Tuesday, October 02, 2012

Reddit: We are the Encyclopedia of DNA Elements (ENCODE) Consortium.

There's been a lot of talk recently about the discussion on reddit concerning the ENCODE publicity fiasco.

Here's the forum ...
AskScience Special AMA: We are the Encyclopedia of DNA Elements (ENCODE) Consortium. Last week we published more than 30 papers and a giant collection of data on the function of the human genome. Ask us anything!
It's interesting to see how some of the consortium members are responding to criticism. My personal view is that none of them seem to be very knowledgeable about genome biology and the work that has been published over the past 40 years.


101 comments :

  1. LM "My personal view is that none of them seem to be very knowledgeable about genome biology and the wrk that has been published over the past 40 years."

    Well, of course not. They probably just got tired of working at McDonald's or the local cineplex and decided to join an international collaboration of research groups funded by the Human Genome Research Institute.

    I was actually thinking about joining as well, but then I thought, meh.

    ReplyDelete
    Replies
    1. My advice would be to keep your job at McDonalds.

      Delete
    2. The thought of me taking advice from steve oberski frightens me to my very core.

      Delete
    3. "Well, of course not. They probably just got tired of working at McDonald's or the local cineplex and decided to join an international collaboration of research groups funded by the Human Genome Research Institute"

      LOL!!

      Delete
  2. Collecting massive amounts of data isn't quite as impressive as conducting hypothesis-driven research, is it? Knowing many digits of pi isn't the same as understanding what pi means. Take a look at the most recent post at the Panda's Thumb about how the creationists have been abusing the data. As Richard Hoppe notes, Birney has a lot to answer for.

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  3. There are a large number of authors involved and some of the ones who do not appear at the press conferences are not happy about the death-of-junk-DNA fiasco. I will not speak for them as my own information is based on a private conversation, but expect to gradually hear some of them back away from the death-of-junk-DNA trope.

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    Replies
    1. Joe:

      expect to gradually hear some of them back away from the death-of-junk-DNA trope.

      Meaning what-- like the way commies gradually backed away from Stalin? OK, 30 years...

      Delete
    2. Let me add to this that backing away is not good enough.

      When somebody publishes a paper saying that drinking piss cures cancer in mice, it winds up on every single newspaper.

      Then later, when 4 or 5 studies fail to reproduce the effect, or show that it doesn't apply to humans, scientists "back away" from the claim-- but you know what? Retractions and "backing away" and failure to replicate never make the newspapers.

      Delete
    3. Diogenes: Retractions and "backing away" and failure to replicate never make the newspapers

      Exactly! And by the time their research proves meaningless, the authors have already taken advantage of all the publicity, advanced their professional career, and life is good! We have to realize that scientists (and lawyers, too!) are among the most educated and smart people around. There are going to figure out how to use the system. And, some people might say: good for them!

      Take, for example, the spokespersons for the ENCODE project. Would they have made the news if they wouldn’t have said that 80% of the human genome is ‘functional’? Likely, not!

      So, the message to other researchers, particularly young scientists, is clear: “adjust to the system or perish into oblivion”

      Delete
    4. Joe: …not happy about the death-of-junk-DNA fiasco

      A few posts back here at Sandwalk, I made the point that the so called ‘junkDNA’ can be under (Darwinian style) evolutionary constrains. Here is a comment I posted on Science’s ENCODE article about this paradigm labeled the “Hummingbird Case” ( http://comments.sciencemag.org/content/10.1126/science.337.6099.1159). What do you think?

      *Evolutionary constrains on genome size evolution: the Hummingbird Case*

      In a previous comment, *Evolutionary questions about junk DNA*, I asked: is the evolution of genome size and junk DNA (jDNA) under host selective constrains?

      One of the main lines of evidence supporting the hypothesis that jDNA serves as a defense mechanism against insertional mutagenesis was the evolution of alternative protective mechanisms such as specific integration sites in organisms that have little jDNA (e.g. Bacteria).

      Indeed, the evolution of specific integration sites is strong evidence for the high selective pressure imposed by insertional elements on their hosts; it should be pointed out, however, that from an evolutionary perspective, the evolution of specific integration sites was a co-evolutionary event, as both the hosts and the inserting elements benefited from this mechanism.

      Unlike Bacteria, which have been under strong selective pressure to maintain a small genome, other organisms, which for various reasons could relax this constrain, used a different strategy for preventing insertion mutagenesis: accumulation of an increasing number of transposable elements including endogenous viruses in their genome in order to serve as a defensive mechanism against insertional mutagenesis. Likely, during its evolution, this novel protective mechanism was enhanced by the presence of additional protective features, such as (sequence-directed) preferable DNA islands for the integration of inserting elements, which relied on the activity of recombination machineries, including homologous recombination.

      Although the process of generating protective DNA was based on the amplifying activity of inserting elements, the sites or regions of the host’s genome in which this DNA accumulated (i.e. was evolutionary ‘fixed’), and its overall quantity, were under evolutionary constraints by the host.

      Whereas the constraints regarding the sites for the accumulation of protective DNA were relatively strict, those on the size of the genome and the amount of jDNA were more relaxed, but at work. Probably, the best example of these host evolutionary constrains at work, even in complex organisms such as vertebrates, is the Hummingbird Case: the hummingbirds have the smallest genome size, not only among birds but all tetrapods, apparently because of the selective force imposed by their high metabolic demands associated with powered flight.

      Delete
  4. Fucking ENCODE has become an issue in my advanced Eukaryotic Microbiology course. While I can explain the issues clearly, it is difficult overcoming the gravitas of Nature, Science, etc.

    ReplyDelete
    Replies
    1. That's funny, where I'm at people seem to realize the hyped nature of what a lot of these big journals publish.

      Delete
  5. Regarding Junk DNA and the definition of "function", the most controversial or widely discussed comments have been those of

    1. Max Libbrecht [mlibbrecht] (who approvingly cites Cryptogenomicon's hype-debunking post)

    2. Rule_30, who says "good riddance to Junk DNA" and then, when he realizes he's talking to Larry, he walks that back. Then he and I have an exchange where he agrees ENCODE did not disprove Junk DNA. He says the same to Larry.

    This comment and thread is often featured in arguments between myself and creationists which I'm sorry to say have been dragged here.

    3. Michael Hoffman's estimate of how much DNA is "functional" is somewhere between 5% and 80%, depending on definition of function. Real specific there.

    ReplyDelete
  6. Being unhappy with the work of close co-workers and backing away on some blogs isn't the same a corrections in the journal that originally published ENCODE's main article. In addition backing away is not the same as admitting an error. E.g., according to faye flam's blog ENCODE researcher John Stamatoyannopoulos assumes that rather 40% than 80% of the human genome are functional:

    He said he thought the skeptics hadn’t fully understood the papers, and that some of the activity measured in their tests does involve human genes and contributes something to our human physiology. He did admit that the press conference mislead people by claiming that 80% of our genome was essential and useful. He puts that number at 40%. Otherwise he stands by all the ENCODE claims:
    “What the ENCODE papers (not the main paper in Nature, but the other length papers that accompanied it) have to say about transposons is incredibly interesting. Essentially, large numbers of these elements come alive in an incredibly cell-specific fashion, and this activity is closely synchronized with cohorts of nearby regulatory DNA regions that are not in transposons, and with the activity of the genes that those regulatory elements control. All of which points squarely to the conclusion that such transposons have been co-opted for the regulation of human genes -- that they have become regulatory DNA. This is the rule, not the exception....”


    IMHO, he completely misses the point that the 80% number is not the heart of the problem. The problem is that ENCODE ignored 40 years of well established genome biology and that ENCODE used an unjustified re-definition of "function". Thus, replacing "functional" by something like "come alive" without defining what the later actually should mean mechanistically in terms of regulation of gene expression doesn't make a better argument than ENCODE's original one.
    It is like saying that not all debris moved on a platform by the slipstream of a passing high speed train but only the paper that is actually lifted is correlated with and thus contributing to the train's velocity. It just doesn't help modifying an argument that didn't make sense from the outset.

