For the past 15 years I’ve been teaching genetics online. When the “genetic code” is mentioned, I often get blasted by fellow atheists mad at me for using the term. This slowed the past few years so I assumed the debate was over, but yesterday it happened again.
I made the following video about it and I’m curious to hear what the crew here thinks, I know people were split on this here in the past: https://youtu.be/1dqvxP6DoU0?si=7jMdl_CbD5EPaRDu&t=446
If you already understand what codons are, what’s meant by a “nonoverlapping triplet code”, how morse code, ASCII and how protein synthesis works; you can skip ahead to 7:26
In the video I ignore many details, such as tRNA, which might make some people frown but you get the idea.
I argue that the genetic code certainly does function as a code under the standard definitions of code found in many dictionaries (I cite the Oxford English dictionary specifically). I show how the genetic code functions as code but then I talk about why, even though it does function as a code, people are free to study it under different paradigms. It’s fine, for example, to just think of it as a chemical system for the same reason it’s fine to think of a person as a colony of cells.
Hi Jon!
I might need to review that last discussion, but my position on this is that genetics are chemistry; nothing about it requires it to be a code. Humans need codes to assign meaning to message, so when we look at a strand of codons and call it a code we are assigning a meaning - and our usage makes it a code.
Shorter: It is not a code in itself, but our description of it is.
Earlier this year @sfmatheson posted an article about a new discovery regarding the order in which amino acids were recruited to the genetic code …
In short, this is evidence that genetic encoding has evolved. Information is being encoded in new ways that were not an original properties of the coding. That is not something that is allowed in any human defined coding scheme, where a sender and receiver must have prior agreement on the encoding to be used. It’s hard to clearly define the notion of what “sender and receiver” means in this context, much less to how they might “agree” to change the encoding.
I don’t know any scientist, regardless of their feelings toward gods or fairies, who has any objection to the phrase “genetic code.” This might mean that I don’t join the kinds of conversations where people are that foolishly pedantic, or it might mean that the objections are tiresome goofy philosophical dances around whatever one means by “a real code.” I won’t watch the video (it’s not you, it’s me) but would you be willing to write a few sentences about the “debate” and what it’s about? I can maybe start us off: is this about whether the code is a code, or is it about whether scientists thought of it as a code from day one? Or something else?
AND
The semantics of language pretty much require we call it a code, but we should keep in mind that semantics is not chemistry. There are other example of “natural” codes, like Fraunhofer lines that derive from the properties of matter, and no one (that I am aware) takes this to be evidence of “design”. Human semantics make this a code too, but these were not created to be any sort of code as humans define it; they just are.
This all springs out of the creation-evolution debate. I kid you not, this is literally like the “all paintings must have a painter”-argument.
So basically, it seems to me there are two possible responses.
Possible response A) Some paintings don’t require a painter.
Possible response B) It’s not a painting.
A-proponents make B-proponents throw a fit by agreeing with creationists it’s a code, which put B-proponents in the unenviable position of having to argue against over half a century of use of the word in the molecular biology literature.
This doesn’t fase them and they insist it’s just a metaphor or an analogy or something to that effect.
So yes, it’s a sematic argument at bottom. What should we include into the set of things we call a code? I’m fine with including the genetic code.
It’s a metaphor, so citing a dictionary is silly.
The primary characteristic of a code is abstraction. There are no abstractions in protein translation. Everything is chemical.
Cite something else that is a code, and I’ll point out the abstraction involved. You can’t do that with the genetic code.
Biology is full of metaphors. They are a field day for dishonest and/or ignorant creationists.-
“All other codes were designed by coders, so the genetic code must have been designed by a coder “
“All other codes were designed by humans, so the genetic code must have been designed by a human?”
Just my opinion.
It really depends how you use the term (of course). Like, I have no problem if anyone says that oil is a “hydrophobic” substance as long as we don’t extend the usage beyond the implied metaphor. From watching the video, the usage for “code” in question is “a system of signs or symbols”. As @Jon-Perry also points out, the crux falls really under how the terms ‘signs’ and ‘symbols’ are used. I think most people would think that a ‘sign’ are abstract concepts. If that’s how we use ‘signs’ then a codon is not a ‘sign’ since it is not abstract.
