity of the Flagellum, as the most popular example.
    Barbara:
    Where in the biochemistry literature has the step-by-step assembly of the flagellum been described plausibly?
    Put up or shut up. Only the credibility of the "inferences" you depend on is at stake.

    ReplyDelete
    Replies
    1. I knew you could not possibly take yourself seriously enough and go on and actually read for comprehension.

      Barbara made quite an effort at writing some explanations for you that you did not bother to read.

      The flagellum has been shown not to be irreducibly complex a plenty. You could save yourself some embarrassment and search this very blog for some answers. But you could not care less. Nah. Understanding the answers would require some effort you're not willing to make, and you rather keep displaying yourself as an arrogant imbecile in the sacrosanct name of your beliefs.

      Keep it up. Like "Quest" comments, yours serve as illustration of the stupidity that it takes to believe the way you do.

      Delete
    2. @Ed Reynolds "Anyhow, rather than nit-picking at my choice of words, why not face the elephant in the room:
      The challenge that biochemistry poses to the Darwinian claim - The irreducible complexity of the Flagellum, as the most popular example."


      Because this pseudo-challenge has already been met beyond all reasonable doubt, multiple times. Irreducible complexity is not a barrier to evolution, not for the flagellum, not for anything. In fact the emergence of irreducibly complex structures is an inevitable result of the evolutionary process.

      The Evolution of Irreducible Complexity
      The Evolution of the Flagellum

      Delete
    3. Re Ed Reynolds

      Read Ken Miller's testimony in the Dover trial.

      Delete
  13. Ed R, you should be wondering, "Why do all these reasonably intelligent people think evolution really happens?" There are better reasons than you silly "indoctrination" conspiracy theories. Dare to read a book that actually explains why. Dare to read the book "Why Evolution Is True." You don't have to tell us you did it -- just quietly work up your courage and do it.

    Even if you don't accept the reasoning in the book, at least your writing here will become more interesting to the group as a whole than the recycled Intelligent Design anti-evolution arguments you've been using so far.

    ReplyDelete
  14. Barbara,
    Thank you for your gracious tone in the face of ridicule. I had forgotten about that.
    You ask me to wonder why so many intelligent people believe in Darwinian evolution. Yeah, I thought of that too, and I did. So I looked into it. And I came to my conclusion.

    You ask me to read Jerry Coyne's book?
    Have you seen Jerry Coyne's lecture on the book? I have.
    His preamble was something like:
    'Just a little background for you: Evolution is defined as a theory that you would have to be DUMB not to believe'.
    Anybody who introduces a topic with 'you'd be DUMB not to believe it' certainly has a dog of his own in that race, to say the least.
    The kindest word to describe that is 'unprofessional'. (hey, maybe I should go ridicule him for a while...)
    You don't understand - the challenge has been made. Irreducibly complex structures and systems are being found by the dozen. You are challenged to back up Darwin's challenge. Will you demonstrate that just one - the flagellum - was built by small, manageable steps by random mutations?

    Okay, I'll go find a blog entry that talks about the flagellum and complain there.

    ReplyDelete
    Replies
    1. You ask me to wonder why so many intelligent people believe in Darwinian evolution

      No idiot, she asked you to ponder why intelligent people think that evolution really happened. Evolution is not just Darwinian. Pay attention and think you imbecile. Your conclusion does not answer the question. People don't decide on working to figure out how nature works only to then sit and allow themselves to be indoctrinated. That just doesn't make sense. We want to understand how nature works. Sitting into indoctrination sessions would be counterproductive to our goals. Maybe you're too much of an idiot to understand something that evident.

      Translation of the rest: Ed Reynolds read a book on evolution by people who know what they're talking about? No way! Flagellum, flagellum! Look at the flagellum! Darwin's challenge!

      Ed, I don't mind if you want to believe that evolution happened or not. I could not care less if you think that "god-did-it" is some kind of an answer. I do mind that you're so arrogant about it while remaining stupidly ignorant about both the theory of evolution, which is far gone beyond Darwin, and about people who accept the theory.

      As an exemplar of creationism, you make a sure good work showing that some actual thinking, and listening and reading for comprehension, are not things people like you are willing to do.

      Delete
    2. Re Ed Reynolds

      Actually, I prefer Richard Dawkins' reaction to hearing a lecture by faux mathematician David Berlinski:

      One who rejects the theory of evolution is either ignorant, stupid, insane, or wicked (but he didn't want to consider that). Berlinski is neither ignorant, stupid, or insane.

      Delete
    3. @Ed Reynolds "His preamble was something like:
      'Just a little background for you: Evolution is defined as a theory that you would have to be DUMB not to believe'.
      Anybody who introduces a topic with 'you'd be DUMB not to believe it' certainly has a dog of his own in that race, to say the least."