    However, although I am skeptic about ENCODE's conclusion on junk DNA some of their data, the design and size of the project as well as the implication big science as ENCODE has on general science and funding I think that ENCODE contains valuable data and that the ENCODE researchers have done serious work. Thus, IMO calling them names like "fucking ENCODE" is not justified.

    ReplyDelete
    Replies
    1. ENCODE scientists can generate valuable data and do serious work AND their spokespeople can fly off the rails to the press. I am dealing with seniors in various biology majors at a major university and am finding that they have heard about ENCODE and that essentially every nucleotide in the human genome is critically important. I do not expect the lay audience to do any better than reasonably well trained students. So I think 'fucking ENCODE' is entirely justified.

      Delete
    2. I would not say 'fucking ENCODE'. The science is not bad, and 400+ people worked on it. It's the interpretation that certain scientists put into the Press Release, egged on by Nature Publishing Group.

      I might say 'Fucking Nature Publishing Group' instead.

      I have looked through a lot of the media coverage. Only about 3 or 4 scientists really hyped these results (Birney, John Stam, Tom Gingeras, a couple of others), out of 400+ scientists in the consortium.

      There are, however, many ENCODE scientists who made statements showing that they never even understood the Junk DNA hypothesis to begin with. Many of them mis-define it and don't even know what it means! (Michael Snyder, Richard Myers, several people at the Reddit interview.)

      There are three problems:

      1. Those 3 or 4 scientists have more sway than the (presumably) hundreds of grad students and post-docs in ENCODE who know the hype is ridiculous, and that junk DNA has not been disproven. Those 3 or 4 scientists have more authority than the grad students, post docs etc.

      2. The media want a Kuhnian Paradigm Shift and will lie to get it. They think "Paradigm Shift" sells papers; while retractions, errata, "the effect is not reproducible", "effect not confirmed", "effect not relevant", etc. do not sell papers.

      3. I have come to suspect that some media people sorted through, and possibly interviewed, many, many scientists who said accurate things (that were boring), in order to find just one scientist who said an inaccurate thing (that was exciting.)

      Consider this quote from Elise Feingold of NHGRI. As far as I know, she's not even in ENCODE and I've never heard of her. So why is she being quoted by NPR? Because she serves the media's "Paradigm Shaft."

      “So the most amazing thing that we found was that we can ascribe some kind of biochemical activity to 80 percent of the genome. And this really kind of debunks the idea that there's a lot of junk DNA or really if there is any DNA that we would really call junk," NHGRI's [Elise] Feingold said. [http://www.npr.org/blogs/health/2012/09/05/160599136/scientists-unveil-google-maps-for-human-genome]

      And why are the media quoting John Mattick as an authority?

      Some suggest that a majority of the genome does have an active role in biological functions. John Mattick, director of the Garvan Institute of Medical Research in Sydney, Australia, who I spoke to in the run up to the publication of these papers, argued that the ENCODE authors were being far too conservative in their claims about the significance of all that transcription. “We have misunderstood the nature of genetic programming for the past 50 years,” he told me. Having long argued that non-coding RNA has a crucial role in cell regulatory functions, his gentle criticism is that “they’ve reported the elephant in the room then chosen to otherwise ignore it”. [Brendan Maher, Nature News Blog, Fighting about ENCODE and junk. 06 Sep 2012, http://blogs.nature.com/news/2012/09/fighting-about-encode-and-junk.html]

      The media people must have sorted through many scientists who told them "It's still mostly junk" to find a few scientists who really didn't even understand the hypothesis to begin with. It takes work to be that inaccurate.

      Delete
    3. "The media people must have sorted through many scientists who told them "It's still mostly junk" to find a few scientists who really didn't even understand the hypothesis to begin with."

      We now see Doigenes oh so delicately weaving a conspiracy theory. Perhaps these clueless scientists could care less about a fading hypothesis in which ideologes sitting in their little corner white knuckle, because they could care less about the advancement of science. Also, you can bet your bottom dollar if the media propped up the Junk DNA idea, the media would be your hero.

      Delete
    4. Also, you have some loose ends dangling over at UD.

      Delete
    5. If any of the UDites ever makes an argument at UD that you think refutes anything I wrote, I DARE YOU to copy and paste their very best argument here. Copy it here, so everyone here can see that your ID authorities, like TheMayan and the UDites, are scientifically illiterate.

      Don't brag and boast about how UDites proved this or UDites proved that. No, copy and paste their very best argument RIGHT HERE.

      For days Anonymous/ "rjop" / "Misc", who stalked after me from Shapiro's blog to here, has taunted me that I must return to UD to face their scary rebuttals!

      Yesterday I did, crushed all the UDites and left. They'll never recover.

      This blog is not UD. Unlike UD or Shapiro's blog, most of the people commenting here are real scientists. People here are not impressed nor fooled by the morons you treat as authorities and their cultist bafflegab-- including TheMayan whom I humiliated at Ewan Birney's blog, and everyone at UD that I crushed yesterday.

      If they ever write anything SCIENTIFIC over at UD or Shapiro's blog, then I dare you to copy and paste it here for the scientists here to see their pathetic blurts.

      Delete
    6. Anonymous, you've got a dangling thing here yourself. You intimated that a paradigm shift was in the air, and then you left it at that. You also said that you were no creationist and that you believed in evolution -- an evolution of sorts, anyway. Shall we ever learn more?

      Delete
    7. Hey Diogenes punk,

      I will be sure to relay the msg to Shapiro he is not a 'real' scientist. I suppose next you will say the ENCODE scientists are not 'real' scientists. Also, get over yourself, this is a public forum and I will respond to anything I choose, you don't like, too bad for you. Also, you never answered my question on what your fist name is. And no I didn't follow you from Shapiro's blog, I followed you from CP after ENCODE hit the news.

      Delete
    8. Also, you crushed the argument at UD, really? I suppose if you call lying and BS 'crushing', so be it. I don't need to copy anything here, anyone is invited to join in > http://www.uncommondescent.com/intelligent-design/ub-sets-it-out-step-by-step/#comment-434621 Diogenes 'crushing' begins at 496. LOL!!!

      Delete
    9. Anonymous writes:

      LOL!!!

      All caps and 3 exclamation points - guess that amounts to QED, eh?

      Delete
    10. Anonymous, rjop, Misc,, etc., said:

      "...anyone is invited to join in..."

      Really? Anyone? "Join in" goes way beyond just looking at that thread or any other thread at UD. Join in means participate, but the hypocritical, cowardly dictators at UD won't allow "anyone" to participate. They often block and ban people who question or challenge their crazy, dishonest, ignorant assertions, and some IDiots often don't allow any comments at all on their dictatorial sermons (e.g. gordon e mullings-kairosfocus), and gordo (kairosfocus) even threatens people with physical violence (six of the best with Mr. Leathers) if they don't kiss his sanctimonious, pompous ass. barry arrington (the UD administrator and evangelical god zombie, lawyer, bill collector, and michele bachman supporter and former employee) even poses incredibly stupid questions and demands that the answers be just as he wants or else he will ruthlessly ban the respondents. He's a power tripping lunatic with delusions of godhood, and so are most of the other IDiots.

      UD is awash with the lies and ravings of impotent, worship demanding, two-faced, IDiotic nobodies who have never accomplished anything productive and only seek to infiltrate and control the lives of everyone on Earth with their insane religious dogma. The so-called "ID movement" or "ID inference" is just relabeled creationism/dominionism.

      Delete
    11. @ TWT

      Diogenes is over there now, Moran, Matzke and others have not been banned. So your whole vampant rant above is moot.

      Delete
    12. @ Jud;

      Pardon me, LoL! Feel better?

      Delete
    13. Unlike UD, most of the people commenting here are real scientists

      'Most of the people'? Well if 'most' of them are scientists here, we are in big trouble.

      Also, no one at TSZ, who interacts with UD, are scientists? Matzke who is on UD quite often, is not a scientist? Oh, Okay...

