29 June 2010

Introns. Let's think about this, people. Part II.

Before we explore what introns are and how they work, let me correct the misuse of my words by one of the ID attack kittens. Months ago, referring to Steve Meyer's claim that introns "are now known to play many important functional roles in the cell," I sought to put intron "function" into context as follows:
The human genome contains at least 190,000 introns (though it's been recently estimated to contain almost 210,000). Together those introns comprise almost 1/4 of the human genome. One fourth. That's 768 million base pairs. And biologists have identified "important functional roles" for a handful of them. How many? Oh, probably a dozen, but let's be really generous. Let's say that a hundred introns in the human genome are known to have "important functional roles." Oh fine, let's make it a thousand. Well, guys, that leaves at least 189,000 introns without function, and gosh, they're snipped out of the transcripts and discarded before the darn things even leave the nucleus.
One critic has interpreted me as claiming that I know that 189,000 introns have no function. That's not my point, and I think most people know that.

No, the point is simply this: finding a "function" for a small number of introns doesn't cut it, at least not if one seeks to claim that introns are generally functional elements in a genome characterized by efficient, streamlined packaging of functional information. And the reason is that introns comprise a huge component of the human genome. So even if one had identified function for a thousand of them, it would be a tiny fraction of the total. It would be like finding a Yugo that's still running.

But let's back up. What is an intron, and how would we know whether it had a "function" or not?

Picture a gene as a set of instructions for making a protein. The instructions are in the form of a code. The code is copied from the DNA in the genome, safely stored in the nucleus. The copy is made of RNA, not DNA, and that copy is shipped to the cellular worksites where the code is translated into a protein. Simple, so far, because we skipped at least one important step. That copy of the coded instructions is often far, far longer than it needs to be. What's all the excess? The excess code is spliced out of the copy before it even leaves the nucleus. It comes in chunks called introns.

Okay, so there's a little excess information that's removed. So? Heh. Hold on. You need to see just how much code is cut out of some genes. Before we look at some specific examples, keep this in mind: less than two percent of the human genome specifically codes for protein, and around 25% is devoted to introns. Come on, think about it: the genes in your genome are interrupted by chunks of information that are spliced out and discarded before the copy is even sent to the worksite for manufacturing protein. Those chunks of information are more than ten times bigger (in aggregate) than the coding sequences.

We have good reasons for suspecting that relatively little of that huge pile of digital information participates in what we would call "function" – that's for the next post. For now, to show you just how pervasive intron sequences are in your genes, let's look at two examples, one from a textbook and one from my own research.

Example 1: the Factor VIII gene

Factor VIII is a protein involved in blood clotting, and it's present in mammals and birds (at least) among the vertebrates. Here is a diagram of the gene from Molecular Biology of the Cell:

Image from Molecular Biology of the Cell online, Alberts et al., 2002.

The red stuff is the coding sequence. The yellow stuff is all introns. The gene is quite large: roughly 190,000 base pairs from start to finish. The coding sequence (in the form of 26 exons) is less than 10,000 base pairs. In other words, about 5% of the gene for Factor VIII is devoted to making the protein. The other 95% is introns.

What functions reside in those 180,000 base pairs of code that is snipped out of the copy and discarded in the nucleus? We don't know. But here are some things we do know. The codes for alternative splicing, that Richard Sternberg points to as evidence for "function" of at least 90% of all introns, are tiny – typically just a few base pairs, and as Sternberg's post notes, only occasionally are these codes more than a short distance from the end of the intron. In other words, those enormous introns in the Factor VIII gene, which are about 8000 base pairs long on average, can harbor tiny codes near their ends which signal the cell to splice in different ways. Folks, that leaves something like 99% of the intronic sequence yet unaccounted for. My assertion is not that we know that the sequence has no function. My point is that we don't know what the overwhelming bulk of that sequence is doing. To say that there are even a few thousand base pairs of sequence that even look functional would be a stretch, and we'd still have tens of thousands more to go. Sternberg mentions microRNAs, which are very interesting genomic elements that influence gene expression. They're called microRNAs for a reason: they're less than 100 base pairs in length. How many microRNAs do you think we can find in the Factor VIII gene? You'll need a lot to make any dent in the huge swaths of discarded sequence in that gene. It's starting to sound like a fiber cereal commercial.

Here's one way we could get a handle on the amount of intron sequence that might have an important function. We could look at similar organisms to see if they have the same stuff, and whether it seems to be conserved. If the introns look the same in some similar but not extremely closely-related species, we might start to suspect that they're important for function. And if they vary a lot in size, we might start to suspect that their makeup isn't mission-critical. Let's see whether the introns in this gene are important to birds, for example.

The chicken has a Factor VIII gene, too. The chicken gene is around 1/10 the size of the human gene: it's less than 20,000 base pairs in length. The coding sequence is just a little smaller than in human, between 5000 and 6000 base pairs. What does this mean? It means that the chicken gene is a tiny fraction of the size of the human gene, and the difference is almost completely due to introns. The chicken introns are far smaller. They're not less numerous – as near as I can tell, both genes have the same number of introns – they're just a whole lot smaller.

