posted 01. February 2004 01:06                   

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We the People of the United States, in Order to form a more perfect Union, establish Justice, insure domestic Tranquility, provide for the common defense, promote the general Welfare, and secure the Blessings of Liberty to ourselves and our Posterity, do ordain and establish this Constitution for the United States of America.

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Original Text
It is even closer to the surface when Hamlet enters his mother's room and holds up, side by side, the pictures of the two kings, Old Hamlet and Claudius, and proceeds to describe for her the true nature of the choice she has made, presenting truth by means of a show.

Hypothetical(?) Student Paper
When Hamlet enters his mother’s room, he holds up, side by side, the pictures of the two kings, Old Hamlet and Claudius, and proceeds to describe for her the true nature of the choice she has made, presenting truth by means of a show.

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Na Cl Na Cl Na Cl ...
Cl Na Cl Na Cl Na ...
Na Cl Na Cl Na Cl ...
Cl Na Cl Na Cl Na ...
Na Cl Na Cl Na Cl ...
Cl Na Cl Na Cl Na ...
Na Cl Na Cl Na Cl ...

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posted 02. February 2004 12:37                   

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For consideration, one class of chemicals is polymers whose monomer elements have a limited likelihood of existing naturally, low occurrence of bonding, and no 100% guarantee of bonds between any given monomer, although there may be favorable bonds, just as long as there are not inevitable bonds. Crystalline structures would thus be ruled out since bonding is likely.

These filters should be sufficient for any committee of chemists to conclude a polymer was synthetic or biological. The filter may reject some polymers developed by intelligent processes, but it must absolutely reject 100% non-intelligently developed polymers. The filter is thus falsifiable. It is sufficient to demonstrate intelligent design, but not necessary.

Consider a monomer alphabet represented by letters of the English alphabet: A,B,C,D,E....

A polymer linearly laid out of the form

AAAABBBBCCCCDDDD......QQQQ

found in a test tube where there are multiple instances of this molecule would be deduced to be of intelligent origin.

Consider the gibberish polymer

QORDZLXCWQRLGVALTLJYHZPQIHHAHZBCMNVNBQUETOPPLJAPQIHHAHY......

Even a gibberish polymer of given length would be considered intelligently designed if duplicates of the molecule exist anywhere. As in my correlation post, anything with a replica is automatically specified.

Because the given polymer is both complex and specified, it is considered of intelligent origin automatically if it is not a biological polymer. However some forms of ID do not distinguish intelligently designed and biological polymers.

This issue came up as there is some discussion of using DNA as a memory storage device (not that I think it's practical, but it gave me ideas). The significance of this method is that one does not need to invoke function or necessity of the polymer or motive for creation to conclude it was intelligently designed.

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posted 02. February 2004 21:21                   

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RBH wrote:
This raises again the notion of defining "specification" in terms of replication. I haven't given it much thought, but I'm suspicious of it. For one thing, if replication is a necessary condition to attribute a specification to an object, then a whole lot of things like snowflakes are not specified.

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Does Salvador really want to exclude stuff like that?

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posted 02. February 2004 22:14                   

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BrO3- + HBrO2 -> 2 HBrO2 + 2 Ce4+

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posted 02. February 2004 23:39                   

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Copies that a self-replicator makes of itself are not detatchable from the original, as they are based completely upon it.

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So what you actually observe, namely lots of copies of the same sequence, and/or low Kolmogorov complexity, is neither detatchably specified nor low-probability.

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Self-replication, in abstract terms, is the same thing as autocatalysis. You start with something, and you end with more of that something. But autocatalysis isn't rare at all. For example, Belousov-Zhabotinsky (BZ) reactions rely upon autocatalysis of simple chemical species.

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posted 03. February 2004 10:39                   

Rex,

Thank you again for responding. I would ask your patience with me here as now you are the first at ISCID to make attempts to engage my assertions. I am not a chemist, so you could be very helpful here. And I believe this has relevance to your thread.

Even if we end up disagreeing, I'm grateful someone on the board is finally examining my claim that ID can be detected all the way down to the molecular level.

What I am saying is, if you as a chemist, with the intent wanting another chemist to recognize your work as designed--could you make a molecule that another chemist would be able to reasonably deduce was desginged by another human??? That is essentially the goal of a human in music and literature. Can you, so to speak make literature of atoms such that another chemist can recognize that you, a human made the molecule?

Where I am headed is that as Denton suggested, we were designed so that one day we would realize we were designed.....

I have to apologize, and correct something of a loose usage of a term I have been using. Dean Kenyon use the term "biochemical predestination" to describe his belief there were favored polymer configurations that enabled life to form spontaneously.

I should not have used the term chemical predestination to describe the autocatalytic reaction. My fault.

