|
Author
|
Topic: IC vs SC: Never Should the Twain Meet
|
Salvador T. Cordova
Member
Member # 959
|
posted 24. December 2003 23:10
This thread presents a brainstorm of a concept I've been bouncing around, namely Irreducible Complexity (IC) is not the same as Specified Complexity (SC). The two are disjoint in my mind. I'm not saying I'm right, but my intuition says it's a serious category error to try to merge the two concepts together!
Consider a Bit-Mapped photograph. At one level it is a highly specified entity, that is to say it has pixels at well defined positions in the Cartesian plane. Each pixel may have color and intensity attributes. The photograph is Specified.
On the otherhand, consider the photograph is a picture of a bride and groom. At one level it is Specified by all bits in the bit mapped image. On the other hand, there are qualities about the picture which are Irreducible.
For example, Irreducible qualities of the photograph would be description of the picture. If the picture were of a bride and groom in an outdoor wedding we could identify the following irreducible descriptions of what the photograph portrays:
1. the couple is near palm trees
2. there is a bride
3. there is a groom
4. his tuxedo is white
5. her dress is white
7. it was a sunny day
8. there were no clouds in the sky
etc.
Such descriptions are not reducible to any mathematical theorems! Yet the those descriptions are completely true!!
I think we in ID are potentially hurting ourselves if we try to merge Specified Complexity and Irreducible Complexity. I think we need to make these distinctions.
We actually have some hint of this in mathematics and physics. In math we can specify the real numbers and their arithmetic properties with a set of unprovable axioms. Because of this, Hilbert, Russell, and Whitehead thought we could then generate every possible theorem of math mechanically given the axioms. That seemed completely reasonable!
Godel eager to prove Hilbert right, ended up proving Hilbert wrong. There are properties of real numbers which emerge that can't be explained or reduced to the governing axioms!!!! These are Irreducible Emergent Properties. Bertrand Russell's whole life work went into a tailspin after Godel! I believe the 3rd volume of Russell's Principia Mathematica was never published because of Godel basically completed the 3rd volume with 'incompleteness' (pun intended).
A possible candidate of such an emergent irreducible mathematical property is Goldbach's Conjecture: "all even numbers are the sum of 2 primes". If Goldbach's conjecture is irreducible, we will never know! We can pose Goldbach's Conjecture to a computer (a universal Turing Machine), and it may never halt!
Likewise in physics. We can fit known laws into one page, but we are getting some very strange emergent phenomon in solid state physics that is not reducible. One of the advocates of "Irreducible Complexity" in particle physics won the Nobel Prize, although I believe he is not an ID advocate, he is considered a renegade. Got to love renegades with Nobel Prizes:)
Salvador
[edited 12/29/2003 to remove erroneous reference to Peano's axioms]
[ 28. December 2003, 12:18: Message edited by: Salvador T. Cordova ]
IP: Logged
|
|
David Bump
Member
Member # 1017
|
posted 26. December 2003 01:00
What? As I understand it, "Irreducible Complexity" has nothing to do with Godel or "reducing" a description to mathematics. You have read Darwin's Black Box by Michael Behe, haven't you? Trying to talk about IC if you haven't read that would be like someone in 1861 trying to talk about Darwinian Evolution without having read Darwin's Origin of the Species.
Something is irreducibly complex if it cannot have even one component removed and still retain functionality. It might be described by mathematics, or it might not. That's how I understand it, anyway.
[ 26. December 2003, 01:01: Message edited by: David Bump ]
IP: Logged
|
|
Salvador T. Cordova
Member
Member # 959
|
posted 26. December 2003 01:54
quote:
What? As I understand it, "Irreducible Complexity" has nothing to do with Godel or "reducing" a description to mathematics. You have read Darwin's Black Box by Michael Behe, haven't you? Trying to talk about IC if you haven't read that would be like someone in 1861 trying to talk about Darwinian Evolution without having read Darwin's Origin of the Species.
Something is irreducibly complex if it cannot have even one component removed and still retain functionality. It might be described by mathematics, or it might not. That's how I understand it, anyway.
Outstanding point. Behe would not exactly like my definition, but I hope he will consider it. I will propose a defintion which Behe's IC will be a subset of greater IC phenomenon such as the one in mathematical structures. I hope board members will contribute.