Do you see how the "introns have function" thing is a problem here? It's not helping us understand the size of the introns, which dwarf the coding sequence in the human, and are suddenly an order of magnitude smaller in a bird. Whether you're a Darwinian hyperadaptationist or just a fan of intelligent design, you're a long way from providing a coherent explanation for this pattern of arrangement of genetic information.

And I didn't pick the most outrageous example. Look up the human dystrophin gene someday. Reputed to be the biggest gene in nature, it's 2.4 million base pairs long. Something like 15,000 base pairs are devoted to making the protein. Yeah. You do the math.

Example 2. The mDia1 gene

This gene encodes a signaling protein that is one of our central research topics. The gene is about 104,000 base pairs long, and the coding sequence is distributed over about 26 chunks (again, these are the exons) which account for less than 6000 of those 104,000 base pairs. Among the 25 or so introns are two very large ones: right at the beginning of the gene is an intron over 30,000 base pairs long, and about halfway through another is about 35,000. So, my favorite human gene is about 6% coding sequence. The rest is composed of introns, including two monsters that could easily harbor the entire chicken Factor VIII gene.

I think that's enough genomics for one overlong post. I hope the point is clear. Those who wish to assign functions to introns need to explain huge stretches of non-coding DNA, sometimes tens of thousands of base pairs long, vastly more than any splicing code or microRNA collection or anything else can account for. I'm not saying I know they do nothing. I'm saying that those who wish to describe genomes as wonders of information storage have an awful lot of work to do.

Next time: the kinds of "functions" we do find in introns.


Bilbo said...

Thanks for a very informative post, Steve.

Davis said...

"I'm saying that those who wish to describe genomes as wonders of information storage have an awful lot of work to do."

And I'm saying that those folks are afraid to do any actual work.

Not only that, they tout an easily testable hypothesis that they are unwilling to test.

John Hansen said...


Good post Steve, but please allow a question from ignorance. There certainly is much more information in the cell than a list of the proteins that are to be made. For example, how is it that my son looks like me? Of course there are slight differences, but his face and facial structure have enough similarities to mine that people easily identify him as my son. Its hard to imagine where the instructions come from to put together a face that looks similar to mine. I can't even tell you what exact details make him "look like" me. But nevertheless he does.

So, by homely analogy, I know a recipe is much more than ingredients. So where is the information in his cells to make his facial image similar to mine.

Now don't accuse me of jumping to conclusions here. Just because I am posting this sincere question on a post about introns does not mean for a second that I have any idea of proposing that the introns are for that purpose. I literally have no idea where this information is kept. But it must be there during development. Is any group currently doing research on this important question?

Knowing what proteins are used for certain processes and identifying introns is interesting, but doesn't there have to be more information in the cell to communicate body plan, size, strength, etc. How does this happen?

Bilbo said...

Hi Davis,

Unable to figure out how to reply to you, I tried the "like" button, and now it says I like your comment. I don't. How do you know "those folks" are afraid to do any work? And are you sure it is easily testrable? I imagine we can try knocking out parts of introns in the germ cells and seeing what happens. How easy is that to do?

John Farrell said...

Hi John Hansen,
I can't speak for Steve, but I would think one answer to your question is: regulatory genes, which form a whole fascinating world of research in their own right.

If I may suggest an informative book, Gerhardt and Kirschner's, The Plausibility of Life.

SteveMatheson said...

Hi Bilbo, the "Reply" button is just to the right of the "Like" button. (I'm using Google Chrome on a Mac.) If you don't see the buttons, I'd like to know. Just let me know which browser and OS you're using.

As for whether ID apologists are "afraid" to do experimental science, Doug Axe is working on protein folds, fruitlessly (and, IMO, hopelessly) trying to show that proteins are completely isolated in sequence space. Mike Behe isn't doing anything that I know of. As far as I know, no ID "scholar" is working on experiments to test the function of non-coding DNA, nor has any ID apologist even proposed one. As I've written before, I would be supportive of any effort to actually test an ID prediction, to the point of arranging a collaboration. Be sure to let me know if/when you become aware of such an opportunity, or even if you know of someone who's remotely interested.

Knocking out a genomic element is generally straightforward, especially in this postgenomic era. Working in the mouse system, the first step is to make embryonic stem cells that lack one of their two copies of the element. This involves making a somewhat elaborate piece of DNA (a plasmid) and that can be challenging. But once the cells have one copy knocked out, there are straightforward ways to make cells that lack both copies. And at that point you can do a whole lot of experiments on cells and differentiation without even making a mouse. And of course you can take the next step: make a mouse with the element missing in its germ cells. That step is costly but generally straightforward.

The mouse is the system I know best, but there are other ways to go, most notably various plants, and those might be much better suited to these types of experiments. The point is that targeted deletion of genomic elements is not merely tractable – it's straightforward.

Davis said...

Hi Bilbo,

Why don't you like my comment? I know that folks like you are afraid to do any work because despite endless jawboning, they don't do any work.

