Creationists, Introns, and Fairly Tales
Richard Sternberg thinks that introns are important. He has to think that way because he's an Intelligent Design Creationist and the idea that introns could be mostly junk and not have a function isn't part of his faith [Matheson’s Intron Fairy Tale].
The segments of our DNA that are commonly called "genes" consist of protein-coding exons and non-protein-coding introns. Initially, the entire DNA segment is transcribed into RNA, but between ninety and ninety-five percent of the initial RNAs are "alternatively spliced."
What is alternative splicing? Imagine that the initial RNA derived from its DNA template has the organization A—B—C—D—E—F, where the letters represent blocks that specify amino acid sequences and the dashes in between the letters stand for introns. Alternative splicing enables multiple proteins to be constructed given the same RNA precursor, say, ABCDF, ACDEF, BCDEF, and so forth. In this way, hundreds or thousands of proteins can be derived from a single gene.
There’s more. The messenger RNAs that are produced by this process—and therefore the proteins that are made in a cell—are generated in a way that depends on the stage of development as well as the cell and tissue type. In the above example, a nerve cell may express the ACDEF version of a messenger RNA whereas a pancreatic cell may produce only the BCDE version. The differences are biologically essential.
What does this have to with introns? Everything. It is the presence of introns that makes this permutative expansion of messenger RNAs possible in the first place.
So let’s do the math. At least ninety percent of gene transcripts undergo alternative splicing, and there are at least 190,000 introns in the human genome. That means we have at least 0.90 x 190,000 = 171,000 introns that participate in the alternative-splicing pathway(s) available to a cell.
It's up to you, dear readers, to figure out all the things wrong with this explanation. You can start with the math. Arithmetic isn't one of their strong points. Or maybe it's an understanding of biology that's the real weak point?
Richard Sternberg thinks that introns are important. He has to think that way because he's an Intelligent Design Creationist and the idea that introns could be mostly junk and not have a function isn't part of his faith [Matheson’s Intron Fairy Tale].
Back in my days doing sequence alignments to examine phylogenetic relationships among primates, I recall 'discovering' that there were conserved sequences in introns, typically near their beginnings and ends. Beyond that, there did not seem to be much constraint.
ReplyDeleteIn other words, beyond those conserved seuences, it appeared to me that the rest of the intron - the bulk of it - was not under selective constraint, ie., quite possibly 'junk.' I'd like to see Sternberg's math on what percentage of the nucleotides within introns are actually employed in facilitating splicing.
90% of high speed collisions are fatal, and there are 100 fatal collisions in my city each year, so that means that there are 100 x 90% = 90 fatal collisions in my city each year.
ReplyDeleteWhat's that you say? Where did those other ten go? They've entered limbo with the 19,000 introns that don't participate in intron splicing yet are called introns anyway.
AL, it's worse than that. Focus on the difference between a transcript and an intron.
ReplyDeleteSeems like Sternberg has responded to this at:
ReplyDeleteLet's Do the Math Again
Sternberg reminds everyone of his calculations that Larry Moran neglected to mention.
Why must Matheson stoop to namecalling and saying Meyer is guilty of "some combination of ignorance, sloth, and duplicity” simply for stating that introns “play many important functional roles in the cell"?
Meyer's claim seems quite defensible--and even if this point about introns is arguable, Meyer does not seem to deserve this kind of abuse.
I just read the "Let's do the math again" post, and Sternberg reminds everyone that although he can perform the operations correctly, he still doesn't get the difference between a transcript and an intron. I don't think he understands what alternative splicing means, either.
ReplyDeleteIf you follow his logic, 90% of the introns end up in one or another mature mRNA.
Sternberg is still wrong.
ReplyDeleteHe should just leave well enough alone. He's already written two essays with errors that I expect my students to avoid. I shudder to think what will follow.
