Uncommon Descent Serving The Intelligent Design Community

Review: The Myth of Junk DNA

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

Myth of Junk DNAJonathan Wells’ The Myth of Junk DNA, is a well-written book that manages to accomplish two separate tasks: to silence the Darwinists who had claimed that recent genomic discoveries supported their dystopic version of The Signature in the Cell; and to bring all of us up-to-date on the breath-taking mysteries being decoded from this most ancient script.

He begins by picking up where Stephen Meyer left off, telling us that within each cell is this memory chip, this software program that directs everything we are and ever meant to be. When Watson and Crick decoded the DNA, there was great expectation that soon we would find the gene to every talent and attribute we had ever wished we had been born with. Sci-fi was filled with stories about a DNA pill that would turn you into a concert pianist, a ballerina, or a nuclear physicist, because the genes for all these talents could manually remedy what evolution had denied you. Soon a billion-dollar government program was begun to decode the human genome, after which, it was widely touted, we would find the cure to cancer and the common cold. The three billion base pairs of the human genome, it was thought, would hold genes stacked up cheek-to-jowl, together encoding some 100,000 different proteins. We knew how to count genes because we had already decoded the way the cell made protein, first by making RNA copies of the DNA, and then sending the RNA to the ribosome factory, which could identify the unique “start” and “stop” codes among the 64 different 3-letter “words” of the RNA software that marked the beginning and end of each gene.

After a decade of work and to everyone’s great surprise, the human genome project found only 10,000 such start-stop pairs, suggesting that you and I are made out of fewer proteins than an amoeba! Furthermore, over 90% of the missing genes were DNA that apparently did nothing. Much of this “dark matter” was in long “stutter repeats” that couldn’t even make a useful protein if you inserted the start and stop codons yourself. All that work, and nothing to show for it! Neither cancer nor the common cold was cured, and instead an even greater mystery was uncovered.

Read more…

Comments
The “Darwinian position” is that even things that happen rarely are quite probable given enough opportunities.
I don't know if that's the Darwinian position or not. It doesn't make much sense to conduct trials without an end in sight, without a goal or target, does it? Take the trilobite eye. It's hardly Darwinian to say that the trilobite, given enough opportunities, would eventually evolve the trilobite eye is it? Rather the Darwinian reasoning goes, there's the trilobite eye. ergo, there must have been enough time and trials for it to come about by Darwinian means. It hardly matters whether such a thing is even possible.Mung
July 2, 2011
July
07
Jul
2
02
2011
12:57 PM
12
12
57
PM
PDT
Yes, but it was clear, surely, that I wasn’t using it [Dawkins' WEASEL program] as a model of evolution,
ok Elizabeth, let's see if I understand you. You do think Dawkins' WEASEL models evolution, correct? But in this thread you were not using Dawkins' WEASEL program as a model of evolution. Do I have it right so far?Mung
July 2, 2011
July
07
Jul
2
02
2011
10:30 AM
10
10
30
AM
PDT
Mung:
Yes, but it was clear, surely, that I wasn’t using it [Dawkins' WEASEL program] as a model of evolution, You can’t be serious. I will go back and harvest your comments if necessary. Dawkins’ sim includes all the relevant aspects. Reproduction Variance Selection What exactly is it about Dawkins simulation that did not model Darwinian evolution?
In that post, Mung!!!!! Sheesh. Yes, I think the WEASEL program models those three evolutionary processes. But I asn't talking about that, I was attempting to explain why, under a Darwinian hypothesis, junk DNA could arise.
I have to disagree. The Darwinian position is that anything can happen, no matter how improbable, because improbable things happen all the time.
No. The "Darwinian position" is that even things that happen rarely are quite probable given enough opportunities. Which is precisely why Dembski attempt to refute the position by saying that even given all the events in the universe, the thing is improbable.Elizabeth Liddle
July 2, 2011
July
07
Jul
2
02
2011
03:47 AM
3
03
47
AM
PDT
p.s. There has been no evidence that there is a limit to improbable things.Mung
July 1, 2011
July
07
Jul
1
01
2011
09:08 PM
9
09
08
PM
PDT
But the default position of the Darwinists is that it is junk because that fits best with their Darwinian hypothesis about the world.
