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…
Who argued that we should base science on word endings? I’m only saying that there is no reason to pretend that the existence of a code does not suggest a coder.
Why is the mere suggestion so threatening?
peace
Who ever said the genetic code isn’t a code? There is more than one definition of “code”. DNA happens to be one that doesn’t use symbolic notation and doesn’t require an intelligence to produce.
There is no reason to pretend that the existence of a non-symbolic coding process requires an intelligent coder either.
Actually, you simply have no argument, it’s just a dumb equation of a false assumption with another false assumption. It isn’t even based on word endings, it’s just based on nothing except for your closed set of assumptions.
I’m only saying that there is no reason to pretend that the existence of a code does suggest a coder. Which is the true statement, not your presupposition.
Why would you portray your pathetic word-game as a “suggestion,” when it’s just a repetition of an old, unsound creationist claim?
The lack of an argument, replaced by mere assertions, is what is threatening to honest discussion. If you wanted to make a decent argument, that would be entirely different, and a welcome change.
Glen Davidson
I see Mung has been busy posting and creating new threads. Pity he couldn’t find the time to post his definition(s) of “code” and “real code”. Not surprising. It’s almost like he’s embarrassed to have been caught bullshitting so badly and is now hoping this thread scrolls into oblivion.
fifthmonarchyman,
Such as? This is a point I have raised before. What do we gain, scientifically, by agreeing it is a ‘real’ code? I mean, we know in great detail what it is – a system whereby c20 AARS enzymes take a subset of the tRNA set each and stick an amino acid on the end, which then bind to mRNA – and people have been calling it a code, including me, for years.
But it’s not really a code! Which is to say a communication or encryption system, a series of protocols, a set of computer instructions or a set of private or public principles. It is what it is. Enzymes sticking specific amino acids on specific RNAs, and them docking against mRNA. A codon ‘represents’ an amino acid the same way someone’s shoes represent their hat – or rather, the impression those shoes make in wet cement.
The definition of ‘code’ has been extended to include the genetic version – a sign that the existing definition was insufficient to contain it. Definitions change of course, but this is fundamentally a semantic point, not a scientific one. I don’t think it’s a ‘real’ code in the same sense that I lament the synonymisation of ‘infer’ and ‘imply’ – as a fairly trivial semantic point. I won’t go to the stake over it, but it’s a perfectly respectable opinion. Other people’s opinions on word usage are equally valid (let’s not get into whether there is One True Definition in the mind of God!).
To label people who do not accept a kindergarten view to be accurately representative of cellular processes as ‘anti-science’ (or ‘pathetic’, ‘desperate’ etc etc) is rich.
Oh? What exactly are those “implications”?
Seems to me it’s quite clear what those implications are. You just said so yourself. But, given that you never once claimed that an existence of a code in the genome proves that God exists I have to wonder what those “implications” actually are.
Please tell.
And if acknowledging that the genome is a code could lead to all sorts of useful scientific advances, then that’s been done already by many people. So the reason Larry’s comment applies to you is that you are in a position of ignorance in comparison to some of the people here, and you think you know better then them. E.G. telling them that it’s really a code and they’d do much better scientifically if they just accepted that fact. You don’t know what you are talking about, again.
fmm,
Plenty of people like you have said “if you’d acknowledge the reality of intelligent design then science would advance much faster”.
Yet they never seem to be able to actually point to a case where that has been true. UncommonDescent is full of claims like this. And that’s all they are – empty claims.
So, once again, in what specific way will acknowledging the genome is an intelligently designed code advance science?
If you can’t say, on what basis are you making the claim?
http://www.wired.com/2015/07/crispr-dna-editing-2/
Honest discussion is threatened when I don’t offer an argument to establish a fact that is not in doubt. How so?
We all know that 2 plus 2 equals 4. Honest discussion is not threatened when I merely assert that 2 plus 2 is 4.
A code suggests a coder. The same way a cake suggests a baker.
A coder does not prove that coders exist any more than a cake proves that bakers exist. It does not have to. We all know that coders and bakers exist.
It’s possible a code (or a cake) could arise spontaneously for the same reason that it’s possible you are a Boltzmann brain. Anything is possible.
I prefer to assume that I am not a Boltzmann brain and that cakes and codes don’t arise spontaneously from the primordial soup.