The only thing I get here is that Matheson and Moran are tenured professors doing some serious research and teaching - Sternberg is a woomeister working for a shady bunch of charlatans and cranks peddling nonsense. If I who has no (in)formal qualifications in biology must control my guffaws, Sternberg should really take a look at the mirror to see the joke he has become.
ReplyDeleteIn the second post, he essentially does the following calculation:
ReplyDelete(t'/t) * t * (i/t) = (t'/t) * i = 0.9 * 190,000 = 171,000
where t is the number of trascripts, t' is the number of alternatively spliced transcripts, and i is the number of introns.
Granting his assumption that introns are approximately evenly distributed among all transcripts (alternatively spliced or not), this means that 171,000 introns will be found on alternatively spliced transcripts. I don't see any errors in the calculation. One slip may be his apparent assumption that all introns in alternatively spliced transcripts are functional (i.e. they are necessary for whatever alternative splicing is going on, and the alternative splicing itself is functional.)
Or I might be completely missing something.
Sounds like Moran and Hunt are much more ready to declare a verdict than to present any evidence. Both of you allege errors. So... what are the errors? One almost gets the impression that the details don't matter... all that matters is, these are "intelligent design creationists" and we all know that such people are unscientific.
ReplyDeleteIf you do know of errors, please do the scientific community a favor and point them out, so they can be corrected. Until then, surely it's a bit odd to be shuddering about something that hasn't yet been identified. Maybe you want us to take it on faith that there are mistakes, bad ones, lots of them?
Alexander and Lars, those 90+% of genes subject to alternative splicing need only produce two mRNA isoforms to be rated thusly. In other words, only one of those 7.6 (on average) introns need be alternatively processed in order for the gene to be considered alternatively-spliced.
ReplyDeleteSternberg is saying that every intron in every gene that gives alternatively-spliced mRNAs will be subject to alternative processing. That's not very likely.
Thanks for clearing that up. I figured one of those assumptions must be wrong.
ReplyDeleteOne more thing - if you read the literature you will see that people who work in this field talk about alternative exons, not introns. There's a reason for this, and it is the source of an even larger math error on Sternberg's part.
ReplyDelete(Sorry if I'm giving away too much here ...)
I know you all will probably laugh at me, but I'm shocked at Sternberg's ignorance here. I've always been baffled by the Smithsonian business, and even suspected that he'd been treated unfairly. His platonism seems weird to me, but I wouldn't have taken him for a fool or an ignoramus just because he helped Steve Meyer get a boring paper published in a nowhere journal.
ReplyDeleteNow I'm genuinely surprised by his stance here, and by his very basic errors. It's clear he doesn't know what he's talking about, and to re-do the math with the same basic mistake in it is really hard to understand. I'll respond on my blog, but I'm not sure what to say. I honestly didn't think the DI could get any worse.
Arthur Hunt's 10:53 PM post tonight states it the simplest.
ReplyDeleteIf one isoform of a gene has 7 exons, an alternatively spliced isoform could have only 6 of those exons. Nothing has changed with the introns. Sternberg assumes that 90% of all introns end up in translated mRNAs. As Steve Matheson says, Sternberg clearly has no idea what he is talking about.
I haven't read the paper that purports to show the breakthrough work on deciphering the splicing code, nor would I understand it if I did. My question is, how big of a role does it assign to the introns in carrying the code? This could be relevant. For example, if introns are responsible for 100% of the splicing code, then that would make their role rather significant, perhaps even in the 10% of the genes where no splicing occurs. It could be the introns in those genes are sending the message, "Make sure you keep all the exons." So is it clear how big a role the introns play in the splicing code?
ReplyDeleteExcuse me but blind, undirected chemical processes (the anti-ID position) can't even explain alternative (gene) splicing.
ReplyDeleteTo splice requires knoweldge and blind molecules just don't have that.
So instead of jumping on Sternberg for his math perhaps you guys should focus on substantiating the claims of your position.
Just a thought...
Joe G,
ReplyDeleteTo splice requires knoweldge and blind molecules just don't have that.
