More evidence for ID in Biology- The ribosome is a genetic compiler
The ribosome is a genetic compiler!
Think about it-
What happens to a newly written or modified computer code that has an error? All new and modified codes have to go through a compiler.
A compiler is nothing if not an editorial perfectionist!
I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free.
Biologists need to be introduced to and experience computer science.
Then this sort of discovery wouldn’t be so “shocking”.
Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids).
The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist.
Think about it-
What happens to a newly written or modified computer code that has an error? All new and modified codes have to go through a compiler.
A compiler is nothing if not an editorial perfectionist!
I bet if we were to watch we would see the compiler doing its thing right up to the point the error occurs and then spits it out much faster than if the code was OK, ie error free.
Biologists need to be introduced to and experience computer science.
Then this sort of discovery wouldn’t be so “shocking”.
Compiler- source code in, object code out. Ribosome- mRNA in (string of nucleotides), polypeptide out (string of amino acids).
posted by Joe G @ 1:14 PM
22 Comments:
At 10:52 AM,
blipey said…
which part of genetic mutation strikes you as being operated by a perfectionist?
At 11:00 AM,
Joe G said…
The RIBOSOME is the EDITORIAL perfectionist.
At least according to the scientific study.
That may be your problem- this is based on science.
No one said anything about mutations being operated by a perfectionist.
Only your twisted and demented little mind would post a question that A) Has NOTHING to do with the OP and B) Has nothing to do with anything that has any relevance to any position I know of.
But thank you for once again proving that you cannot participate in a discussion because you cannot A) stay on topic because B) You don't understand it.
At 11:07 AM,
Joe G said…
Which part of proofreading and error-correction, via deletion, strikes you as being operated by blind, undirected processes?
Ya see proofreading and any error-correction mechanism requires knowledge of what is supposed to be.
But the again "knowledge" is a funny word to you...
At 10:08 PM,
blipey said…
Hmmm. Funny how you connected the supposedly completely unrelated things....
Anywho....
At 7:12 AM,
Joe G said…
Funny how you connected the supposedly completely unrelated things....
What did I connect?
Please be specific.
I know I didn't connect genetic mutations with the premise that the RIBOSOME is an editorial perfectionist.
So what, in your twisted and demented mind do you think I connected and please substantiate the claim with evidence.
At 7:46 AM,
Joe G said…
From the article:
"Johns Hopkins researchers, reporting in the journal Nature January 7, have discovered a new "proofreading step" during which the suite of translational tools called the ribosome recognizes errors, just after making them, and definitively responds by hitting its version of a "delete" button."
So again I ask, what did I connect?
At 10:03 AM,
Joe G said…
which part of genetic mutation strikes you as being operated by a perfectionist?
No one said anything about genetic mutations being operated by a perfectionist.
According to the article:
"The enzyme machine that translates a cell's DNA code into the proteins of life is nothing if not an editorial perfectionist."
That enzyme machine is the ribosome.
Basic word substitution gets us -
"The ribosome is nothing if not an editorial perfectionist."
So the connection to be made is Erik Pratt with a drooling imbecile. You must have a keyboard protector...
At 6:54 PM,
blipey said…
Um...we are talking about translating DNA, right? What part of DNA translation strikes you as perfect, or in other words, how is the ribosome doing?
Are you claiming that Ribosomes are intelligent? If knowledge is what is needed for them to be perfect compilers, they must themselves possess this knowledge.
At 7:40 AM,
Joe G said…
Um...we are talking about translating DNA, right?
Wrong.
I was talking about the ribosome which translates mRNA INTO A POLYPEPTIDE.
Transcription involves DNA to RNA.
What part of DNA translation strikes you as perfect, or in other words, how is the ribosome doing?
DNA gets transcribed into RNA. The edited mRNA gets tarnslated into a polypeptide.
Had you read my blog posts you would have known that. Or better yet had you read a biology text you would have known that.
But anyway according to the scientists the ribosome is an editorial perfectionist.
Did you read the article I linked to?
Are you claiming that Ribosomes are intelligent?
At least as "intelligent" as a compiler.
Ya see if I am correct then the ribosome is programmed to recognize what is to accept and reject- see Biological Information in 3 Dimensions.
If knowledge is what is needed for them to be perfect compilers, they must themselves possess this knowledge.
In the SAME sense that compilers know what is to be accepted or rejected. And in the SAME sense that Word "knows" if words are spelled correctly or not.
At 8:52 AM,
Joe G said…
Erik,
I order for you to discuss a topic you have to have some knowledge about it.
