There are a lot of great resources available on the internet for countering Code Denialism. I’ve gathered a few of them for your convenience. I envision a multi-part series on this topic because the evidence against Code Denialism is so extensive and Code Denialism seems to be surging in popularity here at TSZ.
The 1961 paper by Crick et al. is an outstanding example of the use of thought and logic to solve basic biological problems. In my opinion, it is a superb paper to assign to students in courses because it illustrates how combining knowledge and wisdom can provide answers to important scientific questions.
They demonstrated that three bases of DNA code for one amino acid in the genetic code. The experiment elucidated the nature of gene expression and frame-shift mutations.
…the mutant strains could be made functional again by using proflavin to insert or delete a total of three nucleotides. This proved that the genetic code uses a codon of three DNA bases that corresponds to an amino acid.
“This concept of a phase shift, or a ‘frameshift’ [in the genetic code of an rII gene] as we later called it, was so foreign to people in genetics that we had endless problems trying to explain this work.”
Seems like they still have work to do.
The famous paper:
THERE is now a mass of indirect evidence which suggests that the amino-acid sequence along the polypeptids chain of a protein is determined by the sequence of the bases along some particular part of the nucleic acid of the genetic material. Since there are twenty common amino-acids found throughout Nature, but only four common bases, it has often been surmised that the sequence of the four bases is in some way a code for the sequence of the amino-acids. In this article we report genetic experiments which, together with the work of others, suggest that
the genetic code is of the following general type:(a) A group of three bases (or, less likely, a multiple of three bases) codes one amino-acid.
(b) The code is not of the overlapping type.
(c) The sequence of the bases is read from a fixed starting point. This determines how the long sequences of bases are to be correctly read off as triplets. There are no special `commas’ to show how to select the right triplets. If the starting point is displaced by one base, then the reading into triplets is displaced, and thus becomes incorrect.
(d) The code is probably `degenerate’; that is, in general, one particular ammo-acid can be coded by one of several triplets of bases.
Is the Code Degenerate?
… the code is probably `degenerate’, that is, in general more than one triplet codes for each amino-acid. It is well known that if this were so, one could also account for the major dilemma of the coding problem, namely, that while the bese composition of the DNA can be very different in different micro-organisms, the amino-acid composition of their proteins only changes by a moderate amount.
The Nobel Lecture:
I shall discuss here the present state of a related problem in information transfer in living material – that of the genetic code – which has long interested me, and on which my colleagues and I, among many others, have recently been doing some experimental work.
…It is convenient to have a word for a set of bases which codes one amino acid and I shall use the word “codon” for this.
…There is nothing in the backbone of the nucleic acid, which is perfectly regular, to show us how to group the bases into codons. If, for example, all the codons are triplets, then in addition to the correct reading of the message, there are two incorrect readings which we shall obtain if we do not start the grouping into sets of three at the right place.
In spite of the uncertainty of much of the experimental data there are certain codes which have been suggested in the past which we can now reject with some degree of confidence.
Message, messenger, or genetic message appears 12 times. Other codes were proposed and rejected.
The genetic code is a code.
The evidence against Code Denialism is overwhelming.
There’s really nothing to discuss. But if you insist…
I’m not seeing the point of this.
We use the term “code” in a variety of ways, some precise and some less so. This would not be an issue, except that some creationists and ID proponents are making bogus arguments.
That Francis Crick said that DNA is a code does not constitute evidence for creationism nor does it constitute evidence for ID.
Of course it’s a code in that it’s a process where the input set maps to the output set. It’s just an intelligently designed code that uses symbols to abstractly represent other quantities.
Why IDiots still equivocate over the definition of “code” is the real question.
And I don’t much see the point of trying to discuss codes with people who insist on putting the word code in scare quotes, as if it’s a code “word.” Were you simply unaware of Coding Theory before I brought it to your attention?
Before we can even begin to discuss the relevance of codes in biology shouldn’t we first agree that they actually exist?
Who’s afraid of real codes?
It’s never ceased to amaze me how “skeptics” can deny human exceptionalism and at the same time maintain that only humans are capable of code-making, meaning-making, and semiotics.
Adapa’s posts will be ignored.
If there’s ever been a case of dishonesty and rule-breaking that has been countenanced by the “powers that be” here at the “The Skeptical Zone” it’s been Adapa’s claims that I have a long history of anti-gay bigotry.
