http://www.evolutionnews.org/2.....enial.html

Nakashima, I appreciate that you are asking questions, which is important. Continue to scrutinize, especially in regard to claims that the properties of undirected processes can account for the origin of ribosomes and protein production from symbolic information. Is that a reasonable conclusion?

Best blessings to you and yours,
ericB

Here are some points to reply more directly to your post at 66.

1. Have you read Stephen Meyer’s new book Signature in the Cell? He goes into much more detail than feasible in this space.

2. Sorry, but I don’t see a post by “Art Hunt” about the stereochemical theory of the origin of the genetic code, so it is difficult to respond. Was that under a different column/topic than this one? Can you point it out please?

3. If ones goal were only to explain why this codon is associated with that amino acid in a particular genetic code, even on that level the fact that there is not one universal code does present complications and added difficulty. The fact that there can be variant codes illustrates the observable independence in the 1-1 association. Other associations are possible. (I believe Meyer looks at these issues.)

4. My main objective, however, is to point you toward a deeper and more serious obstacle. This is why I am not particularly concerned about what you call 1-1 associations. Even if they could take place in some isolated sense, perhaps because X chemically prefers to bind with Y rather than Z, that does not touch the issue I am raising.

There are many cases in chemistry, not limited to biology, where X may prefer to bond with Y rather than Z. But that alone does not make them into a symbolic language encoding symbolic information. That only happens in biology (and the creations of intelligent agents).

The question being raised is not why an amino acid is associated with this codon vs. that codon. It is about whether an undirected prebiotic material process could ever build translation machinery, such that a recipe for a functional structure could become stored in a symbolic form and later used to reproduce that functional structure.

NOTE: This molecular machinery would have to be built originally in its entirety without the help of information driven construction. One cannot assume the prior existence of the very thing one whose origin one is trying to explain.

That is the symbolic information hurdle I claim cannot be crossed. Do you believe the stereochemical theory of the origin of the genetic code solves this deeper problem? If so, how?

5. It is not by mere fiat that I say 1-1 associations don’t provide the symbolic information processing I describe. Such associations are not functioning as a symbolic language until they are used for functional translation, i.e. a working system for reproduction of functional structures from separate symbolically encoded information.

That is what makes mere objects into symbols. DNA base sequences can code for proteins they do not even touch because a translation system can reliably convert their specified sequence information into proteins.

But could that machinery and system be constructed without the help of translation machinery driven by symbolic information? Without direction or investigator coercion, how far would isolated strand replication of RNA go toward that goal of a complete integrated and consistent system? Is that a reasonable expectation?

6. Do you claim that functional proteins developed before or after the invention of a working code for representing amino acid sequences using codons? If before, how were proteins created without the help of that system? If after, how did such a system develop to encode recipes for functional amino acid structures that did not yet exist? How does a mindless system develop to pursue future uses?

Perhaps this illustration will help. Think about how a fax machine uses symbolic information. An image that exists at one spot on the globe is reproduced at another. Nevertheless, it is not the visual image that is transmitted. Rather, the electrical signals carry the equivalent symbolic information needed to instruct the other fax machine on how to recreate the visual image.

Notice that the electrical signals does not have the chemical or physical properties of the image. Apart from the existence of a destination fax machine that can translate them back into the image, those signals have no functional value at all.

Likewise, the receiving fax machine would be useless for its designed function if there did not also exist sending fax machines that follow the same conventions, as well as having the means to transmit the information faithfully.

It is this kind of process of information encoding, transmission, decoding and reconstruction of the realized representation that is beyond the reach of undirected mindless chemical processes to invent and construct. They have no need for it, nor any observed unaided inclination toward it.

You are just repeating your assertions at this point. Art Hunt’s post made reference to the stereochemical theory of the origin of the genetic code, how do you respond to that? It seems that you are just by fiat declaring 1-1 associations to not be information.

There are many ways that chemicals might bond. But even if we might generously suppose or imagine various combinations, that would be to no benefit. There is a qualitative threshold that is not crossed. It is not closer to translation.

To say that one has implemented a code for symbolic information means that one can accomplish translation between symbolic information and the realized structure it represents.
To get to translation, one needs not merely chemical bonds or chemical associations, but rather translation machinery that can reliably implement a process whereby the recipe for a structure has been captured by encoding it into a sequence of symbols with the ability to also later traverse that sequence and recreate the intended structure.

This is something different in kind from the many undirected ways that chemicals naturally bind together. An undirected binding simply is what it is. It doesn’t mean anything more. It doesn’t represent something other than itself. It is simply itself — variations on the theme of A is connected with B (or sometimes not connected). Does A represent B or B represent A? Neither. They are just more chemical compounds.

Would undirected processes construct translation machinery and use it to encode and then decode symbolic information? Consider that this machinery must be constructed and reproduced without the benefit of symbolic information, e.g. by the kind of strand replication that RNA might be able to achieve. But that path is not sustainable to the level of such machines, even if it could work for a strand of RNA.

Chemical processes are not pursuing such a goal. The requirements of chemistry can be fulfilled with useless tars and goo. We have no scientific reason, either empirical or theoretical, upon which to rest a faith that the nature of undirected chemical processes is to work toward information driven chemical construction machines.