      No actually Coyne introduces the subject by giving a strong case that the primary reason people reject evolution is because of fundamentalist religious indoctrination.

      Delete
    4. Hey Ed,

      Instead of complaining, why not spent the first 25 years or so of your life educating yourself in the subject at hand, getting an undergraduate degree in the field and then doing graduate and post graduate work in the field, publishing the results of your work in peer reviewed journals and having your work being cited by other experts in the field.

      That's what real scientists do Ed, what you do is lazy, self-centered masturbation.

      And I have to agree with colnago80 and Richard Dawkins, the motives of cretinous idiots like Ed Reynolds are wicked, these tiny little people realize that they will never make any contribution to increasing our understanding of how reality actually works and are gleefully pleased to leave their mark on the world by tearing down the works of others.

      It is easier to destroy than create as religious fuckwits like Ed Reynolds so amply demonstrate.

      Delete
    5. Hey, I'm not the one getting PAID to do the research, buddy.
      I don't claim to be a real scientist.
      I'm your customer, and I expect answers.
      Why don't the Darwinians admit their own bias and assumptions?

      Delete
    6. I'm your customer, and I expect answers.

      Yet you seem resistant to anyone offering you any. You won't read Coyne 'cos he thinks you'd be DUMB not to accept evolution given the evidence (said with a chuckle: 40% of Americans are that 'dumb', with a particular bias towards the Southern states. Turkey must feel really insulted). Your hackles are up before anyone starts.

      So here's a bias I'll admit to: I tend to assume off the bat that someone who has already decided that science is way off in accepting evolution is very unlikely to be persuaded otherwise. Forthright responses like the ones you are getting will probably only reinforce your entrenchment, but it's up to you whether the stridency or intellectual contempt of advocates is really relevant to your desire or otherwise to truly get to grips with a particular field.

      Delete
    7. Hey Ed,

      Let's focus on things you are qualified to talk about and god knows that's a pretty small list.

      How are things between you and Eugenie Scott ?

      All patched up ?

      I'd hate to think to such a promising relationship was going bad.

      Delete
    8. Mr Reynolds,

      you have been given answers, more than enough. But your own bias and assumptions prevents you to admit you're wrong and science is right.

      All the other options you tried failed big time, ENCODE blew up in your face, Behe was shown to be wrong under oath, FLAGELLUM like blood clotting came right back at you.

      It's now time to play the consumer looking for answers ploy? Wow, you really are stupid aren't you...

      Delete
    9. Mr. Reynolds writes: Why don't the Darwinians admit their own bias and assumptions?

      This is typical creationist propaganda: ask a question based on false premises. If we attempt to answer, we acknowledge your premise as valid. We don't accept your premise, that the observations and observed evidence for Junk DNA can be rhetorically waved away by falsely calling them "assumptions" and "bias."

      The accusation of bias is not evidence against Darwinism, nor is it evidence that God did anything. It is an appeal to motive, a logical fallacy, which creationists universally have used as a substitute for evidence.

      The Christian writer C. S. Lewis coined the term "Bulverism" to describe an accusation of bias not backed up by evidence. He predicted it would be the most powerful force in the world. In America's Republican party, this is so.

      Delete
    10. Hey, I'm not the one getting PAID to do the research, buddy.

      Nope. You're not. I am not paid to do that kind of research either. So what? That does not stop me from reaching and getting some proper understanding of the field.

      I don't claim to be a real scientist.

      Yet you do claim to know better than scientists what science and evolution are about, how much we know, how much we don't know, and how we were indoctrinated into "Charly."

      It shows that you're not a real scientist, but you behave as if you thought of yourself as one, despite your obvious ignorance and propaganda-fed mentality.

      I'm your customer, and I expect answers.

      If you expected answers, you would pay attention when answers are given to you. But you ignore and dismiss the answers without even trying to understand them. You don't expect answers. You think that you already know them.

      Why don't the Darwinians admit their own bias and assumptions?

      Go find some Darwinians and ask them if/which, and if they admit to them.

      As of me. I'm not a Darwinian, but I have biases and assumptions Ed. That's why I work hard to discover them and use evidence to either get rid of them or confirm them. That's part of what being a scientist means. We should be able to confront the evidence and accept the answers whether they conform to our expectations or not. For example, I did not want evolution to be true, yet I discovered that I could not deny the evidence. So I moved on.

      It's not enough to admit bias and assumptions Ed. It's about being able to grow up.

      Why won't you admit to your own biases, assumptions, deep ignorance, and then actually listen?

      Delete
  15. Photosynthesis: "No idiot, she asked you to ponder why intelligent people think that evolution really happened. Evolution is not just Darwinian.

    What are you, drunk?
    I know that Evolution includes more than Darwinism.
    And I'm talking about the "Darwinism" part of evolution, not the observed part.