Yes, I am sure that it is easily testable. Why would we knock out parts of introns when Nature does it all the time? Besides, I'm thinking of something much simpler. Instead of arguing with people, you might try arguing with yourself, asking yourself, "What do I expect if I'm right?" and "What do I expect if I'm wrong?"

Davis said...

I should add that the answers to those questions have to be about what you will directly observe. IOW, the answer to the former should never be, "I expect that people will agree that I am right."

Davis said...

John Hansen,

Your question (where is the information) is key to distinguishing something that looks designed from something that evolved.

The answer is that the gene networks aren't nearly as hierarchical as you'd expect if things were designed—that is, there aren't any real instructions. Unfortunately, developmental biologists often have similar blinders and use metaphors.

For example, the key to moving the nostrils from the front to the top of the head is allometry. When we look for big changes in genes that cause big changes in morphology, we are usually disappointed.

The key is that we know that relatively few of these changes are found in introns. They are in promoters, enhancers (which rarely can be found in introns), and 5' and 3' untranslated regions of mRNAs.

You brought up strength. Check out Belgian Blue cattle. That big difference comes from just one gene.

John Hansen said...

But I am not looking for big changes in morphology. I am looking for all the information that makes one face look like the other. Its entirely possible that it really is not much information at all. It may be like an iterative procedure ( such as the simple laws which produce the very distinctive looking Mandelbrot set ), is that what current research indicates or is it an open question?

Davis said...

John, I understand that you aren't looking for big morphological changes. However, that's what researchers have studied first.

If the big ones are that tiny at the molecular level, why would you presume that smaller ones are codified somewhere?

How do you think healing works when you lose a divot of skin and underlying tissue?

Current research suggests that it's not so much iterative as regulatory—hence my question about healing.

John Hansen said...

BTW - I did look up Belgian Blue cattle. Although an interesting example of gross changes in morphology by a single gene, I think it to be a terrible example as far as making the case for evolution. Whether your opponents positions are justified or not, animals which only remain alive because of breeder's intervention are a poor example to try to convince someone who is naturally skeptical of Darwinism that Darwinism is true. I am not saying your opponents are correct, I'm just saying the example is a non-starter in building a case.

Davis said...

I wasn't trying to make a case for evolution, John, I was trying to answer your question. Sheesh.

Doc Bill said...

John, do us all a favor and take a giant step for Creationkind at the same time by not saying stuff like "Darwinism is true." What you mean to say is this: I am skeptical and unconvinced that the modern theory of evolution adequately explains the diversity and relatedness of life on Earth.

Did I express that correctly? Anyone? Buehler?

(There's no such thing as "Darwinism" and scientists don't refer to theories as being "true," John, even in physics.)

Bjstroh said...


Bilbo said...

Hi Steve and Davis,

I now see two reply boxes. Maybe this will work. I didn't understand everything you said, Steve, but it sounds like I'm on the right track with knocking out parts of introns. Since the question of functionality of introns isn't relevant to Behe's thesis, I wouldn't expect him to be working on it. Since it matters to Sternberg, he might be.

I dislike your comment, Davis, because it assumes that you have access to the inner emotions of people that you don't even know. That's reveals a rather arrogant attitude. And as Steve pointed out, the way to test thesis may be simple, it is costly.

SWT said...

I dislike your comment, Davis, because it assumes that you have access to the inner emotions of people that you don't even know. That's reveals a rather arrogant attitude. And as Steve pointed out, the way to test thesis may be simple, it is costly.

Perhaps. However, regardless of their emotional states, ID advocates do appear to be unwilling or unable to bring their speculations into a testable form, and to actually test their speculations. The careful reader will note that most, if not all, of the data about introns was obtained by mainstream biologists and not by ID advocates.

Davis said...

Bilbo wrote,
"Since the question of functionality of introns isn't relevant to Behe's thesis, I wouldn't expect him to be working on it."

But Behe isn't working on anything that's relevant to his thesis. I hypothesize that he is afraid to. Do you have an alternative hypothesis?

"Since it matters to Sternberg, he might be."

Sternberg isn't working on anything either.

"I dislike your comment, Davis, because it assumes that you have access to the inner emotions of people that you don't even know."

I'm open to alternative explanations. Fear of ending the creationist gravy train is the only one that fits the data.

"That's reveals a rather arrogant attitude."

I'm not the one claiming to understand data produced by working biologists better than the producers themselves understand them. That's what you're doing, and your arrogance is off the charts. Quit projecting.

"And as Steve pointed out, the way to test thesis may be simple, it is costly."

But I pointed out a less costly way to test the hypothesis (you'll do anything to avoid that word, eh?). If you were interested enough and not afraid to look, it might even turn out that it's already been tested, Bilbo!

Bilbo said...

Hi Davis,

(The reply function isn't working for me, again.) You've turned your accusation that ID scientists are afraid into a hypothesis. That's an improvement. Now go test it and let us know the results. Until then your speculations about their emotional states are a worthless pile of crap.

RBH said...