You are presenting the typical straw-man argument that always comes up during these discussions. Your assumption of a blind molecule in not correct. These are evolved systems, not random shuffling.
Dr Hunt, thanks for being more explicit, opening your objections to the public so they can be discussed.
ReplyDelete"(Sorry if I'm giving away too much here ...)"
I just don't get this. Is this some kind of quiz game? You are criticizing Sternberg's mental faculties in a way unbefitting scientific exchange, yet when it comes to pointing out what's actually wrong with his reasoning, you're acting like you're only willing to drop hints. How can one evaluate your statements fairly and charitably without full disclosure? Sternberg at least cites sources for his statements. I've looked at Hunt's and Matheson's blogs for a more detailed response to Sternberg, but found none. We all understand that it can take time to find time among other duties to formulate a quality response, but surely in that case, publication of negative statements about the opponent's should wait until the full details are available?
That being said, I see your point that "only one of those 7.6 ... introns need be alternatively processed in order for the gene to be considered alternatively-spliced". I understand the "on average" bit as meaning there are 7.6 introns on average per transcribed gene, not that that one in 7.6 on average is involved in alternative splicing.
That makes sense, and pending Sternberg's response, he seems mistaken in saying that "we have at least 0.90 x 190,000 = 171,000 introns that participate in the alternative-splicing pathway(s) available to a cell". Rather he should have said there are at current estimates somewhere between (0.90 * 190,000 / 7.6) and (0.95 * 190,000) such introns. The lower bound then is 22,500. (The top of the range is 180,500.) Do you consider 22,500 "a handful"?
What is your own estimate of how many introns are involved in alternative splicing? Can you put an upper bound on it?
"if you read the literature you will see that people who work in this field talk about alternative exons, not introns."
Well clearly they do talk about introns too, as we can see from th Nature article abstract... but maybe you're saying that the colored bits labeled 'I' to either side of the "alternative exon" in the middle of the figure are not introns?
"There's a reason for this, and it is the source of an even larger math error on Sternberg's part."
We wait in suspense.
The other Jim,
ReplyDeleteSaying they are "evolved systems" is meaningless because you have no idea if blind, undirected chemical processes can produce such a thing even given deep time.
Also the molecules are blind- that is in the anti-ID scenario.
Deal with it...
Hi Lars,
ReplyDeleteSorry for being cryptic - my lame attempt to keep from taking all of this too seriously.
My remark about alternative exons relates to Sternberg's use of the figure from the splicing code paper. This figure portrays introns as units of ca. 600 nts, 300 associated with one exon and 300 with the other. This reflects the fact that it is the exon that is the functional unit here.
What the figure omits (for good reason - the omitted portion is "junk") is the remaining 90% (very roughly speaking) plus of your average intron. Sternberg would have his readers believe that these thousands of bases, even in alternatively-spliced introns (if one is going to use Sternberg's terminology here), do not exist.
Add them back into the picture and Sternberg's caricature of the alternatively-spliced intron as a unit that teems, end-to-end, with function is revealed to be erroneous. As is his larger argument that alternatively-spliced introns are in some way indicative of a wide-spread functionality that reduces what is for him the "junk DNA" problem.
Joe G,
ReplyDeleteSaying they are "evolved systems" is meaningless because you have no idea if blind, undirected chemical processes can produce such a thing even given deep time.
Yes we do know it is possible. Have you heard of the SELEX experiment?
http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment
Random pool of DNA / RNA. Add some "target". Enrich for things that interact with target. You can, in vitro, evolve enzymatic activity from random RNAs this way. Including an RNA that replicates itself.
So random molecules can develop complex function, without god.
Now removed the human element, and wait a really long time, and it is possible. (http://www.ncbi.nlm.nih.gov/pubmed/19777150)
Bilbo, the question isn't whether introns participate in splicing, to the extent that they contribute to the sequence that identifies the intron-exon junctions where the splice occurs. As I'll explain when I get my response posted, Sternberg is making a really basic mistake here, and he's also playing a rhetorical game.