Pertaining to what you described with autocatalysis, I have to correct my usage and say I was wrong earlier in using the word "chemical predestination" with autocatalysis.

Pertaining to the autocatalysis, you have higlighted something in my definition that needs amendment (that's what brainstorms are for right ) The ability for a simple reaction self-propagate that was never in doubt (salt-crystals, the Belousov-Zhabotinsky (BZ) reaction etc. However, the Hofstadter system is one that is able to self-propagate and capable of storing and processing information. I will have some work ahead of me to improve my defintions. In the mean time:

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You wrote:
But there is chemical predestination in polymerization reactions, too, under appropriate conditions: DNA + free nucleotides + primers + DNA polymerase + thermal cycling produces a remarkably consistent result, at least compared to random aggregation of nucleotides.

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Salvador wrote:
The definition of the polymers I tried to describe is where there is not an inevitable configuration (such as in nylon) but where random polymers are more easily formed vs. identical polymers. Fox's experiments were valuable in strengthening the case that there is no inevitable configuration of protenoid polymers.

Futher research is in order if there exists catalysts which will generate a favored configuration (such as alpha-peptide bonds and homo chilarity). I expect a catalytic reaction may create polymers with amino-acids pairs like ABAB, homo-chirality, and uniformity of pepetide bonds. Fox's protenoids had a mix of alpha, beta, gamma, and epsilon peptide bonds, unlike real proteins which are homo-chiral and have a dominance of alpha petide bonds (some say exclusive, but I don't know).

However, it would be an impressive feat to find a simple process that generates numerous replicas of polymers with all 20 (or some number) of biomonomers. Numerous replicas of biopolymers emerge from a rather long complicated chemical process (the process of living). The question of abiogenesis research is whether a simple (and I mean much much simpler) processes can yield a replicator of biolpolymers.

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This is what I was trying to describe in my second example. There are different Nylon polymers. Nylon 6 is a simple repeating polymer:
H2N(CH2)6COOH --> -NH(CH2)6CO--NH(CH2)6CO--NH(CH2)CO-
Nylon 64 has an ABAB repeat:
H2N(CH2)6NH2 + HOOC(CH2)4COOH --> -NH(CH2)6NH2--CO(CH2)4CO--NH(CH2)6NH--CO(CH2)4CO-

Nylon R (a name I have just made up) has a random sequence:

H2N(CH2)6COOH + H2N(CH2)4COOH --> -NH(CH2)4CO--NH(CH2)4CO--NH(CH2)6CO--NH(CH2)4CO-

Each has been designed to have either a random or an ordered sequence, but each forms from the inevitable reactions of the basic reactants. Proteinoid polymers are actually very similar, for example:

H2NCH2COOH + H2NCH(CH3)COOH --> -NHCH(CH3)CO--NHCH(CH3)CO--NHCH2CO--NHCH(CH3)CO-

As you say, in these last two cases the actual sequence or configuration is not inevitable.
The way to tell if one is from a living system or from a chemical plant is to compare different sequences. Living systems utilise replicators, so the protein sequence will be identical every time. The chemical plant will produce polymers with every polymer sequence unique. As you say:

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However, it would be in impressive feat to find a simple process that generates numerous replicas of polymers with all 20 (or some number) of biomonomers. Numerous replicas of biopolymers emerge from a rather long complicated chemical process (the process of living). The question of abiogenesis research is whether a simple (and I mean much much simpler) processes can yield a replicator of biolpolymers.

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Processes do exist that will stepwise build up a molecule in exactly the way you describe. This can certainly be done for DNA; the experimenter can select a sequence of bases, and then add each base in turn to build up the molecule. I believe the process can be automated, and it is just a case of typing the sequence into a computer and letting it get on with it. This would produce a polymer with a seemingly random sequence of bases, but with every sequence identical. Whether it is a simple process is debatable. I guess this is how artificial insulin is made.

I think what it comes down to is:
1.If we have a "random" sequence that is the same for every polymer, then we necessarily have a replicator of some sort. If we have a replicator, is this evidence for design?
2. If we have a "random" sequence that is the same for every polymer and that sequence is specified externally (eg a protein sequence forming an enzyme with a specific function) is that evidence of design?

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Ghadiri Ligase is not a True Self-Replicator

I will use an analogy that employs the letters of the alphabet and a short sentence in order to demonstrate why the Ghadiri ligase is not a true self-replicator.

For this analogy, I will equate the 23-character “sentence” METHINKSITISLIKEAWEASEL to the Ghadiri ligase. Each of the letters represents an amino acid residue along the length of the GL (my abbreviation for the Ghadiri ligase) where each of the individual “letters” is covalently bonded to its nearest neighbor(s) on the same strand (analogous to the same physical sentence). The covalent bonds between the units will be represented with dashes (-) between the covalently bonded “letters” (M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L).