    Pay attention and think you imbecile. Your conclusion does not answer the question. People don't decide on working to figure out how nature works only to then sit and allow themselves to be indoctrinated.

    -They do if they HAVE TO to get into the profession...

    That just doesn't make sense.

    -Makes sense to me...

    We want to understand how nature works. Sitting into indoctrination sessions would be counterproductive to our goals.

    Yes, it would be. And it IS. But that's the price we pay to propagate Darwinism.

    Maybe you're too much of an idiot to understand something that evident.

    Translation of the rest: Ed Reynolds read a book on evolution by people who know what they're talking about? No way! Flagellum, flagellum! Look at the flagellum! Darwin's challenge!

    -I notice you have nothing evidential to say about the flagellum.

    Ed, I don't mind if you want to believe that evolution happened or not. I could not care less if you think that "god-did-it" is some kind of an answer. I do mind that you're so arrogant about it while remaining stupidly ignorant about both the theory of evolution, which is far gone beyond Darwin,

    -Hey, buddy, I'm not the idiot you make me out to be. I know that. But NeoDarwinism has kept Darwin's assumption that life forms originated by naturalistic factors acting on random variations. This has not been empirically confirmed.
    That has led to a tangled web of rhetorical misdirection that every student has to resign himself to in order to graduate.

    and about people who accept the theory.

    As an exemplar of creationism, you make a sure good work showing that some actual thinking, and listening and reading for comprehension, are not things people like you are willing to do."
    -Right back at you.
    Have you read any books by pro-ID professionals?

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    1. Ed Reynolds, your questions about irreducible complexity and the flagellum have already been answered. See my previous posts.

      "But NeoDarwinism has kept Darwin's assumption that life forms originated by naturalistic factors acting on random variations. This has not been empirically confirmed."

      Yes it has. Ed, do you understand what a substitution model is? Phylogenetic inferences are done explicitly using substitution models as a basis. The fact that they strongly agree with comparative anatomy, embryology and so on is then an incredible and overwhelming confirmation that the process of diversification was a natural, biochemical process of a stochastic distribution of mutations. We can even test this result further by resurrecting ancestral states(using the method known as ancestral sequence reconstruction) and testing them for functionality. What we find in particular (often alternative, more primitive functions from which the extant functions are derived), and the fact that these reconstructed ancestral stages are even functional, is then another level of confirmation of evolution.

      So the problem is, Ed, that you have zero goddamn clue about the subject, because you've got all your information from religious propaganda mills and pop-sci articles/books.

      Delete
    2. Ed - what is it that evolutionary theory is failing to provide - what's the kind of evidence that's missing but might change your mind about it? And how is Design Theory providing satisfactory alternative answers - to an equivalent level of detail - to that on which evolutionary theory falls short?

      Delete
    3. I know that Evolution includes more than Darwinism.

      Then don't paint us as if we all held to Darwinism you idiot.

      And I'm talking about the "Darwinism" part of evolution, not the observed part.

      You wouldn't be able to distinguish Darwinian from other kinds of evolution. Junk DNA are not Darwinian for example. But you did not know that, otherwise you would not insist on "Darwinian evolution" when somebody suggests you to wonder why so many intelligent people think that evolution really happened. "Really happened" is not the same as "happened exactly the way Darwin theorized the process to be."

      -They do if they HAVE TO to get into the profession...

      Really? How exactly would that work? Not once did I sit in a session demanding my allegiance to "Darwinian" or any evolution. Hell, I would have quitted on the spot. How exactly could anybody get us all forced into indoctrination sessions? How exactly would it work so we would never be opposed to the indoctrination? How exactly would it work so as generations pass, we would not just agree that enough is enough? We're talking about people with deep curiosity to actually understand. How exactly would that kind of people get indoctrinated never to speak about it?

      I notice you have nothing evidential to say about the flagellum.

      Then you're an idiot because I repeatedly told you to search in this very blog, while many others gave you direct links to some of the answers.

      Hey, buddy, I'm not the idiot you make me out to be.

      Well, you're working hard to confirm my suspicions.

      But NeoDarwinism has kept Darwin's assumption that life forms originated by naturalistic factors acting on random variations.

      Darwin's assumption? This is science Ed. We are trying to find actual explanations. Primitive peoples thought that volcanoes were gods, and that led them to make offerings to those volcanoes, from food to people to virgins. If only they had assumed that volcanoes were natural phenomena!

      This has not been empirically confirmed.

