Wednesday, May 25, 2011

Junk & Jonathan: Part 7—Chapter 4


This is part 7 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."

The title of Chapter 4 is Introns and the Splicing Code. It opens with a brief description of eukaryotic genes and alternative splicing. Here's a better description of splicing for those who want a quick refresher: RNA Splicing: Introns and Exons. Alternative splicing is when a transcript can be spliced in at least two different ways to produce 2 distinct mRNAs. Each of them will make a different, but related, protein. The process has been known for thirty years and the mechanism is well-understood. It's described very well in a Wikipedia article: Alternative Splicing.

Here's some important background information from Junk in Your Genome: Protein-Encoding Genes.

The minimum size of a eukaryotic intron is less than 50 bp. For a typical mammalian intron, the essential sequences in the introns are: the 5′ splice site (~10 bp); the 3′ splice site (~30 bp): the branch site (~10 bp); and enough additional RNA to form a loop (~30 bp). This gives a total of 80 bp of essential sequence per intron or 20,500 × 7.2 × 80 = 11.8 Mb. Thus, 0.37% of the genome is essential because it contains sequences for processing RNA.
In other words, assuming that introns aren't all junk we can estimate how much of the intron sequence is essential for it's function by taking into account the known regulatory sequences and the amount needed to form a loop.

The rest of an intron sequence may be junk. If it is, then we would expect to see two things.
  • Considerable variation is intron size from species to species.
  • Frequent examples of transposons, endogenous retroviruses, and even other genes inserting into introns.
This is exactly what we see [Junk in Your Genome: Intron Size and Distribution]. There's no indication that intron sequences are conserved or essential.

Jonathan Wells explains that alternative splicing is important in some genes. He is correct. He then explains that there are sequences in introns that regulate alternative splicing. He's correct about that as well. We've been writing this up in the textbooks and teaching it in introductory biochemistry courses since early in the 1980s. The classic example is the determination of sex in Drosophila—it's largely controlled by alternative splicing and we know a great deal about which proteins bind to which sequences in the introns to promote or repress a given splice site [Sex in the fruit fly Drosophila melanogaster].

Nothing new here. We know about binding sites and we know that most of them are 10 bp or less. Their presence makes no significant difference in our calculations of junk DNA. I get the distinct impression that Wells and the other IDiots don't really understand splicing and alternative splicing.

Here's a series of blog posts I did last year when Richard Sternberg tried to pretend that he knew something about molecular biology and alternative splicing. Later on, Jonathan Wells weighs in to try and help his friend but ends up showing that he too, is in way over his head.

Creationists, Introns, and Fairly Tales

IDiots Do Arithmetic a Second Time - Same Result

Jonathan Wells Weighs in on Alternative Splicing

Having "proven" that something like 0.03% of our genome may not be junk, Wells then goes on to describe other sequences that are found in introns. Some of these are regulatory sequences or enhancers. These aren't common, but they do exist. They're usually located in the 5′ intron and they are often associated with alternative transcription start sites. The total amount of non-junk DNA due to regulatory sequences has already been taken into account in my calculations (Junk in Your Genome: Protein-Encoding Genes) and it doesn't matter whether these regulatory sequences are intergenic or included within an intron.

Theme

Genomes
& Junk DNA
Wells also notes that many genes for small RNAs are located within introns. These include some of the genes for the splicing machinery, tRNA genes, snoRNA genes etc. He doesn't mention that introns are also loaded with Alu sequences and other transposable elements (mostly defective). The presence of the these insertions show us that cells don't discriminate between intron sequences that make up 25% of the genome and the remaining 65% that's mostly junk. They are all targets for inserting small genes and transposons. No surprises here.

Finally, on the last page of Chapter 4, Wells devotes two paragraphs to a genuine scientific argument. The idea is that long introns might be necessary to delay transcription. This idea has been around for a long time. It was originally proposed over 25 years ago as an explanation for the long introns found in Drosophila HOX genes, especially Ubx.

If a gene has several long introns it can stretch out over 100 kb (100,000 bp). The typical RNA polymerase II elongation complex transcribes at a rate of 50 bp per second so it will take more than 30 minutes to transcribe these long genes. The idea is that the presence of long introns delays appearance of the regulatory proteins during development. This seems unlikely because there are many other, more efficient, ways of regulating gene expression. As a matter of fact, the argument can be easily turned upside down.

Genes that need to be transcribed quickly have very short introns or none at all. The heat shock inducible genes, for example, don't even have introns. These genes need to be expressed rapidly when a cell encounters stressful conditions. Their non-inducible homologues all have respectable introns so it looks like there has been selection for losing introns in these genes.

Similarly, there are often testes specific genes than lack introns. The supposition is that these variant family members have lost introns so they can be quickly transcribed during spermatogenesis. The globin genes have relatively small introns and they are also expressed at a high rate in erythroblasts.

Genes that are infrequently transcribed tend to accumulate large introns. This includes most developmentally regulated transcription factors that only need to produce a small number of proteins at a specific time in the life of the organism. These observations are consistent with the idea that excess junk in intron sequences is removed when necessary. It's actually evidence that those sequences are junk.