Also the rules that describe how the codons are assigned to the amino acids (or as stop codons) is not abstract, nor arbitrary either. There are clear regularities in the genetic code, which gives us clues to how the genetic code originated (see my commentary here). The first comment here by @Dan_Eastwood also mentions an interesting recent paper on this subject.
But we allow ‘signs’ to include physical things that are representatives of something else besides itself, then I find no issue in calling the genetic code a real code. But we can also say that footprints are a code too. They are ‘signs’ that represents a lot of things: What type of animal left the foot print behind, how much they weighed, and in what direction they went. But I really like the example Fraunhofer lines that @Dan_Eastwood gives, since it is reminiscent of bar codes.
This also deflates any argument from analogy (e.g. watchmaker) that ID/creationists often use to claim that the genetic code must be designed since all other codes are designed. That’s why many online atheists become so upset when anyone calling the genetic code a (real) code. They have opted to the position that the genetic code is not actually a code, but I take a more nuanced position.
I saw the old conversations here. That’s why I thought it was time to share this again.
Did you watch the video? In it I talk about the code’s evolution.
I also talk about who the sender and receiver are. The genome sends messages decoded by the ribosome (and tRNA).
Let me know if you watch the video.
In discussions like this, “arbitrary” is often taken to mean “fully random,” but neither evolved signaling systems nor designed ones are usually fully random. They are usually optimized for a specific use.
Morse code is arbitrary (signs were assigned to letters) but the assignment wasn’t fully random, it was optimized for speed of use and clarity when transmitted over a wire. E is one of the most common letters in English, and so was assigned the shortest possible sign: one dot. T (also super common letter) is one dash. Z, on the other hand, is dash dash dot dot.
Codon assignments are called arbitrary because there’s no law of chemistry that forces a particular codon to correspond to a specific amino acid. Assignments were made by evolution and can be changed by it, much like Morse code is sometimes changed (there are several popular varients).
Codon mapping is dictated by tRNAs, ribosomes, and enzymes which are all evolvable. A single mutation in a tRNA anticodon, for example, is enough to reassign a condon. This means that not only can genomes evolve, the genetic code itself (the mapping of codons to amino acids) can evolve.
Why is Morse code said to be arbitrary even though it’s not fully random? Because there are many equally optimized alt code mappings that could be used instead. The same is true of the genetic code. There are over 1 million alt codes equally optized for the things we think the standard genetic code was optimized for by natural selection.
Messages from the genome are encoded into mRNA, transmitted to the cytoplasm, and decoded by the ribosome using tRNA. This is a real, evolved signaling system. As real as the endocrine system, as real as the signaling system evolved between flowers and bees.
It is arbitrary in that codons were assigned and can be reassigned. There’s no fundamental reason AUA must code for isoleucine. If you don’t believe me, ask your mitochondria.
My main concern was regarding whether codons can be viewed as ‘signs’ or not, in the sense that ‘signs’ are abstract. If one says that ‘signs’ don’t have to be abstract, nor arbitrary, (e.g. footprints being ‘signs’ of an animal past presence and direction) I don’t think we disagree on that.
Regarding the arbitrariness or randomness of codon assignment was a secondary point, but I will address this here.
That’s a very good example. Although, one can point out that E (or the phonetic sounds it represents) being the most common in the English language is also arbitrary, or perhaps more accurately described as ‘historically contingent’. This may not be the case for the amino acids nor the nucleobases.
Well… there are actually are chemical aspects regarding codons that do have a correspondence in the genetic code. When a codon (of an mRNA) interacts with the anti-codon (of the tRNA) each base pair is not equal. For one, GC interactions involve 3 hydrogen bonds while AU interactions have only 2. This has a significant effect on the strength of the interaction, and thus the reliability of one particular codon compared to another. This is also true for the position; e.g. the 2nd base pair of the codon is stronger compared to the first, and both are stronger than the third position which is prone to form wobble base-pairing. Hence, why the third codon tends to be fully or partially redundant, except for a very few interesting cases. There is also an interesting correspondence between the codons and the biochemical synthesis of the amino acids, such that codon assignments may have roots in the physical “rules” of the biochemistry observed in metabolism, which in turn may have roots in geochemistry. I explain such details here as well. The exact reason for that is unclear, but a possible explanation is given by one scientists I like to follow on the topic of the origin of life (Eric Smith). Here is a quote from one of his books.