And if experience is any indicator you don't know anything about biology nor computers beyond the basic 1st grader.
So your only recourse is to inject your ignorance as if said ignorance has relevance.
It does but only to demonstrate that you should not be discussing this stuff.
At 7:16 AM,
Joe G said…
If knowledge is what is needed for them to be perfect compilers,...
No one said anything about "perfect compilers".
IOW Erik, you have proven to be so stupid that you do not even have the capability to read.
At 8:26 PM,
Andrew said…
What you have not explained is why this is positive evidence for ID and not positive evidence for Evolution.
It is clearly evolutionary advantageous to have the Ribosome mop up and translating errors. There is no visible reason, from a high abstract point of view (not considering complex things like, number of mutations required to go from a ribosome that does not fix to one that does limited fixing), that this cannot be evolved.
So this is not something irreducibly complex. And so the title of this post is incorrect in that it implies that it is not evidence for evolution as well (which is not the case).
At 7:23 AM,
Joe G said…
Andrew,
1- "Evolution" is NOT being debated.
2- What part of an editorial perfectionist strikes you as being cobbled together via an accumulation of genetic accidents?
It is clearly evolutionary advantageous to have the Ribosome mop up and translating errors.
How does the ribosome "know" errors exist?
There is no visible reason, from a high abstract point of view (not considering complex things like, number of mutations required to go from a ribosome that does not fix to one that does limited fixing), that this cannot be evolved.
There isn't any visible evidence tat a ribosome can arise in a population that never had one, Never miind arising via an accumulation of genetic accidents.
So this is not something irreducibly complex.
The ribosome itself is irreducibly complex.
And so the title of this post is incorrect in that it implies that it is not evidence for evolution as well (which is not the case).
Again "evolution" is NOT being debated.
At 8:10 PM,
Andrew said…
Evidence changes the probabilities you assign to sets hypothesis that attempt to explain the current evidence, and predict future evidence.
"More evidence for ID in Biology..."
"Evolution" is NOT being debated...."
Lovely, but taken in isolation, it means nothing. Imagine we are tying to figure out the bias in a coin, is it 50% heads 50% tails (hypothesis H50), or is it 75% heads or 25% tails (hypothesis H75). If we see a single instance of heads, it is positive evidence for H50, excellent! but it is also positive evidence for H75, and we can perfectly calculate how much more evidence it is for H75 than H50, Bayes theorem. It is weak evidence for H50, and strong evidence for H75.
So back to ID, another hypothesis is Evolution. Lets just look at those two here.
Evidence: Ribosomes fixes transcription errors.
This is positive evidence for both ID and evolution. For evolution, it is an advantage for an organism to have a ribosomes that does fixing over one that does not, hence if there exists a path consisting ONLY of steps that evolution allows (single mutations, gene duplication, virus insertions and so on) that goes from a ribosomes that does not have this property to one that does, then evolution can evolve this property.
For ID, since any prediction of evolution is a prediction of ID (as it is perfectly acceptable in ID to have an intelligent designer that did nothing: evolution only) it is also positive evidence for ID. Can we quantify which is the stronger evidence? yes we can: ID can 'explain', or predict, far more things than Evolution, so this is very much weak evidence for ID compared to evolution given there exists an evolvable path.
What we don't know here was that it evolved or not, was there a path? this is important because one of the assumptions I made was there exists a path an evolvable path from ribosomes to error correcting ribosomes, I can safely do that for two reasons:
1: The current Theory of Evolution has overwhelming evidence for it at the present time.
2: The space of possible paths is vast, at least exponential in the number of bases in the genes controlling the production of ribosomes, and the possible steps that can be done on each of those bases.
By 2, I mean it is extremely probably that there is at least one path. So to wrap that up, the evidence that the ribosomes does SOME fixing is more evidence for evolution than ID.
This seems unfair on ID, it cannot win can it? well there is a plus side, if by exploring ALL the branches in some way, and proving conclusively there is NO path, then conditioning on that new evidence, the probability that the current Theory of Evolution being true is 0. Evolution requires that a path exists, if you show there is not one, ID wins BIG. Of course scientists might construct an hypothesis of Evolution version 2.0 that takes into this perfectly well.
So ignoring Evolution, you can't actually say it is evidence FOR ID or AGAINSTE ID. As we can see even though it is positive evidence for ID it is MORE positive evidence for evolution. So either it is evidence and the topic is about Evolution, or it is not about evolution... then it is not about evidence. Maybe you could just rename the article to be about this nifty thing ribosomes do, cause it is very cool in itself.
