This is a video published a few weeks ago where Jon Perry interviews Richard Dawkins. Jon Perry is the author of animations posted on his website Stated Clearly. He (Perry) has a very adaptaionist view of evolution—a view that he got from Richard Dawkins.
The main topic of the interview concerns DNA as information and the genetic code. Both Dawkins and Perry give the impression that the only kind of information in the genome is the genetic code (sensu stricto); in other words, the code that specifies a sequence of amino acids using the sequence of nucleotides in a coding region [The Real Genetic Code]. Dawkins makes the same point he has often made; namely, that this is a real code just like any other code.
Perry points out that most people don't understand this, including many atheists who argue that the "code" is merely an analogy and not to be taken literally. Atheists, and others, also argue that the information content of DNA includes lots of other things such as genes that specify functional RNAs and sites that bind proteins. It's hard to argue that a gene for tRNA functions as any kind of a code and it's hard to argue that the DNA binding sites in origins of replication are codes even though you could argue that they carry information.
I don't get excited about arguments over whether DNA carries "information" because there's not much to be gained by such arguments. Who cares whether the genetic code falls under the definition of "information theory"? However, I do get annoyed when people say that the ONLY information in DNA is in the form of the genetic code.
Watch the video and let me know what you think. Jerry Coyne watched it and he wasn't the least bit bothered by the things that bothered me [A discussion on genetics, evolution, and information with Richard Dawkins].
9 comments :
I've never had much patience for semantics either. Whether you want think the genetic code qualifies for the definition of a code or not depends on definitions. But it doesn't matter what label you use to refer to something, nor what category of things you file it under. There is good evidence that the universal(ish) genetic code is a product of a considerable evolutionary history and evolved from a much simpler code, which we do not yet know how originated.
And regardless of how you deign to define information such that DNA sequences in living organisms "have information", we know those DNA sequences are the product of evolution and hence that information can and does evolve.
I agree with you that "code" is not a metaphor, analogy etc, but I think it can be useful to offer some kind of mechanical grounding for the genetic code when explaining it. I've always maintained that the genetic code is pretty much entirely 'located' in the tRNA, as this is where nucleotide sequences and amino acids are physically associated in a Rosetta Stone fashion. What are your thoughts on this attempt to ground the genetic code in something palpable?
Some argue the true location of the code is actually in the aminoacyl-tRNA-synthetase enzymes that charge tRNA with the correct amino acids, as it is these molecules that must simultaneously recognize the correct amino acid and the correct tRNA molecule. They even have editing mechanisms where they can remove incorrect amino acids from tRNA.
Oh, that's very interesting - thanks for pointing this out. Is there anyone that's written compellingly on this specific subject, i.e. the physical "location" of the genetic code, that you would recommend?
Rubio Gomez MA, Ibba M. Aminoacyl-tRNA synthetases. RNA. 2020;26(8):910-936. doi:10.1261/rna.071720.119
Most amazing (actually mind-blowing) thing is these enzymes (there are two "classes" of 10 each, one for each amino acid) appear to have originated as a single gene from opposite, complementary strands of DNA. The anti-parallel(complementary) DNA strand for the common ancestor of all class-I enzymes encodes the common ancestor of all class-II enzymes.
Martinez-Rodriguez L, Erdogan O, Jimenez-Rodriguez M, et al. Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene [published correction appears in J Biol Chem. 2016 Nov 4;291(45):23830-23831]. J Biol Chem. 2015;290(32):19710-19725. doi:10.1074/jbc.M115.642876
One should add here that there is a lot of confusion out there about what is the genetic code. Journalists are always reporting that the sequencing of an organism is discovering its "genetic code". To them, the "code" is the sequence of letters in the genome, not the table that converts them to protein sequences. If I facepalmed every time I heard a journalist do that, my face would be in bad shape.
Hi Larry Moran,
“I don't get excited about arguments over whether DNA carries "information" because there's not much to be gained by such arguments. Who cares whether the genetic code falls under the definition of "information theory"? However, I do get annoyed when people say that the ONLY information in DNA is in the form of the genetic code.”