In Chapter 5 we show that the translation system from RNA to proteins – a system that has clearly been under evolutionary pressure to provide a buffer between the idiosyncratic structure of metabolism and the flatter opportunity space provided by sequence combinatorics – is organized in a way that heavily recapitulates the order of metabolism. Relations between the assignments of amino acids to nucleotide triplets in the genetic code have been recognized since the 1970s [901], but the information we assign to such associations becomes even greater when we recognize that it extends also to the selection of the biological amino acid inventory. Part of the reflection of biochemistry in the code can likely be accounted for by precisely the code’s function of buffering [276, 327, 833]: to minimize the leakage of metabolic pattern through the coding process when errors occur, the assignments must make use of redundancies in the underlying chemistry. We will show, however, that the regularity of the code is even more fundamentally a biosynthetic pathway regularity, which can only be rationalized if it arose when the precursor to the modern translation system was an embedded system coevolving with metabolism.
Evidence?
That’s not what “arbitrary” means. That’s the abstraction involved. No such abstractions exist in translation. I think you’re conflating the two concepts.
Thus it wasn’t arbitrary.
If we wanted to design a secret code, we’d design our abstractions to be arbitrary.
Only you seem to think that it is arbitrary. It’s anything but; it’s highly contingent, an antonym of arbitrary. It’s telling that you haven’t cited anyone but you saying it’s arbitrary.
No, it’s all chemistry. The nouns and verbs you used in that passage are all used metaphorically.
[BTW, bacteria do not have a cytoplasm.]
But there are no real codes involved.
That’s not what “arbitrary” means.
Not that it must, but there are reasons why it does. That’s why it’s contingent and not arbitrary.
I have now watched the video - sorry I missed the link on my first pass.
Genetics are definitely a Signalling System, no arguments there. I think semantics require that it is also a code (what else could we call it?), but I agree with @Mercer that it lacks the abstraction of a human created code. We might need to pin down the difference between arbitrary and abstracted.
AND
In terms of Shannon coding, mitochondria have a different agreement between genome and ribosome over how the code is interpreted than do eukaryotes. If I understand correctly, this difference is contingent on the biochemistry and evolution of each.
An arbitrary agreement on coding is the key idea to cryptography, where the sender and receiver don’t want any third party to intercept the message. I think ascribing this sort of behavior to ribosomes is asking too much. In cryptography or any coded communications the meaning of a message can be completely independent of the coding, and that is not the case for genetics.
I will add that genetic code is unlike computer code. Computer code is a set of sequential logic, giving exact instructions for the task in a specific computing environment. Genetic codes are analogous to a cooking recipe, laying out the ingredients and quantities, and the laws of chemistry/physics takeover to do the cooking. Genetics do not “execute” at all like computer code does.
I agree with Jon as far as the “not a code” a-theist is concerned; Genetics are a “real” code by dictionary definition and semantic usage. I am not disagreeing with @mercer, he is right that genetics lack a key feature of human created codes.
We think we should emphasize that genetics are a natural code that enables an evolved chemical system (life), and unlike the arbitrary and abstract codes that humans create.
I think we should understand that biology cannot be described without metaphors. An example: I have spent decades studying the myosins, known as molecular motors. More recently, biophysicists have shown that the mechanism by which they move is much more analogous to a ratchet than to any motor. That won’t cause anyone, including me, tol stop using the now inaccurate metaphor “motor.”
I’m not sure why you joined those characteristics together, because not all codes that humans create are arbitrary. All designed codes have abstractions as their foundation. The arbitrary ones are designed to keep secrets, while the nonarbitrary ones (Morse code, the single-letter amino-acid code) are designed to promote understanding and/or transmission.
I didn’t explain that very well. I mean that the agreed meaning of a message may be completely arbitrary depending on which receiver decodes it. The words “Genetic code” are a fine example of this, with different people making different interpretations based on different starting assumptions. Strings of codons are not arbitrary in this sense.
