Another Day, Another Bad Day for Darwinism

_{June 23, 2010

Evolutionary biology, Intelligent Design}

Share: Facebook; Twitter; LinkedIn; Flipboard; Print; Email

In the latest issue of Nature, a definitive role for pseudogenes is established. In the last sentence of the Abstract the authors conclude:

These findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs.

Haven’t read the full article* (no time at present), but there’s a related link at PhysOrg.com that gives an overview.

Yes, “junk” DNA now “communicates” with itself. A new “language”, an RNA language, is discovered. Another 30,000 pieces of functional information (over and above proteins) are part of cell architecture. And even more for Darwinists to explain per RM+NS. And the old standard explanation, of gene duplication and pseudogenes ‘evolving’ new function, takes a hit. You’ve got to feel bad for these Darwinists. What’s tomorrow going to bring!?!

*BTW, somehow I gained access to the pdf version of the article.

Comments

Arthur Hunt: Thank you for elucidating your thought. My comments: 1) On the quantitative issue. The important point, IMO, is not "how many nucleotides" are involved in the miRNA competion (I happily accept your calculation), but that a specific subset of "junk" DNA, pseudogenes, which have been traditionally considered mayube the most evidently "error-like" part of non coding DNA, are now shown to be functional, and part of a very complex and integrated regulatory network. We know very well that pseudogenes are only a minority part of non coding DNA, but conceptually they are a very important subset. Other parts of non coding DNA have alredy been shown to be functional in different ways (see our previous discussion about introns), and I am sure that new modalities of function (probably many of them) will be elucidated in a very short time (as research seems now top be justly alerted to these new frontier of knowledge). So, again, I have nothing against your "quantitative" approach: if you want each time a new modality is discovered to count the single nucleotides involved, and stick to how many are still not explained as functional, that's fine form me, but essentially I don't believe that's the right way of getting the real picture. 2) This is more interesting. I believe you really misunderstand the ID point. Let's see: Recall that a pseudogene is the product of a duplication event. In my experience, ID proponents are rather insistent that duplications do not add new information to the genome. So a functional pseudogene is the product of an information-neutral event. That's not completely correct. It is true that a duplication event in itself adds no new information with respect to the sequence itself which is duplicated. For instance, if we are analyzing a causal scenarion where a transition is supposed to happen form one duplicated protein A' to a new protein B, through RV and NS, the act of duplication in itself is not a step towards the new sequence, except for the fact that it can provide a non functional copy of A which can vary without being affected by negative selection (if A' is not translated). So, even in this case there is a variation in the information content of the whole system, if not in the sequence. Let's go to our model of duplication as a pathway to regulation (which is obviously different from the model of duplication as a pathway to a new functional primary sequence). Here, there is a lot of information change implied in the duplication event, and in the following events: a) which gene is duplicated (of all possible gene duplications) b) where it is duplicated c) which parts of UTRs or other flanking regions are duplicated d) which parts of the duplicated gene are not homologous to the original gene, both in the coding and non coding sequence e) how many duplicated genes exist of that particular gene, and how different they are one from the other f) whether the duplicated gene is translated g) whether the duplicated gene is transcribed h) how much the duplicated gene is transcribed, and how its transcription is regulated in relation to the original gene's transcription i) how many miRNA sites are retained, and which, both in the coding and non coding region, and the individual role of each of those miRNA in regulation j) how much the interaction between the pseudogene mRNA and miRNAs influences other genes, and which. k) other possible effects of the pseudogene mRNA, at present not known And so on. My point is, if we believe that transcription and translation of the original gene are finely regulated by a complex network, including miRNAs (and many other regulatory modalities), then the duplication-mutation event must be finely tonuse to integrate in such a network. The point is not that the event in itself is "possible" through known random biochemical mechanisms. It certainly is, exactly as the mutations which can bring to a new functional protein are certainly "possible" from a biochemical point of view. The ID point is that such events are rare functional examples among a huge majority of non functional possible events. The ID point is that, exactly as obtaining a new functional protein is empirically impossible through RV and NS alone, in the same way obtaining a finely tuned duplication, or set of duplications, and the coordinated mutations both in the coding and non coding sequence and in the related regulatory sequences, which perfectly integrates in a complex regulatory system involving many different agents, is empirically impossible through RV and NS alone. Here, while the sequence information varies relatively little (but not really little), differently form what happens when a new protein domain appears, the information in the whole regulatory network changes very much. The problem is that analyzing the information content of a complex regulatory network is much more difficult then analyzing the information content of a primary sequence, especially when the regulatory network is only very partially understood. That's the only reason why ID has focused the attention more on basic protein structures, and less (for the moment) on regulatory networks. But, as our understanding of regulatory networks increases, a quantitative analysis of their information content will follow. Except that it really isn’t. Because the pseudogene must undergo some mutational changes that eliminate the possibility of translation. In my experience, ID proponents are rather insistent that such mutations are actually losses of information. So the bottom line is that functional pseudogenes are the results of losses of information. (Don’t ask me to make sense of this – I’m just following the trail of ID logic here.) From what I have said before, it should be clear that the mutation which disactivates translation is part of a set of coordinated changes which add a specific regulatory function to the system. There is a lot of sense in that. We know how genetic duplications occur – they are the results of typical biochemical processes, and they are, for all intents and purposes, random and unguided. Which means that functional pseudogenes are, for all intents and purposes, the results of random processes that reduce information content. I disagree. We have no evidence that those "typical biochemical processes" are random and unguided, any more than we have evidence that all single point mutations are random and unguided. One of the most likely scenarios for ID is the existence of guided RV. Moreover, many pseudogenes are the result of transposon activity, and transposon activity is a very good candidate as an interface for guided variation. IOW, the main point of ID is that the results usually ascribed to RV and NS are best explained by designed guided variation and/or designed intelligent selection. In other words, new layers of regulation arise from random events that most definitely do not increase information contents of genomes. As I was saying, this is not exactly something that is friendly to ID. And,from what I have said, that is not true: the ID point is that those new layers of regulation arised from design, and that it is empirically not credible that they could arise differently: the facts of pseudogene function are very well explained by an ID scenario, and totally "ID friendly".gpuccio_{June 26, 2010
June
06
Jun
26
26
2010
03:59 AM
3
03
59
AM
PDT}