I have to disagree. The Darwinian position is that anything can happen, no matter how improbable, because improbable things happen all the time.Mung
July 1, 2011
July
07
Jul
1
01
2011
09:06 PM
9
09
06
PM
PDT
Chris said: "To dismiss *any* part of our DNA as “junk” is an argument from ignorance (or even an “evolution in the gaps” argument!) and it is made for purely non-scientific reasons. As “The Myth of Junk DNA” demonstrates, we have found function in ALL of the various categories of Junk DNA: including the so-called “pseudogenes”. And remember, research in the area of non-coding DNA has been restricted by the prevailing attitude that “it would be folly in such cases to hunt obsessively” for functions in it. So scientists should merely be saying: We don’t yet know what most of our DNA does. Will we keep investigating." Excellent point Chris. And if anything, it seems the evidence lies on the side of function as opposed to junk. But the default position of the Darwinists is that it is junk because that fits best with their Darwinian hypothesis about the world.tjguy
July 1, 2011
July
07
Jul
1
01
2011
08:44 PM
8
08
44
PM
PDT
I recently received a copy of Jerry Coyne's Why Evolution Is True. In the index there is no entry for dysteleology. In the index there is no entry for junk dna. In the glossary there is no entry for dysteleology. In the glossary there is no entry for junk DNA. The closest I can see is in the index under DNA: dead genes and And under the entry for genes: dead (pseudogenes)Mung
July 1, 2011
July
07
Jul
1
01
2011
08:27 PM
8
08
27
PM
PDT
Yes, but it was clear, surely, that I wasn’t using it [Dawkins' WEASEL program] as a model of evolution, You can't be serious. I will go back and harvest your comments if necessary. Dawkins' sim includes all the relevant aspects. Reproduction Variance Selection What exactly is it about Dawkins simulation that did not model Darwinian evolution?Mung
July 1, 2011
July
07
Jul
1
01
2011
06:48 PM
6
06
48
PM
PDT
Yes, but it was clear, surely, that I wasn't using it as a model of evolution, just as a mental picture of what a string that was still half junk but had a few words in it that had been selected by some fitness function (say one that gave fitness points for any English word). It was just an image. Don't use it if it doesn't help.Elizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
04:44 PM
4
04
44
PM
PDT
Liz: "maybe still a fair bit of junk (imagine WEASEL half way through)," The example you give is an intelligently designed program programmed to model non-intelligently designed Darwinian evolution that Darwinian evolutionists concede does not model Darwinism evolution because of its design, is an example of accumulation of Junk dna via non-design?junkdnaforlife
July 1, 2011
July
07
Jul
1
01
2011
04:33 PM
4
04
33
PM
PDT
Go have a beer. I’m off to find my cat.
I don't drink beer. Can I have a cider instead? My cat's sleeping on top of the DVR where it's nice and toasty. Do you know what a vacuous claim is Dear Lawyer? It's saying that Design doesn't explain something without any statement of what Design consists of. So if you want to trade misrepresent for meaningless it's ok with me.Mung
July 1, 2011
July
07
Jul
1
01
2011
12:16 PM
12
12
16
PM
PDT
I have to disagree that the DNA being junk is the null hypothesis prima facie. It is now considered the null by many due to the knowledge about its origin. I would expect that when the DNA was initially discovered the null hypothesis was that most of it had a function.myname
July 1, 2011
July
07
Jul
1
01
2011
12:02 PM
12
12
02
PM
PDT
OK, now my turn to be the lawyer! Mung, I did not even attempt to represent (or misrepresent) ID. That's why I didn't use the term. I said "Design". I do not think Design is a good explanation for nexted hierarchies, because human design hierarchies tend not to be deeply nested. I was not talking about "ID". I don't actually think IDist inferences are sound, but not because I don't think it accounts for nested hierarchies. Design could be implement within common descent, for instance, by some "frontloading" mechanism. That's not how human design works, but it could well be how celestial Design works. I'm just saying that the specific pattern of nested hierarchies is not well explained by a Design hypothesis, e.g. the hypothesis espoused, for example, by baraminologists. Go have a beer. I'm off to find my cat.Elizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
11:47 AM
11
11
47
AM
PDT
Elizabeth Liddle:
But Design, to me, doesn’t seem like a good alternative contender, because it doesn’t explain the nested pattern.