By the same token when I hear about the discovery of some Yellowcake uranium I don’t feel obligated to wax eloquently about the many differences between chocolate cake and Yellowcake.
I simply assume both cakes had a “baker” and move on
To each his own.
peace
Yes, and here the environment was the coder. Do you dispute that?
Spontaneous creation is what you believe. A “code” springing into existence all in one go is what you think that biologists actually think happened. They don’t. You are misinformed.
That’s correct. They don’t. And again that’s your ignorance speaking.
Please tell me what biologists think that the DNA code arose spontaneously all in one go?
If you can’t you are now on notice that your claim is wrong and you are in deliberate error if you repeat it.
That does not even make sense. But do nuclear reactors require a designer?
And that’s why your particular brand of ignorance had no involvement in getting us to the world we currently see about us. You are happy with your first answer.
Who is that coder? God? Please be clear, don’t be coy. If you have a claim, even if it’s not scientific, just say it!
If it’s not “god” them what are the implications of “admitting” it’s a code?
not at all.
I long ago said that the whole issue boils down to the argument about other minds. Do you think that “the environment” is an agent?
I never said anyone believed a cake or a code sprang into existence all at once. What ever gave you that idea?
What exactly was the function of the code before it became a code?
My worldview gave birth to science. Yours is a johnny come lately parasite on mine.
If you disagree tell me how you know and I’ll fire up the bot
I don’t have a claim. But I already said that
There are no implications of admitting it’s a code as far as I can tell. That is why I am a little confused at the reluctance to do so. I think it has something to do with not giving the other side even an inch
peace
Define agent.
you saying this:
So what are you saying? That codes can evolve? That seems to contract your suggestion that we take seriously they are designed.
You are confused.
That’s what you tell yourself. Yet your “worldview” enabled nothing more then thousands of years of serfdom.
If you are a representative of your “worldview” then it’s clear you don’t understand science. That’s all the evidence I need.
So you are happy to accept that codes can evolve?
Are all codes intelligently designed? That’s what the reluctance is about. If you say “yes” then of course I’m not going to agree that it’s a code in that case.
I’m not sure how much more simply I can put this.
Just answer yes or no:
Are all codes designed?
Is DNA a code?
It’s really due to the fact that “your side” has so little to go on that the everyday language used to discuss science can be abused by you and yours to claim support that is not present.
The gap you are hiding in is small.
I see your out here as “the designer probably had more then one version of the code” so that’s how it’s possible that “codes have coders” and “I prefer to assume that I am not a Boltzmann brain and that cakes and codes don’t arise spontaneously from the primordial soup.” can be true at the same time.
Yet your weasel words cannot hide the fact you cannot name a single entailment from your suggestion that we treat the genome as a “intelligently designed code”.
fifthmonarchyman,
Answers absolutely nothing. We have known for years about genetic engineering techniques, and the mechanics of transcription and translation. The Crispr system is not directly connected to the genetic code, other than being ‘something to do with DNA’.
I ask again: what do we gain by calling the genetic code a code? How did that influence the approach of the people involved in elucidating or utilising Crispr editing or anything else? In your own words.
design and evolution are not mutually exclusive concepts
http://www.merriam-webster.com/dictionary/agent
I’m unaware of any that are not designed but just because I’m unaware of something does not mean it doesn’t exist.
I see, You will deny it’s a code so as to not give the other side even an inch. Even if your denial is anti science.
In my limited personal experience yes
yes.
peace
fifthmonarchyman,
You will find virtually no-one, other than constructors of straw men, who advance the argument that they do/did.
fifthmonarchyman,
No, it has to do with being entitled to a semantic viewpoint. Appeal to motivation again. It’s a code of sorts, but in significant respects, it’s not. Why do you struggle to concede even that inch to the other side?
More weasel words. Did I say that they were not?
What evidence do you have that intelligent design was involved in the history of life?
That’s correct. Now, let me re-phrase the question again.
Is it your opinion that codes have to be intelligent designed, they cannot arise without intelligent involvement? As we see later, your answer is yes.
No, what I’m denying is that it’s what *you* mean when you say it’s a code. When you define fmm-code then I’ll say one way or the other.
Until they you are just abusing the meaning of words.