The main idea, is that a non-computable or hard-to-compute gap exists. If a genetic algorithm can not converge to an IC structure, that is proof positive the structure is IC. The ultimate in non-computable gaps exists with unprovable statements, but there are lots of IC statements out there that are 'practically uncomputable' given the computational power of the system (such as Darwinian Evolution operating even through millions of years).
I'm not trying to derail Behe's work, I'm a strong ID advocate. I am however on other discussion boards engaging ID critics, and they bring up fair points worth addressing.
Salvador
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 26. December 2003 03:20
This seems to answer the question if irreducibility as defined by Godel has any similarity to Behe's
IP: Logged
|
|
David Bump
Member
Member # 1017
|
posted 26. December 2003 23:44
Oh, so you are first of all proposing that IC can be codified mathematically (or rather, that it deals with questions of mathematical codification/solvability)? And then saying it's not the same mathematics that SC uses?
That sounds about right to me. Are there not mathematical systems that both describe the same phenomena, but in different ways, and with different rules and symbols? Plus, if IC is basically a way of saying that some things can't be subject to -- or described in terms of -- a mathematical algorithm, then by it's very nature it must be different from SC, which by its nature/definition deals with phenomena in ways that can be specified.
So I would agree, it just doesn't work to conflate the two ideas. They can, however, be supplemantary though separate, each addressing phenomena that the other cannot, or revealing things about the same phenomon that the other can't.
[ 26. December 2003, 23:46: Message edited by: David Bump ]
IP: Logged
|
|
Salvador T. Cordova
Member
Member # 959
|
posted 27. December 2003 02:30
Consider a computer system where there are multiple users. Each user is assigned a login and password.
A 10 character password has over 10^14 possibilities. Now, passwords are usually sensible word variants like 'happypep' or something, so the actual space of possibiliies is less than 10^14, however, there is an important point here:
For an amateur hacker, only exhaustive or heuristic search can resolve what your password is. A genetic algorithm is no better than blind chance in resolving the password. Why is this?
An amateur hacker can not know whether he is close to breaking your password. There is no feedback whether he is close to breaking it or not. Say your password is 'happypep' and the would-be hacker enters 'sappypep', he has no feedback to tell him that he is only one letter off.
Selection mechnisms are most successful when an outcome results in improved fitness toward eugenic perfection to the environment (such as peppered moths or finch beaks).
However, the selection mechanism in regard to passwords is of absolutely no use to arriving at the password except to say 'this one didn't work'. The password is effectively irreducible, there are no intermediates or transitionals.
There are mutiple logins and passwords to the system, but each are irreducible. There may be multiple propulsion systems like flagella, cilium, wings, but each could be irreducible.
However, practically speaking, even if there are multiple feasible irreducible propulsion systems, this may not help random chance arrive at these structures. A would-be hacker may explore millions of logins only to be confronted with trillion trillion trillion possibilities of passwords for each login. There may be a trillion ways to build mousetraps, but each is still an irreducibly complex mouse trap.
There are 10^110 possibilities for a polymer of the length of cytochrome-c. There may be 10^55 (a generous value) configurations of cytochrome-c out of those 10^110. That means there are only one in 10^65 are viable configurations of the polymer that are acceptably cytochrome-c proteins when searching through the space generated by a polymer the same length as cytochrome-c . (10^110 divided by 10^55 = 10^65).
Cytochrome-c is now analogous to the login and password idea, but only more so (the password example was only of order 10^14)! A Darwinian mechanism cannot arrive at cytochrome any better than exhaustive search because there are no morphologically useful transitionals or intermediates. Biochemistry lends itself well to mathematical analysis because, by nature, biochemistry is very digital.
Cytochrome-c is only one protein. Denton makes the good point, protein evolution follows Cuvier, not Darwin. Protein formation is untenable via gradualistic steps for the same reason logins and passwords can't be broken through gradualistic steps.
Irreducible Complexity structures defang Darwinian Mechanism of one of its major features: natural selection along a single axis.
The pathway up 'mount improbable' turns out to be a horrendous maze, with chance and luck of Random Mutation the primary mechanism needed to overcome irreducible structures. IC prevents natural selection from being a factor. Natural selection can be more hindrance than a help to arriving at the innovative irreducibly complex structures because the most important ingredient to creating an irreducible structure (short of intelligent intervention) is RAW CHANCE.
----------------------------------------------
I covered 'actually irreducible structure' (like those demonstrated by Godel) to also emphasize the reductionist view is crumbling. Even in the precise world of math, irreducibility exists: there are truths which can not be explained or reduced to more elementary principles. Though Godel is not of immediate consequence to biology, he shows irreducible complexity is a real phenomenon. A system can have meaning that is greater than the sum of it's parts.
Concepts in solid state physics like super conductivity, super fluidity, may be irreducibly complex, we shall see.
From the philosophical and personal side, because of irreducibility, there is justification to believe many of the concepts in our hearts such as intelligence, consciousness, life, health, and joy may be not only be irreducible, unprovable truths, but also the most important truths.
Salvador
[ 27. December 2003, 02:33: Message edited by: Salvador T. Cordova ]
IP: Logged
|
|
Salvador T. Cordova
Member
Member # 959
|
posted 27. December 2003 02:33
quote:
I wrote:
Though Godel is not of immediate consequence to biology, he shows irreducible complexity is a real phenomenon. A system can have meaning that is greater than the sum of it's parts.
Hehe. I spoke way too soon. Godel and computation theory may have supreme relevance!!!
Something deep in side said that true-self replicating machine would have something to do with Godel. I've been fascinated by the idea of von-Neumann self-replicating automata for ages. Biological systems are exactly that.
I just pulled out a Pulitzer Prize winning book by Douglas Hofstadter "Godel, Escher, Bach: An Eternal Golden Braid" It's a gruesomely painful book to read!
Page 530.
quote:
How DNA Self-Replicates
It is not by any means coincidental that the phrases "sufficiently strong support system" and "sufficiently powerful formal system" sould alike. One is the precondition for a self-replicator to arise, the other for a self-referential system to arise. In fact there is in essence only one phenomenon going on in two very different guises...
Even though we know, the Crick Central Dogma may be an approximation, Hofstader attempted an anology.
1. Central Dogma of Molecular Biology
2. Central Dogma of Mathematical Logic (on which Godel's theorm is based)
The analogy he calls, irreverendly, the Central DogMap ![[Big Grin]](biggrin.gif)
For a chemical self-replicator to emerge it's specification (Specified Complexity) must be equivalent to a sufficiently powerful formal system (the real number system is an example of such a system). This formal system is capable of creating emergent irreducible phenomenon (Irreducible Complexity) which describe something like the following:
quote:
proteins acting on proteins acting on proteins.........
Life is an infinitely recursive, self-referential description, an "eternal golden braid".
Such a system is tightly integerated. It is both Specified Complex (since it is self-specified) and Irreducibly Complex on many levels:
1. It ceases to function with certain component removal
2. It generates irreducible emergent mathematical structures that are independent of the specification. (Recall the irreducible phenomenon in the picture and the emergent mathematical structures mentioned above).
Such structures are not ultimately originated through gradualistic Darwinian processes, but only through intelligence, or exceedingly fortuitous raw chance. This is true for biological systems for the same reason logins and passwords are not broken via Darwinian Pathways.
If a mutated cell continues to replicate, it does so because the change was grammatically acceptable, otherwise it results in death, as Maury Eden said in such cases, the computer program just jams.
Thus I have often stated mutations are of 2 basic varieties:
1. accidental
2. designer
Designer mutations are grammatically correct mutations. Accidental mutations may or may not be gramatically correct, and the organism may or may not live, but it's viability may be compromised.
The emergent phenomenon from these strange loops in the formal system generate our biological features (proteins interacting with other proteins interacting with ....).
Phenomenon that are fundamentally irreducible due to emergence from a formal system cannot be arrived at soley via Darwinian Pathways. Darwinian mechanisms may lend only optimization of the system (finch beaks, certain macro evolution).
However the fundamental originating core of many features could not be reached via a Darwinian Mechanism for the same reason logins and passwords can't be broken via Darwinian Mechanisms, and for the same reason emergent phenomon in mathematics are not computable. (Recall the irreducible aspects of the picture above as an illustration of irreducible emergent phenonmeon).
Hofstadter writes:
quote:
The Origin of Life
A natural and fundamental question to ask, on learning of these incredibly intricately interlocking pieces of software and hardware is: "How did they ever get started in the first place?" It is truly a baffling thing. One has to imagine some sort of a bootstrap process occurring, somewhat like that which is used in the development of new computer languages--but a bootstrap from simple molecules to entire cells is almost beyond one's power to imagine.....For the moment, we will have to content ourselves with a sense of wonder and awe, rather than with an answer. And perhaps experiencing that sense of wonder and awe is more satisfying than having an answer--at least for a while.
![[Smile]](smile.gif)
Salvador
[ 27. December 2003, 02:45: Message edited by: Salvador T. Cordova ]
IP: Logged
|
|
David Bump
Member
Member # 1017
|
posted 28. December 2003 01:27
This is very interesting, I like where you're going with this. I think you are again illustrating that while SC and IC are distinct, their applications overlap and complement each other.
I would like to point out that, while it may be helpful to use mathematics such as probability calculations in these matters, we must never forget that we are not dealing with matters of "pure" probability, such as coin flips or rolls of the dice. Such calculations may set boundaries or at least give us a good place to start looking, but there are a number of physical constraints to consider, as well.
For example, amino acids aren't floating around abundantly as multiples of complete sets needed for life. While most have been replicated under what might have been natural conditions sometime, somewhere, I believe there's at least one that has resisted such experiments. And different sets of conditions were required for different acids. Plus, there's the problem of getting all of them the same handedness. A recent experiment with serine produced monochiral groups, but the groups were of both sorts and the serines to which the others were attached were fairly strongly bonded in a non-helical form.
There are a number of other problems, but these begin to illustrate that the powerful probability considerations are only the beginning.
IP: Logged
|
|
Salvador T. Cordova
Member
Member # 959
|
posted 28. January 2004 10:07
The "single target", postdiction fallacy in ID vs. non-ID debates is vexing, mainly because the parameters are so wide open.
To give background:
A penny is flipped 500 times, and each flip is recorded. The history of the flips is beyond the Probablity bound cited by Dembski. The exact configuration of the flips occurs 1 out of 2^500 times. Nothing special. No miracle.
1. We flip a coin 500 times and get a configuration of the flips. No miracle.
2. However to repeat the experiment again and get the exact results is a 'miracle' or some intelligent agency directing the flip somehow.
3. Similarly, if someone specified in advance what the 500 flips would be before they happened, that would be a 'miracle' or intelligent agency directing the flip somehow.
The IDealists wish to make biology analogous to either case #2 or #3. The non-IDealists wish to describe biology as case #1.
(Speak up anyone if you think this is an unfair characterization).
The "single target", postdiction fallacy is analagous to #1. That is to say, we see a cell, look at the arrangement of atoms and say, "it defied probability"! This same objection problem creeps up in analysis of IC systems as well.
I will not solve all of the problems in this thread, nor do I think anyone will soon, however, there are some things I will address that I hope will be useful to IC analysis.
The goal in general of ID is the eliminative approach. It does not prove ID, however part of the methodology is useful to evolutionary biology in that it does help narrow down by elimination which pathways are not likely for evolution to progress. That is a contribution, in my opinion, to scientific understanding.
Pertaining to #2 and #3: The 'miracle' of replicas. Crystalline structures are replicas of each other. Ice collecting on a rock is an approximate "replica". These kinds of replicas are what one would expect from a given set of conditions. No surprise. No intelligence needed.
Crystalline structures are replicas of each other. Ice collecting on a rock is an approximate "replica". These kinds of replicas are what one would expect from a given set of conditions. No surprise. No intelligence needed.
In contrast, the chemical formation of bio-polymers is problematic without:
1. Biological Entity to make the biopolymer
2. Intelligence
Insulin, a bioplymer, can be formed through 1 or 2 or combination of 1 and 2.
The kind of replication achieved chemically by a biopolymer is not the same as in crystalline formation since no configuration is inevitable or heavily favored.
Are formation of biopolymer replicas evidence for ID? That is, does abiogenesis have to be directed by intelligence for it to happen?
Dembski's explanatory filter will be applied to help answer the question. After application of the filter, it is up to the individual to decide
1. Intelligent Agency was the cause
2. Some other non-intelligent causal agency was not accounted for
To answer this question, one must consider the specifics of what specifies a bio-polymer self-replicator. The bio-polymer self-replicator is an IC system.
Life is not possible without a bio-polymer self-replicator. Bio-polymer self-replicators are a necessary but not sufficient condition for life.
I will not insist that such a self-replicator be based on carbon, or a specific chemistry, however, Hofstadter and von Neumann indicate such a self-replicator must have a bare minimum of parts.
Hofstadter provides a mathematical basis from Typographical Number Theory as to how to arrive at a minimum number of parts, but he does not actually come right out and say at what number of parts is needed for "critical mass".
At a bare minimum, one needs, at least -- SURPRISE SURPRISE SURPRISE -- 20 symbolic parts. It is possible to have more and have a functioning system, but Hofstadter's most optimized version is 20 symbolic parts. How many amino acids do we generally see in biology: 20 or more? His astonishment was expressed:
quote:
--------------------------------------------------------------------------------
There is something almost mystical in seeing the deep sharing of such an abstract structure by these two esoteric, yet fundamental, advances in knowledge achieved in our century.
--------------------------------------------------------------------------------
The two structures he was referring to was biological structures and mathematical formal systems capable of Godelian self-reference. Self-reference is a necessary condition for self-replication. Hence a bio-polymer replicator must implement a mathematically self-referential formal system.
Further, Hofstadter related the Godel Codons to the Codons found in DNA/RN. The Godel Codons consist of triplets which correspond to DNA/RNA triplets: like 633 corresponds to UGG, etc.
An arbitrary mapping was made by Hofstadter.
Not that he believes his mapping is the correct one, but he wrote it a starting point for research.
A mapping like this must ultimately exist for the cell to replicate, but the true mapping itself is yet to be discovered.
(page 268,520,535 of Godel Escher Bach elucidates the meaning of the symbols). Allowing for the fact I have to use English letters for some symbols, the fundamental math symbols mapped to DNA/RNA to amino acids by Hofstadter:
0 666 UUU phe phenylalanine
A 626 UCU ser serine
v 616 UAU tyr tyrosine
: 636 UGU cys cysteine
p 611 UAA stop codon
m 633 UGG trp tryptophan
. 236 CGU arg arginine
a 262 CUC leu leucine
< 212 CAC his histidine
~ 223 CCG pro proline
> 213 CAG gln glutamine
+ 112 AAC asn asparagine
^ 161 AUA ile isoleucine
= 111 AAA lys lysine
' 163 AUG met methionine
S 123 ACG thr threonine
( 362 GUC val valine
[ 312 GAC asp aspartic acid
) 323 GCG ala alanine
] 313 GAG glu glutamic acid
E 333 GGG gly glycine
Hofstadter did not account for the 'synonyms' in the DNA/RNA that code for an amino acid, and left it for future research. However, many feel he is onto something. Having myself had an interest in von Neumann's self-replicating molecular automata, I feel Hofstadter is nearer to the mark than most.
This fundamental IC system, the bio-polymer replicator is constrained by the laws of mathematical logic. Thus Dembski's requirement for "detachability" is satisfied. We can build the specification independent of the target. For replication to happen it must satisfy Hofstadter's "Central Dogma of Mathematical Logic".
To Hofstadter credit, the correspondence of 20 symbols to 20 amino acid and the fact Godel codons and DNA/RNA codons are triplets seems too significant to dismiss.
After the system has 20 symbols and 20 codons, plus 1 punctuation codon, the self replicator is realized by arranging the symbols into mathematical axioms and theorems. The system will not work (according to my best understanding per page 216) unless a minimum of 5 axioms of typgraphical number theory are implemented. They are necessary, but not sufficient conditions for function.
I give 2 of the axioms expressed in Hofstadters notation. I give Axiom 3 and Axiom 2 as examples:
Axiom 3
626,262,636,626,262,163,636,362,262,112,123,262,163,323,111,123,362,262,112,262,163,323
Axiom 2
626,262,636,362,262,112,666,323,111,262
There are 3 other axioms of similar length. Now nothing really happens unless theorems are added which utilize the axioms, so now the minimum number of parts grows. These parts must be connected exactly, independent of the chemistry, their sequence is critical. Not a single part can be out of place. It is superbly IC, and liberated from the postdiction, single target fallacy.