1. Some numbers, for a proper perspective: Conservative estimate number of bp in the human genome that is not protein-coding or stable RNA (a very generous estimate for anti-junkites) - 2,400,000,000 Number of nts involved in miRNA decoying (per decoy site) - ca. 25 Maximum number of bp "covered" by the (wildly optimistic) claims of the PhysOrg article - 750,000 Percentage of "junk DNA" that the article cited by PaV eliminates - 0.03. I'd say that we haven't made any dent at all in the "junk DNA" problem. And that's before we correct the hyperbole in the cited article. 2. About my claims about information and functional pseudogenes: Recall that a pseudogene is the product of a duplication event. In my experience, ID proponents are rather insistent that duplications do not add new information to the genome. So a functional pseudogene is the product of an information-neutral event. Except that it really isn't. Because the pseudogene must undergo some mutational changes that eliminate the possibility of translation. In my experience, ID proponents are rather insistent that such mutations are actually losses of information. So the bottom line is that functional pseudogenes are the results of losses of information. (Don't ask me to make sense of this - I'm just following the trail of ID logic here.) We know how genetic duplications occur - they are the results of typical biochemical processes, and they are, for all intents and purposes, random and unguided. Which means that functional pseudogenes are, for all intents and purposes, the results of random processes that reduce information content. In other words, new layers of regulation arise from random events that most definitely do not increase information contents of genomes. As I was saying, this is not exactly something that is friendly to ID.Arthur Hunt_{June 25, 2010
June
06
Jun
25
25
2010
11:38 PM
11
11
38
PM
PDT}

Arthur Hunt (#34): Then there is the fact I see has been ignored – that this mechanism for regulation is quite unfriendly to ID. I have not ignored As you can see in my #33, I have not ignored that statement of yours. And again I ask you: why? Let's discuss this interesting point (it's a serious invitation).gpuccio_{June 25, 2010
June
06
Jun
25
25
2010
03:53 PM
3
03
53
PM
PDT}