Which is why I’m not agreeing that DNA is a fmm-code.
So you think that I’m being anti-science by not agreeing with you that DNA is a designed code?
Presumably you think that’s how science is done. Twist words until your opponent inadvertently agrees with you.
fmm can either do the honest thing, withdraw this claim, or he can provide support for it.
Either way, I look forwards to his response.
I did not see “disembodied intelligence that can live for billions of years.”
I was hoping FMM would finally come up with an argument that didn’t rely on a dishonest equivocation of the term “code”. Alas, it was not to be, We’re getting the same old IDiot word games. Sigh.
There is a bit of a tendency to elide into between meanings of the loose term ‘code’ when talking of ‘the genetic code’. ‘Real code’ or not, it is quite specifically the codon mapping of such DNA as ends up copied to final-edit mRNA and lies between Start and STOP when the same is passed through a ribosome to construct a peptide, perhaps or perhaps not also including posttranslational modifications.
One may talk of other ‘codes’, such as promoters, repressors, methylomes etc etc, but they are not ‘The Genetic Code’ (TM). That is reserved for triplet associations with amino acids.
Well, that’s just it, once again you ignore the step of providing evidence and making an argument, instead merely stating falsely that it is not in doubt (presumably the childish claim that a code requires a coder–which wasn’t actually in the word-game, but we all knew what was meant).
You don’t do decent discussion, you merely assert and claim that your presuppositions are the truth. It’s appalling.
You don’t have to claim that 2 plus 2 equals 4, because it is simply true. You claim that your false claims are the same as 2 + 2 = 4 rather than do the required work to show that it is so.
Why would it? Just because there are codes that have coders doesn’t mean that when we find a code sans obvious coder (and a whole lot of related phenomena not reflecting intelligence) that it necessarily has a coder. It’s really a sort of animism (as ID/creationism typically practice it) that insists that because we’ve only seen humans (or other animals) do a thing placed into a particular category (motion, coding) that it must be a human or superhuman (superanimal perhaps) that made this thing that really is quite a lot unlike what humans have made (but we categorized it with human-made forms–so what?).
That’s your really bad thinking, yet again. You only assert, and then claim that others are inconsistent for not following you down into the abyss of the unthinking.
Your fallacy is to move from the specific to the general sans justification. There’s nothing inherently wrong with saying “design is to designer as code is to coder,” it’s simply the logic of language. What you so badly fail at is in simply assuming that if we call something a code that it must have had a coder. But the genetic code wasn’t a code until we decided that certain things were codes and figured that the genetic code categorized better with “code” than with our other categories. So codes are good for storing information. That’s why life has the genetic code. It’s the functionality that matters, and your pretense amounts to the idea that this functionality must have an author simply because other functionality does. It fails completely as logic.
More importantly, it could have evolved. We have evidence that it evolved, no evidence of intelligence behind it.
And no one here really cares about your assumptions, because we prefer establishing facts rather than assuming them.
Yeah, that’s your logic. The fact that both are “cakes” are what matter to you, not the processes of making them. Well, “yellowcake” exists in nature with no obvious “baker” whatsoever, in pitchblende. It’s not called yellowcake in that (the mineral) form, yellowcake being more a trade name, but it still exists in pitchblende without any “baker” intervening.
No, actually many of us prefer to come to agreement via sound epistemologies and solid science. You may have your own unthinking beliefs, what’s annoying is that you give us no good reason to accept them, yet you parrot them as if they were meaningful.
Glen Davidson
Do you think that Crick would agree with you that DNA is a code that requires an intelligent designer? That it is an intelligently designed code? As that’s how you are defining “code”, as we found out in this comment.
So, given that, do you still say that Crick said that the genome is an intelligently designed code or do you withdraw that?
Think carefully, your eternal fate may rest upon this single decisions…..
What claim?
I’m not sure what your objection is about. Are you concerned about my use of the phrase “primordial soup” or are you concerned about my use of the word spontaneously?
Spontaneously does not mean all at once. It can be very slow and gradual.
from here
http://dictionary.reference.com/browse/spontaneous
quote:
Spontaneous- coming or resulting from a natural impulse or tendency; without effort or premeditation; natural and unconstrained; unplanned:
end quote:
The opposite of spontaneous is planned
Are you saying that the the Genome did not arise spontaneously?