ReplyDeleteThe mistake has already been explained. It's a mistake that indicates that Richard Sternberg is ignorant of the topics on which he writes.
The rhetorical game has not yet been mentioned, and I can't tell how much of it is explained by Sternberg's now-apparent scientific ignorance. The game is to identify the alternative splicing of transcripts, by removal of introns, as a function of introns. As I'll explain on my blog later today, anyone who makes that connection would indeed consider the number of "functional" introns to number at least 20,000, as Lars has already mentioned.
This strikes me as a peculiar way to assign "function" to large sections of non-coding DNA interspersed in coding sequences. Yes, the existence of intron-exon junctions makes splicing possible, and thus makes alternative splicing possible, but to then conclude that the thousands of base pairs in the discarded intron should be credited with that "function" is plainly gratuitous.
To summarize, Sternberg claimed, twice, that because 90% of human transcripts are alternatively spliced, then 90% of human introns are alternatively spliced. By doing this, he demonstrated that he is ignorant of basic molecular biology, and his second error was much worse because he couldn't understand what we were getting at in our comments here. (And yes, Lars, it was a test. He failed. And I was surprised.) He also claims that the existence of alternative splicing, which employs sequence recognition ("codes") that includes sequences in the introns themselves, means that the introns therefore have "function." And if that's what we all mean by "function" of non-coding DNA, then he's right. Gotta go. More later.
Lars says,
ReplyDeleteThat makes sense, and pending Sternberg's response, he seems mistaken in saying that "we have at least 0.90 x 190,000 = 171,000 introns that participate in the alternative-splicing pathway(s) available to a cell". Rather he should have said there are at current estimates somewhere between (0.90 * 190,000 / 7.6) and (0.95 * 190,000) such introns. The lower bound then is 22,500. (The top of the range is 180,500.) Do you consider 22,500 "a handful"?
There are two important problems with Richard Sternberg's article.
First, it's almost certainly *not true* that 90-95% of all human protein encoding genes exhibit alternative splicing. While there's no consensus right now, the majority of biochemists think this number is too high. Whether it's 5% (my guess) or 50% (a common estimate) is controversial.
Sternberg gives us no indication that he understands this controversy. He bases his entire fairy tale on a value that has been pretty much discredited.
His second problem is not even understanding the consequences of his false assumption. Let's assume that Sternberg is correct and 90-95% of all protein encoding genes exhibit alternative splicing. Since there are 20,500 such genes in our genome it follows that about 19,000 are alternatively spliced.
The minimum requirement for alternative splicing is that an intron can be included or excluded in the mRNA. The lower limit for the number of introns is thus 19,000 (actually 18,450 - 19,475).
In other words, as many as 171,000 introns could be (mostly) useless junk. It will be even more if we accept a lower number of alternatively spliced genes.
I don't think this is the message that Sternberg meant to convey in his posting. This is why we call them IDiots.
BTW, Sternberg took the 190,000 introns information from Stephen Matheson who quotes a 2005 paper by Fedorva and Fedorov. According to those authors, there are 23,506 protein encoding genes in our genome of which 21,746 contain introns. Thus, the average number of introns per gene is greater than 8.
We now know there are fewer genes and the total number of introns has been dropping steadily as workers begin to eliminate spurious introns when genes are annotated. I think there are about 150,000 introns (see: Junk in Your Genome: Protein-Encoding Genes).
The exact number doesn't matter so much but the point is you can't mix and match numbers. It's invalid to use a lower estimate of introns per gene (e.g. 7.6) with a high estimate of the number of introns (e.g. 190,000).
Hi Larry,
ReplyDeleteI'm a little confused. You mentioned introns being included in the mRNA. Am I mistaken in thinking that all the introns are initially transcribed and then spliced out of the mRNA?
@bilbo, you're right.
