Tuesday, May 24, 2011

Junk & Jonathan: Part 6—Chapter 3

This is part 6 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

We learn in Chapter 9 that Wells has two categories of evidence against junk DNA. The first covers evidence that sequences probably have a function and the second covers specific known examples of functional sequences. In the first category there are two lines of evidence: transcription and conservation. Both of them are covered in Chapter 3 making this one of the most important chapters in the book. The remaining category of specific examples is described in Chapters 4-7.

The title of Chapter 3 is Most DNA Is Transcribed into RNA. As you might have anticipated, the focus of Wells' discussion is the ENCODE pilot project that detected abundant transcription in the 1% of the genome that they analyzed (ENCODE Project Consortium, 2007). Their results suggest that most of the genome is transcribed. Other studies support this idea and show that transcripts often overlap and many of them come from the opposite strand in a gene giving rise to antisense RNAs.

The original Nature paper says,
... our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another.
The authors of these studies firmly believe that evidence of transcription is evidence of function. This has even led some of them to propose a new definition of a gene [see What is a gene, post-ENCODE?]. There's no doubt that many molecular biologists take this data to mean that most of our genome has a function and that's the same point that Wells makes in his book. It's evidence against junk DNA.

What are these transcripts doing? Wells devotes a section to "Specific Functions of Non-Protein-Coding RNAs." These RNAs may be news to most readers but they are well known to biochemists and molecular biologists. This is not the place to describe all the known functional non-coding RNAs but keep in mind that there are three main categories: ribosomal RNA (rRNA), transfer RNA (tRNA), and a heterogeneous category called small RNAs. There are dozens of different kinds of small RNAs including unique ones such as the 7SL RNA of signal recognition factor, the P1 RNA of RNAse P and the guide RNA in telomerase. Other categories include the spliceosome RNAs, snoRNAs, piRNAs, siRNAs, and miRNAs. These RNAs have been studied for decades. It's important to note that the confirmed examples are transcribed from genes that make up less than 1% of the genome.

One interesting category is called "long noncoding RNAs" or lncRNAs. As the name implies, these RNAs are longer that the typical small RNAs. Their functions, if any, are largely unknown although a few have been characterized. If we add up all the genes for these RNAs and assume they are functional it will account for about 0.1% of the genome so this isn't an important category in the discussion about junk DNA.

Theme

Genomes
& Junk DNA
So, we're left with a puzzle. If more than 90% of the genome is transcribed but we only know about a small number of functional RNAs then what about the rest?

Opponents of junk DNA—both creationists and scientists—would have you believe that there's a lot we don't know about genomes and RNA. They believe that we will eventually find functions for all this RNA and prove that the DNA that produces them isn't junk. This is a genuine scientific controversy. What do their scientific opponents (I am one) say about the ENCODE result?

Criticisms of the ENCODE analysis take two forms ...
  • The data is wrong and only a small fraction of the genome is transcribed
  • The data is mostly correct but the transcription is spurious and accidental. Most of the products are junk RNA.
Criticisms of the Data

Several papers have appeared that call into question the techniques used by the ENCODE consortium. They claim that many of the identified transcribed regions are artifacts. This is especially true of the repetitive regions of the genome that make up more than half of the total content. If any one of these regions is transcribed then the transcript will likely hybridize to the remaining repeats giving a false impression of the amount of DNA that is actually transcribed.

Of course, Wells doesn't mention any of these criticisms in Chapter 3. In fact, he implies that every published paper is completely accurate in spite of the fact that most of them have never been replicated and many have been challenged by subsequent work. The readers of The Myth of Junk DNA will assume, intentionally or otherwise, that if a paper appears in the scientific literature it must be true.

But criticism of the ENCODE results are so widespread that they can't be ignored so Wells is forced to deal with them in Chapter 8. (Why not in Chapter 3 when they are first mentioned?) In particular, Wells has to address the van Bakel et al. (2010) paper from Tim Hughes' lab here in Toronto. This paper was widely discussed when it came out last year [see: Junk RNA or Imaginary RNA?]. We'll deal with it when I cover Chapter 9 but, suffice to say, Wells dismisses the criticism.