A true self-replicator can extract its individual building blocks (monomers/letters) one at a time from its surroundings (a pool of monomers/letters) and construct a functional copy of itself using itself as a template for the sequencing of the units, followed by release of the copy (both the template and the copy should be covalently bonded themselves, but they should not be covalently bonded to each other in order to allow them to separate without also decomposing). Note that the letters would not simply line up according to the template’s sequence, but they would also have to be covalently linked to their nearest neighbors after being non-covalently attached to the template. Forming this bond between units of the same strand requires either a catalyst or the pre-activation of each of the building blocks (and since we are looking for a true self-replicator, the sequence itself should probably be performing this function). The process would involve two basic steps for each monomer added: first, the correct monomer is “chosen” from the stocked pool of monomers and it lines up along the template, then the template sequence itself covalently bonds the new monomer to the elongating string.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M (correct monomer lines up non-covalently with template)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M E (correct monomer lines up non-covalently with template)
M-E (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E T (correct monomer lines up non-covalently with template)
M-E-T (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T H (correct monomer lines up non-covalently with template)
M-E-T-H (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H I (correct monomer lines up non-covalently with template)
M-E-T-H-I (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I N (correct monomer lines up non-covalently with template)
M-E-T-H-I-N (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N K (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K S (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K-S (template sequence covalently bonds new monomer to growing string)

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S I (correct monomer lines up non-covalently with template)
M-E-T-H-I-N-K-S-I (template sequence covalently bonds new monomer to growing string)

[next 26 steps omitted to save space]

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L

So how does the actual Ghadiri ligase measure up? Not very well. Using the same analogy, here is how the GL functions.

The first PREEXISTING half of the sequence, already covalently linked together, lines up with template.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T

The second PREEXISTING half of the sequence, already covalently linked together, lines up with template.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T I-S-L-I-K-E-A-W-E-A-S-E-L

The two halves are covalently bonded together – BUT NOT BY ANY EXTRA ACTION PERFORMED BY THE TEMPLATE SEQUENCE ITSELF, BUT BY THE SEPARATE TWO HALVES THEMSELVES, BECAUSE ONE OF THEM WAS PRE-ACTIVATED.

M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L
M-E-T-H-I-N-K-S-I-T-I-S-L-I-K-E-A-W-E-A-S-E-L

This analogy points out some conceptual reasons why the Ghadiri ligase is not a true self-replicator. It is powerless to recreate itself from the individual building blocks that make it up. It absolutely requires that the correct 15- and 17-aa sequences already be available in the surroundings, with them already being held together by covalent bonds, and with one of them being pre-activated.

So is the GL a catalyst? Yes – it accelerates the rate of the two halves joining without itself being altered in the process. It has been shown that even in the absence of the GL, the preexisting, pre-activated 15-aa and 17-aa fragments will bond together to form the full 32-aa GL. In the presence of the GL, this rate of combination of the halves to form the full template is increased, and after doing so, the original template is ready to align another set of two halves so that they too will bond together. What the GL basically does is to orient two preexisting, pre-activated halves in the correct manner so that they can interact (of course the probability of two halves finding each other and being properly oriented in order to link up is much greater when they are aligned linearly in tandem on a template than when colliding randomly in a solution). So yes, the GL is a true catalyst.

So does the term autocatalytic fit the GL? Yes – it is a catalyst whose product is itself.

So is the GL a true self-replicator? No.

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posted 04. February 2004 00:47                   

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HBrO2 + Br- -> 2HOBr

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posted 04. February 2004 13:04                   

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So one needs a more refined concept than simply having information that can be used to create things beyond oneself.

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If I were to make a molecule that I wanted someone else to decide was made by a human, I'd go into an organic chemistry textbook, find common reactions, and produce something large and weird using a series of standard organic chemistry reactions and common reagents available from Sigma-Aldrich. Since the people who found it would know about Sigma-Aldrich and common O-chem reactions, they'd presumably conclude that it had been made by humans. Alternatively, I could come up with some polymer system and encode in that polymer system a message to the other chemist--maybe the opening paragraph of March's Advanced Organic Chemistry. I'd probably have to include a rosetta-stone-like leader sequence in order for them to understand, though. Without that leader sequence, they wouldn't have any way to know to check March's book, and thus wouldn't come up with a high probability of design by humans. Even if I made thousands of copies, they couldn't tell whether the complex sequence was the result of some unknown regularity and/or copying mechanism, or was a human's handywork. That's why I'd make sure they were pointed to something that had a high probability, rather than leaving everything as a bunch of low probabilities, and therefore a mystery.

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posted 05. February 2004 02:17                   

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Salvador:
The way biology self replicates is overkill design. Salt crystals do a better job of self replicating. Hofstadter's work helps formalize the properties of the way biology self-replicates. That is, relative to salt-crystals, biological self replication is brittle.

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