How does the ribosomes "know" errors exist?
Excellent question, ask the researchers, better yet, what do they mean by 'errors' exactly? for all we know they could be just a set of obvious errors that occur frequently. For example, don't let the sequence ACAGT pass, since no genes use that but they often use ACAGC.
The ribosome itself is irreducibly complex.
So now we should be happy that this statement can only be proven by showing that ALL paths that evolution can take don't lead from A to B. Because if you ignore one path, and declare that statement, you get screwed over when some scientist shows that the path you didn't consider was an evolvable path all along. So basically I ask you, prove THAT statement, or retract it.
As to the ribosomes evolving, why should I spend my time finding that out? google "ribosome evolution" 2 million hits. It is complex stuff, we lamens cannot hope to understand it all so lets be happy in the fact that a bunch of research has shown that yes, the ribosome evolved.
At 7:22 AM,
Joe G said…
So back to ID, another hypothesis is Evolution.
ID is NOT anti-evolution!
Were organisms DESIGNED to evolve or did theyt evolve via an accumulation of genetic accidents?
THAT is the question.
And according to a peer-reviewed paper an accumulation of genetic accidents, if it is greater than 3 genetic accidents, most likely didn't occur- not enough time.
And the theory of evolution via an accumulation doies not have any supporting evidence.
Now I had told you that evolution wasn't being debated and what did you do?
You ignored that and blathered on about "evolution" anyway.
Willfull ignorance.
Please read the following:
Biological evolution- what is being debated
The ribosome itself is irreducibly complex.
So now we should be happy that this statement can only be proven by showing that ALL paths that evolution can take don't lead from A to B.
That is false- you are asking for PROOF and science does not work like that.
Because if you ignore one path, and declare that statement, you get screwed over when some scientist shows that the path you didn't consider was an evolvable path all along.
LoL!!!
The science of TODAY does NOT and cannot wait for what the future may or may not reveal.
And ALL scientific inferences are in the SAME boat- that is future observations may overturn them.
THAT is science!!!!
So what we have is Andrew, who does NOT understand the debtae nor does he understand science coming here and fighting a strawman.
You must be proud of yourself
At 2:58 PM,
Andrew said…
You're right, I don't understand what you are debating.
Were organisms DESIGNED to evolve or did theyt evolve via an accumulation of genetic accidents?
Designed to evolve or evolved? your question is confused. Either they were designed to evolve THEN they evolved, or some other mechanism made life which then evolved. That is more a question of abiogensis.
I think part of the problem is is semantics of 'evolve', I mean it in the sense of evolution which means "evolve via an accumulation of genetic accidents" is a tautology (evolve means they did it that way). Meaning, treat my previous post as if that is what I mean by evolve.
A definition of ID: "Intelligent design is the term used for the assertion that "certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."
Words are important, by this definition of ID, it is trying to explain the same things as evolution.
If you DON'T mean it as this, then it could be anything, but don't use ID then.
ID attempts to explain and makes predictions on the origin of species, why reason why organisms are they way they look now and in the past etc. Just the same things the Theory of Evolution does => any assertion of evidence for ID must, necessarily include Evolution.
Why? think about ignoring the hypothesis that the coin is biased and thinking its fair when it consistently lands 75% on heads.
I'll leave it at that I think, here the problem is semantics of what YOU mean by ID and what I (and the discovery institute) mean by ID :)
If we get confused because of different meanings but the same word taboo your words. Don't use 'evolve' but 'organisms slowly changing in time via evolution via natural selection'. If I am fighting a strawman, it is one you put up with your misuse of the common understanding of ID.
One last thing:
And according to a peer-reviewed paper an accumulation of genetic accidents, if it is greater than 3 genetic accidents, most likely didn't occur- not enough time.
This is obvious stuff if you know Evolution, AND if I understand what you are talking about. One mutation of something needs to confer advantage else it wont set in the gene pool, if it doesn't set then you are not very likely going to see the gene mutated twice (the original mutation followed by another), which is two 'steps'. This is just how Allele frequencies change with time.
At 3:58 PM,
Joe G said…
You're right, I don't understand what you are debating.
I told you- designed to evolve vs evolution via an accumulation of genetic accidents.
THAT is what is being debated.
Were organisms DESIGNED to evolve or did theyt evolve via an accumulation of genetic accidents?
Designed to evolve or evolved? your question is confused.
YOU are confused.
You cut off part of what I asked-
ID = designed to evolve- ie GUIDED evolution
The theory of evolution = evolution via an accumulation of genetic accidents.