Why is it we cannot cite a dictionary definition to support that it’s a code?
By… definition? Where would we find that definition?
You might be conflating the genome with the genetic code. The genetic code is the rules the ribosome/translation system uses when translating an mRNA. While the hardware is different, this works just like simple machine code on punched tape computers. mRNA has a string of instructions read linearly. Each codon is processed one at a time, each codon is a single command telling the system to start, then which amino acid to add, then when to stop.
mRNA does deliver to the ribosome “exact instructions for the task” and they are sequential instructions.
If you were an alien cataloging types of digital coding systems discovered on earth, you’d add this to the pile with ASCII, Morse code, and thousands of other digital encoding/decoding systems without hesitation.
The argument that “the genetic code is not a real code, therefore creationists should stop worrying their pretty little heads about it” is as dismissive as saying “the heart is not a real pump so it doesn’t require an explanation for its existence”.
The argument is dismissive and unconvincing.
Okay 
To the meat of your arguments:
You think I use the word “arbitrary” wrong, that’s fine. I can say this again without that word:
Codons being assigned to represent amino acids was not an automatic consequence of normal chemistry, like hydrogen and oxygen forming water at the right temp and pressure. Some larger-scale process had to have been involved in establishing codon assignments.
Creationists often propose divine action here, but the mainstream scientific answer is: Evolution by natural selection acting on early translation systems. Either way, simply dismissing the question “how did this code get here” by simply saying “it’s not a code so the question doesn’t count” sidesteps a genuine mystery, a mystery not yet fully solved.
Researchers studying the origin of life take the process of codon assignment seriously. Is the standard code a frozen accident, as early workers proposed, or is the code optimized? If optimized, what for? Of the trillions of alternative codon assignments possible, how many are equally optized, or better optimized, but we’re stuck with a mediocre version because of something like the early adoption effect? More interesting still, scientists want to understand what life forms were like before efficient protein coding evolved, and what selection pressures drove it’s evolution.
The paper below points out how rare the standard code is if we assume it is optimized for robustness, error correction and so on, but notice this: If the genetic code is one in a million, that’s still just one in a million out of many trillions of possible codon mappings. AUA did not need to code for isoleucine. Again, if you don’t believe me, just ask your mitochondria.
Regardless of considerations of efficiency or convention, what makes any code abstract is that meaning is entirely a matter of agreement between the sender and receiver. Systems engineering can be notoriously and frustratingly arbitrary and unintuitive. Not only is the Morse code random, but the English alphabet it encodes is random - we could be using hieroglyphics. Secret codes are purposely opaque based on covert agreement. Our agreements on meaning may or may not be optimal or make sense, but there is nothing essential to human codes which is not communication ultimately based on mutual agreement.
The genetic code is our notation for certain chemical species which are involved in physical reactions, with physically determined assignment. As such, while our designations may be deemed a convenient code for scientific communication, the described reality has no degree of freedom. Such language only becomes problematic when there are people who are desperate to prove metaphysical beliefs by playing word games.
Possibly. I’m trying not to use “code” when I mean something else, but I haven’t been consistent about it.
I’m with you so far, but we aren’t done yet. The ribosome spits out a protein which folds (chemistry!) and goes off to combine which other proteins (more chemistry). None of this further action is coded - there is no instruction to go assemble into a cell wall or whatnot, it’s all chemistry, and that is something computer code does not do.
The argument is dismissive and unconvincing.
The claim begs the question that living things are computers; they are not (not yet!). Which brings me to a really important point … Creationists are NOT making scientific arguments; they are making apologetic arguments. Any attempt to respond to apologetics with science is the wrong answer. The right answer is to respond to scientific questions with scientific answers.
You answer the genetic codes just like computer code is fine up to the point you stopped, but you are giving the Creationist a free pass on “computers are like living things”, and tacitly approving the point the Creationist wants you to give away. The trick is to get the Creationist to first ask a scientific question, or make a scientific claim, THEN respond with the science.
This last bit is off the main topic, and I can start a new thread for it if there is interest.
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