The minimal system easily consists of 200 symbolic parts. Replication proceeds via theorems running on the axioms. Using probability arguments, 200 parts and 20 symbols we have:
20^200 is 1.6 x 10^260
and this is the most trivial system. Morowitz, others postulate minimum number of parts in the millions.
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 28. January 2004 12:13
Salvador: This fundamental IC system, the bio-polymer replicator is constrained by the laws of mathematical logic. Thus Dembski's requirement for "detachability" is satisfied. We can build the specification independent of the target.
How? And is the system truely IC? These are important questions to answer and non-trivial. As far as Salvador's calculations, they seem irrelevant as to whether or not (self replicating) biomolecules can arise naturally, which they can. Perhaps Salvador can explain to us how he eliminated regularity in Dembski's filter?
As far as self replicating molecules in nature, he is an interesing one
quote:
Nature. 1996 Aug 8; 382(6591): 525-8
A self-replicating peptide. Lee DH, Granja JR, Martinez JA, Severin K, Ghadri MR.
The production of amino acids and their condensation to polypeptides under plausibly prebiotic conditions have long been known. But despite the central importance of molecular self-replication in the origin of life, the feasibility of peptide self-replication has not been established experimentally. Here we report an example of a self-replicating peptide. We show that a 32-residue alpha-helical peptide based on the leucine-zipper domain of the yeast transcription factor GCN4 can act autocatalytically in templating its own synthesis by accelerating the thioester-promoted amide-bond condensation of 15- and 17-residue fragments in neutral, dilute aqueous solutions. The self-replication process displays parabolic growth pattern with the initial rates of product formation correlating with the square-foot of initial template concentration.
[ 28. January 2004, 12:53: Message edited by: Pim van Meurs ]
IP: Logged
|
|
Salvador T. Cordova
Member
Member # 959
|
posted 28. January 2004 12:25
I should make a distinction. There are replicators, and then there are true self-replicators. A true self-replicating system must be isomorphic to Hofstadter's self-referential system. The von Neumann self-replicating automata must satisfy Hofstadter's criteria.
DNAunion at ARN made a very good analysis of Ghadiri groups "supposed" self replicators.
quote:
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.
[ 28. January 2004, 12:28: Message edited by: Salvador T. Cordova ]
IP: Logged
|
|
Pim van Meurs
Member
Member # 541
|
posted 28. January 2004 12:44
Salvador tries to dismiss the findings by that Ghadiri lab: DNAunion at ARN made a very good analysis of Ghadiri groups "supposed" self replicators.
When DNAunion was given the example he stated
quote:
Could this protein have arisen naturally? Possibly. The point is, that in fact, it did NOT. It was designed – foresight and years of knowledge were used to purposefully construct a molecule capable of performing a pre-selected function.
In fact, this shows how easily intelligent agents can produce complex biological macromolecules with specific functions.
An interesting strawman but admitting that self replicating proteins could arise naturally.
In addition DNAUnion was wondering about the origins of homochirality, even there science may have found the answer(s).
Lets provide the readers with the link
And while DNAunion seems to deny that Ghadiri's protein is self-replicating, scientists seem to disagree with DNAunion's conclusions.
Proc Natl Acad Sci U S A. 2002 October 1; 99 (20): 12733–12740 A self-replicating ligase ribozyme Natasha Paul and Gerald F. Joyce
Link
quote:
Since then, Ghadiri - who is also known for his innovative design of peptide nanotubes (Chem. Br., November 2001, p22) - and his coworkers have developed this molecular toy further, to demonstrate how a simple chemical system can develop some elementary properties of life, such as replication, selectivity for chirality, error correction and interactions between overlapping reaction cycles in a complex 'hypercycle'.1
Link
The Weizmann Institute has a good collection of origin of life links relevant here.
[ 28. January 2004, 12:51: Message edited by: Pim van Meurs ]
IP: Logged
|
|
|
Printer-friendly view of this topic