Joaozinho you asked: My question is, how much of the genome is accounted for? Depending on your level of "proof" for functionality, which seems to be quite high since you want to know "complete" functionality, it varies substantially thus since I maintain that most all of the "Junk DNA will be found to have function, I want you to pick a number, any number for what you think the percentage of Junk DNA is,,, Asking Darrel Falk to Pick a Number, Any Number http://www.evolutionnews.org/2010/03/asking_darrel_falk_to_pick_a_n032871.html Sternberg excerpt: Now, the problem with such a statement is this: While there are ~25,000 protein-coding genes in our DNA, the number of RNA-coding genes is predicted to be much higher, >450,000.1 Some of the latter range in length from being quite short—only 20 or so genetic letters—to being millions of letters long. Since 2004 we have learned that over 90% of our DNA is transcribed into RNA sequences at some developmental stage, in different cell and tissue types.2, 3, 4 (Our brain cells are unusually rich in these non-translated RNAs.) These RNAs are then processed into regulatory and structural sequences of all sizes.2, 3, 4 It could of course be argued, as it has been, that most of these RNA transcripts are themselves junk. But a host of them are packaged into complexes with different proteins.1 So the true number of genes in our DNA is probably >450,000 + 25,000 = >475,000. What is more, these >450,000 genes cover more than 88.5% of our 3 billion genetic letters. That’s right—most, if not close to all, of our chromosomal DNA consists of different types of genes that have only recently been discovered. How do these facts square with this comment made by Falk? "but this still doesn’t negate the fact that almost certainly much, if not most, of the DNA plays no role, and in many cases can be harmful." Well, it all depends on how he is using the words “much” and “most.” I really don’t know. So I have a question for him: Exactly what fraction of the transcribed 88.5% of our DNA are you willing to say “plays no role” or can be harmful? All I am asking for is a prediction, such as “90% of these DNA letters is superfluous” (“or 79.5% of the RNAs are nonsensical”). Since he also said “almost certainly” in the above statement, he must have a figure in mind. So I say pick a number, any number…But to be a good sport, I’ll show my prediction: All of the expressed 88.5% of our DNA has diverse roles in our development.bornagain77_{June 25, 2010
June
06
Jun
25
25
2010
01:25 PM
1
01
25
PM
PDT}

Art, we weren't talking about your upcoming conference. And we're all entitled to our own opinions. You seem to have a conception of how information works, or doesn't work, that differs radically from most of us here. You're free to do so. But that doesn't make it science. It's just opinion.PaV_{June 25, 2010
June
06
Jun
25
25
2010
12:43 PM
12
12
43
PM
PDT}

chrisvander: As far as I can tell from the discussions at the end of the article, a former gene which has been mutated into disfunctionality (a pseudogene) has picked up a second function, unrelated to the first That's how a darwinist would try to explain what is observed. What is observed is that a copy of a very important gene, having been translation inactivated, is anyway transcribed, and the transcribed mRNA acts as a fine regulator of the original active gene. From an ID point of view, that's a very intelligently integrated and finely tuned system. Moreover, the pseudogene in reality has not picked up a second function, as assumed by the imaginative darwinist principle of cooption. Instead, it's exactly because the pseudogene is highly homologous to the original gene that it can work to regulate it, through the means of the miRNA network. So, a specific functional sequence is used both to produce its protein and, after appropriate inhibition of translation, to regulate that production. But isn’t this exactly what evolution says happens? No, it's exactly what we would expect from a very sophisticated design. The conservation of the basic sequence allows the miRNA competition, while the inactivation of the translation ensures the regulatory fucntion. A finely tuned balance between homology and difference is here the key to reach a finely tuned result.gpuccio_{June 25, 2010
June
06
Jun
25
25
2010
09:07 AM
9
09
07
AM
PDT}

gpuccio: Please, greet your friend for me - All the best.
I will. He was sure that you wouldn't accept his bet.
Phaedros: Let me ask you a simple question. Do you think 20,000-30,000 genes is a sufficient amount of information for a complex organism such as a mammal?
Of course not! They are meaningless outside the context of the cell and embryo. That is where I find space for ID, not in the genome.
gpuccio: Again, the point is: functional modalities are being discovered for what was considered non functional DNA. That will go on. There is no reason to just count what is known and stick to the point that there is still much unknown to affirm that it will remain unknown, or that there is nothing to know. Our point is: we are beginning to understand, that’s only the beginning.
But isn't that why the evolutionists are studying this, that they are sure enough that some of what is provisionally classified junk will have function? My question is, how much of the genome is accounted for? That's where I feel deceived by the OP, and it's where I appreciate your honesty, gpuccio.
bornagain: But Joaozinho am I really in a hole?
Yes, you really are. Are you willing to take my friend's bet?Joaozinho_{June 25, 2010
June
06
Jun
25
25
2010
08:37 AM
8
08
37
AM
PDT}