Criticisms of the Interpretation

The other form of criticism focuses on the interpretation of the data rather than its accuracy. Most of us who teach transcription take pains to point out to our students that RNA polymerase binds non-specifically to DNA and that much of this binding will result in spurious transcription at a very low frequency. This is exactly what we expect from a knowledge of transcription initiation [How RNA Polymerase Binds to DNA]. The ENCODE data shows that most of the genome is "transcribed" at a frequency of once every few generations (or days) and this is exactly what we expect from spurious transcription. The RNAs are non-functional accidents due to the sloppiness of the process [Useful RNAs?].

Wells doesn't mention any of this. I don't know if that's because he's ignorant of the basic biochemistry and hasn't read the papers or whether he is deliberately trying to mislead his readers. It's probably a bit of both.

It's not as if this is some secret known only to the experts. The possibility of spurious transcription has come up frequently in the scientific literature in the past few years. For example, Guttmann et al. (2009) write,
Genomic projects over the past decade have used shotgun sequencing and microarray hybridization to obtain evidence for many thousands of additional non-coding transcripts in mammals. Although the number of transcripts has grown, so too have the doubts as to whether most are biologically functional. The main concern was raised by the observation that most of the intergenic transcripts show little to no evolutionary conservation. Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function. But the remarkably low rate of conservation seen in the current catalogues of large non-coding transcripts (less than 5% of cases) is unprecedented and would require that each mammalian clade evolves its own distinct repertoire of non-coding transcripts. Instead, the data suggest that the current catalogues may consist largely of transcriptional noise, with a minority of bona fide functional lincRNAs hidden amid this background.
This paper is in the Wells reference list so we know that he has read it.

What these authors are saying is that the data is consistent with spurious transcription (noise). Part of the evidence is the lack of any sequence conservation among the transcripts. It's as though they were mostly derived from junk DNA.

Sequence Conservation

Recall that the purpose of Chapter 3 is to show that junk DNA is probably functional. The first part of the chapter reportedly shows that most of our genome is transcribed. The second part addresses sequence conservation.

Here's what Wells says about sequence conservation.
Widespread transcription of non-protein-coding DNA suggests that the RNAs produced from such DNA might serve biological functions. Ironically, the suggestion that much non-protein-coding DNA might be functional also comes from evolutionary theory. If two lineages diverge from a common ancestor that possesses regions of non-protein-coding DNA, and these regions are really nonfunctional, then they will accumulate random mutations that are not weeded out by natural selection. Many generations later, the sequences of the corresponding non-protein-coding regions in the two descendant lineages will probably be very different. [Due to fixation by random genetic drift—LAM] On the other hand, if the original non-protein-coding DNA was functional, then natural selection will tend to weed out mutations affecting that function. Many generations later, the sequences of the corresponding non-protein-coding regions in the two descendant lineages will still be similar. (In evolutionary terminology, the sequences will be "conserved.") Turning the logic around, Darwinian theory implies that if evolutionarily divergent organisms share similar non-protein-coding DNA sequences, those sequences are probably functional.
Wells then references a few papers that have detected such conserved sequences, including the Guttmann et al. (2009) paper mentioned above. They found "over a thousand highly conserved large non-coding RNAs in mammals." Indeed they did, and this is strong evidence of function.1 Every biochemist and molecular biologist will agree. One thousand lncRNAs represent 0.08% of the genome. The sum total of all other conserved sequences is also less than 1%. Wells forgets to mention this in his book. He also forgets to mention the other point that Guttman et al. make; namely, that the lack of sequence conservation suggests that the vast majority of transcripts are non-functional. (Oops!)

There's irony here. We know that the sequences of junk DNA are not conserved and this is taken as evidence (not conclusive) that the DNA is non-functional. The genetic load argument makes the same point. We know that the vast majority of spurious RNA transcripts are also not conserved from species to species and this strongly suggests that those RNAs are not functional. Wells ignores this point entirely—it never comes up anywhere in his book. On the other hand, when a small percentage of DNA (and transcripts) are conserved, this gets prominent mention.