Please hearken back to a previous discussion about when ID theory and evolutionary theory do and do not collide. afaik, design theory does not even attempt to offer an explanation for the nested hierarchy. So saying some other explanation is a better explanation than the one offered by design is just ludicrous. So again, you misrepresent ID by suggesting it offers a competing explanation for some phenomenon what it does not even address. Please stop. When in doubt, ask.Mung
July 1, 2011
July
07
Jul
1
01
2011
11:35 AM
11
11
35
AM
PDT
And I really am going to get that response back to Upright Biped this weekend….
That thread is now closed to comments.Mung
July 1, 2011
July
07
Jul
1
01
2011
11:30 AM
11
11
30
AM
PDT
Mung:
ok, so an interesting question is, how did junk dna get it’s start? How did it ever come to gain a foothold in any genome? Is it common to all life, and if so to what extent?
Well, as you pointed out above, "junk" is best set up as the null :) In other words, if we can find a function for a sequence, we can reject the null of "junk", but if we fail to find a function, all we can do is "retain the null" - we cannot conclude the null is true. It is very hard to see how you could tackle the issue the other way round. So it's a very poor flagship for Darwinian "predictions", and I think Dawkins( (if it was he) was silly to put it further. Predictions are far better expressed as H1s rather than H0s. In fact, you could argue that Dawkins is making a "Darwin of the gaps" argument! Not a good idea (which is why Dembski sensible casts Design as H1, heh). But the expectation would certainly be, under a Darwinian scenario, that junk would tend to accumulate, and may even have been present in the earliest proto-genomes. The reason is because DNA isn't very resource-consuming. Sure you need stuff to make it with, but not nearly as much as you need to make a continuous supply of proteins, for instance, because once it's made, it is pretty cheap to maintain, so having extra footage isn't going to cost the organism much. So if there's no penalty at phenotypic level for having a extra footage, then there's no selective pressure to delete stuff that isn't doing any harm, even if it isn't doing any good either. As for where it comes from: well, obviously we know very little about the very earliest genomes, so this is pure speculation, but it's possible (if abiogenesis is possible at all :) that the earliest DNA molecules were mostly random sequences of bases, but that one or two fortuitously happened to code for a protein that fortuitously happened to increase longevity (yes I know, RNA, ribosomes tRNA yadda yadda, but I'm not going there right now). So that genome gets replicated more often than non-coding genomes. If a mutation happens to that bit of sequence, if it results in a less effective protein, that mutation will be "selected out", but if, by chance, it selects a better one, then it will be reproduced more often etc etc. However, mutations that happen in the restof the sequence won't result in differential reproduction, so they will just accumulate, until one of them hits a lucky protein. Fast forward .... We now have populations with lots of coding sequences, maybe still a fair bit of junk (imagine WEASEL half way through), then one of the coding sequences that happens not to be important in the current environment gets broken, or a virus comes along and leaves a bit of its DNA in your sequence, or a bit of junk sequence gets duplicated (repeated sequences very common in alleles, so it seems that the replication process lends itself to mistakes like mistakes like mistakes like this.) Leaving more junk. Fast forward again, and we have lots of remnants of old genes, no longer functional, ERVs, repetitive bits of code that never got weeded out because once a bit of code does nothing, further mutations to it, including repeats, don't have any selectable phenotypic effects. And so, you end up with lots of "junk DNA". So the apparent presence of junk sequences is certainly in accord with Darwinian theory, and it would indeed be surprising if there were none. But as you can't prove a null, it's a very poor prediction to cite as evidence for Darwinian theory. And if IDists can find a use for every single sequence, then Darwinian theory is in trouble (reject the null!) We'd certainly have to look for reasons why it should not be there (for example, it's possible that it's more "expensive", phenotypically, to maintain than we currently think). But that would still be weird - it would mean all those virus sequences all proved functional. Perhaps the Designer uses Designer Viruses! As for your last question: I don't know, but I don't think anyone does, for the reasons given above. Null hypotheses are the very devil to support :)Elizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
10:27 AM
10
10
27
AM
PDT
Mung:
Elizabeth:
This suggests that the way that evolution works is largely by finding (“finding”) new uses for existing proteins rather than new proteins.