      You have it backwards. Non-natural assumptions should be empirically confirmed. Otherwise we’d be dealing with volcano gods on a daily basis. You would have to start explaining what such non-natural factor would be. How to distinguish this factor from mere anthropomorphisms. How to know of this factor and its expected influence. Why is this factor never found in experiments and in the field. Why does random mutagenesis and probability of fixation explain so well the differences we see in different species instead of showing that some non-natural factor intervenes. Etc. We're not talking about a Darwinian assumption, we're talking about the very heart of science, and the most basics of reasoning. If we want an answer, we better start with what the evidence shows. Either we're looking for answers, or we're playing to be primitive tribes worshiping a volcano.

      That has led to a tangled web of rhetorical misdirection that every student has to resign himself to in order to graduate.

      Rhetorical misdirection is calling evolution "Darwinian evolution." Rhetorical misdirection is pretending that we're indoctrinated, while you read only the crap spoon-fed to you by propagandists. Rhetorical misdirection is pretending that somebody could control the whole planet to ensure that people won't graduate unless they swear to evolution, and that then we would just stay quiet.

      Have you read any books by pro-ID professionals?

      Yes. I have talked to them in person too. Their ignorance shows after a few sentences. That when what I discover is not mere propaganda. Professional pro-ID is rhetorical misdirection at its finest.

      There you have it Ed. Now let's see if you can actually think. I bet you'll take bits from here and there, fit them into your propaganda, and miss the points entirely.

      Delete
  16. "
    Really? How exactly would that work? Not once did I sit in a session demanding my allegiance to "Darwinian" or any evolution.

    I's called "classes" and they happen all the time. It's not done overtly, so you wouldn't be able to 'put your finger on it' unless you were given help from the outside to see objectively.

    Hell, I would have quitted on the spot.

    -if you knew it was happening to you.

    How exactly could anybody get us all forced into indoctrination sessions? How exactly would it work so we would never be opposed to the indoctrination?

    Easy. It's a career decision.

    Some people ARE opposed to the indoctrination. Some just keep their mouths shut about it to avoid persecution. Others don't realize they've been hoodwinked until later, when they 'dare' to read literature critical of Darwinism.
    But most people are already indoctrinated by Darwinists propaganda 'cartoons' such as Cosmos before they even hit secondary school.

    How exactly would it work so as generations pass, we would not just agree that enough is enough?

    Yes, very good question! Why hasn't anyone stood up and said "enough! We're not finding the pathways that Darwin predicted we would find. What other explanations could there be?"

    We're talking about people with deep curiosity to actually understand. How exactly would that kind of people get indoctrinated never to speak about it?"

    Good question. Ask the Moron about it; he's part of the textbook writing racket.

    ReplyDelete
    Replies
    1. We've seen your kind 1,000 times before and your arguments are decades old. Hey Disco Stew, wearing your bell bottoms and saying, "Disco rules, man", go over to Panda's Thumb and search the old archives from more than a decade ago!! for the answers to your infantile "flagellum" blurts.

      ShithEd, you're a fantastically dishonest interlocutor who thinks he can make shit up and when we prove you're wrong with evidence, you just make up more shit.

      We will have zero tolerance for appeal to motive fallacy (Bulverism) and accusations of bias not backed up by evidence. The right-wing has gone absolutely bonkers, completely unhinged and insane with Appeal to Motive fallacy. Appeal to Motive is not evidence, ShithEd, and we will have zero tolerance for it.

      You're a robot who's been brainwashed by cultists and Kochists. Your accusations of indoctrination are proof that you have been indoctrinated. Your accusations of bias are proof of how biased you are. We have scientific evidence; you robotically emit old wives' tales, urban legends and creationist lies we've been seeing for decades and refuting for that long.

      You should deprogram yourself, but your narcissistic personality disorder is getting in the way. Right-wing cults know how to exploit the insecurity and narcissistic egomania to brainwash insecure conservatives. Your tedious, robotic accusations of "indoctrination" are simply right-wing propaganda and your Appeals to Motive are not scientific evidence for creationism, or against evolution.

      None of us are interested in your narcissistic personality disorder or your other mental problems. You're just another shithead conservative who thinks he's better than the world's scientists and has NO IDEA what goes on in any classroom or science lab.

      You're not better than us, ShithEd, and every Appeal to Motive and accusation of bias from you proves only how brainwashed and indoctrinated you are.

      Your robotic accusations of bias are proof that YOU HAVE NO EVIDENCE AGAINST EVOLUTION. If you had evidence against evolution, or for creationism, you would have presented it. Instead we get Appeal to Motive fallacy over and over.

      We have the fossils, you have the frauds. You have Paluxy River "man-prints" and a trilobite with a fake "footprint" on it. We have genomic comparisons, you have prehistoric fish's teeth stupidly misidentified as "pre-Flood humans". You have fake diagrams of fossils hoaxed up by anti-evolutionists, we have OBSERVED examples of macroevolution and speciation. We have the human genome project, you have animals lining up two by two to get on Noah's Ark. You have frauds and hoaxes, we have transitional fossils, DNA comparisons, and biogeography.