Bilbo, I've had on public offer a straightforward test of the claim that structures that meet Behe's criteria for irreducible complexity cannot evolve for years. I've published it on ARN and ISCID. None has even bothered to give it a shot. The data are freely available on the web and the test is quite straightforward, employing a knockout procedure and simple probability calculations. Shoot, I've even done some of the work and am willing to ship a spreadsheet containing an example to anyone who wants it (provided I can remember which machine I've got it stashed on). Since I infer from hints in their writings that both Behe and Dembski have read my challenge, I proffer their unwillingness to spend just a few days doing it as empirical evidence for the proposition that they don't want to risk the test.

(And I have to say this new comment submission format is problematic. When I click to add my website I lose the "Submit" button! And there's no preview for us twitch typists)

John Hansen said...

Doc Bill - Please do us all a favor and don't waste space enforcing your personal view of what science is and how it should be talked about. You seem to have a very limited view of what science is. I would guess its your way of somehow (in your mind) undercutting the arguments of those who disagree with you.

Agreement to only discuss universal concepts in a certain vocabulary, is a childish way of establishing your credentials. I don't know why you do this, but that seems to be a favorite tactic of yours. Why a short hand way of expressing myself should evoke some snarky response from you is beyond my comprehension.

JLT said...

Whether faces look similar has much to do with the distances of different elements to one another, like eye distance, distance of the eyes to the tip of the nose, position of the ears in relation to the eyes, stuff like that.
I don't know whether that is researched at present for face development but it is known that in embryonic development gradients play a big role. One example is sonic hedgehog (SHH), a factor that is involved among other things in hand development. It is produced in cells on one side of the hand bud (opposite of the future thumb) and builds a gradient along it. The farther away from the producing site, the lower the SHH concentration, which results in the different looking fingers on our hands, including the thumb.
If SHH or a regulating gene is affected by point mutations or duplicated it can result in polydactyly or a thumb with three phalanges instead of two or other types of malformations. But of course, even if an individual ends up with five fingers and the right numbers of phalanges, there are variations in finger length etc. that are likely determined by variations in expression levels of the corresponding genes or by more or less effective binding of factors to their ligands due to polymorphisms in those genes .
I'd think that something similar determines the distances of eyes, nose, ears and mouth to each other. So, if your son inherited your version of "face factor genes" that would lead to similar gradients and similar distances in which eyes etc. are positioned.

SWT said...

RBH, although I'm no friend of ID, I'd be interested in the test you're suggesting ... you can reach me by email at swt.onpt AT yahoo.com. Send up a flare here so I know you've sent me something, I check that yahoo account very infrequently.

Re: your posting problems, you might be able to sidestep them by registering at Discus, which has the added benefit of enabling email notification of activity on threads you're following. IMO, the lack of a preview function is made up for by the ability to edit a post once it's made (if you're registered and logged in).

doppelganger said...

"I'm not the one claiming to understand data produced by working biologists better than the producers themselves understand them. That's what you're doing, and your arrogance is off the charts. Quit projecting."

Sadly, this attitude seems to be a requirement for one to be a YEC or ID advocate. Such an attitude can be summed up in the work of Dunning and Kruger, or by the earlier but similar concept known as 'Illusory Superiority'. Such work helps us understand how it is that lawyers, theologians, and laymen assert that their opinions on matters of biology not only are vlaid, but in fact trump those of actual biologists.

doppelganger said...

"Agreement to only discuss universal concepts in a certain vocabulary, is a childish way of establishing your credentials."

Interesting. I had my car worked on earlier this week and my mechanic was explaining what he had done and why. He yammered on about rotors and calipers and this and that as though I should have known what he was talking about. And I would have, had I been a mechanic.
Now, the fact is that I did understand what he was talking about, but not because I insisted he use MY preferred terminology, MY preferred understanding of the material, etc., but becuase I took the time to read though my owner's manual and have read things about brakes and such over the years, and I know what the appropriate terminology is.

Point is, when my mechanic was talking to me about my car using mechanic's terminology, it never once occurred to me to dress him down for being arrogant and using those fancy auto mechanic terms. I understood that those are the terms and concepts used in the field.

Matthew S Ackerman said...

In my lab we have several people looking seriously into how introns get into the genome and the evolutionary forces that act on them. It is actually charitable to the creationist arguments to call introns junk DNA. In reality it possible to show that the majority of introns are more than just non-functional, they actually have negative effects on the organisms that possess them.

While the sequence contained in introns are discarded, mutations can arise in introns which alter splicing, and prevent a functional protein from being created. Additionally, there is likely some error rate in splicing that causes the mRNA from genes with many introns to be lost at some rate, post transcriptionally.

Because the negative effects are relatively minor, natural selection is unable to prevent the establishment of introns. The age and phylogeny of introns strongly support the hypothesis that the majority of introns have deleterious effects and are eventually purge from the genome.

Introns: not just useless, but actually (very very slightly) bad for you.

Harold said...

Having read this comment thread, JH, I must tell you that you don't come across well.

You aren't very honest. You initially posed as an "interested person", but you were just trying to set up some kind of gotcha game.

You got the best possible reception - highly knowledgeable people took the time to answer your questions in a polite and informative way.