It remains to this day the shining example of “you’re on our side so we’ll look the other way” hypocrisy of the “moderators” of this site.
There’s not much point in trying to discuss codes with people who insist that “code” only has one meaning – an intelligently designed communication system that use symbols as abstract representations of other quantities.
The simple fact is there are many naturally occurring instances of data being encoded in physical media without the use of abstract symbols or intelligence. The spectral lines in starlight that map to the chemical composition of the star is one. The width of tree rings that map to rainfall/drought conditions in the past is another. The complex chemical reactions that occur with DNA are just another natural instance of coding.
But IDiots will be IDiots. We’ll get the same tired equivocation over the word “code” til the cows come home.
Mung’s anti-science drivel will be laughed at.
In petrushka’s recent OP he thought it important to state that DNA is a template, as if that makes some difference to the debate over the genetic code. Frankly, it just introduces confusion, not clarity, and does nothing at all to dispel the reality of the code.
And:
The coding strand is still there.
THE GENETIC CODE IS A CODE!! A CODE!!
Sure, but it’s not an intelligent designed abstract code.
DIDN’T YOU HEAR ME?? IT’S A CODE!! A CODE!!
Yeah. So?
YOU DON’T UNDERSTAND!! IT’S A CODE!! A CODE!!
Yes. Well?
IT’S A CODE!! A CODE!! That means GODDIDIT!!!
Whatever.
Was that a reply to me?
As far as I know, I did not use scare quotes. I believe that I used quotes properly, according to ordinary English usage. That is to say, I made a reference to a string of letters, rather than to any assumed meaning of that string.
One of my colleagues, at a former position, was a researcher in coding theory. Of course I was aware of it. But it’s a technical area in mathematics which has very little to do with the usual commonsense meaning of “code”.
My claim was that there is a mathematical definition of a code. Can you link to the post where you agreed with me?
Yes, it’s more clearly a code than it is a template, although I wouldn’t really argue much over either one. Maybe it’s not just a name, but the details are what matter, and to simply subsume it under the term “code” and to pretend that it’s thereby no different from Morse Code or some such nonsense is ridiculous.
Then we get to the “all codes are designed” tripe and it’s pretty clear that creationists simply want to define the genetic code as designed. I could as easily say that all significant arches whose origins have been observed were manufactured by humans, hence Rainbow Arch was intelligently designed. No, it doesn’t follow, nor does the notion that the codes we’ve observed being produced were designed (more or less), thus the genetic code was designed.
Life has never been observed to have been designed, hence it makes no sense to claim that the code with which genetic information is stored by life must have been designed. One needs actual evidence, and not to use the fact that almost all of our evolution has been unobserved (by intelligence, anyway) as if that is an excuse to say that “all codes have been designed.”
Glen Davidson
Call it anything you want.
I don’t believe that I ever agreed or disagreed. There are many posts where I don’t bother to respond. That was one of them.
Neil, you were correct.
You were correctly observing the use-mention distinction.
No surprise, Mung missed it. I think it’s not taught, or not taught correctly, in high school English.
But clearly you weren’t using scare quotes. It’s obvious from context that you were sincere. Even if we make allowances for the possibility that Mung doesn’t know about the use-mention distinction, Mung still had no grounds for flying off the handle like that.
Too bad for Mung that he chooses to mistakenly attack you for using scare quotes in the same post where he deliberately uses them while insulting us:
Lord, what fools these mortals be.
Aw shucks. I’ve falsely “accused” people of Code Denialism.
Stand up and be counted.
The genetic code is a real code and the genetic code is not the only real biological code. Defend your stance.
Neil, you’re up first.
Give us your definition(s) of code first Mung. Show that you’re not just another equivocator.
I have not idea what I am expected to be defending. And I have no idea what “real code” is supposed to mean.
Indeed. Code Denialism. Thank you.
Aw shucks. I’ve falsely “accused” people of Code Denialism.
Stand up and be counted.
The genetic code is a real code and the genetic code is not the only real biological code. Defend your stance.
petrushka, you’re up next.
Where are your definition(s) of code Mung? Are you going to bore us with the bog standard IDiot equivocations yet again?
In one post Neil knows what a “code” is. In another post Neil denies knowing what a “real code” is.
Code Denialism.
In post after post Mung refuses to give us the definition(s) of code he is referring to. It’s the usual IDiot evasive tactics of those with just rhetorical bullshit to offer.