      Again: Zero tolerance for Appeal to Motive. F%^& you, we won the debate.

      Delete
    2. Well done Ed, being shown the facts is now indoctrination in your fantasy world.

      Hey, what chance are there for people who deny that 1+1=2?

      In our culture we are constantly bombarded with simple arithmetic statements about addition long before we even enter preschool. What chance is there when they only become aware of the literature critical of 1+1=2 until way later in life?

      How are kids even supposed to know it's happening to them? That there are alternative "views" on addition?

      By the way Ed, it seems you have totally changed the subject now that your "challenges" and questions about evolution and common descent have been answered.

      Delete
    3. he's part of the textbook writing racket.

      Burn them! Burn them all!

      Delete
    4. Mikkel,
      Have you got that definition of "functional" yet?

      Delete
    5. Ed Reynolds,

      You're a lazy idiot who can't be bothered to read, let alone for understanding, and to actually think of what we explain. This is exactly what I predicted, and you just confirmed.

      Given your unsurmountable stupidity, I leave you to it.

      Delete
    6. This is worth repeating from my comment to Ed Reynolds above:

      As an exemplar of creationism, you make a sure good work showing that some actual thinking, and listening and reading for comprehension, are not things people like you are willing to do.

      From another comment:

      Ed Reynolds said:
      Hey, buddy, I'm not the idiot you make me out to be.

      My answer:
      Well, you're working hard to confirm my suspicions.


      Ed surely makes a great job at showing that he's the idiot that I strongly suspected him to be. An unreachable idiot.

      Delete
  17. Mikkel - I'm talking about this:

    "Mikkel:
    Do you agree with wikipedia's definition of a pseudogene:
    "Pseudogenes are dysfunctional relatives of genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell.[1] Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism. Although not protein-coding, the DNA of pseudogenes may be functional,[2] similar to other kinds of non-coding DNA which can have a regulatory role."
    http://en.wikipedia.org/wiki/Pseudogene

    If so, please give your definition of "functional" as used above."

    ReplyDelete
    Replies
    1. No, as a matter of fact, you didn't answer my question.
      A rant is not an answer.

      Delete
    2. Ed -- may I call you Eddie-baby? -- you seem as if you're trying to turn that definition into a claim that all pseudogenes are functional. True? If so, you are grossly misreading it.

      Delete
    3. Ed R, I see you've found an excuse not to read "Why Evolution is True." It's an inoffensive, well written summary how evidence is related to the idea of evolution. Too bad -- you might have learned something. But we can't have that, can we?

      Delete
    4. John:
      Yes, you may.
      Actually, I'm just wondering how function is defined in this context, that's all. It seems to have something to do with the discrepancy between Moran and Collins.
      Anyway, I don't have any doubt that some of our DNA is "junk"; of course mutations happen and I'm sure many of them have stayed in the human genome. My main beef was with Moran imperiously setting the Darwinian "rules" of discussing the topic.

      Delete
    5. "No, as a matter of fact, you didn't answer my question.
      A rant is not an answer."


      Yes I did Ed. Here it is again from futher up in this thread:

      @Ed Reynolds "Do you agree with wikipedia's definition of a pseudogene:"

      Yes I agree with that definition, in it's entirety(As in not just the part that might corroborate my preconceptions). Ed, notice that it says "may have a function" in that description. Not that they DO have a function. Ed, please don't just stop reading once you have found something you think confirms your preconceptions.

      Tell me Ed, what does the L-gulono-gamma-lactone oxidase pseudogene in humans do?

      So you were wrong and lying Ed. I in fact answered you, and it wasn't a "rant". And you haven't answered the question I posed you. What does the vitamin C gene in humans do? (GULOP, L-gulono-gamma-lactone oxidase). What does it do Ed?

      Delete
    6. I sincerely doubt that the definition of function has anything to do with the difference between Moran and Collins. If you think so, you should be able to state the difference you think there is between their definitions. Otherwise you would have no basis for that claim.

      Delete
    7. It seems I stumped you all with a simple question.
      Mikkel is waving his hands, trying to change the subject.
      John has 'sincere doubts' about my intuition that there is some discrepancy in the definitions, but without supplying his (or Moran's) definition, it's kind of hard to back that up.

      Delete
    8. I'll give you a definition of function that will suffice for the question you keep dodging: The gene is functional if it contributes to either organismal development, procreation or metabolism in a way that has a measurable effect on fitness.

      So with this definition in hand Ed, what does GULOP in humans do?

      Delete
    9. Mikkel:
      Why do you specify "a measurable effect on fitness"?
      Do you imagine that you know so much about the genome that you can disqualify functions that are not immediately "measurable" by your standards?
      Sounds like hubris to me.