So far we covered the evidence of probable function in Chapter 3 and seen that Wells does not critically examine the data on pervasive transcription but simply assumes it is correct. He then makes the unsubstantiated claim that evidence of transcription is evidence of function. He's wrong about the claim that most of our genome is transcirbed and he's wrong to assume that all transcripts are functional. Nothing in that chapter supported his claim that junk DNA is a myth.

In this chapter we see the first evidence for specific functions of noncoding DNA. The presence of regulatory sequences in introns has been well known for decades and it has no impact on the estimates of junk DNA. The idea that big introns might be adaptive regardless of sequence is possible but not reasonable. In fact, the evidence suggests strongly that big introns full of junk DNA can be detrimental in some cases. Nothing in Chapter 4 provides convincing evidence that junk DNA is a myth.

What about pseudogenes? Are they a myth? That's covered in Chapter 5.



A note about references
The IDiots are promoting this book by bragging about multiple references that challenge the concept of junk DNA [Jonathan Wells offers over 600 references to recent peer-reviewed literature]. Chapters 1 and 2 were introductions to the problem. They had a total of 51 references. Chapter 3 had 62 references but, as we have seen, they don't add up to a convincing case. There were plenty of references that should have been included if a scientific case was going to be made. Chapter 4 has 63 references but only three of them address a substantive argument against junk DNA in introns. All three make the same point; namely that long introns delay transcription.

That's a total of 176 references so far with nothing much to show for them. There are 432 references in the rest of the book. There are 26 references to known IDiots including 8 references to the work of Jonathan Wells.


24 comments :

  1. You skipped chapter 4, and the title is wrong, it says chapter 4 but the post is about chapter 5.

    ReplyDelete
  2. I guess the Fugu Tetraodon genomes are relevant here too. They contain introns in most of the same positions as ours, but seem to have rid themselves of a lot of the sequence in each one (i.e. their close relatives have long introns, so it reasonable to assume the ancestors of these fish had long introns which have since been reduced). Which suggests that, even if we are locked in to having certain introns now, most of the sequence within them can be lost with no discernible penalty.

    ReplyDelete
  3. He doesn't mention that introns are also loaded with Alu sequences and other transposable elements (mostly defective).

    And it's these exceptions to the rule which are of interest especially to researchers in the medical side of genomics. Which may explain why there is sometimes a bias toward function among researchers who spend their time hunting down mechanisms for a disorder. There's a term for it: Evolutionary functional genomics (EvoFuGeno)

    ReplyDelete
  4. 90% (give or take) of all of the RNA made by RNA polymerase II is degraded - thrown out in the trash.

    In my experience, ID proponents choke on the fact that so much of the macromolecular biosynthetic capacity of the cell is devoted to stuff that is tossed down the garbage chute. It makes perfect chemical sense but no design sense.

    ReplyDelete
  5. A question for Arthur Hunt:
    How is it thrown out in the trash? Is it ejected from the cell?
    That sounds very interesting.
    Do you have a reference link for that?

    Also you say it makes perfect chemical sense. Why do you say that making a lot of unnecessary RNA makes perfect chemical sense?

    ReplyDelete
  6. Also would be interested to here about that more Arthur. thanks.

    ReplyDelete
  7. It looks like we may not be getting an answer from Arthur Hunt. That is a shame since this is an interesting subject.

    ReplyDelete
  8. Here`s an article that may be relevant:
    http://www.nature.com/news/2011/110519/full/news.2011.304.html

    ReplyDelete
  9. Anonymous writes:

    Here`s an article that may be relevant....

    It gets the Central Dogma wrong (for the correct version see Dr. Moran's past posts on the subject). What do you feel the relevance is?

    ReplyDelete
  10. http://www.nature.com/news/2011/110519/full/news.2011.304.html
    "It was already known that some cells 'edit' RNA after it has been produced to give a new coding sequence, but the new work suggests that such editing occurs much more often in human cells than anyone had realized, and that hitherto unknown editing mechanisms must be involved to produce some of the changes observed. If the finding is confirmed by other investigators — and some scientists already say they see the same phenomenon in their own data — it could change biologists' understanding of the cell and alter the way researchers study genetic contribution to disease."

    I wonder if there is a connection with so-called "junk DNA" and "junk RNA". Perhaps their function is related to these new findings.

    ReplyDelete
  11. Here is a quote from one of the comments:
    http://www.nature.com/news/2011/110519/full/news.2011.304.html#B1
    "RNA editing has already been found in a number of organisms and is carried out by a number of mechanisms involving either guide RNAs (gRNAs) or enzymes although there may, of course, be other mechanisms yet to be found if it is indeed as common as this study hints. There is evidence for extensive transcription of noncoding segments of our genome and its possible that some of these rnaS may be involved in editing in some way analagous to gRNAs.

    ReplyDelete
  12. Anonymous writes:

    There is evidence for extensive transcription of noncoding segments of our genome and its possible that some of these rnaS may be involved in editing in some way analagous to gRNAs.