So what happened to the old use? Not needed any more? So the protein went on to do other things? How does that happen?
Well, as I said, "this suggests", not "this is because". But I can tell you where we'd look for answers. First of all, it wouldn't mean that the old use "wasn't needed any more". It could mean that the gene that coded for it was expressed under more than one condition (e.g. to in response to a developmental cellular signal that says "we need a bit more ear stuff here" and also, elsewhere to a signal that says "we need a bit more nose stuff here". A change to the regulatory genes might mean that in one individual, more nose got made, even though the same amount of ear got made. And it might even happen that organisms with long noses and small ears were better adapted for survival in their current environment, and so the old ear & nose protein finally emerges just as a nose protein. Silly example, but you can extrapolate to something more sensible.
If proteins descend from other proteins by descent with modification shouldn’t there be a nested hierarchy? If not why not?
Interesting point. There may be. But Crick was mostly right about the information flow direction (DNA -> RNA -> protein) so phylogenies based on proteins alone are more likely to be blurred - you can deduce a protein (or at least the sequence of amino acids) from a DNA sequence but you can't deduce a DNA sequence from the sequence of amino acids, because some amino acids are coded by more than one codon. Also, coding sequences tend, obviously, to be highly conserved, so you often get more phylogenetic information from non-coding sequences (especially "junk" sequences!) because they can accumulate mutations without phenotypic effects.
If not, why is a nested hierarchy a prediction of Darwinism?
Well, it's not, exactly. Darwinism is an explanation of the observed nested hierarchies. Linnaeus's hierarchies (which he mostly got right, if not entirely) preceded Darwin's theory - it was a non-random pattern requiring an explanation. But Darwinian evolution was not the only possible explanation. Lamarckian evolution was another contender (and even Darwin thought that Lamarckian mechanisms might be responsible for the variation that is subject to natural selection...um... I mean for heritable differential reproductive success). It still isn't. But Design, to me, doesn't seem like a good alternative contender, because it doesn't explain the nested pattern. Most (human) Design lineages are highly cross-referenced.
Elizabeth, it does seem like you raise more questions than you answer when you post your answers to questions.
Yes indeed. A lovely example of a nested hierarchy, in fact! But one not readily explained by Darwinian mechanisms :) And I really am going to get that response back to Upright Biped this weekend....Elizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
09:57 AM
9
09
57
AM
PDT
ok, so an interesting question is, how did junk dna get it's start? How did it ever come to gain a foothold in any genome? Is it common to all life, and if so to what extent?Mung
July 1, 2011
July
07
Jul
1
01
2011
09:42 AM
9
09
42
AM
PDT
lolMung
July 1, 2011
July
07
Jul
1
01
2011
09:37 AM
9
09
37
AM
PDT
Mung:
God is love. Jesus was the expression of that love. That’s not a matter of logic and reasoning. It’s a person, demonstrating love.
I'll still bat for that team. With the odd caveat.Elizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
09:35 AM
9
09
35
AM
PDT
SRI = RSI. lolElizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
09:33 AM
9
09
33
AM
PDT
to = too oops. Now you know why my code is buggy.Elizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
09:32 AM
9
09
32
AM
PDT
Mung:
I also write software that makes my job and the job of my team easier. Why do it manually if you can get a computer to do it!
I hear you. I'd never coded anything until I hit my half-century, but boy has it been useful since! The way I started was I had a really tedious job to do, and it was going to take me about eight weeks and give me an SRI. So I figured if I spent seven weeks learning to code, I could use the eight to write a program that would do it in about an hour! And I did it.
So I do have to think in a certain way to be good at what I do.