Let’s call it the Great Divergence. These poor authors weren’t trying to disprove evolution. They are probably evolutionists themselves. They were simply looking at nature for its own sake, without Darwin’s rose-colored glasses. Something interesting is happening in the hard sciences. The tests have become so sophisticated that they have slipped the surly bonds of Darwinism. Basic research, not driven by any agenda, is taking the human race on a fantastic voyage of discovery. The more we know, the more we realize that nature is highly complex and functional in astonishing ways. This is “bad news” for Darwinism because Natural Selection requires nature to be rather simple. One can, on a dreamy summer evening, imagine the poor girl creating herself through deep time if she doesn’t have very much to do. But each new study finding makes Darwin’s theory look increasingly anthropomorphic. Natural Selection attributes a degree of creativity and ingenuity to nature that cannot be found in nature itself; that exceeds nature’s natural limitations. The worker bees of science have been casting light (unintentionally) on a disconnect between the grand, unifying theory and the particulars of experience. The vestiges of language and purpose they uncover indicate something very different from what Darwin had in mind. Do their discoveries disprove his theory? No; that’s the genius of Darwin. Virtually nothing can disprove his theory. Will Darwinism go away? Not as long as there are people who want to believe it. But basic science is making it possible to become an intellectually fulfilled believer again. What we see with our own eyes and what the Darwinists want us to believe about the nature of being are two very different things. Nothingness is overthrown, and with it the arrogance of those who sought to put themselves in the place of God.allanius_{June 25, 2010
June
06
Jun
25
25
2010
06:03 AM
6
06
03
AM
PDT}

I don't get this. I've read the OP and tried to read the article it references even though it appears to be written in another language. As far as I can tell from the discussions at the end of the article, a former gene which has been mutated into disfunctionality (a pseudogene) has picked up a second function, unrelated to the first. But isn't this exactly what evolution says happens? A gene is duplicated, a mutation disables one copy and then the remainder is available for a new function. How is this "bad for Darwinism"? It looks more like a confirmation of evolution to me.chrisvander_{June 25, 2010
June
06
Jun
25
25
2010
04:42 AM
4
04
42
AM
PDT}

Joaozinho you suggest to me: "When you are in a hole, quit digging." Which is also known as the first law of holes: It is a good thing to follow the first law of holes; if you are in one, stop digging. [1988 D. Healey Observer in J. Care (ed.) Sayings of the Eighties] But Joaozinho am I really in a hole? foras to PaV's cite from the Physorg article in post 32,,,, This means that not only have we discovered a new language for mRNA, but we have also translated the previously unknown language of up to 17,000 pseudogenes and at least 10,000 long non-coding (lnc) RNAs. Consequently, we now know the function of an estimated 30,000 new entities, offering a novel dimension by which cellular and tumor biology can be regulated, and effectively doubling the size of the functional genome.” ,,,,, thus it appears that neo-Darwinists are the ones that are actually in the hole futilely digging themselves deeper. I am quite comfortable with the Intelligent Design postulation of "Junk DNA" being functional and see absolutely nothing in the article that would go against that postulation. I am just left wondering why your friend would "laugh" at such a profound breakthrough as discovering another "language" within the DNA. Does he have some sort of compulsion to dig holes? Dig it - From the Disney Movie "Holes" http://www.youtube.com/watch?v=ybjSSExktzIbornagain77_{June 25, 2010
June
06
Jun
25
25
2010
04:22 AM
4
04
22
AM
PDT}

veilsofmaya: Given the clarifications above, it would appear that ID proponents are merely offend by the very idea of the word “junk DNA” for reasons which would be obvious. God doesn’t make “junk” and the designer ID is referring to is God. You have a point here, but not the way you think. Junk DNA is compatible with Darwinism, because it fits the result of an unguided and unintelligent process. Perfect DNA is also compatible with Darwinism, after all, nature had 4+ billion years to make it perfect. (Actually, both of them are also compatible with ID, in its purest form, because not everything has to be designed.) Why is it then, that Darwinists trumpet that DNA is junk? Why is it that they blatantly allow unjustified leaps of logic to declare something useless, when the we just simply do not understand it? They are intelligent scientists and not so dull that they would not see the trivial flaws in their arguments. It is because, junk DNA, or at least wast amounts of junk DNA is not compatible with an omnipotent, omniscient and good Creator, described in the Bible. The main purpose of Darwinism is to prove the Bible and its historic account false. Once that is done, the moral code described there is also meaningless, so we can do whatever we feel all right. In this battle anything is permitted, because the vast majority of the public will not understand or dare to question those in white lab cloaks. Is the inverted retina unexpected at first sight? Shout it out loud: God would have made it better! Leringeal nerve goes in an unusual path? Stuuuuupiiiid designnnn! Large parts of DNA do not code proteins? Junk, junk, junk!!!!! Truth does not matter here. (It eventually comes to the surface when our puny knowledge is somewhat increased and become able to appreciate these solutions.) Darwinist journalism is not science, but evangelism for atheism.Alex73_{June 25, 2010
June
06
Jun
25
25
2010
01:43 AM
1
01
43
AM
PDT}