Wells doesn't believe in common ancestry so he doesn't believe that sequences are "conserved." (Presumably they reflect common design or something like that.) Nevertheless, when an evolutionary argument of conservation suits his purpose he's happy to invoke it, while, at the same time, ignoring the far more important argument about lack of conservation of the vast majority of spurious transcripts. Isn't that strange behavior?

The bottom line hear is that Jonathan Wells is correct to point to the ENCODE data as a problem for junk DNA proponents. This is part of the ongoing scientific controversy over the amount of junk in our genome. Where I fault Wells is his failure to explain to his readers that this is disputed data and interpretation. There's no slam-dunk case for function here. In fact, the tide seems to turning more and more against the original interpretation of the data. Most knowledgeable biochemists and molecular biologists do not believe that >90% of our genome is transcribed to produce functional RNAs.

UPDATE: How much of the genome do we expect to be transcribed on a regular basis? Protein-encoding genes account for about 30% of the genome, including introns (mostly junk). They will be transcribed. Other genes produce functional RNAs and together they cover about 3% of the genome. Thus, we expect that roughly a third of the genome will be transcribed at some time during development. We also expect that a lot more of the genome will be transcribed on rare occasions just because of spurious (accidental) transcription initiation. This doesn't count. Some pseudogenes, defective transposons, and endogenous retroviruses have retained the ability to be transcribed on a regular basis. This may account for another 1-2% of the genome. They produce junk RNA.


1. Conservation is not proof of function. In an effort to test this hypothesis Nöbrega et al. (2004) deleted two large regions of the mouse genome containing large numbers of sequences corresponding to conserved non-coding RNAs. They found that the mice with the deleted regions showed no phenotypic effects indicating that the DNA was junk. Jonathan Wells forgot to mention this experiment in his book.

Guttman, M. et al. (2009) Chromatin signature reveals over a thousand highly conserved non-coding RNAs in mammals. Nature 458:223-227. [NIH Public Access]

Nörega, M.A., Zhu, Y., Plajzer-Frick, I., Afzal, V. and Rubin, E.M. (2004) Megabase deletions of gene deserts result in viable mice. Nature 431:988-993. [Nature]

The ENCODE Project Consortium (2007) Nature 447:799-816. [PDF]

40 comments :

  1. Do I understand it correctly that 90% of the genome is transcribed?

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  2. (sorry if it double posts – got an error message)

    @Anon

    Depends. Functionally? No. *Especially* not the human genome, if that's what you mean by "the genome" (there are lots).

    I see where the <= 93% data come from (http://bionumbers.hms.harvard.edu/bionumber.aspx?s=y&id=103746&ver=2) – based on the analysis of 1% of the human genome, as Larry mentioned. However, a quick search in the same database shows that only ~2% of the human genome is translated (http://bionumbers.hms.harvard.edu/bionumber.aspx?s=n&id=103748&ver=5), based on the 2004 human genome paper in Nature. So if we take away the percentage translated from the percent transcribed, we're left with 88% transcribed but apparently not translated. Sure some of them are non-coding regulatory RNAs (miRNAs, etc), but 88% of the genome would be a shit ton of regulatory stuff, which is absurd.

    It turns out that the RNA polymerase complexes are not as specific as you would think, and transcription often initiates all over the place. Ie, random stuff gets transcribed all the time, but at lower levels than regions that are "meant" to be transcribed by having the appropriate binding sites. Chemistry is messy. This background transcription can be a problem in EST projects, where they try to get a sense of transcribed genes without knowing the genome by reverse transcribing RNA from the cell – not all the transcripts contain ORFs (open reading frames – carrying start and stop codon necessary for transcription). Since it presumably doesn't kill the cell to have randomly transcribed junk RNA floating around at low levels, these inefficiencies are tolerated. I'd be curious if prokaryotes have lower background transcription 'noise' than multicellular eukaryotes, owing to larger effective population size, etc...