Your response? Childish, defensive petulance and subject changing.

You may call this type of behavior "Christianity" or "skepticism". I call it old fashioned ignorance, rudeness, and dishonesty.

Doc Bill said...

Actually, John, I'm just trying to get the fuzz off the what. I could say, "That leaf is green," and we could have an ensuing conversation about whether it was light green, dark green, sea green, olive green or Mean Joe Green. However, with a spectrometer we could measure the wavelength of the reflected light, determine that it was 510 nm and agree that it falls within what is known as the "green part" of the visible spectrum.

Like the visible spectrum, biological evolution is an observed fact. The modern theory of evolution attempts to elucidate the mechanism of evolution. Since you are skeptical of the theory, John, what aspect of the modern theory of evolution would you like to discuss in order to articulate your concerns?

I find introns fascinating from the standpoint of the genome's tolerance of "errors," akin to the roads around here: patched, potholed and occasionally you lose a tire, but still able to get you from A to B.

Harold said...

I should also add something obvious here.

Individuals who are genetically related tend to look alike unless something in the environment changes their appearance.

Identical twins, who have approximately exactly the same genome, tend to look like each other.

First degree relatives tend to look like each other.

This in itself doesn't rule out some role for non-coding DNA, as non-coding DNA is also shared between the genetically related. However, it is worth noting that mice who have large amounts of non-coding DNA deleted from their genome have normal mouse appearance. The evidence probably favors a major role for expressed genes in the development of morphology.

Your son looks like you because he is, for better or for worse, closely genetically related to you.

For an example from another species, puppies born to a British bulldog mother are very likely to have some morphologic features similar to those of the mother, even if the father was of a different-looking breed.

Harold said...

"There you go again, you repeat the very same error you're trying to disavow. You don't know why it is so long, you just presume it's longer than in needs to be because you are unaware of any other possibility. "

Outrageous. You deliberately create a straw man right from the beginning.

The introns the author was discussing are longer than they need to be for the specific function of alternative splicing, which is what the author was discussing. No-one said they are "longer than they need to be" in some vague, generalized way.

Since you were forced by your overwhelming emotional biases to mis-state the argument you attempt to respond to, the rest of your verbose, incoherent post is irrelevant.

Your very verbosity is a defense mechanism, as you assume that due to the length of your comment, no-one will be able to tear it to shreds piece by piece. But someone probably will.

SWT said...

Who know how many other non-coding functions might be there, but if you keep insisting its junk, we'll have a slower time discovering these things, and that would suck if these other functions have medical significance!


1) How many of the fellows of the DI are actually doing research in this area? Please point me to their publications on this topic. I'm at a university, so subscription walls are often not a problem for me.

2) How many of the functions identified for non-coding sequences have been found by design advocates regardless of their affiliation with the DI? Again, please point me to their publications on this topic.

3) How do the answers to 1) and 2) compare with the number of functions found by biologists who accept the current mainstream theory to explain biological diversity?

Mark said...

While looking through Mr Scordova's post, one question comes to mind; is there any other topic (other than evolution) on which unqualified lay people (or at least those with no relevant training or expertise) feel the need to write so extensively and expect to be taken so seriously?

John Hansen said...


Thanks for the criticism. One of the reasons I like going on web sites where a lot of people disagree with me is it gives an opportunity to see problems with communication. I don't know where you pick up that I am interested in some kind of gotcha game. I don't know where I show myself to be defensive, petulant or dishonest. I fully admit to sometimes expressing myself in a verbose and clumsy manner. I, like most people, wish I was a better writer.

I fully admit to changing the subject sometimes abruptly, because something somebody says sparks my interest more than the main point which I am getting bored about.

I fully admit to being ignorant about genomics. But I stand by being an "interested person". Being "interested" does not mean I don't have some initial biases and even antagonism. But, I do assume that almost everyone who posts here has a goal or arriving at objective truth - whatever position they come from.

I am most definitely a committed Christian. Let me try to make this point by analogy. The type of preaching that turns my stomach is self righteous, self congratulations. The preacher says, "The great unwashed do < fill in sin here > and speak like < fill in mild bad language here>, we do not do that here". The people in the pews get told how righteous they are. They feel good about themselves.

Now, sometimes I think an analogous mindset may infect scientific discussion sometimes. Respected scientist A says, "The ignorant fools keep pursuing < fill in outside of mainstream idea here>, and use vocabulary < fill in not quite formally defined term here>, we do not do that hear" The people in their labs are told how scientific and educated they are. They feel good about themselves.

I think our distinguished host is against that type of behavior, so I don't blame him, but I think his dismissive attitude about certain people promotes that type of behavior. Its too bad because the labeling of "interested but ignorant" people as "ignorant and dishonest" people shuts down communication, and prevents learning.

I would appreciate your thoughts on this. Sorry for going on so long.

harold said...

Yes, finance and economics, at a minimum.

harold said...

