The Sound of The Neutral Theory Exploding
| December 23, 2006 | Posted by Dave S. under Intelligent Design |
Silent Mutations Are Not Always Silent
“Mutations leading to identical amino acid sequences can change protein folding and function”… 12/21/06
Silent Mutations Speak Up
“Biologists have realized that the genetic code harbours a layer of information that they have largely ignored. Again.” 12/21/06
A mutation in a human gene that does not change the resulting amino acid can nevertheless change a protein’s function, according to an online report from Science. The research marks the first time that the phenomenon has been confirmed in mammals.
This time, the focus is on ‘silent’ mutations, single letter changes that were, as their name suggests, generally thought to have little impact on that gene’s instructions for making protein.
But a study published in Science this week shows that two silent mutations are nothing of the sort1. They seem to change the rate at which a drug-pumping protein folds and may help decide whether certain cancers become drug resistant.
Silent  also called synonymous  mutations arise because of the rules of the genetic code. Three chemical letters of DNA, called a codon, instruct the cell to insert a particular amino acid into the string that makes up a protein. But often several different codons code for the same amino acid.
A silent mutation is one that changes the triplet, but leaves the amino acid unchanged. “We were all educated that silent mutations should be ignored, and people really don’t pay attention to them,” says Chava Kimchi-Sarfaty at the National Cancer Institute in Bethesda, Maryland. But it is becoming clear that proteins made of identical amino acids can nevertheless behave differently.
It should be noted that synonymous (silent) mutations are an important part of the neutral theory of molecular evolution and are also an important part of molecular clock theory. If silent mutations are not so silent this handily explains why molecular clocks are such inconsistent timepieces.
One possible explanation is that ribosomes process codons at different rates when the codons differ only by a redundant nucleotide replacement. Think of the ribosome like a caulk gun producing a bead consisting of amino acid polymers that fold as they come out of the gun. If the rate at which the bead comes out changes then the shape it folds into changes as well. Another possibility is post-processing of the protein product where RNA molecules dependent on specific gene sequences alter the way the protein is processed after the ribosome finishes producing it.
Whatever the mechanism it really makes hash out of neutral theory and molecular clock theory.
Also note I’ve blogged in the past about how a design theoretic view predicts things like this. In this comment I described how the NTSC video signal evolved as intelligent designers added additional ways of encoding information to the carrier without effecting the preexisting ways and said we should look for DNA to have multiple encoding schemes one atop the other.
40 Responses to The Sound of The Neutral Theory Exploding
Leave a Reply
You must be logged in to post a comment.
Bob OH:
Ah, the evidence that an agency was around when something appeared is that something appeared.
That is usually the way it goes. Do you think that detectives look for criminals in a case when there isn’t any sign of a crime?
Bob OH:
What if the agency had nothing to do with the appearence?
Then we should be able to test whether ot not nature, operating freely, could bring about what we are observing.
Again when you have two possibilities and you rule one out…
Do you mean besides the fact that science tells us that only life begets life, ie from cells, cells?
Bob OH:
Science doesn’t tell us this:
It has & does Bob. And guess what? No one has been able to demonstrate otherwise.
Bob OH:
it hasn’t shown that abiogenesis is impossible, and indeed is working on showing how it may have come about.
Science doesn’t work like that Bob. Perhaps you should go back to school and learn about science.
Also science isn’t done via promissory notes.
And if scientists ever do observe a living organism arising from non-living matter they would have refuted a long-standing scientific truth (what I stated above).
Bob OH:
Do you have a link to the Max Planck speech? I’d like to see why he argued as he did: otherwise you’re just arguing from authority.
I will take argument from authority over your argument from ignorance any and every day.
What MP stated was based on his years of scientific research. But I could see where you would have a problem with that.
This only applies if they are the only two possibilities. I haven’t seen any demonstration that this is the case here: has anyone ruled out all possible options (e.g. some natural process that we don’t yet know about)? Until they do, as a point of elementary logic, you can’t say “not A implies B”.
A list of my publications in scientific journals. Care to show me your list?
Bob
Impressive list of publications, Bob OH. That and civility is why you can comment here without moderation. I still can’t figure out why you were never able to understand (or concede) that just about every non-specialized cell in a mycelial colony is capable of evolving asexually and spawning new colonies. What’s up with that?
Again when you have two possibilities and you rule one out…
Bob OH:
This only applies if they are the only two possibilities.
That is obvious.
Bob OH:
I haven’t seen any demonstration that this is the case here: has anyone ruled out all possible options (e.g. some natural process that we don’t yet know about)?
This debate doesn’t concern “natural” processes as both design and intelligence are natural.
Can natural processes account for the origin of nature seeing that they only exist in nature?
Bob OH:
Until they do, as a point of elementary logic, you can’t say “not A implies Bâ€Â.
Just what do you think the materialistic alternatives are?
Bob OH:
it [science] hasn’t shown that abiogenesis is impossible, and indeed is working on showing how it may have come about.
Science doesn’t work like that Bob. Perhaps you should go back to school and learn about science.
Regardless of your publications you should know that science does not set out to say that something is impossible. And you should also know that it doesn’t matter who is working on what- if someone starts looking for unicorns and mermaids are they conducting a scientific investigation, just because they are looking?
IOW a list isn’t needed- just a little common-sense.
Personally I find this demand ridiculous since it amounts to arbitrarily raising the requirements for defeating Darwinism. Back in November I had this to say: “This reminds me of the demand that every single conceivable indirect Darwinian pathway must be investigated before Darwinism can be rejected.” So why does this demand keep getting repeated?
Patrick – I think you’re slightly mis-reading my argument. My point here is that there could be a third alternative, other than evolutionary biology or ID. If so, then you can’t prove ID by dis-proving evolutionary biology. I was just trying to show that Joseph’s logic was faulty.
As for disproving evolutionary biology (as a research field), you don’t need to go through and disprove every step. I think Kuhn’s model of scientific revolutions is a good (if not perfect) model: it suffices to show that there are several unsolved problems, and that they are not solved despite a lot of effort. Then a rival paradigm can take the original paradigm’s place. Obviously it needs to be a useful paradigm, i.e. it explains most of the same things as the original, and it provides interesting and fruitful avenues of research.
Joseph – I don’t think we’re going to get anything productive in this discussion, I don’t think you’ve appreciated the points I’m trying to make, and I don’t want to get into a discussion over who has a better idea about how science is done.
Bob
Just about any argument can be pruned down to two choices- A or not A…
Bob, I got your main point but I thought you were extending it to include the position that every conceivable Indirect Darwinian pathway must be researched before a design inference could be made. My bad.
Personally I’m open to a third alternative (do you have a specific naturalistic mechanism in mind, such as the acquisition and fusion of genomes, or are you positing a rhetorical device?). In a designed system of sufficient minimum complexity where the plasticity of the language allows for some variance (chaotic systems) I would not be surprised if under certain limited conditions there could be additional emergent complexity. Doesn’t get rid of the design inference entirely and I’m sure many ID proponents would disagree with me. But it’s not like that has ever been observed…I’m just saying I wouldn’t be surprised if that turns out to be the case. So that’d be a sort of ID/Darwinism hybrid as another option.
[...] The theme of silent mutations that are not so silent has been addressed here at UD before (e.g., go here). Here’s a piece that elaborates on the significance of this recent finding: Silent No Longer: Researchers unearth another stratum of meaning in the genetic code By Ivan Amato [...]
[...] Uncommon Descent | The Sound of The Neutral Theory ExplodingDec 23, 2006 … It should be noted that synonymous (silent) mutations are an important part of the neutral theory of molecular evolution and are also an … [...]