Looking for sources on the information argument

This is completely wrong, if software engineering has anything to teach us. Do you know much about optimization algorithms in machine learning, Gilbert?

You have correctly described the logic. However, for some reason, you failed to mention why the assumption of evolutionary biologists is preferred to the assumption of ID theorists.

In the interest of advancing the discussion, I repeat the empirical basis behind the assumption of evolutionary biologists:

Also, I am still curious about your view of Helder’s credibility, Gilbert. Again:

Best,
Chris

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No, they (the principles of chemistry and physics) don’t. The function of a protein is determined by the amino acid sequence and how it folds. The amino acid sequence is determined by the mRNA sequence which is determined by the DNA sequence. This is all part of Crick’s “Sequence Hypothesis”.

There is no chemical law or law of physics which explains the sequence of DNA bases.

The nucleotide backbone (phosphate and sugar) is generic. It is the same for all nucleotides. The base is attached to the sugar molecule, but there is no bond between bases along the length of the DNA strand (I’m not talking about the bond between the base pairs).

Chemistry explains how proteins and rna products operate, but does not explain the DNA sequences from which they were derived.

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I agree that “DNA is a language” isn’t an apt metaphor. A better metaphor is that DNA is a storage medium, particularly the DNA backbone. The sequence of DNA bases can be seen as the information being stored. The fact that the information is processed chemically is no more relevant than the fact that the information on a smart phone or computer is processed electronically.

I recommend Stephen Meyer’s “Signature In The Cell” as a source for the ID side of “what information is” as used in the ID information argument.

Chapter 4 goes into the differences between information as knowledge and information as sequences of functional characters.

The ID argument is based on the latter, and Meyer cites Webster’s definition:

“1b: the attribute inherent in and communicated by one of two or more alternative sequences or arrangements of something (such as nucleotides in DNA or binary digits in a computer program) that produce specific effects.”

As you can see, the sequence of nucleotides (particularly, the bases) is considered information by definition. But only when it is functional, and, functionality is the “Specified” in Complex Specified Information. You can also look at Dembski’s “Intelligent Design as a Theory of Information”.

More importantly, Chapter 4 makes the distinction between Shannon information and functional sequences (those that “produce specific effects”. Shannon’s work deals with the reliable transmission of strings of bits through a communication channel. Shannon cares about being able to put a string of bits into the channel and getting the same string out at the other end. Shannon’s theorems can’t determine if the string is an important message or just a random string of bits that carries no message.

In short, appealling to Shannon (or Kolmogorov, for that matter) to refute the ID information argument is invalid. It is an improper definition of “information”. It is basically a straw man. Shannon is “any string of bits”. The ID argument is based on “only functional strings of bits”.

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How do you calculate CSI, and what does CSI have to do with whether that information can evolve or not?

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This is not really true of course. There is some series of physical and chemical causes of why some given DNA sequence is the way it is. It’s ancestor used to have some sequence, and then there is some physical cause of a mutation in that sequence, giving us the descendant sequence, same would be true for the ancestor, which itself has physical causes of why it is the way it is, all the way back to the origin of the first genetic sequence.

You might not be able to name a physical “law” as being responsible, but it is false to say it isn’t due to physics and chemistry(there is no physical “law” that explains why yesterday’s weather was the way it was, but physics and chemistry does explain it, through the interactions between the Earth’s atmosphere with the sun and so on).
There is definitely a complex history of physics and chemistry that explains both any extant, and any ancestral DNA sequence. The DNA sequence having a contingent and complex physical history does not mean they have no physical and chemical explanation. That’s a non-sequitur.

That would be like saying there is no physical explanation for the particular arrangement of matter we call the Mt. Everest. We might give a generalized explanation by invoking things like gravity, plate tectonics, and electromagnetism, as all being parts of the explanation for the particular arrangement, but these forces must then be understood in the context of the initial conditions of the solar system and the formation of the planet and so on, and of course we can go back further still to the initial conditions of the universe.
You might say there’s nothing in the force of gravity alone that demands the existence of the Mt. Everest, but if we think about it we can still see that gravity is still very much a part of the explanation for the Mt. Everest. The pressures exerted by the gravitational pull of the planet are part of the explanation for it’s particular size, shape and structure. Then there are all the electrostatic interactions between all the atoms that make it up, and how pressures in the Earth’s crust and mantle have changed over time etc. etc. Thus there really is, in principle, a total physical and chemical explanation for the Mt. Everest, it’s just practically outside our ability to provide. It’s not that physics and chemistry can’t and doesn’t explain it, it’s that we just lack sufficiently detailed knowledge of the system that gave rise to it to give this explanation.

All the same things are true for any given DNA sequence. There really is a physical and chemical explanation for why some particular sequence exists. It’s just much too complicated and too sensitive to local conditions at the atomic level at any given moment in time for us to be able to give a complete world-history for all the subatomic particles that are part of that explanation.

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I completely disagree with the idea that we see everywhere in biology functional gradients connecting functional islands. To start with a very fundamental feature in biology, as @gpuccio noted in a piece called « Defending Intelligent Design Theory: Why Targets Are Real Targets, Probabilities Real Probabilities, And The Texas Sharp Shooter Fallacy Does Not Apply At All », all the functional proteins that we know of, those that exist in all the proteome we have examined, are grouped in about 2000 super families. By definition, a protein super family is a cluster of sequences that have no sequence nor structure similarities with the other groups. IOW, a protein superfamily represents an isolated island in sequence space that is not connected to the others. In the same piece, @gpuccio also mentions another very strong evidence dismantling the idea that functional islands are connected, it is the following rugged landscape paper by Hayashi et al.