I may have over-reacted. I was annoyed because you got good answers to a highly specific question, and came back with something about how it didn't convince you of "Darwinism". But your original question was more or less about the specifics of the development of morphologic features, with the implication that you were wondering in non-coding DNA might be involved. You got very good answers to that question, and came back with something about how Belgian Blue cattle, which were introduced merely as an example of a strong single gene effect on morphology, don't convince you of "Darwinism".

Also, Doc Bill told you EXACTLY what scientifically educated people mean when we talk about biological evolution...

modern theory of evolution adequately explains the diversity and relatedness of life on Earth.

This is EXACTLY what we mean. That's "adequately", not "perfectly". "Darwinian" is a term that is sometimes used, but it is ambivalent. "Darwinism" is a term that is almost never used except in the context of denying or insulting science, and has no valid use.

I strongly respect your right to live and believe as you see fit, but I do prefer it when people who disagree with me - something I don't have a problem with - avoid distorting or misrepresenting what I am actually saying.

Davis said...

Yes, but recent events have shown most economists, unlike biologists, to be clueless...

Davis said...

Shady Sal:
"You don't know why it is so long, you just presume it's longer than in needs to be because you are unaware of any other possibility."

You're simply lying, Sal.

He showed you that we are well aware of other possibilities with evidence. He chose nature's evidence from the chicken, but there's far better evidence that I (and presumably Steve) am aware of.

"The fact is we really don't know whether the " That copy of the coded instructions is often far, far longer than it needs to be."

The fact is that we really do know. cDNA transgenes (even from humans) are used to rescue null mutant mice quite often.

I'm betting that despite your posturing and pretense of superiority to working scientists, you don't have a clue about this.

Arthur Hunt said...

"Search algorithms of AS forms in a variety of Arabidopsis databases showed they contained an unusually high fraction of retained introns (above 30%), compared with 10% that was reported for humans"

Sal, with all due respect, you don't know at all what this quote means. (Trying to explain - this isn't saying that 30% of all Arabidopsis introns are retained in some sense, or that 30% of all transcripts possess retained introns. It means that 30% of all AS events involve retained introns. And it's quite likely that this reflects sloppiness or errors in splicing, rather than function for the retained intron.)

In the case of ncRNA, the DNA is longer than it needs to code proteins because it is creating NON-coding RNA's. Duh! Who know how many other non-coding functions might be there, but if you keep insisting its junk, we'll have a slower time discovering these things, and that would suck if these other functions have medical significance!

Utter rubbish. I was at the RNA 2010 Meeting last week. This is the international venue for researchers who work on ncRNAs, spolicing, AS, etc., etc. And guess what - the ID vanguard was MIA - not a single, solitary soul from the DI or Biologic Institute was there educating the rest of us poor RNA scientists about the functions of non-coding RNAs.

And guess what else - lots and lots of scientists are looking at these things, and have been for, oh maybe 30 years or more. And they have found more medical applications than the ID vanguard will ever uncover. Ever.

Lenoxus said...

The IDist 'junk' argument as applied to another science:

If you ask any astronomer whether there's life on the Moon or Mars, chances are she'll say "probably not". By definition, this means that astronomers' minds are closed to the possibility.

Look, astronomers, just because we haven't found life on them so far doesn't mean that they're uninhabited! The only reason that we haven't found life on those bodies is the close-minded assumption that there isn't any. Since it is, in fact, quite possible that those places are teeming with life (in areas we haven't explored, or in forms we haven't yet recognized as living), this bias is the only possible explanation for astronomers' refusal to admit that Mars and the Moon do in fact have life!

(And won't we be in some trouble if that life turns out to have beneficial effects we had been overlooking for all these years. Or, worse still, detrimental ones!)

Arthur Hunt said...

Um, spolicing is what we study after a few rounds.

Sorry 'bout that.

RBH said...

I've sent an email to your yahoo.com address.

Olorin said...

There seem to be two reasons that ID creationists love "junk DNA".

First, they claim to have predicted functionality for it, accusing evolutionist of dropping the ball for a long time. But, (a) they haven't done diddly squat to investigate or even propose any functions; (b) their prediction would require that all junk DNA have a function, which is a Herculean task---almost like proving a negative; and (c) I'd not be surprised that some mainstream biologist actually found a function for Ohno's "junk" before the creationists first "predicted" it; does anyone know?

Second, because creationists predict functionality, they assume that, ipso facto, evolution predicts (i.e., requires) the opposite--- that junk DNA be functionless. That is, they assume a false dichotomy. Without exposing that fallacy, every new function found for this DNA falsely appears to be a point in their favor.

Davis said...

…and more importantly, not a single one of those working scientists was convinced that ID is correct by producing the data the ID movement claims vindicates their position.

How can the ID movement be so much smarter than working scientists while being so much lazier?

Mattthesk8ter1988 said...

Because, according to them, God is on their side, and he makes it happen. Since it's all perfectly designed, there really is no need to explore. The design will show itself once our kind has been purified of evolutionist illusions.

Actually, I am just making stuff up. Though I wouldn't be surprised if some Idists actually believed in the rubbish I wrote above.


John Farrell said...

Can you send the links? Fascinating.

Doc Bill said...