      Delete
    10. Eddie Baby: You have it backwards. You're the one who claims to see a discrepancy, so you must have an idea about a difference. Why won't you explain what it is?

      Delete
    11. We can measure effect on fitness much smaller than can be observed in the lab over millions of years by observing sequence conservation between species. You got a problem with that?

      Delete
    12. Hey Mr. Reynolds, still dodging the question about GULOP?
      Why not give an answer? Why not explain GULOP from an ID POV. You clearly know all, perhaps I'll even sit back, listen and learn.

      But, I won't hold my breath, while waiting for you answer...

      Delete
    13. OK, let's use the definition of 'functional' that IDists use ...

      Delete
    14. "Sounds like hubris to me."

      Them I'm hubristic in your view, I can live with that. Now answer the question you keep dodging.

      Delete
  18. John:
    Let me just see if I know what you mean:
    You compare the genes of two (or several) similar species, and see which ones are the same in both (all). You conclude that the parts that are the same were inherited by a common ancestor, and the rest arose since the split from the common ancestor.
    Then you conclude that, because they are inherited intact from the LCA, those genes that are the same MUST somehow contribute to fitness.
    Is this right so far?

    ReplyDelete
    Replies
    1. Let me just see if I know what you mean:

      Sort of. But you have stated it strangely. It isn't "the same" that we look at, necessarily, just more similar than would be expected if there were no selection. Bits that have evolved more slowly than we expect from neutral evolution must be under selection. How is it that an expert like you, capable of confounding the professionals, doesn't already know this?

      Delete
    2. Don't forget the biases in the distribution of mutations in neutral regions. What Ed must explain is why, if these mutations didn't happen for well-known biochemical reasons, we see an overabundance of mutations expected on biochemical grounds. No ID proponent have ever even TRIED to account for this fact.

      Delete
    3. No only would Eddie have to account for transition/transversion bias, he would also have to account for the apparent lessening of that bias in increasingly distant pairwise comparisons. The standard view can explain that as saturation due to multiple hits. But how would Eddie do it?

      Delete
    4. Yes that is exactly the question. It's funny because I often see IDists argue that the similarities between different species is because of common design. But there is a whole host of peculiarities in the similarities that are not account for with this ad-hoc rationalization of theirs.
      It simply looks like, if it was all designed, that it was designed to look like evolution happened.

      Delete
  19. Mikkel:
    I'll give you a definition of function that will suffice for the question you keep dodging: The gene is functional if it contributes to either organismal development, procreation or metabolism in a way that has a measurable effect on fitness.

    Okay, thank you. Just wondering.

    So with this definition in hand Ed, what does GULOP in humans do?

    It seems no one knows what GULOP does, if anything.

    ReplyDelete
    Replies
    1. Mr Reynolds, do tell, how does ID explain GULOP? How does ID explain the EV-D68-virus?

      In your rants you seem 'to forget' that ID needs to explain stuff too. Do tell, what's the ID definition of function? Explain with the ID definition of function, GULOP.

      Explain with ID how come the trumpet lily has a genome 30 times larger than human, a very complicated animal like the lungfish a genome more than 40 times larger than H. Sapiens? Care/ dare to explain?

      Delete
    2. So if GULOP doesn't do anything, why is it there in the first place, and why are the inactivating mutations distibuted in multiple different species, such that they agree with the nested hierarchical arrangements we can construct from comparative morphology? Why are the mutations distributed such that they correlate with the kinds of mutations we would expect an overabundance of on biochemical grounds?

      Given that transitions happen more frequenly than transversions, if the GULOP sequence(and countless other pieces of junk-DNA) compared to GULO in species where it actually works have this very same overabundance of transitions, how does that make sense on ID?

      On evolution it makes perfect sense since these are mutations that happened for well-known biochemical reasons. But on design that pattern would make no fucking sense. All you can do on ID is to engage in some senseless ad-hoc reasoning that "it just so happens those are just the mutations the designer wanted to insert".

      Delete
    3. Here Ed Reynolds: http://www.mun.ca/biology/scarr/Transitions_vs_Transversions.html

      Those are the basics. So we can basically restate the question "If the process or mechanism responsible for creating/generating similar gene sequences in multiple independent species was not a natural biochemical one, why do we find the kinds of mutations we would expect if it was a natural, biochemical one?

      Have fun choking on that one.

      Delete
    4. Diogenes: you said:

      "In order to prove that universal common descent was merely Darwin's "assumption" never tested in 155 years, Mr. Reynolds cites as his authority Michael Behe. Michael Behe accepts common descent and has described it as "trivial", that is, given the evidence, proving that common descent happened is trivially easy, according to Behe. "

      Ahh,,, Behe actually said "trivial", not "trivially easy to demonstrate".
      If you read the context of ANY of the times Behe uses the term "trivial" in Edge of Evolution (he didn't use the expression in DBB), you will see what he's talking about.
      For example, if you had read just the FIRST FEW PAGES of Edge, you would have come across Behe's main argument regarding COMMON DESCENT:

      "Yet in a very strong sense, the explanation of common descent is also trivial. Common descent tries to account only for the SIMILARITIES (emphasis Behe's) among creatures. It says merely that certain shared features were there from the beginning - the ancestor had them.
      But all by itself, it doesn't try to explain how either the features or the ancestor got there in the first place, or why descendants differ."
      -Edge of Evolution, P.11,ibooks version.

      Behe demonstrates that common descent is "trivial" in the sense that it's IRRELEVANT to the ID investigation, not that it's "trivially simple" to prove.
      Please stop twisting the words of your professional opponents; it's so unprofessional.

      Delete
    5. I think it's a good time to remind ourselves what the expert, quoted by you guys in this thread, has to say about the definition of FUNCTION:

      "Ewan's Blog: Bioinformatician at large
      Q. Hmmm. Let’s move onto the science. I don’t buy that 80% of the genome is functional.
      A. It’s clear that 80% of the genome has a specific biochemical activity – whatever that might be. This question hinges on the word “functional” so let’s try to tackle this first. Like many English language words, “functional” is a very useful but context-dependent word. Does a “functional element” in the genome mean something that changes a biochemical property of the cell (i.e., if the sequence was not here, the biochemistry would be different) or is it something that changes a phenotypically observable trait that affects the whole organism? At their limits (considering all the biochemical activities being a phenotype), these two definitions merge. Having spent a long time thinking about and discussing this, not a single definition of “functional” works for all conversations. We have to be precise about the context. Pragmatically, in ENCODE we define our criteria as “specific biochemical activity” – for example, an assay that identifies a series of bases. This is not the entire genome (so, for example, things like “having a phosphodiester bond” would not qualify). We then subset this into different classes of assay; in decreasing order of coverage these are: RNA, “broad” histone modifications, “narrow” histone modifications, DNaseI hypersensitive sites, Transcription Factor ChIP-seq peaks, DNaseI Footprints, Transcription Factor bound motifs, and finally Exons."
      -http://genomeinformatician.blogspot.ca/2012/09/encode-my-own-thoughts.html

      I'm sure you guys can make sense of the technical language. Does this sound reasonable to you?
      Why / why not?

      Delete
    6. "But all by itself, it doesn't try to explain how either the features or the ancestor got there in the first place, or why descendants differ."

      And thus Michael Behe is directly lying to you. Directly lying. Yes, I repeat, Michael Behe is unambigously and directly lying to you Ed. And you're buying it, because you don't have enough of a background in the subject to know whether it's true or not. You just trust it, blindly.

      I must ask this question again: If the process or mechanism responsible for creating/generating similar gene sequences in multiple independent species was not a natural biochemical one, why do we find the kinds of mutations we would expect if it was a natural, biochemical one?

      Do you understand the question here Ed? Michael Behe says evolution merely tries to account for the fact that there are shared similarities. This is what is a lie, because it is not JUST the fact that there are shared similarities. There is a specific and peculiar pattern IN the similarities, and that specific pattern is the pattern we would expect if they actually evolved from common ancestors through a process of mutations with particular biased distributions. Behe never mentions this, no ID/creationist ever does.

      Given that transitions happen more frequenly than transversions, if the GULOP sequence(and countless other pieces of junk-DNA) in all primates, compared to GULO in species where it actually works have this very same shared derived pattern in the overabundance of transitions, how does that make sense on ID?

      On evolution it makes perfect sense since these are mutations that happened for well-known biochemical reasons. But on design that pattern would make no fucking sense. All you can do on ID is to engage in some senseless ad-hoc reasoning that "it just so happens those are just the mutations the designer wanted to insert".

      Isn't it curious then, how the designer is going out of it's way to insert mutations in the patterns of distribution the normal chemistry of the cell would produce on it's own?

      Delete
  20. Mikkel: you said:
    "I'll give you a definition of function that will suffice for the question you keep dodging: The gene is functional if it contributes to either organismal development, procreation or metabolism in a way that has a measurable effect on fitness.

    So with this definition in hand Ed, what does GULOP in humans do?"

    I don't know what GULOP in humans does. Do you?

    ReplyDelete
    Replies
    1. "I don't know what GULOP in humans does. Do you?"

      Yes, nothing. It does nothing. If you don't believe this, or you disagree, then please account for the pattern of mutations found in GULOP and many other similarly mutating regions of the genome, in all of the primates.