By the way what was the function of the code before it was a code?
peace
I never once said that a code requires a designer. You are arguing with a phantom fundy of your own construction and not me.
I only said that codes in my limited experience codes are the result of intelligent design.
What evidence do you have that the genetic code evolved?
What was the function of the code before it became a code?
How can evolution occur if there is no code to carry the mutation?
peace
I did not ask about a “disembodied intelligence that can live for billions of years” I asked if you thought “nature” was an agent?
peace
from here
https://en.wikipedia.org/wiki/Uraninite
quote:
Uraninite is a radioactive, uranium-rich mineral and ore with a chemical composition that is largely UO2, but due to oxidation the mineral typically contains variable proportions of U3O8. Additionally, due to radioactive decay, the ore also contains oxides of lead and trace amounts of helium. It may also contain thorium, and rare earth elements.It used to be known as pitchblende —————-
Uraninite is a major ore of uranium.—————Uranium ore is generally processed close to the mine into yellowcake,
end quote:
peace
from here”
quote:
I note a commenter at Uncommon Descent calling himself Virgil Cain has asked Larry Moran
Do you think the genetic code is a real code (like Morse Code is a real code)?
and Larry Moran responds:
Yes. That’s how I describe it in my textbook.
end quote:
peace
You’re the one who made the faulty claims (ignoring all that had been written before, since you utterly lack manners), so suck it up and provide evidence for your claims. I’m not here to feed you knowledge that you’ll either ignore or dismiss based on your made-up beliefs.
Glen Davidson
Yes, pretty much what I wrote, you dolt.
Glen Davidson
Perhaps I should note that the important fact of yellowcake is that it is U3O8, and as the Wiki page noted, U3O8 is present in the uraninite (or pitchblende), since FMM seems typically ignorant of what he writes. In essence, that’s yellowcake, what people are buying when they buy yellowcake.
No baker. FMM is wrong about that, as typical.
Glen Davidson
what claims?
quote:
Uranium ore is generally processed close to the mine into yellowcake,
end quote:
So? gluten is present in wheat, that does not make it chocolate cake.
from here
https://en.wikipedia.org/wiki/Yellowcake
quote:
Yellowcake (also called urania) is a type of uranium concentrate powder obtained from leach solutions, in an intermediate step in the processing of uranium ores. It is a step in the processing of uranium after it has been mined, before fuel fabrication or enrichment. Yellowcake concentrates are prepared by various extraction and refining methods, depending on the types of ores. Typically, yellowcakes are obtained through the milling and chemical processing of uranium ore forming a coarse powder which has a pungent odor, is insoluble in water and contains about 80% uranium oxide, which melts at approximately 2880 °C.
end quote:
why does this stuff have to be so hard?
peace
How about all of them? But especially the one about a code meaning that there is a coder, even the genetic code.
Yes, dullard, I didn’t say that U3O8 was actually called yellowcake, I said that it wasn’t.
Obtuse as usual. Yellowcake is U3O8, essentially nothing else. When it says “gluten” on the bag it had better be gluten.
from here
Yes, moron, that’s what is sold as yellowcake. The same damned thing exists in pitchblende, but clearly it’s not processed for sale at that point.
I don’t know, because you’re really dumb? Or is it because you’re too stubborn to admit that the same thing is found naturally? I said it wasn’t called the same thing, noting the point about minerals and trade names, and you just blither along as if I hadn’t noted the non-chemical differences between the two. I wouldn’t have mentioned them if I didn’t know, but you’re either too stupid to, or simply unwilling to, read what I wrote for comprehension.
I never claimed that the presence of code means there was a coder.
I only pointed out that in my limited experience code comes from coders,
Exactly, “processing for sale” is the sort of thing bakers do.
peace
Look, no one cares about your weaseling BS. You wrote:
No, you weren’t straightforward, you just wrote as though other than a Boltzmann-brain type appearance of codes it would require a coder. So cut out the literalist excuses, they’re neither clever nor a part of reasonable discussion.
fifthmonarchyman:
Baker’s bake cakes, dullard. In making yellowcake the point is pretty much to make sure that it has the right form and chemistry, namely, U3O8.