ReplyDeletePre-mRNA is transcribed with introns in it, after which it is processed out by RNA and protein splicing factors to yield the mature mRNA. This mature mRNA is then exported out of the nucleus.
Bilbo asks,
ReplyDeleteI'm a little confused. You mentioned introns being included in the mRNA. Am I mistaken in thinking that all the introns are initially transcribed and then spliced out of the mRNA?
The whole point about alternative splicing is that sometimes certain "exons" are spliced out and sometimes certain "introns" are retained in the mRNA.
There aren't many examples of alternative splicing that only involve intron exclusion/inclusion. They tend to be concentrated in the noncoding region at the beginning and ending of a gene. However, they do correspond to the definition of a "functional" intron.
Thanks, Larry. This is fascinating. So occasionally an intron can actually code for part of a protein?
ReplyDeleteThanks, Larry. This is fascinating. So occasionally an intron can actually code for part of a protein?
ReplyDeleteoops. double post
ReplyDeleteYes, an intron can sometimes include a bit of coding region.
ReplyDeleteBut I was actually thinking of 5'UTR introns that do not contain any codons. Here's a short presentation of 5'UTR introns [Systematic Analysis of Human 5’UTR Introns Reveals Their Importance in Expression. Sometimes these introns are involved in alternative splicing.
There are also 3'UTR introns at the "tail" end of the gene.
Dr Hunt,
ReplyDelete"... my lame attempt to keep from taking all of this too seriously."
Do you expect the reader to take your side of the argument seriously?
"Add them back into the picture and Sternberg's caricature of the alternatively-spliced intron as a unit that teems, end-to-end, with function is revealed to be erroneous."
This is the "even larger math error" you accused Sternberg of? Looks to me like no error at all, but a difference of opinion over what the discussion ought to be focusing on. Sternberg makes very clear that he is talking about the number of introns, not the number of base pairs, that have function. In addition, he is specifically responding to Matheson's statements, which again are very clearly talking about the number of introns, not the number of base pairs in introns, that have function. (He mentions base pairs once, but then repeatedly offers counts of introns.) You all may argue that the number of functional introns is less pertinent than the number of base pairs, but that does not make Sternberg guilty of a math error.
It's nice that Matheson has now apologized on his blog, though he still shifts the blame on Sternberg. I wonder if Hunt will apologize as well. The pattern I still see here is that the abuse heaped on Sternberg is vastly out of proportion to sins committed.
Darwinists are frequently pointing out that the scientific process is characterized not by one scientist's conclusions being right the first time and forever, but by the dialog (multilog) of publishing, having results examined by others, corrected, and superseded. Making an error does not make one unscientific; rather, dishonesty does, e.g. failing to acknowledge a legitimate error once it is pointed out; throwing ad hominems when you can't find a weakness in your opponent's argument. In this regard, I think it's clear which side has been a better exemplar of the scientific process. Nevertheless, again, I'm glad to see Matheson's apology, as mixed with ad hominems as it may be.
Regarding the idea that introns are functional only insofar as their boundaries are functional (Matheson):
"Yes, the existence of intron-exon junctions makes splicing possible, and thus makes alternative splicing possible, but to then conclude that the thousands of base pairs in the discarded intron should be credited with that "function" is plainly gratuitous."
The claim about count of base pairs has been partially addressed above. Sternberg did not say anything about how many base pairs should be credited with function.
However your implication that it is only the intron-exon junctions that are necessary to direct alternative splicing has already been addressed in Sternberg's post, and in the Nature article; you have not addressed this point. Sternberg writes, "such an argument would be false. In order for alternative splicing to work properly, it is necessary not only that exons be demarcated from introns, but also that the splicing process be correctly modulated. And introns contribute significantly to such modulation. How do I know this? Take a look at this figure: [Figure from Nature article, and discussion] ... It is clear that introns are just as rich in splicing-factor recognition sites as are exons. The authors of the article—titled 'Deciphering the splicing code'—conclude that the evidence 'predicts regulatory elements that are deeper into introns than previously appreciated.'"
Since Sternberg has already addressed your argument, and you have not responded to his point, the best appearance at this point is that he is correct. Being publicly "shocked at his scientific ignorance" makes you more qualified perhaps as a dramatic actor, but does not advance your side of the argument; rather the reverse.
P.S. I'll post any further comments over on Matheson's blog, as he is more central to this discussion.
ReplyDeleteHi Lars,
ReplyDeleteThanks for clarifying your disagreement with my statements. I would ask that you understand that my criticisms of Sternberg's claims about introns are made in a larger context, one that gets to the heart of the matter as to why Sternberg is asserting functionality in essentially all introns.
Basicaly, Sternberg is committed to finding function for 88.5% (his number) of all transcribed RNA, including intronic RNA. I am inclined to take everything Sternberg says about introns in this larger context. This is the basis for my comments. One may not like that I am holding Sternberg responsible for his larger "body of work" in this regard, but that's too bad.
I'll toss out an expectation: Sternberg is committed to finding function for 88.5% of all DNA in the cell. I'm pretty sure that, somewhere down the road, Sternberg will cite his own erroneous calculations (90% of all introns have function) to conclude that he has in fact met his goal, at least when it comes to polII transcription units. When he gets to this point, I would ask that you recall my comments in this thread.
One has to wonder how Sternberg got his position at the National Center for Biological Information and how he is able to fulfill the duties outlined in his CV (see: http://www.rsternberg.net/CV.htm)
ReplyDeleteWhy even bother with a calculation like this when you go can directly to a genome browser like Ensembl and look up the empirically determined number of (known) gene transcripts:
ReplyDeletehttp://uswest.ensembl.org/Homo_sapiens/Info/StatsTable?db=core
That number is 148,000.
Oh, I know why. Because Sternberg wouldn't know where to find information like that.
In the debate (with Matheson and Hunt) against Meyer and Sternberg, all Moran does is bluster his usual invectives all while proudly but fecklessly declaring himself as 'right'.
ReplyDeleteWe are to apparently just trust him and his fellow priests of materialism's metaphysical "science" - Darwinism in its latest guise.
"Pay no attention to the man behind the curtain please", one reads between the lines.
Moran even calls one far more educated in evolutionary biology than himself an "idiot".
You people can't debate worth shit and your vacuous accusations come right beck in your faces.
Self-appointed priests of Darwinian fundamentalism need psychological help for living in denial of reality.
"Artificial life investigators and most applied biologists accepted this reality early on. Steering is required to achieve sophisticated function of any kind. Much of the life-origin research community, however, continues to “live in denial” of this fact."
-biosemiotic research trends
Moran wrote: "Richard Sternberg thinks that introns are important. He has to think that way because he's an Intelligent Design Creationist and the idea that introns could be mostly junk and not have a function isn't part of his faith."
ReplyDeleteAnd likewise, the opposite can be said of you Mr. Moran. You are ever so quick to jump to the conclusion that introns are mostly junk. Hence Matheson's ridiculous statement of faith that "biologists have identified functions for only a “handful” of the 190,000 or so introns in the human genome. “How many? Oh, probably a dozen.” he says, but then he gets really generous and says maybe even a thousand introns in the human genome are known to have ‘important functional roles.’ I think he is going to have to be a lot more generous than that as more functions are discovered. This prediction of evolution will fall in the same way that the "junk DNA" idea has proven false.
But the idea of junk DNA and junk introns fits well with the evolutionary fairy tale so evolutionists are quick to jump on this as evidence supporting their theory. The problem is that as functions are identified, they have to wipe egg off their face. Here, Matheson and now Moran are left having to defend a dying idea. At least the other side has some real science on their side. These guys have not given us anything to support their case. We need current articles or articles that respond to the scientific research that Meyers and Sternberg based their views on.
But evolutionists are so dedicated that even though functional introns are not a part of their faith, I'm sure that they'll find a way to alter the original infallible revelation and somehow include functional introns in their statement of faith.
tj
"Steering is required to achieve sophisticated function of any kind."
ReplyDeleteTaken from some book called Biosemiotics Research Trends. I suggest Gary and the authors of that book look into the work of Richard Lenski. Forget artificial life. Lenski has demonstrated sophisticated function evolving, without steering, in *actual* life.
Anonymous (of course) says,
ReplyDeleteBut the idea of junk DNA and junk introns fits well with the evolutionary fairy tale ...
Actually the idea of junk DNA does not sit well with many evolutionists. That's why they are opposed. Junk can't be adaptive and the dominant worldview among many biologists is that life looks designed and the designer is natural selection.
But evolutionists are so dedicated that even though functional introns are not a part of their faith, I'm sure that they'll find a way to alter the original infallible revelation and somehow include functional introns in their statement of faith.
I first started teaching about the legitimate roles of alternative splicing back in 1982 and it's been in every textbook I've written since 1989. All my textbooks describe the functional roles of intron sequences. How do those little facts fit into your description of me?
"First, it's almost certainly *not true* that 90-95% of all human protein encoding genes exhibit alternative splicing. While there's no consensus right now, the majority of biochemists think this number is too high. Whether it's 5% (my guess) or 50% (a common estimate) is controversial. "
ReplyDeleteIt's important to distinguish whehter we are talking about the sheer physical number of transcripts or the variety of kinds of transcripts. The distinction is important. As I pointed out:
regarding Sternberg's claim:
"At least ninety percent of gene transcripts undergo alternative splicing, and there are at least 190,000 introns in the human genome. "
A charitable reading is 90% of the KINDS of transcripts existing emerged from alternative splicing.
How can this be? a manufacturing analogy is inorder.
Say we have 1000 cars, 900 of them are identical, but 100 of them are unique, and the unique cars emerged out of Alternative Manufacturing (Splicing if you will). Thus we have 101 different kinds of cars, and 100/101 = 99% emerged via Alternative Splicing.
Thus even though 90% of the physical cars did not go through alternative splicing, 99% of the kinds of cars went through alternative splicing (so to speak).
The context of the discussion is the variety of kinds of transcripts, not the sheer physical number of them.
Also, finding instances where a system is not used is not evidence it has no function.
I should point out there are legitimate and illigitimate ways of characterizing functions.
It would be illegitimate to cherry pick all the days where spare tires on cars are not used. It would be illegitimate to say, "the spare tire wasn't used on July 19, 2001, therefore the spare tire serves no function".
In similar fashion, it would be illigitimate to say certain features of an operating system (like Windows 7) aren't functional merely because we find computer users who don't use all the features of the operating system!
We certainly might find introns in some cells that are not used, but it would be deeply improper to generalize the behavior of introns in one cell type to all cell types. In fact Mattick argues introns are used differently in each cell type.
If indeed the cell uses operating systems like modern computers, and if cells have backup systems like spare tires, we would actually expect cells to have functional capabilities that are not always utilized. The lack of utilization 100% of the time is not evidence against function anymore than the lack of use of a spare tire or unused feature of an operating system is evidence against its function.
Many researchers characterize cells have operating systems, by the way.
Citations of where an intron isn't used in one particular cell type is a pretty lame argument in light of modern understanding of systems engineering where backups, contingencies, and unused copies are the norm, not the exception.
Anonymous says,
ReplyDeleteCitations of where an intron isn't used in one particular cell type is a pretty lame argument in light of modern understanding of systems engineering where backups, contingencies, and unused copies are the norm, not the exception.
Unfortunately for you, the human genome wasn't designed by an engineer, unless it was the same one who works for BP.
Dr. Moran,
ReplyDeleteI should have identified myself in the previous comment as scordova of Uncommon Descent. That was an oversight on my part. I was stating what I had stated at UD.
Apologies for not affixing my name to the earlier post.
scordova