PaV, As I look through the abstracts for the RNA 2010 meeting in Seattle, I find lots of stuff that reveals the quotes you bring up to be incredible hyperbole. The authors' findings do not apply to many long ncRNAs (look up some work on these - you'll find lots of stuff that has nothing to do with miRNA decoying), and they don't apply to the thousands of pseudogenes that are not transcribed to any great extent. (Please spare us the "95% of the genome is transcribed" line - the transcripts IDists are so excited about are so exceedingly rare that they cannot possibly be involved in miRNA decoying.) In a nutshell, their extrapolation is unwarranted and has already been refuted by numerous studies. Then there is the fact I see has been ignored - that this mechanism for regulation is quite unfriendly to ID.Arthur Hunt_{June 24, 2010
June
06
Jun
24
24
2010
11:21 PM
11
11
21
PM
PDT}

Arthur Hunt (#10): Um, I count 12 (or thereabouts) objects of study in the cited paper. Even if we count every miRNA target site in these as a separate “piece of information”, I don’t see how we get to 30,000. Again, the point is: functional modalities are being discovered for what was considered non functional DNA. That will go on. There is no reason to just count what is known and stick to the point that there is still much unknown to affirm that it will remain unknown, or that there is nothing to know. Our point is: we are beginning to understand, that's only the beginning. Just how much of each pseudogene actually participates in the described decoying? Again "how much". I don't think that's a good way to be quantitative. We are discovering informational networks. Only a little bit of them. Some parts work in a way, other parts will be probably shown to work in another way. That's complexity. If one does an informational inventory, I am pretty sure one will find that this mode of regulation is pretty unfriendly to ID, what with its insistence on high amounts of information and inaccessibility to random processes (neither of which applies to miRNA decoying by pseudogenes). So, the question is, why bring up the subject on this blog? I disagree. While the comnplexity of regulatory networks is certainly more difficult to assess than the complexity of a single protein domain, it should be obvious, and it will be demonstrates in tfime, that regulatory networks are even more unlikely to arise by chance and necessity than "simple" first level structural information. On what do you base your statement that "this mode of regulation is pretty unfriendly to ID"? Not again, I hope, on your point that biological machines are different form mechanical machines? I have already answered that elsewhere, but if you want we can take again the discussion here.gpuccio_{June 24, 2010
June
06
Jun
24
24
2010
11:13 PM
11
11
13
PM
PDT}

Art Hunt[10]: Read the PhysOrg link:
This means that not only have we discovered a new language for mRNA, but we have also translated the previously unknown language of up to 17,000 pseudogenes and at least 10,000 long non-coding (lnc) RNAs. Consequently, we now know the function of an estimated 30,000 new entities, offering a novel dimension by which cellular and tumor biology can be regulated, and effectively doubling the size of the functional genome."
The fact that the authors are speaking of a new genetic "language" is very problematic for Darwinism: Darwinism can't answer the question, Whence the DNA code? Now it has to answer another question: Whence the RNA code? And, if that weren't bad enough, the supposed uselessness of pseudogenes is now demonstrated to be in error. See Sal's quote from Ken Miller. As I posted, "Another Bad Day for Darwinism"! veilsofmaya [16]:
And what factors prevented them from accepting Heliocentrism? Intuition, a conflict with the current day interpretation of scripture and personal incredulity.
Your initial argument ran roughly like this: "PaV says that the bias of Darwinism blinds researchers to the function of junk DNA. Yet the researchers are studying junk DNA. If they thought it had no function, then why are they studying it." In invoking Ptolemeyism, I was pointing out that though the astronomers were wrong in their understanding of planet motion, this didn't stop them from studying the motion of planets. You didn't respond to this point I made. Instead, you sped forward to the Copernican revolution (BTW, you do know, of course, that Copernicus was a Catholic cleric? See here) and now want to infer that it is perfectly permissible to draw an analogy between that paradigm shift and the current one taking place, implying that ID thinkers are blinded in some way. But you invoke a two-edged sword. And the "scripture" of today is Nature magazine. And the chief high priests are the evolutionary biologists. And they make sweeping statements like "nothing in biology makes sense without the theory of evolution" (meaning Darwinisms). So, your attempt at smearing gets you nowhere.PaV_{June 24, 2010
June
06
Jun
24
24
2010
10:34 PM
10
10
34
PM
PDT}