    Again, key point here is that biochemistry is messy, and you can only say whether something is transcribed by comparing its transcription levels relative to others. This is why you need a crapload of controls when trying to test for transcription even of known coding genes – if you look hard enough, you can find your pet gene "expressed" under whatever conditions you want! This is why transcription levels are generally spoken of in a relative sense...

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  3. Larry said:

    Wells doesn't believe in common ancestry so he doesn't believe that sequences are "conserved." (Presumably they reflect common design or something like that.) Nevertheless, when an evolutionary argument of conservation suits his purpose he's happy to invoke it

    This is what I've always found particularly pernicious about these people. Where science is concerned, they're like monkeys with matches. They're happy to indulge themselves in whatever science furnishes them, but they want nothing to do with the discipline itself. They would, and do!, happily retard it in favour of their superstitions and mind control.

    These people couldn't give a flame fudge bag about whether junk DNA exists or not, inasmuch as it impacts how life actually functions. No, it only concerns them to the extent that if they can argue it out of the public mind, then they can claim the genome is the work of a perfect creator and couldn't possibly be any better than it is, so therefore Jesus is Lord and do what we say he says. That's it. That's all this argument is really about for them. That we are sharing the Space Age with these Galileo-bashers is a literally disgrace to our species.

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  4. If we consider matters from an evolutionary standpoint, and allow the possibility that our DNA information store was preceded by an RNA-only informational store (the 'RNA world)', then the apparent high transcriptional rate does make sense, without forcing us to conclude that the transcripts are functional. Genes have always been 'identified' by the RNA-translation machinery. The more recent job of passing viable transcripts from DNA to that system does not need to have 'knowledge' as to whether it is wasting its time with a given segment of DNA, any more than meiosis needs to have such knowledge to perform its task of shunting chromosomes about.

    It seems energetically wasteful to polymerise nucleotide triphosphates to such a ridiculous extent in order to squeeze out a tiny drop of functional 'juice' from the metaphorical lemon. But if you eat organisms stuffed with nucleotides, and well-provisioned with the energy needed to polymerise them, there need be no compulsion to save this notional cost. We might design the system differently - but unintelligent design is characterised by such bodging.

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  5. Any ongoing/future research you're aware of on this general subject matter that we should be watching for?

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  6. PSI Wavefunction:
    "we're left with 88% transcribed but apparently not translated.".

    So 88% is transcribed but not translated?

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  7. Questions for Larry: I've only read bits and pieces of some of these papers so

    1) I seem to remember a paper that used a much improved technique that claimed the ENCODE project was picking up false positives ( perhaps thats the paper you mention)?

    2) Even if the transcripts are real I've gotten the impression that they're so scarce- perhaps 1 per site/day that its very unlikely they could have any fuction?

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  8. OK I have another question for Larry or Psi: now that I think about it I'm surprised theres any transcription at all from most sites. The DNA should be wrapped up so tight in heterochromatin that not a singe RNAP could get in. Is it possible that they isolated RNA from actively dividing cells and the transcription they're seeing is a brief burst after S phase?

    Rod

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  9. Lantog asks,

    1) I seem to remember a paper that used a much improved technique that claimed the ENCODE project was picking up false positives ( perhaps thats the paper you mention)?

    There are several papers like that. The most important one is von Bakel et al. (2010) [PLoS Biology 8:e1000371]

    2) Even if the transcripts are real I've gotten the impression that they're so scarce- perhaps 1 per site/day that its very unlikely they could have any fuction?

    That's correct. Such rare transcripts are consistent with spurious transcription.

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  10. Lantog says,

    now that I think about it I'm surprised theres any transcription at all from most sites. The DNA should be wrapped up so tight in heterochromatin that not a singe RNAP could get in.

    There aren't many transcripts from constitutive heterochromatin—those regions tend to be full of highly repetitive sequences. The rest of the genome is in dynamic flux with respect to open and closed domains so RNA polymerase can bind anywhere if it waits long enough.

