I can’t even.
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So, what you are saying is that what makes a code a code is that it began as abstractions in the human mind, hence codes are by definition intelligently designed. But this simply confuses how the method or process for how something comes to exist with the things essential nature. And that just isn’t the definition of a code anyway, that it has to begin as an abstraction in the mind of some intelligent designer(human or otherwise).
What something is does not necessarily tell us how it originated(and the reverse is not a necessary relationship either). There’s nothing that prevents us from just saying the genetic code is also a code, and that categorizing it as one in order to argue in favor of intelligent design merely commits a question-begging fallacy. By categorizing it as something they think is by definition intelligently designed they have merely assumed what they’re being asked to prove. There’s just no good reason to agree to define the concept of a code that way.
It seems to me we really can in some cases separate somethings essential nature from it’s method of origin. What are codes - and how do codes come to be - can be two separate questions. Codes can be codes without having been conceived of abstractly in the minds of intelligent designers.
Some codes can evolve physically and chemically. And the genetic code is a code because of it’s nature: the physical storage of the information required to produce protein sequences, in nucleic acid sequences, in a way analogous to innumerable other codes.
Their defining commonality is this concept of a systematic mapping from one thing to another, and that this is what makes them qualify as a being a code. But this accomplishes nothing with respect to determining how it came to be if we’ve merely begun by defining codes to be intelligently designed.
Then why is the genetic code’s origin in physical and chemical reactions negating my ability to consider in the abstract the concept of the genetic code? Why is the causality only one-way here? Began abstractly → doesn’t negate physical implementation. Began physically → negates abstract consideration. There’s no reason why. I’m pretty sure none of these rules are agreed upon anywhere, are found in no dictionary, and you’re just sort of making them up as you go.
The rules in the computer are all concrete too. Concrete in the genetic code and concrete in the computer. But again you appeal to what has happened in the past - someone at some point made an abstract decision(btw are you sure you don’t actually mean arbitrary here? Because what’s an “abstract decision”?) - to argue why the genetic code doesn’t qualify as a code. Ultimately it’s just a really weird way of defining the concept, by how it began, rather than by what attributes it currently has right now.
Imagine we did something similar with a car. We say it’s only a car if it’s made in a factory, so if someone builds one by hand it’s not a car. So they didn’t actually build one, they built something entirely like a car, it’s just not one. Milk only comes from cows, so if we some decide to recreate it entirely synthetically it’s no longer milk despite having exactly the same constituents.
Can you point to which verse mentions DNA?
Or perhaps you are just saying that those descriptions are so broad, that they fit anything.
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The marks do show the mechanism and they are entirely logical. Change(s) = Branching = mutation(s) including existing variation. That is the mechanism.
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Can you explain how this mechanism logically accounts for the pattern? Considering-
-The waiting times for changes in a population.
-Genes have almost an infinite possible way to arrange their sequences.
-Changes in gene expression and splicing changes
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No, I didn’t specify human. The criterion is abstraction.
I think that you are tying yourself in knots. The essence is the abstraction.
Correct, assuming that you meant “converse” instead of “reverse,” but it’s irrelevant to my point.
Yes, there is. There are no abstractions to be seen. If in 20 years we learn that God definitely provided the abstraction, then it would be a code. Today, it’s a metaphor. Are you aware that metaphors are common explanatory devices in biology?
No, because the distinction applies outside of biology.
I think you’re missing the point.
Name one outside of biology, then, please, and notice that you went from the simple criterion “abstraction” to adding two additional ones. Why?
“Analogous” doesn’t mean “identical.” Analogies are explanatory devices, not arguments.
The word “it’s” is a contraction of “it is.”
It’s irrelevant, because now you’re equivocating between the creation of an abstraction and your later consideration of it. Where did that come from?
Now you’re combining your false equivocation (creation/consideration) with returning to your false claim that “abstract” is the antonym of “physical.” It’s a twofer!
Say, does this abstract painting not exist physically?
The reason is that you don’t understand the basic concepts.
I’m pretty sure you’re projecting, as I just pointed it out in the dictionary link you provided above for “abstract”!
Again:
Thought of apart from any particular instances or material objects; not concrete.
Is that a characteristic of ASCII?