Joaozinho: Let me ask you a simple question. Do you think 20,000-30,000 genes is a sufficient amount of information for a complex organism such as a mammal?Phaedros_{June 24, 2010
June
06
Jun
24
24
2010
09:37 PM
9
09
37
PM
PDT}

Joaozinho: Please, greet your friend for me :) - All the best.gpuccio_{June 24, 2010
June
06
Jun
24
24
2010
09:32 PM
9
09
32
PM
PDT}

bornagain, When you are in a hole, quit digging. You did not give me what I asked for. The function discovered in this case required transcription, but transcription is not sufficient to assume function. Even I can see that this would not have been a Nature paper if they had just shown transcription. Clearly, if a pseudogene is not transcribed/expressed, it can't possibly have the function that PaV was generalizing from. I'm not being disingenuous here. I came here looking for answers, not further exaggerations.Joaozinho_{June 24, 2010
June
06
Jun
24
24
2010
08:55 PM
8
08
55
PM
PDT}

But Joaozinho you stated: "My friend, who is a genome scientist, asked me to ask you how much you are willing to bet that there have been no surveys of pseudogenes to see if they are expressed—I think he used the word transcribed." and I gave you this: A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way. Thus I gave you exactly what you had asked for Joaozinho, and by the way Joaozinho transcription is in fact completely unexpected from the neo-Darwinian framework. And is indeed a very strong indication of function though we are just barely beginning to understand the unmatched complexity being revealed in the genome,, that was what was completely surprising about the ENCODE study! That you would imply I was misleading you by implying function is disingenuous to what you actually asked for and what I actually gave you and is also misleading to what the current state of the evidence is for Intelligent Design framework to the neo-Darwinian framework. frankly if I had wanted to impress you with 100% functionality, that teams of leading scientists can't even fully unravel, I would of used recent proteome studies.bornagain77_{June 24, 2010
June
06
Jun
24
24
2010
06:18 PM
6
06
18
PM
PDT}

bornagain, Yes, it helped me to see that my friend was right about everything. First, gpuccio was gracious enough to politely point out PaV's exaggerations. Then, you did exactly what my friend predicted someone would do—try to pass off transcription as sufficient to demonstrate function. I'm really disappointed.Joaozinho_{June 24, 2010
June
06
Jun
24
24
2010
06:00 PM
6
06
00
PM
PDT}

"Are you claiming this researchers are actually pro ID, but operating under the radar out of fear of being censured? If so, please indicate how you’ve reached this conclusion." I wont speak for GP, but I have personally interacted with researchers that did exactly as you say. I once emailed an author of a published paper and asked him to clarify a topic in his research. I told him I did not know his metaphysics and did not care to know, but admitted that I was pro ID and then asked the question I wanted clarified. He emailed me back the answer, which then lead to follow up email by me. He then sent me an email and said that he would follow up, but preferred to use regular mail. Several days later I received his letter. In that letter he was clear about his thoughts, and asked for confidentiality (which was already a given). And then - get this - he asked me to destroy the envelope he had used to mail the response. - - - - - - - Materialists like to pose such questions as the one above. They like to spit challenges at anyone who would dare to observe them as they very often are. They dismiss their intolerant hegemony in one breath then talk of consensus in the next. It won't last though. That's what facts are for.Upright BiPed_{June 24, 2010
June
06
Jun
24
24
2010
03:54 PM
3
03
54
PM
PDT}