    However, as you might expect, most of the spurious transcripts come from regions near active genes.

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  11. @Psi Wavefunction:

    "I'd be curious if prokaryotes have lower background transcription 'noise' than multicellular eukaryotes, owing to larger effective population size, etc..."

    I don't know how prokaryotes compare to eukaryotes, but I do know there's evidence for substantial 'noise' in E. coli. For example, this paper shows that random eukaryotic sequences are often transcriptionally active in E. coli.

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  12. I am trying to get the big picture here.

    PSI Wavefunction has said:
    "we're left with 88% transcribed but apparently not translated.".

    So it looks like the genome is conserving and transcribing as much as 88% of the genome. And less than 1% of that transcribed material is actually translated.

    Is that a correct understanding?
    If not, what are the actual numbers roughly?

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  13. Larry: Of course, Wells doesn't mention any of these criticisms in Chapter 3. In fact, he implies that every published paper is completely accurate in spite of the fact that most of them have never been replicated and many have been challenged by subsequent work. The readers of The Myth of Junk DNA will assume, intentionally or otherwise, that if a paper appears in the scientific literature it must be true.

    Very funny. They assume that every paper in the literature is correct, except (let's add) for all the evolutionary biology papers showing evidence of common descent. A double standard.

    And of course Larry has made, forcefully, the analogous point about evolutionary conservation of sequences -- Wells assumes that the argument from conservation to function is valid but he forgets to apply the same logic to all the nonconserved sequences. And he accepts the evidence for common descent, but only when when he needs it.

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  14. Hey Larry, I appreciate this series that supports my philosophy. Could you do many of us a favor after you finish the series by combining the content of all these posts into a single downloadable PDF? I would prefer a free download, but would understand if you have commercial interests. :)

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  15. Genomic DNA doesn't have to be transcribed for it to be important to cell function - whether you call such DNA "functional" or not, it's not junk. An obvious example is a transcription factor binding site, though these are not going to take up a significant fraction of the genome.

    Do you think chromatin is worth considering in this junk/no-junk debate? Chromatin is particularly important in multicellular organisms for its role in genetic silencing (e.g. heterochromatin), and I can tell you from my own work studying nucleosome positioning that DNA sequence has an influence on chromatin. I speculate that a segement of DNA may appear to be evolving neutrally even though its G/C content, the most important sequence feature for nucleosome positioning, is actually conserved. As I say, this isn't much more than a guess, but it indicates a possible biological function for DNA irrespective of transcription. DNA folding and bending are other sequence-dependent effects on chromatin that do not rely on sequence motifs, the usual metric for mutation.

    Higher organisms tend to have more junk DNA, and they also have a greater need for genetic silencing. All I'm saying is that this is one speculative possibility that may provide function to a significant fraction of junk DNA.

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  16. flies, I don't think we can accept anything like what you are describing because it will have the unacceptable result that Wells might be correct.
    Better to just rally around the idea that it is junk and show Wells to be wrong.

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  17. flies says,

    Genomic DNA doesn't have to be transcribed for it to be important to cell function - whether you call such DNA "functional" or not, it's not junk.

    That's correct. If you want to see a summary of those functional DNAs then check out: What's in Your Genome.

    BTW, none of these are mentioned in Wells' book except for centromeres and regulatory sequences. Isn't that strange?

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  18. anonymous says,

    I am trying to get the big picture here.

    No you're not.

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  19. Here is the rest of the post that Dr. Moran left out:

    "I am trying to get the big picture here.
    PSI Wavefunction has said:
    "we're left with 88% transcribed but apparently not translated.".
    So it looks like the genome is conserving and transcribing as much as 88% of the genome. And less than 1% of that transcribed material is actually translated.
    Is that a correct understanding?
    If not, what are the actual numbers roughly?"

    I am still interested in the answer.

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  20. If in the future at some point, functions are found for the "junk DNA" will the line be that Wells was right but that he did not know he was right? Or that he did not know why he was right?
    There will have to be some way to ensure he gets no credit.

    Of course the basic line will be that even if it has function, that is not a problem for evolution theory.

