tag:blogger.com,1999:blog-37148773.post5324564226815613719..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Sean Eddy on Junk DNA and ENCODELarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger83125tag:blogger.com,1999:blog-37148773.post-89919216983092000352012-12-12T08:30:48.413-05:002012-12-12T08:30:48.413-05:00Pedro,
I appreciate the fact that you are keeping...Pedro,<br /><br />I appreciate the fact that you are keeping our discussion here on scientific issues, rather than turning it into meaningless personal attacks.<br /><br />I just want to clarify that the ‘Hummingbird case’ was intended to address the issue whether evolution of the genome size and of the so called ‘junk DNA’ (jDNA) can be under host selective constrains? As discussed in the original paper, the presence of jDNA can be explain simply because its rate of origin is higher than that of its deletion, or because jDNA offers a selective advantage. The hummingbirds are a clear example that even in vertebrates the amount of jDNA can be under selective constrains and that it can be reduced if necessary. Therefore, the fact that many species maintain high level of jDNA, supports the idea that it has a selective advantage.<br /><br />So what about the paradigm change associated with my model? As you know, despite ECODES’s conclusion that 80% or our genome is functional, most scientists continue to claim, as they have done for almost half of century, that the vast majority of our DNA is non-functional, or junk. However, the current data and observations clearly show that the so-called jDNA provide a defense mechanism against insertional mutagenesis. This is an indisputable, statistical fact, which no reputable scientist denies. If that is the case, and the so-called jDNA provides a defense mechanism at the genome level (just as the immune system which provides hundreds of defense mechanisms at the organismal level), then it makes sense to consider it functional DNA.<br /> <br />Again, say goodbye to the concept of ‘junk DNA’!<br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15765459270697577402012-12-12T04:41:07.120-05:002012-12-12T04:41:07.120-05:00Claudiu:
"Clearly, the protective function o...Claudiu:<br /><br />"Clearly, the protective function of jDNA against insertional mutagenesis is a fact, and no reputable scientist disputes that."<br /><br />My problem is not really with the insertional mutagenesis part but with the claim that those with less jDNA are due to metabolic/energetic reasons. If we check a representative number of species for which we have metabolic data, does that map well to jDNA size? You should do that, because right now the model is too vague and without clear confirmation. Things like "evolutionary constrains on genome size" sound good but lack solid evidence that actually confirms it. What constrains are those specifically? Metabolism? Remains to be shown, in my opinion. It's too vague. I think your model may be a good hypothesis, but it is certainly in no state to be a paradigm changer for now unless you come up with strong data to support it. I can't blame people for remaining skeptical for now. <br /><br />Anyway, I'm not attacking you. But I'd prefer that you worked on your model instead and delivered the goods. As it is it will not convince anyone. It's just an hypothesis that needs far more data to turn into something solid.<br /><br />:)<br /><br /> Pedronoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67731335820264864502012-12-11T12:48:19.780-05:002012-12-11T12:48:19.780-05:00http://en.wikipedia.org/wiki/Medical_Hypotheseshttp://en.wikipedia.org/wiki/Medical_HypothesesFaizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62656224181248488752012-12-11T12:31:54.606-05:002012-12-11T12:31:54.606-05:00@lutesuite,
As I said in an earlier comment, unli...@lutesuite,<br /><br />As I said in an earlier comment, unlike the conventional scientific publishing, where you are protected from ‘unpleasant’ comments, here on Blogosphere, you are fully exposed. The only bad part about that, is that it is usually done by people, such as <b>lutesuite</b>, who hide behind anonymity.<br /><br />I suggest that if you respect yourself enough to stand behind your words, and if you respect the other members of this blog, you should reveal who you are.<br /> <br />Also, I think that the editors and the thousands of scientists and clinicians who have published in one of the oldest scientific medical journal <b>Medical Hypothesis</b>, where I published my hypothesis, are highly offended by your remarks about the journal.