Joaozinho does this help? How The Junk DNA Hypothesis Has Changed Since 1980 - Richard Sternberg - Oct. 2009 - Excellent Summary Excerpt: A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way. http://www.evolutionnews.org/2009/10/how_the_junk_dna_hypothesis_ha.html here is another gem from Crevo: Pier Paolo Pandolfi of BIDMC explained, “This means that not only have we discovered a new language for mRNA, but we have also translated the previously unknown language of up to 17,000 pseudogenes and at least 10,000 long non-coding (lnc) RNAs. http://www.creationsafaris.com/crev201006.htm#20100624abornagain77_{June 24, 2010
June
06
Jun
24
24
2010
03:31 PM
3
03
31
PM
PDT}

gpuccio, thanks for your reply. When you say growing evidences, what do you mean exactly? That most of junk dna is now accounted for? And if the amount of pseudogenes that are expressed is absolutely not known, isn't it deceptive to use this as an example? I'm asking this because I feel like I am being left without an IDist leg to stand on. My friend, who is a genome scientist, asked me to ask you how much you are willing to bet that there have been no surveys of pseudogenes to see if they are expressed—I think he used the word transcribed. What I meant about his observation was that it disproves the claim that ID-friendly research cant be funded or published.Joaozinho_{June 24, 2010
June
06
Jun
24
24
2010
03:18 PM
3
03
18
PM
PDT}

Interesting the ways in which materialist try to rewrite/deny the written history of thought as it concerns junk DNA.Upright BiPed_{June 24, 2010
June
06
Jun
24
24
2010
03:18 PM
3
03
18
PM
PDT}

Intelligent design cannot explain the presence of a nonfunctional pseudogene, unless it is willing to allow that the designer made serious errors, wasting millions of bases of DNA on a blueprint full of junk and scribbles. Evolution, however, can explain them easily. Pseudogenes are nothing more than chance experiments in gene duplication that have failed, and they persist in the genome as evolutionary remnants... Ken Miller
ROTFLscordova_{June 24, 2010
June
06
Jun
24
24
2010
02:51 PM
2
02
51
PM
PDT}

Joaozinho: He laughed at it and said that only a tiny bit of junk dna is pseudogenes, That's true, but there are growing evidences for regulatory fucntions of the other parts too (like introns). Pseudogenes are only the new entry. only a minority of pseudogenes are expressed as rna, That's absolutely not known. and this paper was only about one pseudogene. True, but this paper is only the beginning. The approach is new, just wait and see. He also made the same observation that the darwinists did here, that it disproved any claims about bias. What does that mean? Please, explain. We IDists are notoriously not intelligent...gpuccio_{June 24, 2010
June
06
Jun
24
24
2010
12:54 PM
12
12
54
PM
PDT}

veilsofmaya (#14): I would like to clarify my personal positions about this subject: 1) Pro ID or non pro ID research: You say: Are you claiming this researchers are actually pro ID, but operating under the radar out of fear of being censured? If so, please indicate how you’ve reached this conclusion. I don't know and I don't care. Other researchers have IMO been pro ID, and have operated for some time with what we could call "reasonable caution". Of these reasearchers I know nothing, and they probably have nothing to do with ID. But that is not the point. The point is that, as I have always openly stated, research in itself is neither pro ID nor against ID, as long as it finds true facts and data. Let's say it is pro scientific knowledge. Obviously, the inspiration of research and the interpretation of the results are usually done according to one's paradigm: as ID and darwinism are antagonistic paradigms, the interpretation of scientific results, or at least of some of them, is different in the two fields. But, as I firmly believe that ID is the best theory, I always welcome all new findings, confident that, beyond the first partial interpretation of them made by official darwinist biology, in time they always reveal their importance for ID. What I have never understood is the arrogant position of some darwinists who think that the results of research in some way "belong" to darwinism because the scientists who obtained them adopt a conventional "darwinist" approach. That is not true. Facts belong to all. So, when you say: I’m asking because the study of alternative functions of non-coding DNA is not exclusive to those who support ID. I obviously agree with you. 2) The relationship between the concept of junk DNA, darwinism and ID. That's more tricky. You say: Nor is it necessary for junk DNA to be universally non-functional to collaborate evolution. To a point, I can agree with you. The problem of non coding DNA is not essential neither to ID nor to darwinism. But some facts are certainly true: a) Coventional darwinism has freely chosen to interpret non coding DNA as "non functional". More than that, it has been considered as "evidence" of non intelligent evolution. b) Many important darwinist biologists ((Moran, Matheson, Hunt), even today, believe that most non coding DNA is non functional, and argue in that sense. Again, their choice. c) I have never believed that non coding DNA is non fucntional. While this instinctive conviction can be partially related to my ID approach, it more explicitly derives from two facts: - I have never considered credible that 95% or more of the human genome is non functional. That concept seems so ridiculous that I have never seriously considered it as true. Call it an argument for incredulity A good argument form incredulity. - I have always been aware of the important problem, many times discussed here, which I call "the problem of the missing procedures". IOW, I always thought that the protein coding genes were only the gross effectors of biological information, but that all the fine regulatory software, the "procedures", were missing. So, I always thought that non coding DNA (95% of the human genome of which we don't understand the function) was a very good candidate for at least part of that information. I believe that all the evidences that have accumulated in recent yeras, and continue to accumulate about this subject, are a very good confirmation of that idea. d) So, finally, is the function of non coding DNA a falsification of darwinism? No, it isn't. But it is certainly a falsification of some very silly interpretations made by some darwinists, and encouraged by the possible support that those interpretations could give to the main theory. Moreover, the new functions discovered for non coding DNA certainly "make things more difficult" for darwinian theory. Indeed, any new level of functional complexity which is daily discovered in living beings has that effect, because the greatest weakness of darwinism is that it is utterly incapable to explain functional complexity. So, the more the functional complexity, the more the difficulties for darwinism. Especially if that complexity is multilevel, stratified, regulatory, integrated, realizing increasingly growing networks of software-like information whose existence was not even suspected 10 or 20 years ago. Therefore, I do believe, today like years ago, that most of non coding DNA will be found to be functional, and highly functional. And that includes probably all types of it: introns, transposons, pseudogenes, and so on. Is such a non protein coding function a falsification of darwinism? Not especially. Not alone. But it does help!gpuccio_{June 24, 2010
June
06
Jun
24
24
2010
12:46 PM
12
12
46
PM
PDT}