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  21. I've added an update to my article to explain how much of the genome should be transcribed on a regular basis.

    I don't believe any result claiming that more than 40% of the genome is transcribed on a regular basis.

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  22. So more than 40% of the genome could transcribed, but just not on a regular basis.
    What percentage do you think is transcribed if you included that which was transcribed but not on a regular basis?

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  23. Anonymous asks:

    "If in the future at some point, functions are found for the "junk DNA" will the line be that Wells was right but that he did not know he was right? Or that he did not know why he was right?
    There will have to be some way to ensure he gets no credit."


    Whatever the factual truth about junk DNA, Wells' current arguments are inconsistent with the evidence, and frequently fallacious and disingenuous to boot. I think Dr. Moran has demonstrated that quite abundantly already.

    What sort of credit would Wells deserve if it turns out that there really is very little junk DNA? IMO, about as much credit as a student who reduces the fraction 16/64 by cancelling the 6 digits in both the numerator & denominator. They get the correct result of 1/4, but they get no credit for actually understanding the problem or approaching it correctly.

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  24. And if it turns out that there is no junk, then evolution theory is shown to be wrong.
    Oh I forgot. Evolution theory is right if there is junk and right if there is no junk.
    Gotta love a theory like that!

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  25. And if it turns out that there is no junk, then evolution theory is shown to be wrong.
    Oh I forgot. Evolution theory is right if there is junk and right if there is no junk.
    Gotta love a theory like that!


    Well, yeah ... a theory that copes with all the known facts - gotta love it! If evolutionary theory hinged on the amount of junk, then your sarcasm might have a point. But evolution does not demand either lots or little. Only ID has a problem with junk. We have many organisms with virtually none - including those causing the vilest of diseases. No-one ever suggested their lack of junk as evidence against their having evolved. Do we suppose necrotising fasciitis to have been designed?

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  26. Allan Miller said:

    Do we suppose necrotising fasciitis to have been designed?

    Yes! By a "loving" god! But only after humans became aware of the difference of good and evil, and so, somehow, deserved it... gotta love a theory like that! ;)

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  27. @Anonymous
    This has been repeated over and over. I will repeat it one more time, slowly.

    Evolutionary theory does not rest on whether there is junk DNA or not. Junk DNA is irrelevant to evolutionary theory in the same way that humans existing on Earth are irrelevant to General Relativity or Quantum Mechanics. The theory make no definitive statement on the matter, and the presence or absence changes nothing.

    This controversy is an intelligent design strawman argument. Both presence and absence of junk DNA are permissible within evolutionary theory. The fact that there are extremely compact, efficient genomes and big sloppy ones can both be explained by current population genetic models. Within the scientific community, the argument boils down to It is all about whether extra DNA has an evolutionary cost or a selectable benefit to that specific population you are looking at.

    In contrast, an intelligent creator seems less likely if a large proportion of the human genome is wasted nucleotides. This is why Wells and the DI care so much. Their theory stands to suffer if most of the genome (especially the Human genome) is dispensable junk. The ID claim of an intelligence that designed a machine that cannot suffer insult makes specific claims on the topic.

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  28. Well that is interesting. The posts by Dr. Moran and others here are filled with sarcasm.
    But Allan Miller notes sarcasm in my post and does not like it.
    People here want to use sarcasm but do not like it when it is turned back against them.

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  29. We humans waste things. Does that mean we are not intelligent?

    If an engineer, using trial and error, creates things that turn out to be junk, does that mean the engineer is not intelligent?

    People here have some child-like picture of this intelligence called "God" but you never actually think in a practical way about how that intelligence might operate.

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  30. By the way, for those of us who perceive the influence of a higher intelligence, we do not believe that everything that happens on planet earth is the intention of that higher intelligence.
    Crime/evil/corruption occur at various levels and are not the intention of the higher intelligence.

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  31. Anonymous writes:

    So it looks like the genome is conserving and transcribing as much as 88% of the genome. And less than 1% of that transcribed material is actually translated.