Is that a characteristic of the genetic code?
They are, and they are all implementations of the abstraction, as are the code wheels. We’ve been over this. The initial mapping to create the code was an abstraction. All it takes is one.
I am sure.
Once an initial abstraction in a code is deciphered, the rest can be comprehended more easily. For example, once you are told that the ASCII for A is 01000001, B, C, and D follow sequentially–that sequence is not arbitrary, because it was not designed to conceal anything. The degree of arbitrariness is roughly proportional to the difficulty in deciphering a code. That’s why passwords that are less arbitrary, like your dog’s name, are weaker.
I don’t see the analogy, sorry. You appear to be creating straw men. Analogies are explanatory devices, not arguments.
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Your idea of waiting times relies on the Texas sharpshooter fallacy. Nobody is waiting for a particular gene to be gained or lost. Some gene or other is merely being gained or lost all the time. In the great majority of gene duplications, one of the pair is lost without ever becoming fixed. What you see are the small fraction that aren’t lost. The great majority of non-coding sequences never give rise to new genes. What you see are the small fraction that do and that aren’t lost. Etc.
The other two things you want to consider are entirely irrelevant and/or nonsensical.
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Perhaps it is all in code?
Yeah I don’t care whether you meant only human or not, which was clear from my post if you had read it in it’s entirety. The point remains that you think it’s a code because it began with “abstract decisions” in someone’s mind.
The one that was once in someone’s mind, right? It’s not enough that we can currently create those same abstractions in our minds right now, or on a piece of paper. The abstraction has to have been in someone’s mind in the chronological past? LOL.
I think that you are tying yourself in knots.
Sure there is. They’re the rules that determine why one particular nucleotide triplet maps to some particular amino acid.
This is exactly why I asked you why the physical implementation of, for example, morse code in electronic or mechanical hardware, would count as an abstraction to you, but the physical implementation of the genetic code does not. And this is where you made up a new rule: The past in someone’s mind.
So there we have it. If something specific happened in the past then it would be a code. Hence not a current property of the code makes it a code, but some causal explanation in the past about how the code came to be is what makes it a code.
Hence my analogy to hand-made versus factory-made cars. How did the car come to exist? If by a factory, it’s a car. If by hand, it’s not. Clearly idiotic, but that’s the essence of your argument.
Are you aware that your condescension here is without merit? I really am following this discussion just fine.
But it just isn’t when codes can be physically implemented in hardware and there is no abstraction. Oh wait I forgot, you think what goes on in a computer is a form of abstraction too. Okay, but then the genetic code can be a code too because it also involves abstraction that is physically implemented in a set of physical and chemical rules. Oh wait I forgot, then you made up the rule that it is the fact that a code began as an abstraction(a set of rules) in a mind that makes it a code, not because of some property it happens to have in it’s current physical implementation. In other words, it must have the property of being abstract in someone’s mind, it’s current physical implementation is irrelevant. But then the genetic code can still be a code, because we can still conceive of the genetic code abstractly (we can just make that mapping wheel for the genetic code too, in our minds, and consider the physical and chemical rules in the abstract.
Oh wait new rule! The property of being abstract in someone’s mind must lie chronologically prior to the code’s physical creation somewhere because well why the fuck not? It’s just yet another new made up rule that never was the definition of a code anywhere.
I’m not equivocating when I am asking why it doesn’t count. I’m not saying the two are identical, but I am asking why one counts and the other does not. Merely saying they are not the same does not explain that.
Beginning abstractly, in the mind, is to you something’s “creation” then, right? What you mean when you say a code begins abstractly is that someone thought up the concept of the code in their mind(it’s rules, the mapping), and that this thinking about the code in the mind is the code’s creation. Well excuse me but, isn’t thinking about a code (the part you would presumably call it’s ultimate creation) a form of consideration? I’m pretty sure thinking about something is to consider it, even if those thoughts are not the thoughts that originate the concept.
So it seems to me there is really no equivocation going on, and I have not in this instance considered(heh) “abstract” to be the antonym of “physical”. Though, I must add, that is a common interpretation of the word and there are situations where that really is the intended meaning.