<br /><br />Moreover, I only joined the Blogosphere less than two years ago, so your assertion about “trolling’’ is incorrect. The fact is that, although I published my model on the evolution of genome size and of so called junk DNA (jDNA) more than two decades ago, I never brought it up until now, which might explain why it is not known. <br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88956602426706127342012-12-11T11:29:40.042-05:002012-12-11T11:29:40.042-05:00No, I get the "essence of your model" ju...No, I get the "essence of your model" just fine, Claudiu. And I don't think I'm missing anything, now. But I was earlier, when I was treating you as a serious scientist. <br /><br />I also don't appreciate being quote mined. I now realize why most of the longterm posters here seem to be simply ignoring you, as I will endeavour to do henceforth.<br /><br />A bit of internet sleuthing reveals that your "hypothesis" was not published in a peer-reviewed journal, but in a magazine best known for promoting pseudoscientific ideas like AIDS denialism. Since then, you have spent much of the past two decades trolling internet discussion groups complaining that your idea has not been accepted because of the ideological rigidity of the scientific establishment. <br /><br />If you really want your idea to be accepted, you would get back into the lab and produce some evidence worthy of passing the peer-review process, rather than just whining about how your genius is not appreciated by the blinkered scientific elite. Until you do so, you deserve to be treated as nothing more than a crank.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-16157630920395771152012-12-11T10:48:30.185-05:002012-12-11T10:48:30.185-05:00Petro,
I think if you review your comments on th...Petro,<br /> <br />I think if you review your comments on this post, you’ll see that I answered most of your specific questions and that you thanked me for that several times.<br /><br />Obviously, this model on the evolution of genome size and of so called junk DNA (jDNA) needs further studies and discussion. However, this model fundamentally answers the very old C-value enigma (which commonly and metaphorically is expressed as the Onion Test):<br /><br />: <i><b>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</b></i>.<br /><br />Clearly, the protective function of jDNA against insertional mutagenesis is a fact, and no reputable scientist disputes that. <br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-63349027134855979032012-12-11T09:45:53.184-05:002012-12-11T09:45:53.184-05:00I don't think you actually answered any of my ...I don't think you actually answered any of my questions above. <br /><br />"Moreover, like any major paradigm change, it needs to undergo full validation, and that usually requires many new studies and numerous discussions."<br /><br />But until those studies show that your model correlates to all the points I made above you don't have a case. You say that your model solves the C-value enigma, and you could very well have a case for the high values of jDNA as being functional by your definition. But until your model passes the "onion test" (see my posts above that you have not commented on) it hasn't solved anything. You have to explain both the high and low levels of jDNA, otherwise your model isn't an alternative to the current paradigm.<br /><br />Pedronoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-37057489997368842632012-12-11T08:49:38.571-05:002012-12-11T08:49:38.571-05:00Pedro said: What do you think?
Well, I think we a...Pedro said: <i>What do you think?</i><br /><br />Well, I think we are making progress. Indeed, as stated by <b>lutesuite</b> this is <i>“a revolutionary overturning of the standard scientific understanding of the topic”</i>, so it is not going be an easy transition. Although relatively straightforward, this model on the evolution of genome size and of so called junk DNA (jDNA) challenges much of the thinking and dogma in the field, so it should be expected to be met with some reluctance. Moreover, like any major paradigm change, it needs to undergo full validation, and that usually requires many new studies and numerous discussions.<br /><br />However, fundamentally, this model solves the C-value and jDNA enigmas: <i><b>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</b></i>.<br /><br />Obviously, there are many issues and specific cases (e.g.amoeba) that need to be further addressed in context of this model. However, one of the major undertakes would be to clarify what <b>biological function</b> means. Like <b>lutesuite</b> mentioned above, the current dogma implies that in order to be considered functional, the DNA must have an informational function. In context of this dogma, only ‘informational DNA’ (iDNA) has a function, so unless we clarify the problem with this dogma, it will continue to obstruct progress. <br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-58100169356359700652012-12-11T07:59:56.272-05:002012-12-11T07:59:56.272-05:00Let me make the missing post again:
If you want t...Let me make the missing post again:<br /><br />If you want to pass the "onion test" you have to show that your model is consistent all across the board, not just with a single example from humming-birds. Does two different breeds of onion have significant different metabolic demands that correlate well with the huge difference in jDNA amount? Does a cheetah, which has high metabolic demands, have correspondingly low amounts of jDNA? We know that birds of prey apparently have relatively low jDNA content, but what about other species with also high metabolic demands? What about grazing animals in Africa, in which thousands of animals die for lack of water and food while migrating all the time? Do they all show lowjDNA content? What about migrating birds that travel from northern latitudes to lower latitudes in extreme metabolic stress?<br /><br />Can we see a clear correlation between a representative number of species that show consistent levels of jDNA that are consistent with your model? It seems to me that it can't. I think you are far from passing the "onion test". You have to eliminate the null-hypothesis and also show that low jDNA amounts correlate all across the board with a representative number of high metabolism species. Otherwise you don't have a strong case.<br />Pedronoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14698341670876353202012-12-11T07:39:24.428-05:002012-12-11T07:39:24.428-05:00Hum, my posts are not being posted in real time in...Hum, my posts are not being posted in real time in the thread. Kind of difficult to have a discussion like this with posts missing.Pedronoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-31559471033123227882012-12-11T05:37:03.496-05:002012-12-11T05:37:03.496-05:00Some more food for thought: if I remember correctl...Some more food for thought: if I remember correctly, most if not all, birds of prey show relatively low amounts of jDNA (someone please confirm). That could help with your idea that metabolic rates could have something to do with it. But what about migratory birds that are under extreme metabolic stress? What about migratory mammals in Africa that spend most of their time under nutrient stress, always traveling from one place to the other in great migrations to find water and food? You would have to analyze all these cases, calculate what the energetic needs would be for all representative species and see if metabolic rates correlate with jDNA content all across the board. Just using the humming-bird case is not enough. It's only a single example. Your theory has to demonstrate the capacity to coherently explain most cases under an unified model. Otherwise it won't convince anyone to abandon the current jDNA model. It seems to me that right now the metabolic explanation for low amounts of jDNA is far from clear. probably it doesn't even correlate across most cases, much less jumping to the conclusion of causation.<br /><br />What do you think?Pedronoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43181572239980357932012-12-11T04:43:36.716-05:002012-12-11T04:43:36.716-05:00"Pedro, I hope I didn't lose you during t..."Pedro, I hope I didn't lose you during this rant!"<br /><br />No worries. I'm not attacking you at all, just asking questions.<br /><br />"Please take a serious look at the Hummingbird Case and see if it silences the Onion Test?"<br /><br />In here I have to agree to a certain point with Lutesuite. It's not that your model appears to me as necessarilly wrong, it's that the explanation is seems shaky and needs a lot more testing, including clearly invalidating the null-hyphotesis. Even if the humming-bird case did explain without any doubt that particular case you'd still have to have a coherent explanation to most other cases, including the good old different onions, etc. I don't think it is ready to pass the onion test as it is, unless I'm missing something. As for the amoeba case you say that the enourmous size of its genome "MIGHT HAVE something to do" with lateral transfer of genetic material, but this is far from being a good explanation. It COULD be, but you need a unifying concept that fits most observed cases, and at the moment you don't appear to have that. Therefore it's normal that other people will not see your case as a solid alternative to the present model of jDNA. Maybe it will turn out to be correct eventually, but right now it is not in a form that can overthrow the current models.<br /><br />Not sure I was clear in my point. What do you think? <br /><br />Pedronoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55475422724936883942012-12-10T19:37:26.381-05:002012-12-10T19:37:26.381-05:00@lutesuite
Obviously you are “missing something.”...@lutesuite<br /><br />Obviously you are “missing something.” And, I’m rather surprised because I though you got the essence of my model on the evolution of genome size and of the so called ‘junk DNA’ (jDNA), when you said:<br /> <br /><i>“If anything, your hypothesis strengthens this claim, by providing a reason that a smaller C-value would not be selected for, and that there might be an advantage in retaining these junk elements, rather than having them eliminated thru deletion.”</i><br /><br />Apparently, I was wrong about your take, but let’s see what Pedro or the OT fans have to say, if anything!<br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-38292327474148779632012-12-10T10:36:29.449-05:002012-12-10T10:36:29.449-05:00Maybe I'm missing something, but I fail to see...Maybe I'm missing something, but I fail to see how your "Hummingbird Case" even remotely addresses the "Onion Test." You seem be claiming that the reason the hummingbird has an unusually small genome is because of the high metabolic demands its mode of flight imposes. Umm, OK. Any supporting evidence? Is there an overall correlation between metabolic demands and genome size? Do humans have much higher metabolic requirements than, say, salamanders? Of the two types of onions Pedro mentions, does one fly about collecting nectar from flowers while the other just sits quietly in the ground? I can't say I've ever seen a flying onion, but you never know.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67435681672552767672012-12-10T10:17:55.369-05:002012-12-10T10:17:55.369-05:00Pedro: What would be the reason an amoeba has 100...Pedro: <i>What would be the reason an amoeba has 100 times more jDNA than a human? Do amoebas get cancer? Why does a breed of onions have so much jDNA and another onion breed with little genetic differences that can be cultured in the exact same conditions doesn't? How does your model cope with that?</i><br /><br />These are all great questions and any model on the potential function of the so called ‘junk DNA’ (jDNA) should address them. I don’t know if you had the chance to read my comment entitled <b>‘Five reasons why my theory on the function of ‘junk DNA’ is better than theirs’</b> in which I made strong case for this:<br /><br /><i>“The Onion Test is so formidable and inconvenient that, to my knowledge, it has yet to make it through the peer review into the conventional scientific literature or textbooks.</i> (<a href="http://selab.janelia.org/people/eddys/blog/?p=683" rel="nofollow">http://selab.janelia.org/people/eddys/blog/?p=683</a>)<br /><br />When confronted with the ‘Onion Test,’ do you know what the leaders of the ENCODE project, who stated that 80% of the human genome is functional, said? They said that the Onion Test is ‘silly ’ (see: <a href="http:http://www.genomicron.evolverzone.com/2012/09/birney-thinks-onion-test-silly/" rel="nofollow"> http://www.genomicron.evolverzone.com/2012/09/birney-thinks-onion-test-silly/</a>.<br /><br />So, if the leaders of the ENCODE project, which has consumed more than 200 million dollars of our tax money, can get out of addressing inconvenient questions about their conclusion by saying that they are ‘silly’ (or by using an even more efficient strategy of dealing with difficult questions or alternative paradigms which is to pretend that they don’t exist), do you expect me to really address these questions here?<br /> <br />Don’t you think that reasonable answers to such important questions would be worth a page or two in some of our flagship scientific journals? After all, understanding the evolution of the genome side and the potential role, if any, of the so called jDNA are among the most significant scientific questions in biology, aren’t they? And they are worth investing hundreds of millions of dollars in addressing them, aren’t they? So, how much would reasonable answers to your questions be worth? For goodness sake, even Pepe might end up a thousand bucks richer from this fiasco about jDNA!<br /><br />Well, unlike in traditional scientific publishing, here in the Blogosphere you <i>‘answer the questions or perish’</i>! So, I did! I answered the Onion Test challenge. And in doing so, I proposed the Hummingbird Case (you can find a narrative of this paradigm here: <a href="http://sandwalk.blogspot.com/2012/09/ewan-birney-genomics-big-talker.html" rel="nofollow"> http://sandwalk.blogspot.com/2012/09/ewan-birney-genomics-big-talker.html</a>).<br /><br />Pedro, I hope I didn't lose you during this rant! Please take a serious look at the Hummingbird Case and see if it silences the Onion Test? Maybe the author and other proponents of the OT might jump in, unless they think that Hummingbird Case is silly!<br /><br />In regard specifically to amoeba’s freakish genome, its enormous size might have something to do with their enormous appetite for ingesting tons of other genomes that are full of transposable, inserting elements. What do you think?