Because Ada Lovelace could use imagination, she was able to write programs for Charles Babbage’s Analytical Engine — even though the engine did not yet exist. But chemical processes cannot use imagination, and cannot be expected to develop complex translation machinery in a universe where no symbolic information exists to be translated, or to design such information in a universe that cannot yet translate it, or even to use both to encode for functional chemical structures (e.g. proteins) that do not exist.

Thank you for taking the time to reply. I’m traveling myself, and I know it is difficult to maintain continuity in the conversation.

I agree that evolution before the first cell must mean something else than change in allele frequencies. With respect to chemical evolution of RNA, at least we can count the variants and how often they appear. A discussion of the evolution of vesicles involves more handwaving, I think.

By focusing on aaRS molecules, I’m trying to add clarity by specificity to the discussion. I understand your position (and Mr. BiPed’s, I think) is that the genetic code could not have evolved.

If I understand you correctly, even if amino acids could be created pre-biotically, and even if RNA could be created pre-biotically, a regular association of RNA sequences with amino acids could not have evolved. For example, there could never have been a wobbly loose association of some sequence of RNA bases with a broad category of amino acids (such as hydrophilic AAs) that became more specific over time.

I think that if these associations were looser, then the rest of the circuitry would have been looser as well – the ribosome would have been simpler, more prone to error, jamming, running backwards, whatever. But that is my position. Am I correct that you don’t think any of that was possible?

I’m using someone else’s computer, so this will have to be brief.

The idea of structures evolving is itself problematic before you have living cells. Replication of RNA molecules, even if it could be achieved by undirected processes is not the same.

Nevertheless, the coding system requires much more than you mention. One needs not just the individual parts at the core of the association, but an entire functioning translation system. Plus you need not only decoding ability (such as we see now), but also encoding ability. Else, there is no encoded symbolic information for the decoding to work upon.

Finally, you need to have independently created structures to be represented by the symbolic information via encoding. A mindless undirected process cannot invent the symbolic representations based on imagined realized structures.

If anyone supposes that random processes can find meaningful symbolic information (rather than starting with encoding from actual models), that is hopelessly implausible.

The core difficulty is that undirected material processes have no need for any of this. They don’t care about or pursue symbolic representation. There is no basis upon which they can prefer pursuing the future value of such inventions.

Lutepisc @39: RickToews @ 30, you didn’t listen to the lecture, did you? (I could tell…)

You are correct: I had listened to only about 10-12 minutes. I have since made time to listen to the entire lecture. Maybe I didn’t listen carefully enough, but I don’t recall hearing anything that addressed the difficulties I raised with more or less dismissing the history of early Genesis. Perhaps she does so in another lecture.

She’s very easy on the ears, very pleasant to listen to; and I agreed with her on at least most of the “myths” she listed concerning the Hebrew Bible.

—First, I am not at all sure why you’d consider Ken Miller to be a neo-thomist. If he has said word one about Aquinas (I know he’s catholic, but not every catholic knows that much about thomism), I’ve missed it. Can you point me at where he’s mentioned this?”

I think you have a point about Miller, in the sense that he is probably more Kantian than Thomist. I included him because he draws heavily on and makes too much of the Thomistic idea that God can create from contingency, yet he probably does not buy into the Thomistic thought system. Indeed, it is the only quote from him coming from Aquinas that I can think of. I think I was trying to hard to find a fourth category.

—-”As for Barr, considering Barrxpressly denies the ‘random’ part of Darwinism in the relevant way (see his discussion with John West), I don’t think he’d be in any “Darwinist” camp typical by normal UD measures. ‘Unguided, unplanned’ is essential for Darwinism – remove that and you’re left with something other. If you agree to that, realize this is Barr’s position.”

Right again. I would call Barr a “vitalist.” I need to eliminate my first category, it doesnt’ work.

—-”All I can do is recommend Edward Feser’s book “The Last Superstition” (or at least check out his blog). I think you’d enjoy it, but it helps to illustrate why Aquinas’ teleology (and his Fifth Way in particular) is something utterly other from design in the ID sense. His objection, and the objection of some other thomists I’m aware of, is that ‘modern ID’ concedes mechanistic metaphysics – ruling out formal and final causality to begin with.”

That one I can’t buy, but I will check it out. I think this is the same error pointed out in section 2 in different form.

—-”Also, one caveat: Yes, I believe detecting ‘design’ (certainly on the level of God) is not science. Please note, I also believe detecting or declaring ‘not-design’ is -also- not science. Darwinism, insofar as it requires a complete lack of guidance (either in terms of front-loading or direct intervention) a commitment to truly random variation (as opposed to randomness for the sake of a model, etc) and otherwise is not science either.”

Right. I know that you take a balanced position on that one.

Overall, I think the Oakes,
Templeton, Feser connection is the problem and the idea that function = mechanism. Equally important, I think all these good folks need to realize that Aquinas revamped Aristotle’s fourfold causality, and, included something called an examplary cause, which is the equivalent of what we call “agent” cause.