No Mercer, me not understanding the basic concepts(I still do just fine) is not a reason why you think our ability to consider the genetic code in the abstract does not suffice to make it qualify as a code. That makes no logical sense.
I’m talking about the definition of a code, not the definition of abstract.
Yes, and yes. I can in point of fact think of the genetic code apart from any particular instance or material object. Which is my goddamn point here. Why does that not count? Why does me being able to think of the genetic code NOW in the abstract not suffice to make it a code. Why must this thinking lie in the chronological past at the creation of the code in someone’s mind, for it to be a code?
There is no reason why. You are just making that up arbitrarily.
I find that astounding. Implausible, actually.
I know, and I was making that analogy in order to try to explain what I think is wrong with your argument. In order to make it obvious why appealing to events in the chronological past makes for a pretty shitty definition of something, rather than it’s current essential attributes. And I used an analogy for that to make it more obvious.
Someone first thought about the milk → therefore it’s milk. The milk was first produced physically in a cow → therefore it isn’t milk, even if someone can subsequently think about it. Unless we learn in the future someone thought about the cow’s milk before the cow physically made it, then it can be milk again. But until then, it isn’t.
And that children is why the genetic code isn’t a code. Because someone didn’t think about it first.
Your discussion is right that a new gene generated from gene duplication is rare. A rare event however contributes to the waiting time problem as per the Lynch/Behe discussion. An important factor in time to fixation is the mutation rate. This is why Michael Lynch argued for the majority of mutations being neutral prior to gene duplication.
If the Howe diagram was caused by replication and divergence the results of the Lenski experiment would be very different then what we observed. A billion mutations over 60000 generations but only a small fraction (around 30) getting fixed in the population.
Based on the models we have today there is no way to explain the Howe pattern with known natural mechanisms. I conclude that based on current knowledge that humans, mice, chickens and zebra fish do not share common ancestry.
Maybe we should have a competition to see who can design the best Virtual Creationist. 
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This is the waiting time until a specific mutation or fixation happens, which is irrelevant to the waiting time for some mutation or fixation to happen. As you might know but seem to forget, in neutral theory the number of fixations per generation is equal to the mutation rate.
You are very confused. Bacteria are quite different from eukaryotes, with much smaller genomes, stronger selection for efficient replication, and very little junk DNA.
Even if your premise were true (it isn’t), I will note that you are still confusing the pattern of changes with the causes of changes. You can’t go from “known mechanisms can’t account for the changes” to “must be special creation” without ignoring the hypothesis that unknown mechanisms (maybe even God) cause changes in evolving lineages. That hypothesis would fit the data much better than yours. How is it possible for you to fail to understand this? Do all my statements on that subject just wash over you without penetrating your brain?
If I had read it in it is entirety? That makes no sense.
It’s (hey, you used it correctly there!) not what I think, it’s the definition:
a system for communication by telegraph, heliograph, etc., in which long and short sounds, light flashes, etc., are used to symbolize the content of a message: Morse code.
a system used for brevity or secrecy of communication, in which arbitrarily chosen words, letters, or symbols are assigned definite meanings.
That symbolizing is the abstraction common to all codes. Secret codes are a subset of codes in which the abstraction is arbitrary.
There are no such abstractions in the genetic code. We can, and do, describe them in abstract terms all the time. Denoting adenosine with A is a code.
In the cell, there are no human rules. It’s all non-abstract interactions between molecules.
Yes, if it involved an abstraction.
No, the abstraction remains in the code and is generally obvious. Using 0100001 for A is an obvious abstraction, whether your keyboard does it electrically or you do it in your mind. Didn’t a person/committee make that completely abstract rule in the past?
I know. Your failure to understand “abstract” is at the heart of your failure to understand the definition of “code.”
Yes and no. “Think” is present tense. “Thought” is past tense. We’re talking about their origins, not how we think of a code after it has been created.
Really? Many definitions involve past actions. Are you really not aware of this? Is Finnish like my barely-enough-to-get-by Spanish or Portuguese, in that I only use present tense?
Not even remotely analogous, because the milk is not the product of the thought. You’ve got quite a cognitive block going there! And again, analogies are not arguments.
“Conspiracy” is more analogous because it is defined entirely by what people thought and did in the past:
1 : a secret plan made by two or more people to do something that is harmful or illegal
The CIA uncovered a conspiracy against the government.