      And unless you have asked every one of the UD commenters if they are scientists, one can conclude you have made yet another false assumption.

      Delete
    14. @Anonymous / rjop / "Misc":

      Here's a brief compendium of FOUR TIMES where you insanely misrepresent my words.

      Falsehood #1: "I suppose next you will say the ENCODE scientists are not 'real' scientists."

      Jesus Tapdancing Christ, you're stupid. How many times have I said the opposite of that.

      What I wrote, on this very thread: The [ENCODE] science is not bad, and 400+ people worked on it. It's the interpretation that certain scientists put into the Press Release... Only about 3 or 4 scientists really hyped these results... out of 400+ scientists in the consortium.

      So on this very thread, I said there are 400+ scientists in the consortium, and you run and tell people I said there are NO scientists in the consortium.

      Here's what I wrote at the REDDIT thread.

      I know that work like ENCODE results mostly from man-centuries of labor by an army of nameless grad students and post-docs who do most of the bench work... So, I want to appreciate the labor of that army of nameless grad students and post-docs for their work in compiling the ENCODE data, which I agree will be a valuable resource for years to come. ...the ENCODE data are valuable; 2. however, its true value is not what the PR says it is.

      I have big problems with the PR version of ENCODE, but I do not challenge the accuracy, fidelity or value of the massive amount of data compiled.


      So you go tell people I said the ENCODE people are not scientists, you lying shit Anonymous.

      Falsehood #2: I will be sure to relay the msg to Shapiro he is not a 'real' scientist.

      I never wrote that. I never said Shapiro was not a real scientist. I said most people who comment at his blog were not scientists.

      What I wrote: Unlike UD or Shapiro's blog, most of the people commenting here are real scientists.

      You gonna dispute that?

      Falsehood #3: Matzke who is on UD quite often, is not a scientist? Oh, Okay...

      I never wrote that. Matzke was banned from UD, so you cannot use him as counter-example. He was polite and respectful, but he brought scientific evidence, so Arrington banned him. I said MOST commenters at UD are not scientists, and that's true, but Matzke's not a commenter there.

      What I wrote: Unlike UD or Shapiro's blog, most of the people commenting here are real scientists.

      Falsehood #4: Also, no one at TSZ... are scientists?

      I never mentioned TSZ and I've never been there. This is your fantasy-- irrelevant to anything I wrote.

      Falsehood #5: And no I didn't follow you from Shapiro's blog, I followed you from [Christian Post]

      So you admit stalking me-- but you stalked me from Christian Post, where I've never been. I don't know if that's more creepy, or less. Either way, you couldn't follow me from a place I haven't been.

      You have Fregoli delusion and you think I'm everyone on the internet who's smarter than you. (But there are so many...)



      Delete
    15. Anonymous, rjop, Misc belched:

      "Diogenes is over there now, Moran, Matzke and others have not been banned. So your whole vampant rant above is moot."

      No it's not. Three or four people posting there against the IDiots does not mean that what I said is wrong. Many people have been blocked and banned at UD. More than 20 were banned, within a very short time, not long ago, for no good reason. Even an IDiot or two said that arrington was wrong for banning all those people.

      Regarding this:

      "Also, no one at TSZ, who interacts with UD, are scientists? Matzke who is on UD quite often, is not a scientist? Oh, Okay..."

      TSZ isn't UD. Most of the IDiots are afraid to comment at TSZ or anywhere else where they can't block and ban people who question or challenge their lies and bullshit.

      And Diogenes obviously meant that most of the IDiots at UD aren't scientists. If you're going to nitpick every word that Diogenes or anyone else that you don't like says, how would you like to have the same thing done to every word of yours? Do you really want to go there?

      Instead of picking fights over irrelevant trivialities and your own lack of comprehension, you should consider making points that are actually relevant to the Encode claims and whatever agenda you have, and back up those points with credible, scientific evidence and arguments.

      Delete
    16. "you go tell people I said the ENCODE people are not scientists"

      No I did not, I said, "I suppose next you will say the ENCODE scientists are not 'real' scientists. Can you read?

      I never wrote that. I never said Shapiro was not a real scientist. I said most people who comment at his blog were not scientists.

      My mistake, but your recent comments at Ewan's blog and elsewhere, indicate you have a very low opinion of him, which weighs in on why I might have came to that conclusion, such as:

      "Go tell your cowardly wuss Shapiro"

      "Gutless Shapiro will never return"

      "like your cowardly Ken doll, that ignorant gutless Shapiro

      http://www.blogger.com/comment.g?blogID=1688712549144760104&postID=4399636876507026413

      What I wrote: Unlike UD or Shapiro's blog, most of the people commenting here are real scientists.

      You gonna dispute that?


      You gonna answer my questions regarding that above?

      Matzke was banned from UD, so you cannot use him as counter-example

      http://www.uncommondescent.com/intelligent-design/darwinists-spin-encode-findings-more-than-even-i-thought-possible/

      Please provide valid evidence he was banned, or we can again conclude you are lying.


      I never mentioned TSZ and I've never been there. This is your fantasy-- irrelevant to anything I wrote.

      TSZ is a blog by Elizabeth Liddle who is an evolutionary biologist > http://theskepticalzone.com/wp/

      Who do you think they are going back and forth with on the UD thread you spread more BS on earlier today? Joe provides the link throughout the comments.

      So you admit stalking me-- but you stalked me from Christian Post, where I've never been. I don't know if that's more creepy, or less. Either way, you couldn't follow me from a place I haven't been.

      You mean you have never been there as "Diogenes" and no I do not admit to 'stalking you', we have been having ongoing discussions on ENCODE, which started at CP under your real name, in which you then switched out to Diogenes on Shapiro's blog, after I challenged you to go there. Also, after the ENCODE news, you linked me here and to T Ryan's blog on CP while under your real name. Why don't you just come clean and tell me your first name so I can check it out? The more you refuse to do so, the more my suspicions are validated.

      You have Fregoli delusion and you think I'm everyone on the internet who's smarter than you

      Has nothing to do with who is 'smarter', this is only your warped mind.

      But there are so many,

      So many what?








      Delete
    17. TWT:

      Three or four people posting there against the IDiots does not mean that what I said is wrong

      Did you not say this:

      "Join in means participate, but the hypocritical, cowardly dictators at UD won't allow "anyone" to participate"

      This is what I was responding to. And sorry, there are more than 3 or 4 with opposing views. They probably don't want to waste a bunch of time dealing with people like you, who are obviously absorbed in hate, evident by the spewage in your first comment. Also, the banning goes both ways, I know Joe has been banned from of several 'your sides' blogs. But I guess in your book that doesn't count.

      Delete
    18. Anonymous: My mistake, but your recent comments at Ewan's blog and elsewhere, indicate you have a very low opinion of him [Shapiro],

      Ya think? Wow. With deductive skills like that, you should work for Scotland Yard.

      As for Matzke, I might've been wrong about him being banned during Arrington's freakout. I emailed Matzke for clarification.

      What is the bug up your ass with this person at the Christian Post? He's a horrible person and you're obsessed with him-- OK-- tell us his name.

      What are you afraid of? What do you think you're losing by saying the name of this person at CP?

      So if it's my real name, then go get me. Expose me. Tell everybody here my real name, since you claim to know it. Do you think if you say my name three times, I will appear?

      Delete
    19. * Correction on TSZ: *Joe provides the link throughout the comments starting 21, 44 and continuing through the comment thread.

      Delete


    20. You 'might' have been wrong? Oh Okay.. If he was banned during Arringtons freakout, he wouldn't have been able to post there just recently. Duh..

      Also, why do you continually side step revealing your fist name, what are YOU afraid of? Someone will catch you in another lie if you give a bogus name perhaps?

      Delete
    21. Also, it is interesting you play the 'stalking' card, if you're who I think you are. We were recently discussing this very thing, regarding another CP commenter. You me to get off your back, all you have to do is give me your fist name and try not to lie..

      Delete
    22. **You want me off your back, all you have.....

      Delete
    23. Anonymous, rjop, Misc said:

      "TSZ is a blog by Elizabeth Liddle who is an evolutionary biologist..."

      She does know lot about evolutionary biology but that's not her professional gig:

      http://www.nottingham.ac.uk/chs/divisions/psychiatry/people/staff/elizabeth.liddle

      She might be able to help you with your delusions and aberrant learning patterns.

      Also see this:

      http://theidiotsofintelligentdesign.blogspot.com/2012/01/gordo-threatens-elizabeth-liddle-with.html

      And this:

      http://pandasthumb.org/archives/2012/02/a-purge-of-comm.html

      And this thread:

      http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=506d535bd0f1d1ad;act=ST;f=14;t=5141

      Delete
    24. TWT,

      What is your point? Like I said the banning goes both ways. And again you are wrong that no dissenting views are allowed, which was your first assertion.

      Delete
    25. Anon: If he was banned during Arringtons freakout, he wouldn't have been able to post there just recently.

      No. He might have been re-instated.

      Delete
    26. Well if he was re-instated, that would mean he is not banned, so what is your point. BA77 was banned then re-instated a while back. And why have you not answered my question on your first name?

      Delete
    27. No. You say I'm this person at Christian Post, so just say this person's name. If this person's name = my name, then you saying his name = my name. All up to you, pal.

      Delete
    28. I am not going to post someone's name without their permission in the extreme narrow event you are not them.

      However, your complete refusal to post your first name is beyond logic. What this tells me and any logical person is you are hiding something and most of all shows just how disingenuous you are.

      Therefore, my suspicions are further validated by your refusal to do so. It is also uncanny how you and this person on CP exhibits the same pathetic diversion tactics and complete inability to answer simple questions. You also have some questions waiting on UD, are you going to answer them?

      Delete
    29. Anonymous, rjop, Misc said:

      Did you not say this:

      "Join in means participate, but the hypocritical, cowardly dictators at UD won't allow "anyone" to participate"

      Yes, I did say that. You obviously need another lesson in reading comprehension. The word "anyone" in that sentence is meant in the same way as you originally meant it, and that's why I put quote marks around it. You said "anyone is invited to join in" and the obvious meaning in that is that everyone is invited to join in, which of course is not true at UD.

      Another way to look at what you said is 'any one is invited to join in', or 'any person is invited to join in', or 'every person is invited to join in', but not just any one or every one or every person is invited to join in (participate/comment) at UD. Many people are blocked and/or banned for no good reason.

      The words any and every are interchangeable at times and this is one of those times, and that's due to the way YOU used the word anyone.

      Now, go back and read what I said and this time maybe you'll get it. I doubt it though.


      You also said:

      "Also, the banning goes both ways, I know Joe has been banned from of several 'your sides' blogs. But I guess in your book that doesn't count."

      Do you mean joey g? The deranged IDiotic coward who threatens people, and who posted a picture of a woman's crotch on TSZ just to be an asshole and called it "tunie", and who goes on massive, spamming tirades filled with over the top abuse, and who is one of the most disruptive and arrogant trouble makers on the internet? Yeah, he gets banned from some sites for GOOD reasons. He should be banned from planet Earth.

      UD only allows a few people at any one time to question or challenge their bullshit, and the only reason they allow anyone at all to do that is because UD was DEAD without it. If the UD gang were actually interested in open and honest discussion, as they claim to be, they wouldn't block and/or ban 'anyone' simply because they question or challenge the lies and arrogant, ignorant crap the IDiots spew.

      I'm beginning to wonder if you're joey g. Or maybe mung. Are you?

      Delete
    30. @ TWT

      Got it, and no I am not Joe or Mung, I am a female. Will look into your claims about Joe G. When I said it goes both ways, there are other examples such as BA77, whom was banned a while back from UD and then reinstated, and if I'm not mistaken, Joe was also banned from UD and then reinstated. I really don't see what the issue is, it is their blog and they should be able to 'ban' if they see it as warranted. As for Joe being abusive, I suggest you look at some of your own stuff, as you seem to think you are pure as the driven snow.. Also, Diogenes is still posting there with quite an opposing view, wonder why he hasn't been banned yet?

      Delete
    31. Anonymous:

      What this tells me and any logical person is you are hiding something and most of all shows just how disingenuous you are.

      Wow, that's hypocritical. You wouldn't tell me your ID at Mike White's blog and wanted me to deduce it like Sherlock Holmes. That's OK when you do it. Now it's your turn, now you're Sherlock, you deduce my ID.

      I don't owe you a damn thing. You say you followed me here, that's your damage.

      You don't give a shit about genetics. The people here do care about genetics. We come here to talk about science and use technical jargon freely. You haven't made a single scientific point here or at any other blog-- and no, blathering about how science should be free of "ideology" is not a scientific point. That's armchair psychoanalysis.

      You also have some questions waiting on UD, are you going to answer them?

      Don't ever tell me that again-- I don't owe anyone at UD a damn thing. I've never once said you have to answer questions on some other blog. You do this more than once a day. Don't order me around.

      Why are you here? We like science. You don't. You say you have kids? How can someone with kids be on the internet 24/7? Go give your kids a cookie and leave us alone.

      From now on, I will not respond to any comments nor questions from you AT ALL unless they are limited to SCIENTIFIC, not PERSONAL, content. Allegations about "ideology" are not science. I will NOT let you order me to go to any other blogs anywhere else on the internet.

      Delete
    32. In fact, I'm not going to be back here for several days.

      Delete
    33. Wow, that's hypocritical. You wouldn't tell me your ID at Mike White's blog

      Yes I did, on the Ewan blog here, I provided a link with my ID, Friday 9/28. If you mean directly on White's blog, you never asked for one.

      I don't owe you a damn thing. You say you followed me here, that's your damage.

      Then my suspicions are 100% Confirmed.

      The people here do care about genetics. We come here to talk about science and use technical jargon freely

      Oh really, is that why there is 'Rationalism v Superstition' where bashing people of faith is a regular occurrence. I suggest you look around, there is much more being said than a simple discussion on science using 'technical jargon'.

      Don't order me around.

      'Order' you around, I don't think so. Perhaps you are confusing me with the little voices in your head. And who wrote this: "In my previous post I gave you a direct order" and "This was a direct order" YOU did, on Ewans blog here.

      You say you have kids

      Now in order for you to know this, you would have had to go back to the Axe blog in where I was responding to NE, but you said nothing there today. Were you stalking me? If you can accuse me of doing so, I can do the same.

      I will not respond to any comments nor questions from you AT ALL unless they are limited to SCIENTIFIC, not PERSONAL, content

      You mean like making scientific statements such as Shapiro is 'terrified' and 'scared to death' of you. You mean scientific statements such as:

      "Go tell your cowardly wuss Shapiro"

      "Gutless Shapiro will never return"

      "like your cowardly Ken doll, that ignorant gutless Shapiro"

      There are many more like these..

      In fact, I'm not going to be back here for several days.

      Good, why don't you make it forever. And make sure you put CP on that list where you continually berate, ridicule, and hound almost every single person there, while telling them you're a theist and believe in one God. If I catch doing this I will be back. You are one demented low life.

      Delete
  7. The Lorax says: While I can explain the issues clearly, it is difficult overcoming the gravitas of Nature, Science, etc

    If your students are already ‘hooked’ to the idea of ‘functional junk DNA’, maybe you should offer them to take a look at a more sensible model on a presumed function for ‘junk DNA”.

    You can start with a comment entitled: “Five reasons why my theory on the function of ‘junk DNA’ is better than theirs (http://sandwalk.blogspot.com/2012/09/read-what-mike-white-has-to-say-about.html), and continue with five brief comments I posted in Science discussing this model: http://comments.sciencemag.org/content/10.1126/science.337.6099.1159

    To entice you and, hopefully, your students, I’m posting here the fifth, and concluding comment in Science:

    *C-value paradox and ‘junk DNA’ enigma: case solved?*

    The concept of ‘junk DNA' (jDNA) has its roots in the C-value paradox, which designates the fact that the haploid genome size (C-value) varies enormously among eukaryotic species, and that the C-value doesn’t correlate with the presumed number of genes as expected from the apparent organismal complexity. For example, the size of genomes in vertebrates and animals varies by a factor of more than 300 and 3000, respectively.

    The C-value paradox led to the paradigm that only a relatively low percentage of the genome is occupied by functional DNA; the rest, up to 99% in some species, such as humans, constitutes non-functional, or jDNA.

    Part of the enigma surrounding the C-value paradox and the evolutionary origin of jDNA was solved by the discovery that it's composed primarily of transposable elements, including endogenous viruses. However, the puzzle at the center of C-value paradox and jDNA paradigm has remained: (i) is jDNA functional, and has it been maintained because the host organisms possessing it have a selective advantage (i.e. is jDNA symbiotic)?; or (ii) is jDNA nonfunctional, and has it accumulated simply because its rate of deletion has been lower than the amplification (i.e. is jDNA is parasitic)?

    As previously pointed out (1), by its bare presence in the genome, jDNA has an effect on cellular physiology (e.g. nucleotide metabolism; division rate), structure (e.g. nuclear and cellular size), and genome ‘fluidity’ (e.g. increased recombination versatility and evolutionary co-option of jDNA).

    Also, by its bare presence in the genome, jDNA gets replicated and it can, for example, undergo transposition and transcription, or it becomes non-specific target for diverse DNA binding proteins, as shown in the ENCODE project. However, these features and correlates do not solve C-value paradox and ‘junk DNA’ enigma; on the contrary, they confuse these issues.

    As argued in the original hypothesis (1) and in the comments I posted here, by serving as a defense mechanism against insertional mutagenesis, which in humans and many other multicellular species leads to cancer, all jDNA is functional. Expectedly, as an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the insertional mutagenesis activity and evolutionary constrains on genome size.

    1. Bandea CI. A protective function for noncoding, or secondary DNA. Med. Hypoth., 31:33-4. 1990.

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    Replies
    1. Maybe there are good reasons that according to Thomson Reuters Web of Knowledge your paper has never been cited during the last 22 years. According to TR Gregory even back in 1990 your idea wasn't really new.

      Delete
    2. Anonymous, do you have any ideas of your own, anything you would be prepared to share and discuss as a scientific topic, or do you come here only because you enjoy cowpie fights? You present yourself as a non-creationist (oh no, thank you sir!), I suppose your views are not merely scientific but represent the cutting edge of scientific progress: the whole world will come round to share them soon as Larry Moran and his junk-worshipping fans sink into oblivion. Why not tell us openly what those views are? You are out to re-define evolution, right? In what way?

      Delete
    3. Anonymous says: Maybe there are good reasons that according to Thomson Reuters Web of Knowledge your paper has never been cited during the last 22 years

      I agree with that, there must be some very good reasons! The question is what the reasons are?

      In a previous post, Larry Moran, our Host, asked a similar question ( http://sandwalk.blogspot.com/2012/09/athena-andreadis-writes-for-sceintific.html):

      ”I note that you published this hypothesis in 1990 and now after 22 years nobody has stepped forward to claim that it solves the problem. Why do you think that is?

      As I responded to Larry, I think it was primarily my fault because I did not pursue it. And, the fact that the paper was published in a small journal did not help; and, I did not have the name recognition to go with it.

      As to why other scientists, such as Ryan Gregory, who knew about the paper (at least starting with February 2008, when I corresponded with him about it) never mentioned it, I can’t give you an answer.

      However, I think that in my comments here at Sandwalk and other sites, I made a sensible case that this hypothesis might "solve the problem", to put it in Larry’s words! And, I summarized this in my comment above, *C-value paradox and ‘junk DNA’ enigma: case solved?*

      Maybe now, people will consider taking a look at this model, and I think they should do it not only because it might solve the problem of C-value paradox and ‘junk DNA’, but also because of its potential medical and public health significance, as this model opens the door for better understanding of one of the most devastating maladies: CANCER.

      Indeed, as emphasized in a previous series of comments ( http://sandwalk.blogspot.com/2012/09/ewan-birney-genomics-big-talker.html):

      “insertional mutagenesis, it’s just a fancy way of saying CANCER”

      Delete
    4. @Piotr,

      I believe there are two Anonymouses on Sandwalk, at least.

      The Anonymous who argues with Claudiu is a rational person.

      The Anonymous / rjop / "Misc" who argues with me is not. This could of course be cleared up if Anonymous would just sign his comments, but no.

      Delete
    5. A good point. However, some of the anonymous responses to Claudiu sound pretty irrational too. Either they come from the second Anonymous, or there is only one Anonymous with a wavering level of rationality. I understand the advantages of Internet anonymity, but why not use a nickname?

      Delete
    6. I’m relatively new at blogging, so I’m still learning. But, is it possible that, sometimes, even people who have a ‘name’ sign as Anonymous?

      Delete
    7. Dunno. The Anonymous who argues with Claudiu knows a little science and raises scientific issues.

      The Anonymous / rjop / "Misc" who argues with me never raises issues of evidence and seems uninterested in it-- his concern is ideology /worldview.

      Delete
    8. Note that the Anonymous above hyperlinked to TR Gregory's blog.

      Creationists never cite TR Gregory's blog!

      Delete
    9. I don't find the "junk DNA is protective" vs. cancer to be convincing, because:

      1) The junk DNA is largely caused by retrotransposons, so it might be reasonable to suppose the the number of active retrotransposons will scale with the amount of junk DNA. In other words, even if the junk DNA is protective through mass action effects, the additional burden of having more active parasitic sequences balances out any such effects.

      2) Cancer caused by insertional mutagenesis is almost never observed. If the junk DNA were functionally adaptive as a cancer preventive measure, I would expect there would be a sufficient amount to reduce the cancer burden to levels at which pre-reproductive age cancer caused by insertional mutagenesis was reduced, but not eliminated, with an increasing frequency of occurrence related to chronological age of the individual. We don't see this. If selection has resulted in the protective junk DNA, then selection has done its job too well.

      Look at it this way: we know that errors in DNA replication can cause cancer. So, how well does the DNA replication/repair machinery work? Well enough to keep levels of pre-reproductive age cancer at low levels but not any better than that. In other words, if defense against insertional mutation really were subject to selection, I would expect the incidence of post-reproductive age cancer caused by insertional mutation to not be at the essentially negligible levels that we observe.

      Delete
    10. Short version of the 1990 Bandea paper: Junk DNA exists to protect genomes from other junk DNA.

      Delete
    11. Matt G: Short version of the 1990 Bandea paper: Junk DNA exists to protect genomes from other junk DNA.

      Thanks Matt for reducing my already short paper to one sentence! Leaving humor aside, your abbreviation is excellent; metaphorically, I said: fighting fire with fire!

      For those who want to read the one-page version, it is posted here at Sandwalk:
      http://sandwalk.blogspot.com/2012/06/tributre-to-stephen-jay-gould.html

      Delete
    12. Metaphorically, I can also say that that the ‘Good Junk DNA’ is protecting us from the ‘Bad Junk DNA.’

      The worst of all ‘Bad Junk DNA’ might be retroviruses, such as murine leukemia viruses or HIV, which can bombard our cells with an extraordinary large number of insertional mutagenesis events. Without strong protective mechanisms such as ‘Good Junk DNA’ to defend us from these events, we would be evolutionarily drowning.

      In my previous comments, I pointed out that the data supporting the model already exists. This data was generated in context of hundreds of different studies; however, these studies were not designed to address this model, and therefore the results were not interpreted in context of this model.

      For example, there are hundreds of studies showing that insertional mutagenesis by endogenous transposable elements and exogenous viruses, such as retroviruses, cause cancer.

      As a matter of fact, insertional mutagenesis has been one of the most productive experimental approaches used for mapping the genes and regulatory sequences that have oncogenic potential, as well as for studying the paths to neoplastic transformations (e.g. reviewed in http://www.ncbi.nlm.nih.gov/pubmed/20844553

      Moreover, there is very strong data provided by several gene therapy studies demonstrating the oncogenic activity associated with insertion mutagenesis of viral vectors used in these studies. For example, 4 out of the 9 infants enrolled in a X-linked SCID gene therapy study developed leukemia within 3 to 6 years after therapy as a result of gammaretroviral vector mediated oncogenesis (see: http://www.ncbi.nlm.nih.gov/pubmed/12529469, and http://www.ncbi.nlm.nih.gov/pubmed/18688285)

      Delete
    13. Anonymous: I don't find the "junk DNA is protective" vs. cancer to be convincing, because…

      Does my comment above answer some of your points?

      Delete
    14. In my comment above, I said that the evidence that ‘junk’ DNA (jDNA) is not under evolutionary constrains in regard to its sequence is supported by many lines of evolutionary, genetic, and biochemical evidence.

      One of the strongest recent evidence is a study by Lindblad-Toh et al., entitled “A high-resolution map of human evolutionary constraint using 29 mammals” slowing that 4.2% of the genome is evolutionary constrained (http://www.ncbi.nlm.nih.gov/pubmed/21993624).

      I’m surprised that the ENCODE’s messengers (managers) did not know that: “Nothing in biology makes sense except in the light of evolution”

      Delete
    15. CB: Does my comment above answer some of your points?

      It's a good try, but not really. Can you cite evidence that endogenous transposable elements are important for cancer?

      Delete
  8. I have done a google search for 'ENCODE fiasco', 'Junk DNA fiasco', 'junk DNA PR fiasco', and for all three, the entire first page of links leads directly, or indirectly, to this very site.

    It would seem that most of the world, including the larger portion of the scientific community, has a more sanguine, or at least tolerant, view of the whole ENCODE enterprise than this site's author.

    Repeatedly calling something a 'fiasco' when nobody else seems to find it to be such (even Richard Dawkins, in a recent debate, didn't rush to distance himself from the findings when a perfect opportunity was given him) doesn't de facto MAKE it one.

    Of course LM may feel that the world will face dire consequences if our precious children are not taught the vital message that they are 92% junk, but most people seem more interested in the possibilities for medical advancements that may emerge from the data as it is assessed. Priorities, priorities.

    ReplyDelete
    Replies
    1. Of course LM may feel that the world will face dire consequences if our precious children are not taught the vital message that they are 92% junk, but most people seem more interested in the possibilities for medical advancements that may emerge from the data as it is assessed. Priorities, priorities.

      The difference between seeing ourselves as the pinnacle of the perfection of creation on one side and as a highly entropic offshoot of genome evolution on the other looks quite important to me.

      The process started with Copernicus and Galileo when geocentrism wad destroyed, then came Darwin, the design argument was destroyed and we became part of the tree of life, the molecular revolution of the 20th century conclusively showed that there isn't anything special about us on the molecular level, and finally, in the last 15-20 years we have been able to sequence the genomes of wide variety of species and by examining them fully appreciate the role that neutral evolutionary processes have played in our evolution. Which was the last nail in the coffin of human exceptionalism as it became clear that if anything is "perfect" and "highly evolved" it is bacteria and not us, while a better description for ourselves would be genomic degenerates full of maladaptive features.

      These advances in our understanding of the world around us also represent fundamental shifts in our understanding of who and what we are - if that's not important I don't know what is, however the majority of people in the world have not yet even gotten the news from 150 years ago, let alone walked the full path I outlined above.

      Now that ENCODE has done a lot of medical relevance is very much true - but while this should have been much more of a focus on it, it was not what dominated the coverage of the project, which was all about the death of junk DNA; something quite unfortunate, as I have said before, as it caused most of the good work of scientific importance that the consortium did to be ignored.

      Delete
    2. Georgi, you have made this argument before, and I hope you realize that your viewpoint is almost exclusively western. You thus pin environmental degradation on religious belief, specifically a human interpretation of it that posits human beings as the ultimate creation. But one can hold many types of religious beliefs outside of that paradigm. 'All life is sacred' is a concept that science, certainly not labeling everything 'junk' is going to bring you. One of the reasons there are so many vegetarians (nearly all) in India has to do with the concept of ahimsa, meaning to harm no living thing.
      The Gaia concept, that Mother Earth is a sacred being that we should revere and honor, not destroy and lay waste to is a religious (or at least spiritual), not scientific, concept.

      I respect your opinions and I think we share the same concern about the crises our current path has led to and is leading to, but I continue to think you are barking up the wrong tree with your faulting of 'human exceptionalism'.

      Delete
    3. I didn't say anything about sustainability here - what I said above is 100% true without going there at all. Yes, it is related, but it stands on its own.

      Delete
    4. Georgi, understood. I brought up sustainability because I have seen you write about it in the past.
      If your argument is going to be that science has destroyed the notion of human exceptionalism, I think the point remains that you are referring to a paradigm shift that has taken place in a relatively limited part of the world.
      you could talk to people who hold many different beliefs who would perhaps say to you, "science killed the idea of human exceptionalism? That's nice. As for me, I never thought we WERE all that exceptional."

      Delete
    5. Andyboerger: I have done a google search for 'ENCODE fiasco', 'Junk DNA fiasco', 'junk DNA PR fiasco', and for all three, the entire first page of links leads directly, or indirectly, to this very site.
      Did you google "ENCODE and junk"? All resulting links go directly or indirectly to the abstract of ENCODE's main paper, the ENCODE press release or the irresponsible comments by Ewan Birney and other leading figures of the ENCODE project.

      Andyboerger: It would seem that most of the world, including the larger portion of the scientific community, has a more sanguine, or at least tolerant, view of the whole ENCODE enterprise than this site's author.
      Most of the criticism is not directed against the whole ENCODE project but against its weakest, IMHO, false claims. There is no place for tolerance in science.It has to be scrutinizing.

      Andyboerger: Repeatedly calling something a 'fiasco' when nobody else seems to find it to be such (even Richard Dawkins, in a recent debate, didn't rush to distance himself from the findings when a perfect opportunity was given him) doesn't de facto MAKE it one.
      Please note that calling ENCODE a "fiasco" worked without redefining what a fiasco actually is. Compare this to the way "function" is treated by Ewan Birney. And do a google search to find out how often the claim that Junk DNA is functional has been repeated during the last weeks. Repeatedly calling Junk DNA functional doesn't MAKE it so.

      Delete
    6. 'google "ENCODE and junk'

      This one is interesting:

      http://debunkingdenialism.com/2012/09/16/the-current-creationist-abuse-of-encode-and-junk-dna/

      This pretty much shoots the Junk DNA crowd down, and I agree ID jumped the gun, but what they don't understand, is ID is fighting against the Moran's and Ilk..

      Especially like this line:

      "“junk DNA” has never been a major part of modern science. It is a fictitious construct by the media and some eccentric scientists of the past"

      Delete
    7. Andyboerger: It would seem that most of the world, including the larger portion of the scientific community, has a more sanguine, or at least tolerant, view of the whole ENCODE enterprise than this site's author.

      There is a difference between the data of ENCODE and the Press Release, as we have all emphasized over and over.

      As for the Press Release and "Death of Junk DNA" hype, a large number of science bloggers have in fact reacted with, well, disgust to the PR. This would still be true even if Larry Moran and this blog didn't exist. Do you want a list of hyperlinks? I have them. It's a long list.

      Most molecular biologists I know would not actually believe most of your genome ISN'T junk-- if you define junk properly. If you define junk DNA as 'not constrained as to sequence by an organism-level function', most molecular biologists will go, 'DUH, obvious!'

      If you define junk DNA with some bullshit definition like 'non-coding DNA' or 'DNA whose function we don't know', they'll dispute that most of it has no biochemical activity at all.

      Repeatedly calling something a 'fiasco' when nobody else seems to find it to be such... doesn't de facto MAKE it one.

      Duh. "Nobody else"? A large number of science bloggers have in fact reacted with disgust to the PR. Many such commenters are part of the ENCODE project, including Michael Eisen, Max Libbrecht-- and even Ewan Birney walked back his 80%.

      Moreover, virtually NO science bloggers have advanced fact-based arguments supporting the 'Death of Junk DNA'-- that is, except for twits who think Junk was defines as 'non-coding DNA' or 'DNA whose function we don't know.'

      Should we really worry about the opinions of people who can't even define Junk DNA? Whenever you tell scientists the actual definition of Junk DNA, the great majority go, 'Oh, obviously that's most of the genome.'

      I wrote a blistering, over-the-top denunciation of the PR hype at Reddit, and one ENCODE scientist, Rule_30, wrote back-- he could not defend the PR. His thoughtful response is wrenching, and you should read it before you think we're the only ones who consider this is a debacle.

      Delete
    8. @SPARC:

      Compare this to the way "function" is treated by Ewan Birney. And do a google search to find out how often the claim that Junk DNA is functional has been repeated during the last weeks. Repeatedly calling Junk DNA functional doesn't MAKE it so.

      It is ironic that Andyboerger should present himself as defending objective reality against ad hoc redefinitions of words! And also presents himself as defending Birney and his "80% functional" which involves inventing a new definition of "function"!

      You cannot defend objective reality against re-defining words, and ALSO defend the ENCODE PR machine. Those two forces are utterly opposed.

      Sorry Andy, we are the ones defending objective reality against ad hoc redefinitions of words!

      Delete
    9. Any way you look at it, and as valuable as it might be, the data produced by ENCODE does not support its major conclusion and message.

      And, if it wasn’t for heroic effort by Larry, Diogenes (way to go!), SPARC and many other contributors at this site, the messengers of ENCODE might have gotten away with it, at least for a while, until the science process takes its course in eliminating flaws.

      Delete
    10. @ Claudia

      If you consider belittling, disrespecting and berating scientists, a "way to go"!, this is alarming and I'm not referring to Larry or Sparc.

      Delete
    11. I might not have read all Diogenes’ comments, and I might only focused on the message, but my take on his position was that he was “belittling, disrespecting and berating” ENCODES’s message.

      Well, he might have spill his ‘rage’ over the face of some of the ENCODES’s messengers (or managers), but they might deserve it considering that they took an otherwise remarkable project performed by hundreds of good scientists and colleagues and smear it with pseudo-science mud!

      Delete
    12. Sorry, he went way beyond the ENCODE msg. Sparc deserves the applause much more..

      Delete
  9. If you consider belittling, disrespecting and berating scientists, a "way to go"!, this is alarming

    Your concern for scientists is heartening.

    ReplyDelete
  10. @ Jud

    My concern is scientific progression not being stifled or held down by ideologies on both sides of the debate.

    ReplyDelete
    Replies
    1. Both sides? What sides? There is no ideological conflict between, say, Larry Moran and the ENCODE team. "Junk DNA" is not an ideological concept. Or do you mean mainstream science vs. ID? If so, keep it in mind that ENCODE is a scientific project and its participants would laugh at you if you called them champions of the ID cause.

      Delete
    2. "If so, keep it in mind that ENCODE is a scientific project and its participants would laugh at you if you called them champions of the ID cause"

      I'm sure they would, the point I was trying to make, is both sides should hold more of an agnostic view at this point, regarding 'Junk DNA', which like I pointed out above from a neutral source: "junk DNA” has never been a major part of modern science. It is a fictitious construct by the media and some eccentric scientists of the past" Shapiro also holds this view.

      Delete
    3. Anonymous:
      which like I pointed out above from a neutral source: "junk DNA” has never been a major part of modern science. It is a fictitious construct by the media and some eccentric scientists of the past"

      If you think that's a neutral source, you're ignorant of the subject and its history. It's a wildly inaccurate quote. I see no reason to believe the quoted person does not even know the definition of Junk DNA. Lots of people don't.

      It's like someone saying they've refuted Kepler's laws of planetary motion, but they don't know what's the difference between planet and star. Why should we care?

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    4. "Why should we care"

      Who exactly is 'we', you mean the idealoges who white knuckle Junk, such as yourself?

      "even know the definition of Junk DNA. Lots of people don't. "

      And lot's of scientists don't know the definition of Junk DNA and have given many indications they don't care about it. Wonder why?

      Sparc suggested doing a google search, which is what I was responding too, get over it.

      Delete
    5. Come on, Anonymous, even the ENCODE folks are backing away from the claim that most human DNA is somehow "functional". As far as is known, most of it is nonfunctional now, even if it was functional in the distant past and if on rare occasions some of it may be co-opted in a new function. The ENCODE data have not changed this picture. Some scientists may dislike the popular ring of the term "junk DNA". Call it more technically "nonfunctional DNA", then. Whatever name you give to it, it is there, and it is the historically accumulated decaying debris of broken genes, retroviruses, runaway repeats and what not. I do not understand why you must interpret the debate in ideological terms. It is not ideological, but the insistence that it is makes you sound like an agitprop activist. Even if the human genome were mostly or entirely functional, it would not constitute evidence of Intelligent Design -- only of purifying selection being sufficiently strong.

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    6. Why don't you post this on Shapiro's blog at Huff Post and see what his thoughts are? My personal view is instead of 'function', 'activity' should have been used. However, since there is so much more to explore, this 'activity' suggests 'function', but of course this is yet to be determined. It does seem however, you guys seem to white knuckle the Junk idea quite voraciously..

      Delete
    7. Anonymous: And lot's of scientists don't know the definition of Junk DNA and have given many indications they don't care about it. Wonder why?

      Why?

      Delete
    8. Anonymous: My personal view is instead of 'function', 'activity' should have been used

      I don’t think ‘activity’ will do it, either.

      As, I said in my comment above (*C-value paradox and ‘junk DNA’ enigma: case solved?*):

      As previously pointed out (1), by its bare presence in the genome, jDNA has an effect on cellular physiology (e.g. nucleotide metabolism; division rate), structure (e.g. nuclear and cellular size), and genome ‘fluidity’ (e.g. increased recombination versatility and evolutionary co-option of jDNA).

      Also, by its bare presence in the genome, jDNA gets replicated and it can, for example, undergo transposition and transcription, or it becomes non-specific target for diverse DNA binding proteins, as shown in the ENCODE project. However, these features and correlates do not solve C-value paradox and ‘junk DNA’ enigma; on the contrary, they confuse these issues.

      Delete
    9. @ Claudia

      I don't know why, perhaps many scientists do no believe the Junk idea is that important. Time will tell how it all pans out, as there is much more to investigate and research...

      Delete
    10. Why don't you post this on Shapiro's blog at Huff Post and see what his thoughts are?

      I have seen the discussion there and know what his thoughts are.

      My personal view is instead of 'function', 'activity' should have been used. However, since there is so much more to explore, this 'activity' suggests 'function'

      Non sequitur. Lots of things in this universe are "active" without being "functional".

      It does seem however, you guys seem to white knuckle the Junk idea quite voraciously

      I don't think so. Some living things (prokaryotes) have got little or no junk DNA. We can live with it, can't we? We know why it doesn't accumulate in them, and we know why it accumulates in Eukaryota. An "extreme Darwinist" (meaning someone who sees selection at work everywhere) would probably be inclined to predict that all DNA should be functional (because it if it weren't, purifying selection would eliminate it), but apparently there are no hardline Darwinists on Sandwalk.

      Delete
    11. Anonymous writes:

      both sides should hold more of an agnostic view at this point, regarding 'Junk DNA', which like I pointed out above from a neutral source: "junk DNA” has never been a major part of modern science. It is a fictitious construct by the media and some eccentric scientists of the past"

      I think you would find from an objective review of the research of the past 40 or so years that Shapiro's ideas are almost uniformly the outliers, the ones that would be considered "eccentric," to quote your source. I think you would also find a tremendous amount of research showing affirmatively that a very high percentage of the genome - 60+% - is not functional; and finally, that how much of the genome is functional (and thus how much is non-functional) has indeed been a major topic of scientific inquiry during those 40-odd years.