Meanwhile over at Uncommonly Dense, Mung waddles back to brag to the rest of the IDiots how he stumped the scientifically knowledgeable posters at TSZ.
More IDiot bullshit
Pathetic.
I don’t know why this is difficult to understand.
Code=Goddidit.
Why is that hard to understand?
Yep, that’s bullshit. Goddamn.
Neil never said what Mung claims he did.
It’s a short thread. All anyone has to do is look up.
I mean, I could see getting confused about people’s positions in a thousand-comment thread with lots of complicated replies and sub-conversations. But Mung has no excuse for getting Neil wrong here.
The fact that Mung flew over to ID to crow about it convinces me it’s not just an honest misunderstanding on Mung’s part. Goddamn. Is there any one of them who’s not a walking advertisement for the slogan “religion poisons everything” ?
I’ve not claimed that Code=Goddidit.
Is the belief that Code=Goddidit a good reason to adopt Code Denialism?
Then explain why the definition of code is important.
I started a thread, the main thrust of which is it doesn’t matter.
You had little or no participation in that thread.
Now that you have your own thread, perhaps you will explain whit the definition is important.
It seems to me that the important thing is what DNA does, not what it is called.
Is the belief Code=Goddidit a good reason to make up IDiot lies and bullshit and ignore the actual scientific evidence?
Adapa accused me of a long history of anti-gay bigotry. Adapa was asked to produce evidence in support of that claim. If the evidence was ever produced it escaped my attention.
At least hotshoe_ had the courage to also challenge Adapa’s false claim when it was first posted, a fact that I shall not forget. But now it’s as if it never happened. One wonders what ever motivated her defense at the time.
So while I remain grateful, people who quote Adapa will likewise be ignored.
If you have an argument of your own, make it. No need to piggyback on the claims of lying cowards.
Yes, that’s pretty much why I am ignoring most of what he posts.
petrushka, my very first post in that thread ended up in moderation and never saw the light of day. Didn’t even get sent to Guano. That was my last post in that thread. The current theory is that I requested that it be deleted. I’m skeptical.
Your thread has the title: What Is A Code? You did not answer that question in your OP. Has anyone in that thread answered that question?
When people deny that the genetic code is really a code, or that there are other biological codes in addition to the genetic code, what is it that they are denying?
Definitions are almost always important. If one is to affirm X or deny X, it is important to be be able to say what is being affirmed or denied. Even if one wishes to argue that it is not important whether or not the genetic code is a code, it seems to me that the argument would need to say what a code is and why whether or not the genetic code is a code, in order to make sense of the argument that whether or not it is a code is not important.
But to me, that’s not where we’re at. And that is the point of my OP.
It’s not as if everyone here agrees that the genetic code is a code. It’s not as if everyone here agrees that other biological codes exist. It’s not as if the only question is the import of codes.
First, let’s get beyond Code Denialism. It’s not anything that ought to be taken seriously. Then perhaps we can move on to what the existence of biological codes mean in the context of the debate over Intelligent Design.
DNA doesn’t do anything. The important question is what is DNA for.
🙂
Lots of people did Mung. But I suppose you didn’t see any of the answers either.
Yep. That’s why IDiots will never commit to a definition, because they know they’ll get called on the dishonest equivocation.
So Mung, what is your definition(s) of code as you are referring to it here? How much longer will we get the IDiot Two Step from you?
Good for you. Given that you also ignore most of what you post, the circle is now complete.
Your second post in this thread assured everyone that you were not using scare quotes when you used the “code” word.
One could perhaps be forgiven for making the assumption that at that time you were claiming to know what a code is.
However, your claim that you don’t know what a real code is, is beyond dispute:
Neil Rickert: I have no idea what “real code” is supposed to mean.
Don’t post at UD if you don’t want to be exposed. Here at TSZ you can hide behind “the rulez.”
As opposed to why you gossip at UD where you can hide at a site where almost all pro-science people have been banned. Speaking of lying cowards, why did you lie at UD about what Neil posted here?
Of course brave Sir Mung still won’t post his definition(s) of code.
He was pointing out he didn’t know what YOU meant by “real code” since you’ve been too afraid to provide your definition.
That’s a bit like saying that oxygen doesn’t do anything when it combines with hydrogen to form water.
What does DNA do that isn’t chemistry?
petrushka,
That’s a bit like saying that hydrogen doesn’t do anything when it combines with oxygen to form water.