A problem of the philosophy of science. A simple example from genomics:
5'-GCA-3' “coded” for Alanine.
In chemistry, the corresponding term generally refers to a catalytic reaction mechanism. In the language of biochemistry, on the other hand, one can speak of an enzymatically catalysed reaction. Systematically, enzymatically catalysed reactions are of course only a subset of chemical reactions. But since enzymes are in a biological context, they form a special category: without the presence of organisms, biocatalysts cannot of course be determined empirically. Consequently, this is only a special level of description.
The use of the term "coding", which is based on the theory of science (!), is also a special level of description, which, however, satisfies a corresponding information-theoretical coherence. Thus, biological information exists here, which by definition only occurs in living beings. "Coding" here is more precisely biological coding, terms such as sequence, reading direction, codon, stop codon, anticodon or redundancy of a code table are derived from this without information-theoretical contradictions.
The subject area of the theory of the genetic code comprises, in terms of information theory, the process of transferring a nucleotide sequence to that of an RNA single strand in the amino acid sequence of the polypeptide chain of a protein.
“Who cares whether the genetic code falls under the definition of "information theory"?”
Little surprise: You...! For example, "junk" is a term that can only be found in a very narrow field in chemistry. In information theory, this kind of thing is neutrally called redundancy (whereas in biology there are many forms of redundancy, so this is one reason why we also have to die). And when you speak of "code" above, what exactly are you talking about?
“It's hard to argue that a gene for tRNA functions as any kind of a code and it's hard to argue that the DNA binding sites in origins of replication are codes even though you could argue that they carry information.”
Let's put it this way: A programmable molecular computer can also be built from DNA. The rest is an analogy (In which the genome can be viewed as the biological representation of a Turing machine).
“Dawkins makes the same point he has often made; namely, that this is a real code just like any other code.”
Dawkins is right. And this means the corresponding code table and nothing else. Of course, a code set can also be built on doublets instead of triplets (wobble base pair). But everything else is in a different information-theoretical context.
In general: In the information-theoretical interpretation of thermodynamic entropy, entropy measures the potential information of the observer. Now you should also know who wrote the genetic code...
Cheers,
Lamarck
Thanks for sharing my interview with Dawkins & for your comments. It's always nice to see how I'm being interpreted.
Calling me an adaptionist is fair. Any mutation that doesn't affect phenotype is a bore unless you're trying to build phylogenies. I also find phenotype variation that doesn't affect fitness to be a bore, again, unless you're trying to construct phylogenies.
I'm curious why you think we suggested "that the only kind of information in the genome is the genetic code"
The genetic code is the set of rules governing protein synthesis. Obviously we never said that's the only information in a genome. If so, we'd all just be clouds of ribosomes, tRNAs and synthetases in search of a membrane.
What we did say is that the specific type of information DNA and RNA pass on (when a strand is replicating) is "sequence information". Do you disagree with that statement?
Most sequence information in a genome is, as you know, non-coding. Neither of us deny this, neither of us denied the importance of functional RNA. In fact, we spent about 15 minutes talking about ribozymes and RNA evolution experiments. Neither of us deny the importance of sequences that act as binding sites. Obviously, that all falls in the "sequence information" bucket.
There was a point in the video where I said "sequence information is what's passed on when nucleic acids replicate, it's the information passed from parent to child".
By "parent" and "child" there I meant "parent strand" and "daughter strand". In retrospect my phrasing was poor.
I don't know about Dawkins by I don't deny the importance of methylation patterns and non-DNA/RNA gamete content. I've made videos specifically about them. These things, along with many environmental interactions, clearly play a role in phenotype determination but they were beyond the scope of our short conversation.
The conversation was about the nature and possible origin of the genetic code: The 64 codons and their specific assignments to amino acids & start/stop commands in protein syntheses. Our aim was to compare this natural code structure to the code structures we've engineered for our computers.
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