DNA duplication, mutation, and information

[Dan_Eastwood]

@colewd

Can it falsify it in a practical way? I think so if you can build a mathematical model that explains it. Although you could make the same comment with gravity that we can not eliminate Gods actions we can attribute most of the observed action to the properties of matter.

ID cannot be falsified by demonstrating evolution. Not being able to eliminate God’s actions is exactly the point.

@colewd

In the case of a 3D printer the generated code is algorithmically processed to form a function. The same case for biology. The laws of chemistry are not the sole determining factor. It’s also the architecture of the cell that determines the outputs such as protein synthesis and reproduction.

In both cases algorithms are involved vs direct mental interpretation. The ultimate source of the original code and the code receiving algorithms can be inferred to require a mind.

Don’t be silly. Think about the implications of what you just wrote with regard to chemistry.

[Faizal_Ali]

@colewd

In both cases algorithms are involved vs direct mental interpretation. The ultimate source of the original code and the code receiving algorithms can be inferred to require a mind.

You, along with every other ID proponent, have not substantiated that inference. Could you please spell out your reasoning behind this supposed inference? Be as specific as you can.

Helpful hint: If we know for a fact that some swans are black, it still does not mean that most swans are not white.

[colewd (Bill Cole)]

@Dan_Eastwood

ID cannot be falsified by demonstrating evolution. Not being able to eliminate God’s actions is exactly the point.

Science cannot eliminate any cause as it is tentative. If a mechanism is identified that explains the observation then it can be tentatively attributed as the cause. Biology can certainly tentatively infer the transcription translation mechanism without invoking God as a direct cause.

@Dan_Eastwood

Don’t be silly. Think about the implications of what you just wrote with regard to chemistry.

This simply may be a difference in how we define Chemistry. You may be using a broader definition for rhetorical reasons. If you want to try to support your claim it is only chemistry a working definition would be required. We all need to be careful of labeling fallacies.

[colewd (Bill Cole)]

@Faizal_Ali

You, along with every other ID proponent, have not substantiated that inference. Could you please spell out your reasoning behind this supposed inference? Be as specific as you can.

I think I will avoid getting into a you “got to do better than that” loop. If you don’t think the explanation is adequate for what ever reason I will accept your opinion. To me the inference is obvious.

[scd]

@Rumraket

using nothing but the frequency with which the function exists in protein sequence space, in total ignorance of any knowledge of starting point, mutation spectra, natural selection, or anything else that clearly would be relevant.

@Michael_Okoko

The calculation appears to have nothing to do with the evolution of the N-terminal domain of lambda repressor, just its formation from scratch. However, we know the protein did not emerge spontaneously, it most likely evolved from simpler precursors, so the calculation is irrelevant to the origin of its fold or any other fold in nature

@Mercer

I don’t see how. What I do remember is that there aren’t that many different folds–they are greatly outnumbered by the number of different functions. The immunoglobulin fold is a fine example of this.

hey guys, there are many topics here so i will try to stay on focus. lets take a specific case such as new organ. suppose that we need for that at least 2 match changes. first we need to agree on that number. i dont think its possible to evolve a new biological system (such as new organ) by only a single change. this seems to be impossible, like getting a flagellum from non flagellum by a single change (or by analogy like getting a cell-phone from a GPS (or any other complex object with different function) by a single change). so do we agree on that so far?

@Witchdoc

Both Homoplasy and Homology are types of similarity. If common descent were true, we would expect to see mainly Homology, with some Homoplasy, and that is what we see

there are few problems with that argument. for instance: according to that paper (at least at the morphological level) homoplasy is more common than homology (fig 1):

https://www.sciencedirect.com/science/article/abs/pii/S0169534704001429

so even if homoplasy was more common than homology at the molecular level- it will not be a problem for evolution. there are other issues with that argument but i realy dont want to get into them right now.

[Michael_Okoko]

@scd

lets take a specific case such as new organ

From protein folds to organs and the cycle continues.

@scd

suppose that we need for that at least 2 match changes. first we need to agree on that number

We don’t agree. Why should we agree to this?

@scd

i dont think its possible to evolve a new biological system (such as new organ) by only a single change

But you cited a paper that showed exactly that: the Starr paper wherein SRE-specificity was achieved in one mutational step from ERE-specific ancestors by some variants. In addition, “single change” is vague: it could something as trivial as a single amino acid/nucleotide substitution or large scale event like a single whole genome duplication event; it might even be a single recombination event.

I am not saying single changes are sufficient in all cases, but evolution happens with them as well.

@scd

this seems to be impossible, like getting a flagellum from non flagellum by a single change (or by analogy like getting a cell-phone from a GPS (or any other complex object with different function) by a single change). so do we agree on that so far?

Its not impossible, but is certainly not applicable to all evolutionary events that transpired in the last 3.5 billion years.