As a religious studies major, I was excited by this post and emailed this to a biologist friend of mine as soon as I saw it here. He laughed at it and said that only a tiny bit of junk dna is pseudogenes, only a minority of pseudogenes are expressed as rna, and this paper was only about one pseudogene. He also made the same observation that the darwinists did here, that it disproved any claims about bias. So I felt embarrassed and had no good response. How should I have responded to his points?Joaozinho_{June 24, 2010
June
06
Jun
24
24
2010
11:16 AM
11
11
16
AM
PDT}

veilsofmaya :
"I'm confused"
Well that part is certainly clear enough. Most Darwinian fundamentalists are.Borne_{June 24, 2010
June
06
Jun
24
24
2010
10:21 AM
10
10
21
AM
PDT}

@BornAgain77, It seems you've made my point for me. Given the clarifications above, none of these things in the post you linked to are controversial. The "problem" is one that ID'ists manufacture to suit their agenda.veilsofmaya_{June 24, 2010
June
06
Jun
24
24
2010
10:03 AM
10
10
03
AM
PDT}

@PaV (#11) PaV, And what factors prevented them from accepting Heliocentrism? Intuition, a conflict with the current day interpretation of scripture and personal incredulity. Please see here and here. @Alex73 (#12) Please see the clarification links in my previous comment. The term Junk DNA is used in the context which we commonly use the term junk. For example, I have a few of items that did one perform a function, some of which still may work. However, I no longer use them and I keep them around for sentimental value. If someone called them junk, I would not be offended because I understand the context by which they were using the term. I've kept them around, despite the fact that they currently do not serve a functional purpose. Nor does this refer to an assertion of universal non-function or some vague function as Matheson elaborates using the following analogy.
Paint cans are sometimes found in piles of rubbish in vacant urban lots (VULs). Paint cans can be used to prop up old cars, or to fight off intruders, or to make music. Therefore VULs are useful in auto repair, home security, and musical composition.
As such, Junk DNA is a way of referring to a specific class of genes that are currently thought to be non-coding. This is non-controversial, yet brought up by ID supporters time and time again. That anyone says some Junk DNA is non-functional is a like saying some of the genes of class Z are non functional. There is no necessary assumption that genes in class Z are universally non-functional. Attempt to conflate the class of junk DNA with universal non-function are disingenuous and opaque. Given the clarifications above, it would appear that ID proponents are merely offend by the very idea of the word "junk DNA" for reasons which would be obvious. God doesn't make "junk" and the designer ID is referring to is God.veilsofmaya_{June 24, 2010
June
06
Jun
24
24
2010
09:58 AM
9
09
58
AM
PDT}

Prev 1 2 3 4 Next

You must be logged in to post a comment.

Leave a Reply