2 : the act of secretly planning to do something that is harmful or illegal
They were accused of conspiracy to commit murder.
So is that a ridiculous definition because it requires people thinking of (and doing) something in the past?
Objecting to a definition having a temporal component makes no sense, sorry.
No, you completely misunderstand. The rate at which spontaneous gene duplication mutations occur is actually quite high, but the rate at which new gene duplications get fixed is much lower than the rate at which the mutations occur because they’re mostly just lost to genetic drift.
There is only a waiting time problem if you’re waiting for a particular duplication, rather than just some duplication.
And that’s exactly why waiting for particular pre-conceived target genes to be duplicated commits the Texas sharpshooter fallacy.
A much more important factor still is the idea of picking out particular genes and waiting for their spontaneous duplication to become fixed, rather than just waiting for just any of the many duplications that nevertheless occur, to become fixed.
Please try to wrap your head around the difference between the specific and the general. Waiting for specific outcomes takes a long time, while waiting for just any equivalent outcome is much faster.
That statement is completely nonsensical. If the divergence of genes in the Howe diagram owed to divergence of duplications, that having occurred in the past to give rise to those genes wouldn’t somehow magically travel through time and alter what has occurred in the Lenski experiment. You’re not making any sense.
Incidentally the data depicted in the Howe diagram DOES owe to the divergence of the included species, since the pattern of gene gain and loss fits a tree
Some of the novel genes are diverged duplicates that are no longer detected as homologous because they’ve diverged too far, or moved to alternate chromosomal locations. Some of them are novel genes that owe to things like recombination and fusion of fragments of other genes, some of them evolved de novo from junk DNA, and heck, even some of them are likely to be false positives.
So what? How is that a problem again Bill? It’s a completely meaningless number because you don’t know the rate at which genes that can’t be detected as homologous due to de novo evolution, recombination and fusion, mutational divergence, and chromosomal relocation, evolves.
Merely calculating how many mutations that happens in some amount of time tells us none of that. You simply have no idea how one number relates to the other, so you have zero basis for claiming there is any problem. Instead you just have some completely baseless belief that novel genes evolving is incredibly rare and infrequent.
That is just flat out false. There is nothing in any current model that supports that statement.
That’s hilarious because Michael Behe, who originated the arguments you are relying on, still thinks they do. What do you know that Michael Behe and pretty much the entirety of the rest of the worlds molecular biologists, biochemists, and evolutionary biologists don’t?
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That is only partly correct.
The rarity of gene duplication did not factor at all into Behe’s analysis, because he assumed the population started out with a fixed number of duplicate genes, and assumed that this number remained constant (i.e. if one gene duplicate was removed from the population, another one would instantly appear.)
Lynch, OTOH, started from the point before a gene was duplicated, and included the time spent “waiting” for this to happen in his analysis. On its own, this increased the waiting time that would be calculated in his model. But because his other parameters more closely approximated what is observed in reality, his waiting time was still orders of magnitude lower than what Behe calculated.
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Hi Rum
Can you provide evidence for this that quantifies the rate of duplication in vertibrates. Thanks.
That may have been part of the reason Behe came up with such unrealistically large numbers, but not the only one and maybe not even necessarily the main one. If you read Lynch’s response, he can’t even figure out what Behe was trying to do. It appears Behe and Snoke just used a bunch of equations they made up and which are not part of standard population genetics. At least, that’s how I understand what Lynch wrote.
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While true, that’s a bit deceptive. The diagram is of orthologous genes, so detectable paralogs still count. And I suspect that the majority of the genes in that picture do have paralogs in the same genomes.
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The Howe diagram was derived from (not caused by) a very incomplete dataset. You appear to be using it to avoid most of the relevant data.
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My understanding is that part of the detection pipeline involves looking at synteny, so it is possible there are some genes that are missed as paralogous in some species because low overall similarity at the locus.
Of course. One of the biggest problems with the figure is that it only shows 4 species. With more primates, rodents, birds, and ray-finned fishes, the numbers of “unique” genes would go down a lot and we would just see the majority of these novel genes proliferate in numbers in their own clades over time.
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