    So more than 40% of the genome could transcribed, but just not on a regular basis.

    What percentage do you think is transcribed if you included that which was transcribed but not on a regular basis?

    First, let's deal with your statement about "conserving." That is incorrect. In general, the non-coding parts of the genome that Dr. Moran has characterized as junk are not conserved between species. There is a higher rate of mutation here than in known non-junk, suggesting it is not important enough to keep.

    Second, regarding "transcribed" and "translated:" The material in introns that is transcribed must all be thrown away in the process of translation, i.e., turning RNA into protein. Think of panning for gold, the exons as nuggets, and the introns as dirt. Why on earth would digging up more dirt than necessary, then going through the laborious process of getting rid of the dirt, indicate the dirt was somehow as good as gold? Lots of DNA in introns that must be gotten rid of before making protein means the process is less efficient than it could be, exactly the opposite of good design.

    The overall sloppiness of the process is emphasized even more by irregular transcription. Think of mechanized shovels that occasionally get diverted from the more productive parts of the stream where the gold is, that dig up and dump plain dirt into the pans. That is irregular transcription - RNA wandering off from the locations it's supposed to be transcribing, and transcribing DNA from somewhere else, that is never translated into protein. This isn't an indication the DNA isn't junk, it's RNA performing its transcription function in unproductive places.

    "But it's transcribed, just like non-junk. Must mean it's not junk, right?" Nope. The dirt goes into the pans just like gold; doesn't mean it is gold. So the next time you read someone using transcription of introns as evidence supporting design, realize they either don't understand what they're talking about, or are deliberately misleading you.

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  32. People here have some child-like picture of this intelligence called "God" but you never actually think in a practical way about how that intelligence might operate.

    [Sigh, another irony meter fricasseed.]

    Oh, actually we do. We carefully observe and test and corroborate and document this thing called "reality." If there's a God, then we know how He's made the biological world, and it's described by the theory of evolution.

    Then there are the people who claim God is unfathomable to mere mortals, who somehow manage to fathom Him oh-so-exactly that they can tell the folks who actually work at gaining knowledge they're all wrong.

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  33. anonymous says,

    Crime/evil/corruption occur at various levels and are not the intention of the higher intelligence.

    How do you know? Did the "higher intelligence" discuss his/her/its intentions with you?

    Maybe the one true god is evil.

    Anyway, I assume you disagree with the IDiots about junk DNA. They say that Intelligent Design Creationism predicts that it's not junk. (They also say this has nothing to do with god!)

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  34. Intelligent Design can accommodate junk or no junk.

    Dr. Moran still is so biased against religious thought that he distorts everything.
    It is sad really.

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  35. Jud as usual is confused.

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  36. Anonymous writes:

    Intelligent Design can accommodate junk or no junk.

    Please, please let me sell tickets to a debate between you and Jonathan Wells on this subject.

    Have you told him yet he was wasting his time with his new book? I know he'll be heartbroken that a brilliant - umm, scientist? theologian? - such as yourself has agreed with Dr. Moran and determined he's all wrong.

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  37. I have not seen anyone as consistently confused as Jud.
    He seems not to be able to follow the logic of any discussion.
    But we can expect some confused response to this as well.

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  38. Well that is interesting. The posts by Dr. Moran and others here are filled with sarcasm.
    But Allan Miller notes sarcasm in my post and does not like it.
    People here want to use sarcasm but do not like it when it is turned back against them.


    No, no, you're wrong - I love your sarcasm! I'm also delighted that you managed to completely miss the substantive point I was making.

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  39. We humans waste things. Does that mean we are not intelligent?

    If an engineer, using trial and error, creates things that turn out to be junk, does that mean the engineer is not intelligent?

    People here have some child-like picture of this intelligence called "God" but you never actually think in a practical way about how that intelligence might operate.

    ReplyDelete
  40. But in fairness to the folks here, even religious people rarely think in a practical way about how that higher intelligence might operate.
    Almost everyone has a child's picture of it, based on the picture they formed when they were children.

    ReplyDelete