Either they were designed to evolve THEN they evolved, or some other mechanism made life which then evolved. That is more a question of abiogensis.
And that is why the question of "origins" cannot be separated from the question of "evolution".
I think part of the problem is is semantics of 'evolve', I mean it in the sense of evolution which means "evolve via an accumulation of genetic accidents" is a tautology (evolve means they did it that way).
But "evolve" does NOT mean that. And that is why it is misleading.
Perhaps you should read more about ID than some wikipedia article.
Then it would help your case to show that my use of ID differs from any other IDist's use.
Bring it on.
If I am fighting a strawman, it is one you put up with your misuse of the common understanding of ID.
Prove it.
Your bald accusations are meaningless.
Dr Behe:
Scott refers to me as an intelligent design "creationist," even though I clearly write in my book Darwin's Black Box (which Scott cites) that I am not a creationist and have no reason to doubt common descent. In fact, my own views fit quite comfortably with the 40% of scientists that Scott acknowledges think "evolution occurred, but was guided by God." Where I and others run afoul of Scott and the National Center for Science Education (NCSE) is simply in arguing that intelligent design in biology is not invisible, it is empirically detectable. The biological literature is replete with statements like David DeRosier's in the journal Cell: "More so than other motors, the flagellum resembles a machine designed by a human" (1). Exactly why is it a thought-crime to make the case that such observations may be on to something objectively correct?
Oops that supports what I have been saying!!!
Now what?
And according to a peer-reviewed paper an accumulation of genetic accidents, if it is greater than 3 genetic accidents, most likely didn't occur- not enough time.
This is obvious stuff if you know Evolution, AND if I understand what you are talking about.
The following is the paper:
Waiting for two mutations: with applications to regulatory sequence evolution and the limits of Darwinian evolution
And the following is Dr Behe's response:
waiting longer for two mutations
And again- that allele frequencies can change over time is NOT being debated.
At 4:04 PM,
Joe G said…
And WTF is this?:
Don't use 'evolve' but 'organisms slowly changing in time via evolution via natural selection'.
Via "evolution"?
Changing over time IS "evolution"!!!
Did they change over time via an accumulation of genetic accidents?
What is the scientific data that supports THAT premise?
If living organisms arose from some population(s) of single-celled organisms via an accumulation of genetic accidents, what should we observe?
Any analogies to complex information-rich data systems arisng via an accumulation of accidents?
Anything? Anything at all?
At 5:13 PM,
Joe G said…
What is ID?:
"Intelligent design refers to a scientific research program as well as a community of scientists, philosophers and other scholars who seek evidence of design in nature. The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection. Through the study and analysis of a system's components, a design theorist is able to determine whether various natural structures are the product of chance, natural law, intelligent design, or some combination thereof. Such research is conducted by observing the types of information produced when intelligent agents act. Scientists then seek to find objects which have those same types of informational properties which we commonly know come from intelligence. Intelligent design has applied these scientific methods to detect design in irreducibly complex biological structures, the complex and specified information content in DNA, the life-sustaining physical architecture of the universe, and the geologically rapid origin of biological diversity in the fossil record during the Cambrian explosion approximately 530 million years ago."
and
"The theory of intelligent design is simply an effort to empirically detect whether the "apparent design" in nature acknowledged by virtually all biologists is genuine design (the product of an intelligent cause) or is simply the product of an undirected process such as natural selection acting on random variations. "
And even more support that my view of ID is THE view of ID.
At 7:41 PM,
Joe G said…
Evolved by design
vs.
Evolved by an accumulation of genetic accidents
See Also "Not By Chance" by Dr Spetner (non-random evolutionary hypothesis)
At 2:30 PM,
Gary H. said…
Good article.
The one thing I find myself repeatedly having to explain to Darwinists in topics like this is that error detection/correction absolutely, necessarily demands pre-knowledge of correct system state.
For some reason, probably related to their other mental illnesses, they never get this.
The illness is called "cognitive dissonance" and all real Darwinists (and atheists) suffer from it.
Test: write a coherent sentence in English on a piece of paper. Make sure to include several glaring grammatical and spelling errors.
Now, find a monolingual Chinese person and ask them to find and correct the mistakes.
See? No pre-knowledge of English grammar, symbolism, spelling etc. (information encoding) = no ability to either detect or correct anything at all.
Same applies to any such error trapping/correcting in any such system - including biological ones.
Design is the inevitable and only scientifically correct explanation. Period.
At 2:38 PM,
Joe G said…
Thanks Hitch.
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