Your “argument” amounts to saying that any existence of lead yellow implies a lead yellow-maker, because titanium isn’t found in nature. Oh no, because the same chemical found in nature is called “crocoite,” not lead yellow. So the chemical just happens to be found in nature, but clearly not as a dye–and so is U3O8 (as in, you could separate it out, mechanically process it in a certain manner, and it would then be yellowcake–which, as I noted, it wasn’t called when part of the rock, common when “minerals” are turned into “chemicals”). All you do is blither on meaninglessly, since you don’t even begin to think properly, let alone discuss anything as you should.
Glen Davidson
GlenDavidson,
I don’t think FMM is a dullard or a moron or a particularly awful person, but his posts are awash in result orientation. He will not leave his goal for a moment and just, you know, “disinterestedly” watch the sky or crack a science book. It’s this “presuppositionalism” that makes him so frustrating. Even when he says “I’m not saying X” he’s suggesting X with every breath in his body.
GlenDavidson,
I can’t edit the referred-to post now, so note that it should be “yellow lead” where it says “lead yellow” and also where it says “titanium.”
Glen Davidson
Well, depends on what is meant by “dullard” or “moron.” If it’s results, as it tends to be when you’re dealing with such wretched nonsense, then it really is the result of poor thinking, at least. If it’s a general statement, sure, there’s no reason to think he’s dumb, just not interested in thinking well.
And that’s just it, one ends up with endles pointless arguments based on the opposite of any good discovery mode, and so much verbiage is written (iow, time spent when one doesn’t want to deal with such dumb stuff), over basically nothing at all.
Glen Davidson
You posted this evasion before. Moran was speaking of the superficial similarities, both have outputs which map to their inputs. You were asked to explain the differences between Morse code and the genetic code. You were also asked for your definition of “real code”.
You ignored the questions and kept right on with the dishonest equivocation.
I should also note that one often writes “dumb” or the like here when “bad faith” or “intellectual dishonesty” might be preferred. Rules, you know.
Glen Davidson
1) I think that would be your job?
2) there are lots of differences for example
a) Morse code was invented in the mid 1800s the genetic code appeared much earlier.
b) Morse code works with dots or dashes the genetic code works with cytosine, guanine, adenine, or thymine
c) In Morse code one sequence of dots and dashes corresponds to just one Latin letter the genetic code is much more flexible and robust with lots of ways to get to a particular protein.
All codes have differences and similarities analogy is about similarities.
Off the top of my head I would say a “real code” is a set of rules by which outputs map to corresponding but somewhat arbitrary inputs.
hope that helps
peace
Here is the deal. We see the world from polar opposite perspectives. You begin with you (as judge) I begin with God, there is no way to bridge that gap between us.
You will never be argued into admitting that God exists and I will never be argued into denying his existence. This is just a fact of life.
Frustration results when you expect me to act as if God’s existence is an open question when his existence is undeniable.
Face it that is not going to happen.
These discussions will be more fruitful if you all can just relax and learn to accept that that is just the way it is . The same way I accept that I won’t be able to lead you to Christ with some magic argument that you haven’t heard before.
What we can do is try to get past the tired old culture war footing live in peace with each other as much as possible and work together in the places where our perspectives overlap.
I think our perspectives overlap when it comes to an interest in science. I would hope we could discuss science here.
peace
You omitted the crucial one. Morse code uses arbitrary symbols to abstractly represent letters of the alphabet. There are no arbitrary symbols, no abstract representation of anything in DNA’s function. Only the former requires an intelligence to decide and assign the symbols and abstractions.
Analogies aren’t evidence.
So having DNA be a “real code” isn’t an indication it was intelligently designed. Got it.
I’m fine with that.
I never said they were
I would disagree. There is no necessity in the DNA to protein connection ever hear of RNA world?
Proteins can and do arise in the absence of DNA. and then there is this
http://www.wired.com/2015/07/chemists-invent-new-letters-natures-genetic-alphabet/
peace
More weaseling. You posted the Moran quote about Morse code being like genetic code twice. If that wasn’t trying for evidence by analogy what was it?
Then show us the arbitrary symbols and where they are used as abstract representations in DNA or RNA.
It was to show that the genetic code is a code
Is this what you are looking for?
https://en.wikipedia.org/wiki/DNA_digital_data_storage
peace