Furthermore, stop attacking strawmen. No one here has ever argued flagella arose via a single change, so its pointless to even mention it. So no, I don’t agree to any of the strawmen and baseless assumptions you keep making here.

[scd]

@Michael_Okoko

But you cited a paper that showed exactly that: the Starr paper wherein SRE-specificity was achieved in one mutational step from ERE-specific ancestors by some variants.

that was not a new function. only a reduce in function actually. im talking about new function that was not existed before.

@Michael_Okoko

I am not saying single changes are sufficient in all cases, but evolution happens with them as well.

ok. so im talking about these cases were it was not possible. and there are probably many such cases.

[Michael_Okoko]

@scd

@Michael_Okoko

But you cited a paper that showed exactly that: the Starr paper wherein SRE-specificity was achieved in one mutational step from ERE-specific ancestors by some variants.

that was not a new function. only a reduce in function actually. im talking about new function that was not existed before.

I’d suggest you take a starter course in biochemistry, because everything you wrote up there is pure BS.

First, the transition from ERE-specificity to SRE-specificity is a gain of new function.

Second, there was no reduction in function, just a change in ligand type (the ancestral ERE-specific receptors and derived SRE-specific receptors still bind steroids and hormone response elements {HREs}, only different HREs now). In fact, as the study showed, some other possible SRE-specific receptor variants performed better than the historical one.

Third, the SRE-binding function didn’t exist until evolution rewired the steroid ligand preferences of ERE-specific receptors. So yes, it meets your definition of a new function.

[Michael_Okoko]

@scd

@Michael_Okoko

I am not saying single changes are sufficient in all cases, but evolution happens with them as well.

ok. so im talking about these cases were it was not possible. and there are probably many such cases.

Of course there would be cases where a single change won’t suffice and this is a fact we all agree to, so why do you keep bringing it up?

Furthermore, the relative instances of single changes to multiple changes is irrelevant, because evolution works with all of them.

[Mercer (John Mercer)]

@scd

@Mercer

I don’t see how. What I do remember is that there aren’t that many different folds–they are greatly outnumbered by the number of different functions. The immunoglobulin fold is a fine example of this.

hey guys, there are many topics here so i will try to stay on focus. lets take a specific case such as new organ.

Which one?

@scd

suppose that we need for that at least 2 match changes.

Why would we suppose that? Let’s focus on your supposition.

@scd

first we need to agree on that number.

Why aren’t we looking at a known organ?

@scd

i dont think its possible to evolve a new biological system (such as new organ) by only a single change.

I don’t think that your assumptions about how organs evolve is consistent with reality.

@scd

so do we agree on that so far?

No.

[Faizal_Ali]

@colewd

I think I will avoid getting into a you “got to do better than that” loop. If you don’t think the explanation is adequate for what ever reason I will accept your opinion. To me the inference is obvious.

I really didn’t expect that you had an actual argument. I was quite sure you were bluffing as usual. But I thought I’d be fair and give you a chance.

So can we expect you, in the future, to refrain from making this claim since you are unable to defend it?

@scd

so do we agree on that so far?

I don’t. If we are going to be simplistic about it, at some point something went from being not what you consider a flagellum to being a flagellum.

I see no reason that the difference could not have been a single mutation. So you need to substantiate your claim. It would probably be helpful as well if you had a rigorous definition of “flagellum” and “not-flagellum” if you are going to insist on thinking dichotomously on this.

[scd]

@Michael_Okoko

Third, the SRE-binding function didn’t exist until evolution rewired the steroid ligand preferences of ERE-specific receptors. So yes, it meets your definition of a new function

are we talking about the same paper? i was referring to this one actually:

https://science.sciencemag.org/content/312/5770/97.full

“Using ancestral gene resurrection, we show that, long before the hormone evolved, thereceptor’s affinity for aldosterone was present as a structural by-product of its partnership withchemically similar, more ancient ligands.”

@Michael_Okoko

Of course there would be cases where a single change won’t suffice and this is a fact we all agree to, so why do you keep bringing it up?

because i think there is a time problem here for evolution. if we agree that at least 2 parts are needed in order to evolve a new organ (or any other complex biological system), then we need to calculate how long it takes to evolve them. so we need to calculate how many mutations are needed to evolve a single part and then multiple it. so if the chance to get a new functional part is say one in a billion, then we will need billion^2 mutations to get that new organ.

@Mercer

Why would we suppose that? Let’s focus on your supposition.

@Faizal_Ali

I see no reason that the difference could not have been a single mutation. So you need to substantiate your claim. It would probably be helpful as well if you had a rigorous definition of “flagellum” and “not-flagellum” if you are going to insist on thinking dichotomously on this.

well, can we make an object move in the direction of light just by adding or changing one component? if we cant do that then its not possible in animals either.