I think that DNA doesn’t do anything. What do you think DNA does?
Sure. Let’s pretend that Code Denialism isn’t popular here at “The Skeptical Zone.” Let’s pretend that Code Denialism doesn’t exist at all here at “The Skeptical Zone.”
It base-pairs by forming hydrogen bonds between complementary bases. It also folds into a double-helix. This is all chemistry 🙂
Why do you think DNA doesn’t do anything when it clearly does?
@ Adapa
Moved a couple of your comments to guano as they break the rule regarding accusations of lying.
Yeah, whatever, it’s a code.
Mung,
What, again?
Beat that drum until we all agree that ID is the only way to go, and semiosis the banner under which we will march into this new dawn. Where’s Frankie? – c’mon man, grab an end.
Mung writes:
The genetic code is a code.
Who could argue with that? On the other hand, looking at standard definitions, a code is:
here
and
here
*links to this definition: Definition of GENETIC CODE
Mung, words are a shorthand for discussing human-described categories. “Code” (see what I did there?) has several unrelated uses depending on context. “Life” is another word that is so broad that a definition is meaningless. When we look at life, we can consider categories more specifically by qualifying it: human life, plant life, alien life etc. We do the same with “code”. Talking of the “genetic code” is a perfectly clear way of setting the parameters of a discussion of biochemical replication and translation. What information is added by saying the genetic code is a code, other than trying to draw an inappropriate analogy?
Some of us don’t have the choice of posting at Uncommon Descent. I find it most irritating that people might get the impression that the reason I don’t post there is because I can’t rather than I am boycotting the place. (Aside to Neil and any others still tempted to post there. Please support our boycott!).
Participation at TSZ is entirely voluntary, Mung. Any commenter is free, within the rules, to post or not, reply or not, ignore or not any other commenter. I’d like you to either support an allegation that Neil is somehow “hiding behind the rulez” or withdraw it. I can see no evidence whatsoever for such an allegation.
All Mung has done is extract a few quotes which show that people freely use the term ‘genetic code’ (non-scary quotes). As I do myself, and have done since uni days. He is not seriously suggesting we deny that. But nowhere does Crick, Brenner or anyone else appear to discuss whether it is ‘really a code’ (whatever that might mean).
To the extent that they did, I might argue with them, but since they aren’t active in this thread, we are left with quote mines supporting a point that is not disputed – that the term ‘genetic code’ has a long history and is established and meaningful terminology.
Citations? The moderation issues thread awaits.
By other real biological codes, do you mean things like Neural Coding?
According to this theory, the patterns of connectivity in our brains encode our perception and experience in a manner which implements a trade-off between encoding as much as possible of the information in those perceptions and, at the same time, compressing it to minimize the neural resources needed to do so.
I think that would meet your Wolfram-reference (in the Noyau thread) to coding theory as the way to define codes.
So our brains are creating new encodings using the biochemistry of neurons. It is not a pre-created code; each of us has led different lives leading to individual trajectories of perceptions and hence different encodings.
So when I go to a lecture to understand what scientists mean by the genetic code, what I hear is encoded using the neural code. Similarly for the scientists who first created that genetic code as a way of understanding DNA in action (or discovered it, depending on your viewpoint on scientific realism).
Of course the capability for neural encoding is partly based on the genetic code. It’s all codes implemented by codes driven by codes.
Codes, codes, codes, codes! Now my brain hurts. Must be a coding error. Why didn’t the compiler pick that up?
What’s the difference between a code and a real code? Are there codes that are not real codes then?
I wanted to end my last post with the Monty Python allusions, so I’ll use this post to clarfy one point.
I see two separate issues here.
1. Is the genetic code real? The genetic code is part of the theory of the biochemistry of the cell. If you are a scientific realist, and if you think the genetic code plays the appropriate role in the scientific theory of the cell, then you would conclude the genetic code is real. This issue is a philosophical one, not a scientific one.
2. Regardless of your answer to 1, there is the scientific question of how the genetic code developed. That question does not depend on whether you are a scientific realist about the existence of the code. There is an active scientific research program trying to answer that question, it has produced fruitful work, and there is no reason to think it will be a failure in the end. That research program does not use a designer in its theories.
Here is the full content of the “very first post in that thread” which currently sits in trash:
Clearly this is a very important post, and completely settles the issue of what is a code.
</extreme-sarcasm>