I invite you to look in the piece below how, according to gpuccio, the paper by Hayashi et al also demonstrates that functional islands exist, and that they are isolated in sequence space.

https://uncommondescent.com/intelligent-design/defending-intelligent-design-theory-why-targets-are-real-targets-propabilities-real-probabilities-and-the-texas-sharp-shooter-fallacy-does-not-apply-at-all/

Uhm, no, that’s not the definition of a protein super family. A protein super family is defined as one in which all members of the family are inferred to share ancestry, it is not a part of that definition that there should be no sequence or structural similarities with other superfamilies. In so far as there might be any such similarities, they are generally throught to have arisen by convergence, rather than divergence from a common ancestor.

And it should be noted that the unrelatedness of some superfamily classifications are actually disputed, as modern work (employing for example ancestor reconstruction) is beginning to indicate that some superfamilies previously thought to be unrelated, could have derived from very simple common ancestral structures. For example the ubiquitous P-loop NTPase and Rossman-fold superfamilies have been suggested as possibly sharing common ancestry.

And another point, it’s not really clear that @Chris_Falter’s suggestion that functional gradients are everywhere in biology, is meant to imply that any and all functions can be sort of turned into each other, nor is that in any way are requirement for the reality of biological evolution. That seems like a strawman reading of his words.

Gpuccio’s stuff on Hayashi and so on has all been discussed to death around here before. The fitness landscape around a particular domain being rugged has zero implications for the possibility of connections between other functional proteins and/or proteins with other functions.

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With due respect, Gilbert, you have made a category error in thinking that protein super families and functional gradients are the same thing.

In biology, a functional gradient describes how a small evolutionary change can yield a selectable advantage to a population or portion of a population–and that’s it! The concept of protein super families is, AFAICT, basically orthogonal to the concept of functional gradients.

Accordingly, Gilbert, you have not in any way refuted the observation that functional gradients are ubiquitous in biology, in my opinion.

Additionally, I commend @Rumraket’s latest post. He understood the issues we were discussing quite aptly.

Finally, we have all noted that you have no response to the observation that Helder is an unreliable witness with respect to biology and paleontology. It matters because the same poor handling of evidence she exhibited with respect of pre-Cambrian fossils also shows up in her entirely speculative, contrary-to-the-real world assumption that no functional gradients exist with respect to sponge structures.

Respectfully,
Chris Falter

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Marvelous post, and very apt. It drives me nuts to see people say that no “law of physics” determines something like a DNA sequence and you have ably dismantled that.

Of course, most of those I’ve known to say things like that would also say that if you can’t give that sub-atomic, local-conditions, history-of-the-universe level explanation, then they’re not going to believe it can happen. I recall pointing out to someone once that we were never going to have the genomes of all of the extinct creatures of the ancient world, and getting the response that, well, if that’s the case, there’s no reason to believe evolution happened. So many facepalms, so little time.

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Yes, chemistry does explain both the sequence of amino acids and the sequence of DNA bases. Amino acids fall into different chemical classes based on their side chains - some are acidic, some are neutral, some are polar, some are non-polar, etc. And the chemistry of these side chains affect what they will bind to. For example, arginine and lysine are positively charged amino acids that interact ionically with DNA’s phosphate backbone.
There is also a fair amount of flexibility in swapping amino acids without losing function. Since arginine and lysine are chemically similar, substituting one for another probably won’t cause loss of function. But replacing arginine with glutamate or glycine will probably cause loss of binding activity.

Similarly, certain DNA sequences are capable of binding to these proteins and other sequences aren’t, again due to chemistry. For example, promoter regions tend to be AT rich or GC rich.

There are literally thousands of papers on this topic. Here is just one example.Effects of lysine-to-arginine substitution on antimicrobial activity of cationic stapled heptapeptides - PubMed
Disclaimer, I didn’t have time to read the paper, but I skimmed the abstract. I can provide more references later if necessary.

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If you don’t believe that DNA sequence matters or that it matters because of chemistry, read about mutations in the promoter region. Here is just one reference.Mutations in the promoter reveal a cause for the reduced expression of the human manganese superoxide dismutase gene in cancer cells | Oncogene
Again, I skimmed the abstract because I’m supposed to be paying attention in a Zoom meeting, but I can post more references later. There are thousands of papers to choose from.

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Welcome to Peaceful Science @DaveB! :smiley:

Can you tell us a bit about yourself?

Great, there’s some common ground. Do you agree that metaphors and analogies are not arguments?

What information is being stored in a promoter or enhancer, exactly?

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The metaphor I like is, “DNA is a recipe.” Chemistry and physics do the cooking.

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I don’t think it’s fair to call this a straw man. Dembski (2005) applies concepts from Shannon and Kolmogorov (Algorithmic) Information. Algorithmic Specified Complexity (Marks, Ewert, and Dembski 2014?) is a direct application of Kolmogorov theory. @EricMH applies Shannon theory in his efforts (Hi Eric!). Functional Information (Hazen 2007 et. al.) is an Information Measure and Information Theory concepts apply.

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The recipe analogy is inaccurate. I think the most accurate is that it is like a notebook that contains multiple lists of ingredients. Of course, chemistry and physics wear the Chef’s hat.

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All analogies are inaccurate, it’s just a matter of how they are inaccurate. :slight_smile:

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Sure. The recipe analogy is grossly inaccurate. :smile:

But it suits my taste. :slight_smile: