Uncommon Descent Serving The Intelligent Design Community

Metaprogramming and DNA

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

In informatics metaprogramming is a technique consisting in developing computer programs (sets of instructions) that output other programs. While simple programming means instructions generating data, metaprogramming means instructions generating instructions. In general the prefix “meta” means a thing/cause that stays at a higher semantic/ontological level than another thing/effect (in the case of metaprogramming we have a two-level hierarchy where a parent program creates child programs). For a tutorial introduction to metaprogramming see for example the following Jonathan Bartlett’s brilliant articles:
one, two and three.

DNA contains instructions, biological code for working-out various constructive cellular jobs (making proteins, setting developmental parameters, etc.). Question (inspired by the above ascertainment and readings): does DNA contain also meta-programs beyond simple programs?

Much DNA (outside its coding-for-proteins portions) seems without function (junk-DNA). Is it possible that some junk-DNA is meta-code able to assembly other DNA code? This could be an interesting ID prediction. Many have noted as the information amount contained in the genomes seems really too little to account for the overall complexity of organisms. Metaprogramming would be exactly one of the techniques able to compress the biological information.

If the “DNA-metaprogramming” ID prediction were confirmed in the lab this would provide additional terrific evidence of design inside the cell. In fact metaprogramming involves an additional level of abstraction upon the classic programming level. After all intelligence is what can construct hierarchies of unlimited levels of abstraction. Who would bet that the intelligence that designed life limited itself to simple programming only and didn’t use advanced programming? In my opinion just the bottom programming level is absolutely outside the range of what undirected evolution can reach (for reasons of principle). But unfortunately we see not even the discovery of programming in the cell convinced evolutionists about ID. May be would the discovery of biological metaprogramming convince them finally?

Bartlett himself also provided some insights about the presence of metainformation in the cell here and here (last two pages). I think these works represent genuine ID research and go in the direction of confirmation of a possible ID prediction about the presence of metainformation in the cell.

The analysis contained in these docs of the VDJ recombination system as a metaprogramming system is persuasive. It is likely that in front of the difficult problem of generating “millions or billions of antibodies out of a relatively few number of genes” a skilled software developer would resort to metaprogramming. Really it seems the designer of life used such advanced technique (or something like that) to solve difficult biological tasks (like to engineer parts of the immunitary system).

Usually metaprogramming implies the development of a new metalanguage that serves to assembly constructs of an object language, which in turn will be run by the hardware. Eventually metalanguage and object language can be the same (e.g. “nihil obstat” that one writes a metaprogram using the C language to output another C program). In this case the syntactical level remains the same, nonetheless the semantic level of the former respect the latter is higher. Only intelligence can stack semantic levels. The double level of abstraction superimposed on matter implied in metaprogramming applied to biology is a thing that sure is very far from the low material level of the natural laws and randomness and should help to convince anybody about the sophisticated design of life.

As last note, this issue emphasizes again the importance of the involvement in biology of computer science experts (and specialists of other fields too) who are in the same time ID supporters. Before the many applications and explanations suggested by ID one doesn’t understand as evolutionists might say that the ID perspective is not useful to science.

Comments
Biological information can be explained by stereochemistry just as a computer's information can be explained by electricity. Too bad there isn't anything in chemistry that can explain biological information just as electricity does not explain a computer's information.Joseph
August 24, 2009
August
08
Aug
24
24
2009
06:41 AM
6
06
41
AM
PDT
There isn't any evidence for a RNA world. The experiments conducted to date demonstrate the difficulty in getting two nucleotides- hint it takes the work of chemists to get the two. Experiments conducted on RNA's catalytic properties have also been disappointing- one bond is made. So the bottom line is the RNA world exists only in the minds of those who need it.Joseph
August 24, 2009
August
08
Aug
24
24
2009
06:37 AM
6
06
37
AM
PDT
jerry, Modern tRNA attaches itself to the amino acid differently than its ancestor did, but close to the original binding site. Is that clearer?Dave Wisker
August 23, 2009
August
08
Aug
23
23
2009
02:01 PM
2
02
01
PM
PDT
"Instead, the amino acid is attached via an ester bond to the 3? end of the stem. The anticodon sequence is further down the stem and is not involved." Then why should the amino acid bind at some other place on the tRNA just because the anti codon will bind to it. There should be a connection or am I missing something.jerry
August 23, 2009
August
08
Aug
23
23
2009
01:31 PM
1
01
31
PM
PDT
jerry, One more quick comment: This is the first I was aware that the anti codon sequence was responsible for the protein binding as well as the codon binding. Sounds interesting but is it true that the binding part of the tRNA for the protein is the same as the anti codon? No. As I said, the anticodon sequence is found in the acceptor stem of the tRNA, but it no longer actively binds to the amino acid. Instead, the amino acid is attached via an ester bond to the 3' end of the stem. The anticodon sequence is further down the stem and is not involved.Dave Wisker
August 23, 2009
August
08
Aug
23
23
2009
09:45 AM
9
09
45
AM
PDT
Hi jerry, Let’s see if I can reduce your explanation even further. Somehow a protein comes into existence. That can be a subject of some other study. This protein contains a series of amino acids. On some of these amino acids a small RNA polymer binds. One of these binding RNA polymers is three in length and represent a three base combination that is attracted to a specific amino acid. I'm on mny way out the door right now,and will comment later, but I can make two quick points: 1. Don't assume the protein, i.e., polypeptide, has to occur first. 2. The RNA binding sites on the RNA aptamers are usually longer than than three ribonucleotides, but the codon or anticodon sequences are contained within the binding site.Dave Wisker
August 23, 2009
August
08
Aug
23
23
2009
09:34 AM
9
09
34
AM
PDT
Upright, If you have been reading my comments about the stereochemical hypothesis on other threads here (my discussion with Paul Giem specifically), you would know that I have pointed out that it rests on certain assumptions, some of which are speculative. That has nothing to do with the basic premise I have been talking about. Good hypotheses make predictions about what should be observed, but always the predictions are based on the supposition that the hypothesis is true for the sake of argument. That includes, therefore, some of its foundational assumptions. I'm not (and have not, at least not intentionally) demanded that everyone here accept that all of the assumptions are true, just as you shouldn't for ID. It is good enough to evaluate the hypotheses and see if what they predict is what we observe. If they at least pass that initial test, then we can work on the assumptions and requirements to see if the hypotheses and the overall frameworks within which they fit are plausible. Many hypotheses fail at this point, or prove to be incomplete. That's life. That's science.Dave Wisker
August 23, 2009
August
08
Aug
23
23
2009
09:23 AM
9
09
23
AM
PDT
Dave Wisker, Let's see if I can reduce your explanation even further. Somehow a protein comes into existence. That can be a subject of some other study. This protein contains a series of amino acids. On some of these amino acids a small RNA polymer binds. One of these binding RNA polymers is three in length and represent a three base combination that is attracted to a specific amino acid. This three base combination then duplicates somehow and there is a string of the same two RNA sequences. At some time later the string gets longer so that at one end is the RNA sequence and at the other end a duplicate is there. Now this RNA sequence will also bind to its opposite base combination. So the opposite base combination is the origin of the codon and the original base is now the anti codon? So we have the anti codon binding to the codon and also the same combination, binding to the amino acid at the other end. Let me know if this is a correct interpretation. This is the first I was aware that the anti codon sequence was responsible for the protein binding as well as the codon binding. Sounds interesting but is it true that the binding part of the tRNA for the protein is the same as the anti codon? Seems like that would have been obvious years ago and we would be here much sooner.jerry
August 23, 2009
August
08
Aug
23
23
2009
08:50 AM
8
08
50
AM
PDT
Dave, you have now made my points succinctly. 1) your premise relies completely upon a laundry list of speculative assumptions - many of which are contrary to present knowledge. 2) you tranfer the problem of information out of sight by simply attributing it all to chance (which is again, contrary to present knowledge). 3) you use the word "establishes" when, in truth, nothing whatsoever has been established about the origin of information.Upright BiPed
August 23, 2009
August
08
Aug
23
23
2009
08:27 AM
8
08
27
AM
PDT
Hi jerry, If you have time, maybe you could explain in layman’s English just how the reactions work in the Yarus et al study. What attracts each other and how does this end up relating codons or anti codons to amino acids. As far as I know the anti codon and the amino acid are on opposite ends of the tRNA and there is no special reason why they should be on the same polymer. Why is there a relationship between the two of them when on the tRNA they are separated by a fair distance? I’m not sure how well I can explain, but I’ll give it a try. Yarus’s paper is a review of a lot of work done by his lab and others on the origin of the genetic code. It fits in to an overarching view of the origin of protein synthesis under the RNA World hypothesis. Yarus believes that the genetic code and translation mechanisms came into their modern form in stages. The earliest stage was handled purely by RNA and its catalytic properties. The associations between codon or anticodons and amino acids were established by small RNA sequences that bound to specific amino acids. What Yarus and others noted early on was, the binding sites on small RNAs tended to contain the codon or anticodon that corresponded (from the modern genetic code table) to the amino acid to which they bound. Isoleucine was the first one they looked at, I think, and it remains the most intensively studied. The first thing they did was to try and rule out the possibility that this was just due to chance. To do this, they generated thousands of small RNA sequences randomly, and evaluated the binding sites of those that did bind to eigjht amino acids. Then they subjected the data to a statistical analysis to determine the probability of the results being due to chance (they used was a goodness-of-fit technique known as a ‘G- test’). The authors found the overall probability of this kind of association for the eight AA’s being due to chance was 5.4 X 10-11 They have taken this information and other work to develop an hypothesis which states that early translation was RNA-mediated, in ancestors to modern cells called ribocytes (mentioned in the second paper I cited). Modern tRNAs and enzyme-assisted translation mechanisms came later as the modern translation system developed, but the gist is, modern tRNAs are descended from proto-tRNAs derived from the original binding RNAs, but with the anticodon sequences no longer part of the actual amino-acid binding apparatus. If we look at a modern tRNA molecule, we see that it contains anticodon sequences in two places: in the acceptor stem, where the amino acid attaches to the tRNA (Rodin et al, 1996), and in the anticodon loop which binds to the codon in the transcript mRNA. De Guilio (2000) suggests that the anticodon sequence in the acceptor stem is the original one, and the sequence in the anticodon loop is a copy produced by duplication. References: De Guilio, M (2000). The RNA World, the genetic code, and the tRNA molecule. Trends in Genetics 16(1): 17-18 Rodin S, A Rodin & S Ohno. The presence of codon-anticodon pairs in the acceptor stem of tRNAs. PNAS 93: 4537-4542Dave Wisker
August 23, 2009
August
08
Aug
23
23
2009
06:31 AM
6
06
31
AM
PDT
I'm sorry I haven't had time to post on this one - I have a lot going on in my family life right now. However, I am disturbed because it seems that my critics haven't read anything that I wrote. In any case, besides the obvious overlaps between VDJ recombination and regular metaprogramming, what I am most curious if there is enterprise metaprogramming going on in the cell. That is, whether there are mechanisms which allow a single mutation to make coordinated changes in multiple tissues. So, if a segment of DNA might exist that is used in different ways by different parts of the cell, so that _one_ change would change different proteins in different cells in a coordinated fashion.johnnyb
August 22, 2009
August
08
Aug
22
22
2009
08:50 PM
8
08
50
PM
PDT
Dave Wisker, You may have missed my comment up above at #38 but could you lay out the attractions and how they work. Thanks.jerry
August 22, 2009
August
08
Aug
22
22
2009
07:50 PM
7
07
50
PM
PDT
Dave, No one can make you believe that which you are not prepared to believe. Against human will, no amount of evidence can accomplish such a feat. I simply point out that for your assumption to be of any actual value whatsoever (and I do mean, WHATSOEVER) many many almost chemcially incoherent events must occur. You dismiss it all as if nothing had even been said. So be it. You might want to consider: there is a reason there has not been headlines around the world that the actual source of DNA has been found; the bottom line of the bottom line. That reason is manifest unto itself: No one beleives it, even for a minute. My humble suggestion at this point is that you grab a codon table and stare at it until the light comes on.Upright BiPed
August 22, 2009
August
08
Aug
22
22
2009
03:45 PM
3
03
45
PM
PDT
kf: UB's points are misdirected, and do not address the basic point that the information (i.e., the association of codon/anticodon and amino acid ) does not require intelligent input, since much of the association can be explained by stereochemistry. UB wants to look at other aspects underlying the overall evolution of translation itself, which, while interesting, avoids the actual issue of interest.Dave Wisker
August 22, 2009
August
08
Aug
22
22
2009
01:42 PM
1
01
42
PM
PDT
DW and Cabal: Looks like UB adn Joseph have done a good enough job of addressing your talking points. GEM of TKIkairosfocus
August 21, 2009
August
08
Aug
21
21
2009
11:21 PM
11
11
21
PM
PDT
Peter,
Common descent is an extraordinary claim. I require more than circumstantial evidence to accept evolution.
Me too Peter, me too. And common descent is an extraordinary claim, which most assuredly requires more than circumstantial evidence to be accepted. Well put.Clive Hayden
August 21, 2009
August
08
Aug
21
21
2009
10:43 PM
10
10
43
PM
PDT
Dave Wisker, If you have time, maybe you could explain in layman's English just how the reactions work in the Yarus et al study. What attracts each other and how does this end up relating codons or anti codons to amino acids. As far as I know the anti codon and the amino acid are on opposite ends of the tRNA and there is no special reason why they should be on the same polymer. Why is there a relationship between the two of them when on the tRNA they are separated by a fair distance? I don't have access to the article and don't know if I would have the time to plow through the technical jargon to get at this.jerry
August 21, 2009
August
08
Aug
21
21
2009
08:40 PM
8
08
40
PM
PDT
Billb,
Are similarities between you and your grandparents circumstantial?
You make the same mistake again. My grandparents and myself are both humans. This is not an example of evolution. Your point does not support your argument. An extraordinary claim requires extraordinary evidence in science (unless you are a secularists in desperate need of a worldview). Common descent is an extraordinary claim. I require more than circumstantial evidence to accept evolution.Peter
August 21, 2009
August
08
Aug
21
21
2009
07:17 PM
7
07
17
PM
PDT
Cabal:
Whereas in DNA, a specific code results in chemical activity. So you don’t think the molecular makeup of DNA matters?
It matters in that it is the hardware that carries out the instructions of the software. The the sequence specificity is linked to the pre-specified code, ie software. All the resources for all the chemical reactions required are there and those reactions are carried out under the direction of the software. Protein transport knows its destination the same way your email does- it is programmed in- again not the sequence- the sequence is just required to carry out the instructions. These instructions ride on/ in the sequence. The DNA would hold a program. When any RNA is formed from it it downloads the data that RNA requires to carry out its particular job. When DNA is replicated the program is downloaded from parent to daughter across the newly formed bonds.Joseph
August 21, 2009
August
08
Aug
21
21
2009
04:51 PM
4
04
51
PM
PDT
Cabal, have you ever heard of any code reassignment studies?Upright BiPed
August 21, 2009
August
08
Aug
21
21
2009
02:22 PM
2
02
22
PM
PDT
Dave,
Stereochemistry establishes the relationship (i.e., the ‘meaning’) between amino acid, anticodon and codon.
Woese and Gilbert would be proud of you, but perhaps you use the word “establishes” with an unwarranted level of confidence. Or, more precisely, an unwarranted conclusion as to applicability of the observation, particularly given the assumptions that precede it. Start Here: 1) The building blocks of RNA form on Earth (very, very modest evidence) 2) Functional RNA oligonucleotide chains appear on Earth (no evidence) 3) An RNA replicase appears on Earth (absolutely no evidence) 4) RNA templates are used by RNA enzymes to produce proteins (no evidence) 5) Proteins take over the synthesis of proteins from RNA (no evidence whatsoever) 6) Reverse transcription appears from RNA to DNA (absolutely no evidence in any shape, form, or manner) So, ignoring such minor details as a self-replicating membrane, or the deamination of the fragile RNA complex in pre-biotic conditions, or the half-life of cytosine, or the necessary formation of ribose, or the formose reaction in the presence of amino acids, or the issues of cross contamination, or the problem of getting polyribonucleotides to form in any length to be practically functional, or the list of protein functions that RNA can’t fulfill, or the plausibility of an ex nihlio synthesis of the full gamut of mRNA and tRNA constituent parts to move the system (by some unfathomable means) from ribozyme-based protein synthesis to protein-based protein synthesis, or even the activation of energy and control into all these systems, or… Perhaps suggesting that affinities between the constituent parts of the translation system (which are in fact required by the process to begin with) and indeed, coded for, available, and organized by means of that process IS a bit too much to bite off. You posited a minor hypothesis that rests upon a larger hypothesis that is riddled with assumptions that have little or no evidence that any of them did occur, or even can occur. In essence, you have simply pushed the problem of information out of the way. What templating mechanisms RNA used to form proteins to take over forming proteins (while it formed the proteins itself) you do not say. And what of reverse translation? It’s as if it hardly even matters. - - - - - - - - - The RNA world is a chemical nightmare and a joke. The same joke as the multi-verse.Upright BiPed
August 21, 2009
August
08
Aug
21
21
2009
02:21 PM
2
02
21
PM
PDT
The molecular make up of the medium does not determine the information it contains.
Really? I agree that the molecular make up of a computer is irrelevant - it works by abstraction; i.e. the hardware is organized to act as logical devices: it is digital circuitry only capable of performing binary logical operations. Whereas in DNA, a specific code results in chemical activity. So you don't think the molecular makeup of DNA matters? Then any arbitrarily selected molecular medium to make up the code set expressed with adenine, cytosine, guanine, thymine would perform equally well? No chemistry?Cabal
August 21, 2009
August
08
Aug
21
21
2009
01:40 PM
1
01
40
PM
PDT
What you need to explain, instead, is — per your materialist premises — how the whole system originated by forces of chance plus blind necessity, wiothout intelligent input, without just so stories or other strain- out- a- gnat- but- swallow- a- camel implausibilities. Actually, what you need to do is address the stereochemical hypothesis by evaluating its claims and predictions. You could start by examining the empirical experimental evidence supporting the hypothesis as described in the paper and show how it is implausible or wrong, instead of simply handwaving and playing the hoary old "just so story" gambit. In the meantime, we can continue to explore the stereochemical hypothesis and how it fits into the RNA World by looking at this: Yarus M (2002). Primordial genetics: phenotype of the ribocyte. Annu Rev Genet 36:125-51
The idea that the ancestors of modern cells were RNA cells (ribocytes) can be investigated by asking whether all essential cellular functions might be performed by RNAs. This requires isolating suitable molecules by selection-amplification when the predicted molecules are presently extinct. In fact, RNAs with many properties required during a period in which RNA was the major macromolecular agent in cells (an RNA world) have been selected in modern experiments. There is, accordingly, reason to inquire how such a ribocyte might appear, based on the properties of the RNAs that composed it. Combining the intrinsic qualities of RNA with the fundamental characteristics of selection from randomized sequence pools, one predicts ribocytes with a cell cycle measured (roughly) in weeks. Such cells likely had a rapidly varying genome, composed of many small genetic and catalytic elements made of tens of ribonucleotides. Thereare substantial arguments that, at the mid-RNA era, a subset of these nucleotides are reproducibly available and resemble the modern four. Such cells are predicted to evolve rapidly. Instead of modifying preexisting genes, ribocytes frequently draw new functions from an internal pool containing zeptomoles (<1 attomole) of predominantly inactive random sequences
Dave Wisker
August 21, 2009
August
08
Aug
21
21
2009
11:34 AM
11
11
34
AM
PDT
The DNA, RNA, proteins, ribosomes, etc., are the hardware. Each also contains software. The sequence specificity is not that software, rather the software of living organisms is very much like a computer's software. A computer's program is not reducible to the medium on/ in which it resides (disc, chip, tape). The molecular make up of the medium does not determine the information it contains. And yes I would say it is a safe bet that there are layers of instructions- ie software. Do people really think that molecules just set off to make other molecules, which are then further prepared by other molecules to just go build yet another molecule, just because a sequence was matched?Joseph
August 21, 2009
August
08
Aug
21
21
2009
10:56 AM
10
10
56
AM
PDT
To the Sussman/Minsky quote must be added the classic AI programmer's graffiti, "I'd rather write programs that write programs, than write programs!" ;) Of course, GP is just programs writing programs via evolutionary changes.Nakashima
August 21, 2009
August
08
Aug
21
21
2009
10:21 AM
10
10
21
AM
PDT
Cabal etc: Your stereochemical affinities of tRNA anticodons for codons are of course how the codon triplet bases are coded for and read, triggering elongation of the AA chain in the coded for protein. (They are not materially different from how the double helix has complementary pairs encoding the same information.) So, by saying the technical basis for the coding in suitably technical terminology, you have obfuscated the basic facts of the matter: digital codes expressed in data structures and programs. What you need to explain, instead, is -- per your materialist premises -- how the whole system originated by forces of chance plus blind necessity, wiothout intelligent input, without just so stories or other strain- out- a- gnat- but- swallow- a- camel implausibilities. For, in the cell the mRNA string is plausibly constructed from the DNA information on demand, then slips through a nuclear port to access Ribosomes, which thread the mRNA and advance them codon by codon to start, elognate and then terminate the AA sequence for the required functional protein, which is then despatched to the chaperone structure, and is then folded and put to work. All of this is a step by step information and code based sequence of triggered operations, i.e. digital processing based on programs and data structures. In short, Onlookers, what I see above looks uncommonly like willful obtuseness leading to refusal to acknowledge unwelcome facts. GEM of TKIkairosfocus
August 21, 2009
August
08
Aug
21
21
2009
07:53 AM
7
07
53
AM
PDT
BillB Thank you for your post. You wrote:
Are the apparent similarities between processes in the cell and human design evidence that the cell was designed.
No. The case for design rests on the fact that cells instantiate certain features (FCSI, meta-information and possibly meta-programming) which no known natural process can generate, but which intelligent activity is perfectly capable of generating. If someone manages to find a natural process capable of generating these features, then the case for design in the biological world is overthrown. Hence ID is falsifiable. Referring to evolution, you wrote:
As I understand it (a) Speciation has been observed (although others here will claim that they aren’t really new species) (b) The major mechanisms for this have been verified and (c) Beneficial or near neutral mutations can propagate in populations. This is why some intelligent people are convinced.
Your three premises, taken by themselves, would not convince me. All they show is that one species can evolve into another. To establish universal common descent you need two more premises: (d) The kinds of genetic changes which are capable of causing speciation are also capable of accounting for ALL of the differences between the various kinds of organisms in the world today; (e) Supposing these changes to have occurred, the postulated intermediate forms would have been viable, and hence capable of passing on their genes to their descendants. Premises (d) and (e) go well beyond the available evidence at the present time. Hence Darwinian (i.e. undirected) evolution can remain nothing more than a bold, speculative hypothesis.vjtorley
August 21, 2009
August
08
Aug
21
21
2009
07:20 AM
7
07
20
AM
PDT
My favourite it the impossibility of rats to evolve into bats. The intermediary life form could not survive.
ROTFL - flying squirrels! Are similarities between you and your grandparents circumstantial?BillB
August 21, 2009
August
08
Aug
21
21
2009
07:20 AM
7
07
20
AM
PDT
BillB,
"Are the apparent similarities between processes in the cell and human design evidence that the cell was designed."
Evolutionists make the claim of universal common descent. This implies a pathway. Similariites are only circumstantial. There may or may not have been a speciation based on random chance and necessity. There could have been other undescovered mechanisms or divine fiat. So similarities do not proof a pathway. Good science can replicate a claim in a lab. Evolution theory can not do this. ID on the other hand is not claiming universal common descent. It does not postulate speciation therefore they do not have to prove speciation. They are only saying the complex entities come from intelligence. There are millions of examples every day of intelligence creating complex phenomenons. a) The fossil record contradicts universal common descent. My favourite it the impossibility of rats to evolve into bats. The intermediary life form could not survive. b) wishful thinking. c) mutations that don't produce new species.Peter
August 21, 2009
August
08
Aug
21
21
2009
07:08 AM
7
07
08
AM
PDT
Similarities are convincing evidence of similarities.
Are the apparent similarities between processes in the cell and human design evidence that the cell was designed. As I understand it (a) Speciation has been observed (although others here will claim that they aren't really new species) (b) The major mechanisms for this have been verified and (c) Beneficial or near neutral mutations can propagate in populations. This is why some intelligent people are convinced.BillB
August 21, 2009
August
08
Aug
21
21
2009
05:48 AM
5
05
48
AM
PDT
1 2

Leave a Reply