<br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-52001956515931906112012-12-10T06:24:33.303-05:002012-12-10T06:24:33.303-05:00What would be the reason an amoeba has 100 times m...What would be the reason an amoeba has 100 times more jDNA than a human? Do amoebas get cancer? Why does a breed of onions have so much jDNA and another onion breed with little genetic differences that can be cultured in the exact same conditions doesn't? How does your model cope with that?Pedronoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57524291433285654082012-12-08T15:55:01.555-05:002012-12-08T15:55:01.555-05:00My comments here and elsewhere about the paradigm ...My comments here and elsewhere about the paradigm that the so called “junk DNA” (jDNA) provides a protective mechanism against insertional mutagenesis, which in humans and other species is a common cause of cancer, come more than two decades after I published it. <br /><br />For whatever reason, the model I proposed has not been embraced. So, now that we know that this paradigm represents a fact that cannot be disputed (any statistician will confirm that), I decided to re-introduce it. I think that's reasonable, don’t you?<br /><br />Obviously, Pépé did not make his argument based on my model. But, it just happen that he won his bet with our host Larry. To his credit, Pépé (if indeed he/she is a real person and not a fictional character invented to spike or discussion on jDNA) has not jumped yet up down demanding his ‘cash’, as he probably realized that he was right but not for the reasons he thought. So, kudos to Pépé!<br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56778338641742750882012-12-08T13:36:31.583-05:002012-12-08T13:36:31.583-05:00However, if you read previous discussions here at ...<i>However, if you read previous discussions here at Sandwalk, you’ll find that some of our colleagues have circumvented the data and the rationale supporting this model based on what I consider ideological (anti-religion in this case) reasons, which are in line with to those articulated by you. My point is that we should not let the truth and science become hostage to ideological pursuits.</i><br /><br />And if that's the case, then I have to say with all due respect you may share a large portion of blame. You could be more modest and realistic in the appraisal of your model as being a complement to the understanding of the nature of non-coding DNA. But when you instead present as a revolutionary overturning of the standard scientific understanding of the topic (eg. when you suggest that this means Pepe has won his bet, when in fact it does not), you sound suspiciously like a creationist. And, to be clear, I am not accusing you of being one. But if others are coming to that conclusion, you may have to consider you part in fostering that impression. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-75935741075858003042012-12-08T13:24:21.829-05:002012-12-08T13:24:21.829-05:00lutesuite said: "Your claim of the structura...lutesuite said: <i>"Your claim of the structural role for non-coding DNA may well be correct. I won't pretend to be knowledgeable enough of the field to hold an informed opinion. But assuming it is, that is a peripheral issue to the question of the origin and nature of "junk DNA." More specifically, it does not refute the hypothesis that much, if not most, of non-coding DNA consists of remnants of transposons and similar "selfish" genomic elements. If anything, your hypothesis strengthens this claim, by providing a reason that a smaller C-value would not be selected for, and that there might be an advantage in retaining these junk elements, rather than having them eliminated thru deletion “</i><br /><br />I completely agree with most of what you are saying. Indeed, my model on the evolution of genome size and the function of the so called “junk DNA” (jDNA) as a protective mechanism against insertional mutagenesis is based on the fact that <i>“much, if not most, of non-coding DNA consists of remnants of transposons and similar "selfish" genomic elements”</i>. Probably, you did not have the chance to read the original paper and the numerous comments I posted here and elsewhere, in which I address these issues in more detailed; for links to some of this material, please see my comment below in response to a question by Pedro.<br /><br />However, I don't think that the putative protective function of the so called jDNA is a peripheral issue. This function might be key to undestanding the evolution of genome size (in your words, it provide <i>“a reason that a smaller C-value would not be selected for”</i>), which is a very important scientific goal. Moreover, this model might have significant biomedical implications and applications (see my previous discussions).<br /><br />Also, I think that most if not all evolutionists are open to truth; I also belive that they will embrace this model if they would get the chance to evaluate it. However, if you read previous discussions here at Sandwalk, you’ll find that some of our colleagues have circumvented the data and the rationale supporting this model based on what I consider ideological (anti-religion in this case) reasons, which are in line with to those articulated by you. My point is that we should not let the truth and science become hostage to ideological pursuits.<br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-92057919822449807502012-12-08T10:47:50.686-05:002012-12-08T10:47:50.686-05:00I don't see where any scientists are "cir...I don't see where any scientists are "circumventing the truth." Your claim of the structural role for non-coding DNA may well be correct. I won't pretend to be knowledgeable enough of the field to hold an informed opinion. But assuming it is, that is a peripheral issue to the question of the origin and nature of "junk DNA." More specifically, it does not refute the hypothesis that much, if not most, of non-coding DNA consists of remnants of transposons and similar "selfish" genomic elements. If anything, your hypothesis strengthens this claim, by providing a reason that a smaller C-value would not be selected for, and that there might be an advantage in retaining these junk elements, rather than having them eliminated thru deletion. <br /><br />So, again, it comes down to the language one chooses. One can present the evidence objectively and accurately, saying this finding expands our understanding of the nature of non-coding DNA but does not overthrow or falsify our current understanding.<br /><br />Or, you can engage in hyperbolic claims that all those "evolutionists" who have been "circumventing the truth" have been proven wrong, thereby providing succour to the <i>actual</i> liars who want to create the impression that all DNA was specifically designed for a purpose by God. <br /><br />Your choice.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4993152468870858302012-12-08T09:58:48.668-05:002012-12-08T09:58:48.668-05:00lutesuite,
In regard to your second point, I do n...lutesuite,<br /><br />In regard to your second point, I do not think that we should obscure scientific findings and facts because they might “be exploited by religious propagandists.”<br /><br />On the contrary, the effort by some scientists and bloggers to circumvent the truth might create a deceiving academic and intellectual framework susceptible to, and encouraging, misleading propaganda and unproductive discussions. <br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-61294298704936220912012-12-08T09:40:02.886-05:002012-12-08T09:40:02.886-05:00lutesuite,
You bring forward a critical issue reg...lutesuite,<br /><br />You bring forward a critical issue regarding the concept of “junk DNA” (jDNA), namely : <i>the meaning of the word "functional"</i>.<br /><br />Fortunately, we have some very knowledgeable members in linguistics here at Sandwalk, including <b> Piotr Gasiorowski </b> and <b>andyboerger</b>, so I hope they will help us here.<br /><br />I agree with you that in terms of “informational content as defined by its base sequences”, the structural DNA (sDNA) can be called “junk”. But, I think, you would agree that in terms of structural role, the informational DNA (iDNA) can also be called “junk.”<br /><br />However, from a scientific perspective, both sDNA and iDNA have a biological function, and neither is “junk.” <br />Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10767849491184672882012-12-08T07:54:53.419-05:002012-12-08T07:54:53.419-05:00Claudiu Bandea,
Not to dispute the scientific val...Claudiu Bandea,<br /><br />Not to dispute the scientific validity of your claim, but it seems to me you are making much the same error the ENCODE people have, by equivocating on the meaning of the word "functional". That non-coding DNA might serve "functions" independent of its informational content does not change the fact that, in terms of that informational content as defined by its base sequences, it can still be called "junk". This is the usual context in which the term "junk DNA" is used.<br /><br />While I can see the argument for not allowing creationists do dictate the terms of scientific discussion, I believe it is an error to ignore the possible ramifications of making grand eye-catching, but not strictly accurate, claims about having overthrown the paradigm of junk DNA without considering how easily such statements can be exploited by religious propagandists. That is the error ENCODE made, and I fear you are making it as well. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-67517687615993657282012-12-07T10:50:13.126-05:002012-12-07T10:50:13.126-05:00Just want to add my endorsement, FWIW. This artic...Just want to add my endorsement, FWIW. This article is very clear and persuasive to a layperson like myself. A must read for anyone interested in the topic.Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28172706565289018862012-12-07T10:26:57.002-05:002012-12-07T10:26:57.002-05:00Joe, I agree with you. It will take many years for...Joe, I agree with you. It will take many years for the misleading message trumpeted by the ENCODE to fade. We have to realize that the leaders of this project are very smart and ambitious people, who will not let facts stay in their way. That’s why there occupy those positions. But forget about their misleading message, what’s important here is that the project has generated valuable data that can be used to make progress in understanding our genome.Claudiu Bandeahttps://www.blogger.com/profile/04987489537796352657noreply@blogger.com