    So let's assume the possibility is true (you never closed the quote, so I don't know whether the possibility is mentioned in the comment or is something you are proposing). Then instead of simply having the RNA use the DNA as a template to make protein in the "classic" way, in your proposal the RNA is not only edited in the usual way to take out the introns and throw them away before making protein, there is RNA from some non-coding region doing additional editing before protein is synthesized. Does this "many cooks" procedure seem like good design to you?

    ReplyDelete
  13. I believe that at least some non-coding genes produce RNAs that provide a regulatory function.
    Right?
    That gives tremendous flexibility.
    Like parameters controlling standard code. Making standard code able to produce a variety of outcomes.
    Does what I am saying make sense to you?
    Or are you just interested in pretending not to get it and arguing?

    ReplyDelete
  14. Jud says:
    "So let's assume the possibility is true (you never closed the quote, so I don't know whether the possibility is mentioned in the comment or is something you are proposing)."

    I gave the link itself. I guess Jud does not realize he could follow the link himself and see.
    But he would rather strain to find something to criticize.

    ReplyDelete
  15. Anonymous didn't answer my question, so let me pose it again:

    Does this proposed "many cooks" procedure (much of the coding from the original DNA template being thrown out at two different stages before a protein is made) seem like good design to you?

    ReplyDelete
  16. This answers the "many cooks" point:

    I believe that at least some non-coding genes produce RNAs that provide a regulatory function.
    Right?
    That gives tremendous flexibility.
    Like parameters controlling standard code. Making standard code able to produce a variety of outcomes.
    Does what I am saying make sense to you?
    Or are you just interested in pretending not to get it and arguing?

    ReplyDelete
  17. Anonymous writes:

    I believe that at least some non-coding genes produce RNAs that provide a regulatory function. Right?

    That gives tremendous flexibility.

    Like parameters controlling standard code. Making standard code able to produce a variety of outcomes.


    Why, Anonymous - I'd never have imagined reading such a pro-evolution argument from you!

    Have a look at Sean B. Carroll's books. The flexibility of standard code, such as the HOX genes, able to produce a variety of outcomes (i.e., morphologies/species) under varying regulatory regimes is an excellent counter-argument to IDers and the like trying to use probability (incorrectly) to argue against evolution.

    ReplyDelete
  18. Jud is all over the place.
    He thinks at first that the flexibility is an argument against design, then suddenly it is an indication of good design.
    Evolutionists say anything whether it is consistent with their theory, or their previous ideas, or not.
    But they do not see that and do not acknowledge it when it is pointed out to them.
    It reminds me of Moran's fiasco in thread:
    Junk & Jonathan: Part 4—Chapter 1
    http://sandwalk.blogspot.com/2011/05/junk-jonathan-part-4-1.html

    ReplyDelete
  19. Evolutionists interpret any evidence as support for evolution theory, whether it makes sense or not.

    That is the pattern that plays out at the end of the era of a paradigm.

    Intelligence is the new paradigm. Intelligence at the level of Nature, down to the level of the cell.

    ReplyDelete
  20. Anonymous writes:

    Jud is all over the place.
    He thinks at first that the flexibility is an argument against design, then suddenly it is an indication of good design.
    Evolutionists say anything whether it is consistent with their theory, or their previous ideas, or not.


    Oh I've been quite consistent, but you lack sufficient understanding of biology to know that. "Flexibility" is a meaningless term unless it is attached to particular biological facts. There are some aspects of biology that can be called flexible, and some that very definitely aren't.

    I'm just staying consistent with the facts. Like anyone else without a map, you think I'm meandering when I'm actually following the factual "topography."

    ReplyDelete
  21. Anonymous writes:

    Intelligence is the new paradigm. Intelligence at the level of Nature, down to the level of the cell.

    But unfortunately not up to the level of the IDiot.

    [Sigh. Not another one of these "Cells have smarts!" kooks.]

    ReplyDelete
  22. Jud, talking to you is a waste of time.

    ReplyDelete
  23. Anonymous writes:

    Jud, talking to you is a waste of time.

    It doesn't have to be. Right now, you're obviously unfamiliar with a lot of basic biology, making much of concepts that have no intrinsic scientific meaning, like "flexibility." It's as if you were on a cooking website, got one Italian recipe with garlic and one without, and said "You guys are wildly inconsistent! Does Italian cooking have garlic or not?"

    I'm sure you understand in that hypothetical situation, you wouldn't leave the other forum members questioning the validity of Italian cuisine; they'd understand you didn't have the necessary level of knowledge and perhaps try to educate you, or maybe just ignore you. Perhaps if you persisted in posing uninformed questions rather than learning, they'd mock or insult you. (Sound familiar?)

    This really isn't going to get any better for you, with me or anyone else here, unless you're willing to educate yourself in the fundamentals. (Not that I have so much education in that regard, but I'm willing and eager to learn.) Persisting in spouting "questions" that reveal an agenda accompanied by a basic level of ignorance, rather than sincerely engaging in dialogue, is going to continue to have the predictable result.

    ReplyDelete