"The genetic code is a real code" is this debate over yet?

[Mercer (John Mercer)]

@Rumraket

Why is it we cannot cite a dictionary definition to support that it’s a code?

Because the definition wouldn’t apply to a metaphorical use. Are you unfamiliar with metaphors?

@Rumraket

@Mercer

The primary characteristic of a code is abstraction.

By… definition?

No, because it’s the primary characteristic. You name a human-designed code, and I’ll point out the abstraction at its center.

@Jon-Perry

The genetic code is the rules the ribosome/translation system uses when translating an mRNA.

Rules are things made by people, IIRC, so your usage is metaphorical.

@Jon-Perry

While the hardware is different,

There is no hardware. Proteins generally have the consistency of a bathtub rubber ducky.

@Jon-Perry

this works just like simple machine code on punched tape computers.

No, it is very different because there are no abstractions. Abstractions are the meat that you are avoiding.

@Jon-Perry

mRNA has a string of instructions read linearly.

Really? Explain the allegedly linear mechanisms by which “instruction” for adding the poly(A) tail to an mRNA is read.

@Jon-Perry

The argument that “the genetic code is not a real code, therefore creationists should stop worrying their pretty little heads about it”

Nice straw man! The point is not that, but that the argument “The genetic code is a real code, therefore it was designed” is bunk.

@Jon-Perry

…is as dismissive as saying “the heart is not a real pump so it doesn’t require an explanation for its existence”.

There you go again, falsely putting words in my mouth.

I would say that the heart is definitely a real, not a metaphorical pump. Its valves are real, not metaphorical valves. The myosins that power the pumping, however, are metaphorically referred to as molecular motors–that has to be true because we know they function as ratchets, not motors. I’d say that “ratchet” is very close to not being metaphorical.

Again, the meat you are avoiding is abstraction. Pumps like the heart don’t involve abstractions, so that’s an absurd analogy.

@Jon-Perry

The argument is dismissive and unconvincing.

Your straw man definitely is! How about if you address what I’m writing and stop manufacturing quotes?

@Jon-Perry

Okay

To the meat of your arguments:

No, the meat is abstraction, which you completely avoid addressing.

The more accurate metaphor is “straw man.” You even put words that I did not write in quotation marks, which ethically should only be used to enclose the literal words that someone used, not your fabrication.

@Jon-Perry

You think I use the word “arbitrary” wrong, that’s fine.

I know you do. It’s not fine, because it suggests that you don’t understand codes. Or metaphors. Or analogies, for that matter.

@Jon-Perry

Codons being assigned…

There is no actor to assign them. That’s another metaphor.

@Jon-Perry

to represent amino acids

They don’t represent anything. You’re sneaking in at least one metaphor in every sentence! Do you really not understand that virtually nothing in biology can be explained without extensive use of metaphors?

@Jon-Perry

Some larger-scale process had to have been involved…

That would be evolution.

@Jon-Perry

…in establishing codon assignments.

Two additional metaphors sandwiching the term you’re trying to claim is not a metaphor! Slick!

@Jon-Perry

Creationists often propose divine action here,

You’re completely missing the point. They propose design because the abstractions in human-designed codes are designed. However, there are no abstractions in translation. It’s all chemistry.

@Jon-Perry

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”

Jon, why can’t you address my point as stated? Why resort to fabricating a quote? Again, They propose that our use of “code” necessitates design because the abstractions in human-designed codes are obviously designed.

@Jon-Perry

Researchers studying the origin of life take the process of codon assignment seriously.

They do. And unlike you, they tend to know when they are writing metaphorically.

@Jon-Perry

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.

Fascinating. Why are you referring to scientists as a third party in this context?

What point are you trying to make with your link?

[Nesslig20]

@Rumraket

@Mercer

It’s a metaphor, so citing a dictionary is silly.

Why is it we cannot cite a dictionary definition to support that it’s a code?

That’s exactly the case. I think we first need to come together and agree on a definition before this. I propose the following from what I am able to find from the field of semiotics (not that I am an expert on that or anything, far from it).

A ‘code’ is the defined as a system of rules that describes the relations between signs (signifier) and objects (signified). How the signifier and signified are connected can be very different. Charles Sanders Peirce classified the types of ‘signs’ under the following (non-mutually exclusive) categories.

• Icon: a sign that in some way resembles the object (e.g., a photo, or the gendered stick figures on bathrooms).
• Index: in cases where there is/are causal links between signs and objects (e.g., smoke means fire, footprints indicates type of animal).
• Symbol: In cases of an arbitrary, or historically contingent conventional link (e.g., words, flags, green/yellow/red street lights).

I think the codon-aa relationship in the genetic code are mostly an index-based code, even if the causal relationship are not directly obvious to us as is the case with smoke and footprints. Although, some details of the genetic code could be due to historically contingency, in the sense that if we replayed the tape of life (a la Stephen J. Gould) back to just the point before the genetic code emerged, some codon assignment could’ve ended up being different.

I do suspect that most people don’t consider the footprint-animal relationship as a type of code. The difference in how people use the same word presents a high risk of equivocation.

[Mercer (John Mercer)]

@Nesslig20

A ‘code’ is the defined as a system of rules that describes the relations between signs (signifier) and objects (signified).

That system of rules is the abstraction. There’s neither signifier nor signified in the genetic code.

@Nesslig20

I do suspect that most people don’t consider the footprint-animal relationship as a type of code.

Agreed. I sure don’t.

@Nesslig20

The difference in how people use the same word presents a high risk of equivocation.

The other problem is that we have multiple human-designed codes that we use to explain translation, creating confusion, but science educators should be aware of this.