Thank you, harold, Delta Pi Gamma forever and a kegger on Friday. My place!

I'm going to guess that Hansen balks at biological evolution being a fact, but I'm captive by my "worldview" on that one.

However, my question to Hansen would be this. Did you have a direct relative alive during the reign of Elizabeth I? One could answer Yes, No or Don't Know. The answer would be Yes, obviously.

Now, Hansen, answer this. Did you have a relative alive in 1000BC? 2000BC? 5000BC? 10,000BC? 50,000BC?

I'm curious as to how Hansen would answer those simple questions. The answer is obvious, of course.

I had my DNA tested by National Geographic and my ancestors inhabited Europe about 60,000 years ago. I'm pretty chuffed by that.

John Hansen said...

Let me try to clarify the remark about Belgian Blue cattle. Please reread what I wrote. It was not a challenge, it was advice. All I was trying to say, is, if you believe that ID is a scourge and you want to get rid of it, you might not want to use Belgian Blue cattle as an example of anything. Being a animal from animal husbandry, it plays into all of the IDist type arguments against evolution and may distract more than it illustrates. I wasn't arguing anything.

Doc Bill said...

John, animal husbandry is not "intelligent design creationism." It's regular old evolution. The farmer doesn't manipulate the genome. The farmer just mates the livestock. Evolution, regular old evolution, does the rest.

For the farmer to be an "intelligent design creationist" he would have to manipulate individual base pairs in the genome to get the results he desires, and it wouldn't take him many, many generations.

However, the farmer just mates big and strong to big and strong and lets ordinary evolution do its thing.

ID isn't a "scourge," rather, it's simply WRONG. Nobody wants to "get rid" of ID because it's non-existant to begin with. John, how many BS Biologists graduated in the US alone in 2010? Something like 50,000. How many ID creationists graduated? Zero. What's to "get rid of?"

Rather than arguing a point of contention about the Modern Theory of
Evolution, John, it appears that you were simply cursing the darkness.

Get a candle.

John Hansen said...

Doc Bill, I have to admit your thinking process is beyond me. What on earth would you mean by such a foolish inquiry? I really don't know how anyone could be quite as contemptuous of others as you seem to be. I feel sorry for you.

Doc Bill said...

Well, John, I'll tell you. The answer is YES in every instance. In fact, you had a relative living 6 million years ago, 65 million years ago and 600 million years ago. Answering the question would be your acceptance of common ancestry and descent with modification, in essence the outline of the theory of evolution. I'm not surprised you failed to answer. I don't think you'll commit to any position.

As for being contemptuous of others, once again you are completely wrong. I do not hold those who are willfully ignorant in high regard and I am quick to mock them. I am contemptuous of those ideologues who hold positions on our state board of education (Texas) and I work diligently to get them replaced.

John Hansen said...

Doc Bill,

In the case of Belgian Blue cattle, animal husbandry is not just plain evolution, because an animal which develops a mutation that should cause it to die out ( not to many wild animals out there that regularly have caesarian deliveries ) instead survives.

John Hansen said...

I did not answer because the question was stupid and it was painfully obvious what answer you were looking for. I'd do find you interesting though. What is your worldview? Are you a TE like Steve, are you and agnostic? an atheist? a materialist?

You don't have to answer, I just would like to know where you are coming from.

Doc Bill said...

So how far back do your ancestors go, John? Do you come to a screeching halt at October 26, 4004 BC or, like me, do you go back 3.5 billion years when Grandpa/Grandma joined lipids around a black smoker deep in the ocean and feasted on iron, sulphur and carbon dioxide?

Do you understand what Steve wrote about Factor VIII and the chicken? Do you know what that implies?

As for a worldview, it's irrelevant in a scientific discussion. I do have a fondness for curry, guacamole and bold coffee.

Efren TS said...

To answer your question, he understands none of what has been painstakenly shared with him. That is why he is trying to change the discussion into "evilution is your religion!"

Doc Bill said...

Honnnnnnkkkkkkkk! Wrong answer, John! Humans aren't magical. They're just another selective pressure. Over a period of 15,000 years or so dogs and cats adapted to an environment that gave them food, shelter and protection: living with people. Even with your sacred cow you're dealing with random mutation and selection.

People make a semantic distinction between artificial selection and natural selection, but it's the same process under the hood. Besides glass, what's the difference between artificial and natural insemination? How about 4-Hydroxy-3-methoxybenzaldehyde and natural vanilla?

Suppose Hurricane Alex is coming and I put some of my cows in a barn and leave some in the field. The ones in the barn survive and the ones in the field are killed by a flying Volvo. Aside from the Volvo, is natural evolution somehow interfered with? Suppose the barn blows down and kills the cows, but the ones in the field dodge the Volvo? (get it, "dodge" the volvo? Never mind) Does Evolution care at all? No, it doesn't.

How about Craig Venter creating Synthia complete with poetry built into her DNA and other bits snipped out? Did Venter mess with evolution? Arguably, yes, because he directly manipulated the genome but the new organism is now subject to evolutionary processes.

SWT said...