Yes, me to. But we seem to have different operating systems :)Elizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
09:32 AM
9
09
32
AM
PDT
Mung, When I was in grad school in physics, we all posted cartoons on our doors. One door had a picture of fellow standing underneath a car on a lift, messing with the muffler or something, and he's answering the owner of the car. "Well I wanted to do Quantum Mechanics, but I must have made a wrong turn somewhere" I tell people I started out wanting to be a physician but had some sort of difficulty with the spelling...Robert Sheldon
July 1, 2011
July
07
Jul
1
01
2011
09:31 AM
9
09
31
AM
PDT
Mung:
Can you quote from your book how they reasoned in this way and came to the same conclusion?
Well, I'll see if I can dig it out. It was mostly fairly heavy biochemistry. And may still be on one of our cardboard boxes :( But I'm fairly sure I've seen it on the shelf in recent times, so I will take a look.
But why could regulatory genes not code for proteins that control the expression of other proteins?
A regulator gene, regulator, or regulatory gene is a gene involved in controlling the expression of one or more other genes. A regulator gene may encode a protein, or it may work at the level of RNA, as in the case of genes encoding microRNAs.
Now if it is in fact the case that regulatory genes can and do encode proteins, how does it follow that there must be non-coding DNA?
You know, I guess you have a point there. Perhaps non-coding DNA really is useless junk. Seriously, you do have a point. Perhaps you are right that early on, people postulated that regulation was done by all done by suppressor proteins. I will double check :)
It doesn’t. Another non prediction of evolutionary theory.
Well, no. That would be (if it was) a non prediction of biochemical theory, or even genetic theory. I'm just aware that throughout my (earlyish) life, people talked about what DNA did apart from code proteins, because there must be some mechanism for determining which proteins should be produced. i.e. which genes should be expressed. It was fun being a nerdy teenager in the sixties! And the general principle (Crick's "Central dogma") was that the information flow goes DNA-> RNA -> Protein rather than the other way round. But in fact of course, that is not correct, because as you point out, proteins do play a role in regulating gene expression. Thanks for keeping my toes to the fire :)Elizabeth Liddle
July 1, 2011
July
07
Jul
1
01
2011
09:28 AM
9
09
28
AM
PDT
You are a lawyer aren’t you?
Actually, no. I'm an engineer, of a sort. But I probably could have been a lawyer. Can you believe I started out wanting to be a doctor? Ah, how life gets in the way of plans :) I got my start in electronics in the Navy. I work in the mobile telephone industry and have since 1985. Mobile telephone switches have to be told what do do, and I basically write the stuff that tells them what to do. I also write software that makes my job and the job of my team easier. Why do it manually if you can get a computer to do it! So I do have to think in a certain way to be good at what I do.Mung
July 1, 2011
July
07
Jul
1
01
2011
09:22 AM
9
09
22
AM
PDT
What’s a girl to do?
Have a beer. Show that cat some loving. Set off a few fireworks in celebration of American independence. Go yanks! :)Mung
July 1, 2011
July
07
Jul
1
01
2011
09:13 AM
9
09
13
AM
PDT
Elizabeth, there is no ‘convincing’ you of anything for you ignore evidence that disagrees with your ‘chosen’ worldview, instead of follow the evidence to the truth.
It wasn't easy, but I think I convinced Elizabeth of a thing or two. So I think it can be done. I think I convinced her that I am a complete jerk, for example. ;)Mung
July 1, 2011
July
07
Jul
1
01
2011
09:10 AM
9
09
10
AM
PDT
But I’m better at debating for what I think is supported by evidence and argument! If you want me back on “team Jesus” you’ll have to convince that you are right
God is love. Jesus was the expression of that love. That's not a matter of logic and reasoning. It's a person, demonstrating love.Mung
July 1, 2011
July
07
Jul
1
01
2011
09:08 AM
9
09
08
AM
PDT
Thanks mung for your continued stabs in the back. I'm building quite the knife collection.bornagain77
July 1, 2011
July
07
Jul
1
01
2011
09:03 AM
9
09
03
AM
PDT
1 2 3

Leave a Reply