      Delete
  21. ...And just in case anyone missed the expert's point about % function of the genome:

    "Q. So remind me which one do you think is “functional”?
    A. Back to that word “functional”: There is no easy answer to this. In ENCODE we present this hierarchy of assays with cumulative coverage percentages, ending up with 80%. As I’ve pointed out in presentations, you shouldn’t be surprised by the 80% figure. After all, 60% of the genome with the new detailed manually reviewed (GenCode) annotation is either exonic or intronic, and a number of our assays (such as PolyA- RNA, and H3K36me3/H3K79me2) are expected to mark all active transcription. So seeing an additional 20% over this expected 60% is not so surprising."

    So it appears here that there had been previous studies done that resulted in 60% function. Were these studies also contested by Moran et al?

    ReplyDelete
    Replies
    1. Nothing of the sort appears.

      Apparently the difference between exon and intron has never properly entered your mind.

      Delete
    2. Ed Reynolds, based on what you've said, it's obvious that you are a creationist and that you really don't like the concepts of junk DNA, common descent, and especially descent of humans from an ape-like ancestor and other previous life forms.

      I'm curious, besides your religious beliefs, why do you care whether any of those things are true or not? Why do you care whether evolutionary theory is on the right track or not? Is your 'faith' in your religious beliefs so insecure as to need confirmation of your beliefs from science? Is your 'faith' so insecure that you feel the need to question and condemn scientific findings? Is there a voice inside you that is telling you that your religious beliefs are or may be wrong but the religious voice inside you is telling you to fight against scientific findings that contradict that religious voice? Why does it matter to you what science finds? Why does it matter to you what your ancestors were? Why does it matter to you whether you're related to other primates and other life forms or not? And why does any of that matter when it comes to feeling good about yourself? Does your self-esteem depend on who or what your ancestors and relatives were and are? Does believing that you and your ancestors were 'specially created in the image of God' make you feel as though you're way above all non-human life forms? Does believing that you're 'specially created in God's image' and that 'God' doesn't create non-functional DNA (especially in humans) make you feel as though you're a pure and flawless example (or nearly so) of humanity and 'God's' creative power? Why does the thought of being an evolutionary mutt instead of a specially created purebred bother you so much?

      And one more question for now: If evolutionary theory only applied to non-human life forms and all evolutionary scientists were to assign humans to a unique 'specially created in the image of God' category, would you still question and condemn evolutionary theory?

      Delete
  22. Georgi,
    "Nothing of the sort appears."
    Okay, it was just an inference.

    Apparently the difference between exon and intron has never properly entered your mind."

    Without a degree in biology, I can tell by the context that our expert considers both exons and introns to be "active" in the genome.
    So, my ignorance of the details notwithstanding, 80% of the genome is considered functional, and that shouldn't have come as a big surprise, according to the expert.

    ReplyDelete
    Replies
    1. "Without a degree in biology" isn't the important thing about you. It's your inability or perhaps disinclination to read and understand. Exons are for the most part under selection and are clearly functional; introns, except for a small number of regulatory bits like splice signals, are not. I assume you got "active" from "active transcription"; introns are transcribed but are spliced out before translation. By the nature of the mechanism, the cell has to transcribe the intron to transcribe the eons, but that doesn't mean they're functional.

      And if you've been reading any of Larry's blog, you should know that the ENCODE definition of "functional" has nothing to do with what anyone else would have considered functional.

      Delete
    2. Ed, the ENCODE definition of functional is meaningless. How do we know this? Because we could, deliberately, design a long piece of nonfunctional DNA and insert it into a cell. We could then measure the "biochemical activity" of that DNA and find that it was "active" in the way ENCODE defines it.

      Are we now to believe that the piece of DNA we designed to be nonfunctional has a function anyway? Obviously not. So there's something wrong with the definition used by ENCODE, it ignores our knowledge of how DNA interacts with the rest of the biochemistry of the cell nucleus. The mere fact that some piece of DNA is "biochemically active" says nothing about whether that piece of DNA has some actual organismal function the cell is dependent upon. All DNA, once inside the nucleus, would start having some small activity in the sense ENCODE defines it, so it's a meaningless definition they use.

      Now it would take too much space to explain all of this in this thread, but Larry has multiple posts on the subject. You should read them if you want to understand why ENCODE has garnered so much criticism regarding their function pronouncements. And some of those criticisms do not rely on evolution to show that there's a problem with their definition. For example the argument I just here is not an evolutionary argument.

      Delete
    3. Mr. Reynolds writes:
      "So, my ignorance of the details notwithstanding, 80% of the genome is considered functional, and that shouldn't have come as a big surprise, according to the expert."

      OK, is this the ID definition of function? If not, do tell, what is the exact ID definition of function?

      You haven't answered my question. Do enlighten us on the exact ID definition of function?
      And using this definition, predict the amount of functional DNA in our genome. It should be easy to find in ID scientific literature, I expect.

      Delete