Suppose the barn blows down and kills the cows, but the ones in the field dodge the Volvo? (get it, "dodge" the volvo? Never mind)

As much as I like the rest of your post, I'm really not interested in your Saab story here ...

John Hansen said...

Efren TS,

Why do you assume that someone who believes ( admittedly mostly by faith ) that the modern theory of evolution CAN'T adequately explain the diversity and relatedness of life on Earth has inadequate brain power to understand what has been said.

What Steve said about the introns is very easy to comprehend. For one thing Steve seems to be an excellent teacher. But I am afraid that if I try to explain the obvious inferences from this, in my ( not approved by Doc Bill ) jargon, I will be chastised again for some grievous offense.

So you make the assumption that because the introns are of different size it implies that the large size of the human genome can't have a function or else the same functionality can't even be approached in the chicken gene. This is not a difficult concept. You further imply that this means the existence of introns which match each other in various genes make common descent the best explantation for the observed facts. These are not difficult concepts to grasp.

Doc Bill, I only want to know what you believe because I feel that we have been speaking past each other. Every time I say something, you project beyond what I want to say by assuming me to have some motivation I don't, pose some dumb question, and continue to mock. I don't understand what you are trying to prove. You are in sharp contrast to Harold who politely offered his opinion, he did not tell me I was a moron, just pointed out that I came across badly.

My only agenda in asking your belief system was to figure out something about where you come from in discussions. It was not ( as Efren TS contributed ) to pivot to any "evolution is your religion" type argument. I seriously am not trying to lay any rhetorical traps here. I enter into discussions mostly with the hope of learning something - even when it is a discussion with someone I disagree with, or someone who speaks with hostility.

Efren TS said...

Why do you assume that someone who believes ( admittedly mostly by faith ) that the modern theory of evolution CAN'T adequately explain the diversity and relatedness of life on Earth has inadequate brain power to understand what has been said.

Whether you possess adequate brain power is a separate issue from whether you understood what was laid out for you. As far as the second issue, I don't think you have the foggiest clue what they are talking about because any question they ask of you for you to demonstrate your understanding or explain the data from your perspective is met either with silence, complaints because they insist you speak in the common language of the scientific field, or an attempt to change the subject. If you had the goods, you would have wowed us by now.

Davis said...

John Hansen: What on earth would you mean by such a foolish inquiry? I really don't know how anyone could be quite as contemptuous of others as you seem to be.
John, you seem to be in need of an irony meter given your juxtaposition of those two sentences. I would have loaned you mine, but it blew up upon reading them.

John Hansen said...

Sorry for not responding about this earlier, but Doc Bill IMHO this is just a wrong statement. You can't count conscious decisions of Human Beings as Evolution. Then everything is Evolution even if God did it by miraculous intervention. Intelligent manipulation of the "selection" part of evolution is the same thing as intelligent manipulation of the "variability" part of evolution. It is conscious decisions to manipulate the course of animal development. It is design. Did Mendel allow his plants to just evolve naturally. If he did, he would not have been able to answer his questions.

Do you really want to define Evolution so sloppily that it includes all things? Then you really don't have a falsifiable theory. So IMHO I don't think Evolutionists would want this to be defined this way. I could be wrong, of course, and am open to correction if Biologists want to define it this way.

tuibguy said...

Re: (1) and if they aren't doing any research into this area, what is stopping them? A bad attitude of self-defeatism by non-ID researchers? I have a feeling that it is because they really don't want to do any research.

Davis said...

It's because they have zero faith that their hypotheses will stand up to real hands-on research in the lab or in the field.

It's a complete fraud.

Ash said...

And it's quite likely that this reflects sloppiness or errors in splicing, rather than function for the retained intron

No, since in some cases the retained introns are likely to yield
functional proteins in others not.

HornSpiel said...

I am glad to see the results of your research.
Thanks for sharing it.

HornSpiel said...

Thanks Steve for these explanations of "junk DNA."

In future posts I hope you will address a) how introns came to exist in the genome (what was the mechanism), and b) why it exists in the quantities that is does.

However I find it strange that the existence of this junk DNA should cause any problems for IDists. If we think of DNA as part of an information transmission system. It might be useful to think of the introns as Noise DNA and exons as Signal DNA. Due to the second law of thermodynamics , all physical information transmission systems need to cope with the introduction of noise. Apparently the DNA system can cope with a lot of it.

Any scientist (especially one who specializes in information systems) should not be surprised to find noise in the DNA signal a well as mechanisms for filtering it out.

Now to explain the low S/N in DNA: I would hypothesize that there is a component in the transmission system that produces intron noise. I would also predict that it was more efficient or cheaper or easier to make or enhance an error correction mechanism that filters out the intron nose after it has slipped into the DNA, than to prevent the introns from getting in or to fix the noisy component.

I would be interested to see how my predictions compare with the evidence.

Arthur Hunt said...

No, since in some cases the retained introns are likely to yield
functional proteins in others not.

References, please.

Nicholas Hibbeler said...

"Among the 25 are so introns are two very large ones"

Should be "Among the 25 or so introns are two very large ones"