[colewd (Bill Cole)]

@Faizal_Ali

I really didn’t expect that you had an actual argument. I was quite sure you were bluffing as usual. But I thought I’d be fair and give you a chance.

So can we expect you, in the future, to refrain from making this claim since you are unable to defend it?

This subject has been litigated many times over the years. People have different opinions whether the design inference is viable. Harry can infer design from the observation but Pete cannot. I have tested this with secular friends and after reading Behe’s book they all agree the design inference is legitimate.

What argument that takes realistic observations into account would convince you? If you take a hyper skeptical position you can categorically deny evidence is evidence and we end up in a stale mate.

[Mercer (John Mercer)]

@colewd

People have different opinions whether the design inference is viable.

Those who do tend to ignore the vast majority of evidence while blatantly misrepresenting critical pieces of the objective evidence itself. Dembski is a fine example of that.

It’s not a difference in interpretation.

[Faizal_Ali]

@scd

well, can we make an object move in the direction of light just by adding or changing one component?

Sure.

You’re building the object, one component at a time, and it can’t move in the direction of light.

Then you add one more component, and it can.

Why is this impossible?

@colewd

I have tested this with secular friends and after reading Behe’s book they all agree the design inference is legitimate.

I have no idea to exactly what you are referring with the term “the design inference.”

I was referring to the specific claim you were making: “The ultimate source of the original code and the code receiving algorithms can be inferred to require a mind.” I guess if I were to take you absolutely literally there, your statement is trivially true. Anyone can “infer” anything from anything, if they really want to.

It does not follow, however, that a DNA sequence can only produce a functional protein if intelligence is involved. It is an observed fact that evolution can do this.

[colewd (Bill Cole)]

@Faizal_Ali

It does not follow, however, that a DNA sequence can only produce a functional protein if intelligence is involved. It is an observed fact that evolution can do this.

I am not sure what you mean by this statement. DNA produces proteins through the transcription translation mechanisms.

[Faizal_Ali]

@colewd

I am not sure what you mean by this statement. DNA produces proteins through the transcription translation mechanisms.

Is it more clear if I word it this way? “It does not follow, however, that only those DNA sequences, if any, that have been arranged by an Intelligent Designer can produce functional proteins.”

[Puck_Mendelssohn]

@scd

lets take a specific case such as new organ.

This reminds me of a strange conversation I had over on Amazon once. Somebody was obsessed with “the human kidney” (as though it didn’t have homologues in other creatures) and with the notion that kidney-having is, as the kids say these days, “binary.” You either have one, or you don’t. And since a kidney is complicated, and since you either have one or you don’t, well, “checkmate evilutionists.”

It led me to do a bit of reading on renal function in a variety of critters, and in the thread we also had a paleontologist who knew quite a lot about this precise subject, and no amount of explaining seemed to be sufficient to get the poor fellow to understand that kidney-having and not-kidney-having were not two radically different states, with a great gulf lying between them, but rather were points on a spectrum easily traversed by evolutionary processes. As @Mercer points out, of course, it’s important WHICH organ we’re talking about, if we’re going to start agreeing in principle that an “organ” requires X number of mutations, but this is going to be the type of problem for practically any organ structure. Yes, sudden de novo origin of a complex organ, where no similar structure or function previously existed, would be really unlikely. And no, nobody proposes that such things happen, so it’s a straw-man.

P.S. – I should add that after we were some distance into that conversation, it became evident that this poor fellow also supposed that the second kidney had to evolve separately, and by gum, it came out just the same, and what are the odds? We would have started explaining how development proceeds in a bilaterian organism, but it seemed like time for the pub so we just wandered off for a pint of Waddy’s 6X.

[Tim]

@colewd

I have tested this with secular friends and after reading Behe’s book they all agree the design inference is legitimate.

Did this “test” involve either:

1. friends who were actually experts on the evolution of the systems that Behe claims were IC, or

2. showing them any of the many scientific critiques debunking Behe’s claims?

If not, then your “test” is as worthless as your “design inference.”

It is comparatively easy to fool people who understand less about a topic than you do – even if your own understanding of the topic is deeply flawed. This makes it unsurprising that Behe was able to fool your friends (in spite of his own badly flawed understanding of evolution, whose flaws have been repeatedly documented on this forum).

This is why ID makes its case in church halls, not scientific conventions.

[colewd (Bill Cole)]

@Tim

It is comparatively easy to fool people who understand less about a topic than you do – even if your own understanding of the topic is deeply flawed. This makes it unsurprising that Behe was able to fool your friends (in spite of his own badly flawed understanding of evolution, whose flaws have been repeatedly documented on this forum).

This is why ID makes its case in church halls, not scientific conventions.

These friends were highly educated individuals and the exercise was comparing Darwins black box to The Blind Watchmaker. All thought Behe had the easier argument.