      Some good tips in terms of getting started looking at the research are in the following excerpt of a comment from T. Ryan Gregory, who as someone active in research and publishing on this topic is in a good position to know:

      First, there was never a time when non-coding DNA was *all* dismissed as “useless junk” such that functions were not considered. Quite the opposite — functions were seriously considered for every new type of non-coding DNA when discovered. The early authors of the “junk DNA” concept explicitly mentioned possible functions for *some* non-coding DNA. Comings (1972) suggested 20% of the genome is actively used, for example.

      Second, the concept of non-functional, non-coding DNA was not based on ignorance or giving up and just calling it “junk”. There were (and still are) positive arguments for expecting much of the genome to be of little or no relevance to fitness. Mutational loads, variability in genome size, neutral evolution at the sequence level, 2/3 of the genome being transposable elements, etc. Several of these arguments have been around since the 1970s and they remain valid today.

      Third, there is no evidence that a majority of the human genome is “functional” in any meaningful sense of that word. Of course some non-coding DNA is functional (regulatory regions, centromeres and telomeres, ribosomal RNA, etc.), but no one ever said otherwise. There are more examples coming up all the time, which is very interesting. But the total still hasn’t even approached Comings’s (1972) original figure of 20%. And even if some people are willing to interpret the current evidence as indicating that most DNA in the human genome will turn out to be functional, they still have to explain why a pufferfish does fine with only 1/10 as much whereas even the smallest salamander genome is 5x larger. This suggests that, even if 100% of the human genome is functional, a lot of eukaryotic DNA out there is not. That is, that the notion of non-functional, non-coding DNA remains valid. Claiming that humans are complex and so need more DNA is an expectation that was refuted in the 1950s. And, in any case, the human exceptionalism required to maintain the view that 100% is functional in people but the amount of non-coding DNA is irrelevant in pufferfishes and salamanders is biologically nonsensical.

      Delete
    12. Many contributors to this blog support the hypothesis that jDNA, which represents 90% or more of the human genome, is not under evolutionary constrains in regard to its sequence. Accordingly, jDNA does not code for proteins or functional RNAs, and it does not have gene regulatory functions. In other words, replacing the jDNA with arbitrary sequences would have no phenotypic defect. I fully agree with this paradigm, which is supported by many lines of evolutionary, genetic, and biochemical evidence.

      However, I have been advocating a model on the evolution of genome size, which I think solves two of the major enigmatic issues in genome biology, the C-value paradox and the evolution of ‘junk DNA’ (see comments above). According to this model, jDNA which has originated from the activity of transposable elements and endogenous viruses has been used by their hosts as a defense mechanism against insertional mutagenesis, which in humans is “…just a fancy way of saying CANCER.”

      Leaving aside the issues of how this jDNA originated, or whether it has been ‘adaptive’ or ‘functional,’ does jDNA protect against insertional mutagenesis by transposable elements and retroviruses?

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  11. Anonymous doesn't quite get it. The scientists responsible for stirring up the hype damaged their own reputation with their own hands (as did the publishers who staged the unprecedented media event). They were terribly concerned about publicity and headline drama, and not so much about the honest and accurate reporting of their findings. Calling their bluff and was a great service to the scientific community, and kudos to Larry Moran for his coolheaded response to those inflated claims. To be sure, anyone without a reading comprehension problem should have been able to detect false notes even in the initial press release, not to mention the pathetic explanation on Ewan Birney's blog that "the bigger number ... brings home the impact of this work to a much wider audience". It certainly set off my personal BS alarm, and I was relieved to find a few enclaves of common sense left in the blogosphere.

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  12. This is off-topic, but Anonymous / rjop / "Misc" has repeatedly taunted me to return, again and again, to Uncommon Descent, where I was crushing the last couple of days. Anonymous / rjop / "Misc" insists that I am frightened of the UDites, who have so far presented only insults and personal attacks in rebuttal to my scientific points.

    Now as most of you are aware, visiting UD is like scuba diving in a river of garbage. You just feel dirty afterward. It is the most horrible place on the internet, filled with horrible people who know no science, but just overturn their shopping carts full of cultist bafflegab.

    You will learn about no science at UD, except one: abnormal psychology; but perhaps some people here are curious about the worst site on the internet with the most horrible people.

    If that's your cup of tea, here's your chance, but you've been warned. I've been posting a lot of comments at one thread, that rebut their ID bafflegab. In response the UDites are up in arms insulting me and attacking me. They're not just ignorant about science, they're also infantile.

    It's a long thread and most of it is insults and personal attacks, but I'll try to guide you to some substantive stuff.

    Anonymous / rjop / "Misc" has this to say about it.

    I suppose if you call lying and BS 'crushing', so be it. I don't need to copy anything here, anyone is invited to join in > http://www.uncommondescent.com/intelligent-design/ub-sets-it-out-step-by-step/#comment-434621 Diogenes 'crushing' begins at 496. LOL!!!

    No, if you're interested, you don't need to start at comment #496. You could best skip to my comment #749.

    The topic of the thread is the so-called "semiotic argument", which says that the genetic code is made of "symbols" (though the poster Upright Biped calls them "representations".) And human language is made of "symbols"/ "representations". And only intelligence can make symbols or a code, therefore the genetic code must be intelligently designed.

    So I summarize the vague, undefined terms at comment #746, and I demolish the argument at #749. The response was long, vituperous insults and personal attacks.

    That's what's interesting about it: the psychology of people who care NOTHING about science.

    So if you want to take a scuba dive in a river of garbage, here you go.

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  13. "who have so far presented only insults and personal attacks in rebuttal to my scientific points"

    Sorry, I don't see that unless it is warranted, and what about your personal attacks? There are plenty of them. Also, Upright asked you a question @ 778, which instead of answering, you just continue on your rampage against Joe and Meyers. Why don't you address Upright's argument, which is what the thread is for. He has been quite respectful towards you. Wonder why they haven't banned you yet? Oh yeah, UD doesn't allow dissenting views....

    Also, why did you post this here verses above, where the discussion was about UD?

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    1. I presume that our Anonymous / rjop /"Misc" posts at UD under a FOURTH identity. Am I right?

      Why don't you address Upright's argument, which is what the thread is for.

      Already refuted UB's argument at #749. UB just pretended like my refutation does not exist.

      Wonder why they haven't banned you yet?

      A mystery indeed!

      Also, why did you post this here verses above, where the discussion was about UD?

      Unparseable.

      So Anonymous / rjop /Misc, what is your identity at UD?

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    2. "I presume that our Anonymous / rjop /"Misc" posts at UD under a FOURTH identity. Am I right?"

      How about you answer my question I have been asking for days now on what your first name is, and I will answer yours. You're diversion are quite pathetic.

      "UB just pretended like my refutation does not exist"

      This is only in your warped mind, any objective observer (which I'm sure we won't find here) will agree this is yet another pathetic proclamation by you.

      Delete
    3. ** 'Your diversions' are quite pathetic....

      Delete
    4. Also Diogenes,

      Notice how onlooker can have a reasoned debate by asking questions and sticking with the argument at hand, something you completely lack.

      And this little gem to Joe by you: "Two sentences would be enough to prove me wrong– if I were wrong. So what was he afraid of?"

      Yet YOU cannot answer ONE simple question, which requires ONE word I have asked of you for days now. Such hypocrisy...

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  14. Anonymous, rjop, Misc,

    How much CSI or FSCO/I or dFSCO/I is there in a banana? Show your calculations.

    How much semiotic information is there in a banana, what is the content of that information, and what symbols does a banana use to process that information? Show your calculations and evidence.

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  15. Larry, your pic looks great in "Debunking junk" by Daniel James Devine in World Magazine at http://www.worldmag.com/2012/09/debunking_junk/page1 .

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    Replies
    1. Oh no, the DNA worldmag displays in that article is left-handed.

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  16. From the page linked by Denny: Researchers are showing that the old Darwinian ideas about 'junk' DNA were simplistic.

    Yeah, Ol' Charlie Darwin was completely wrong about junk DNA.

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