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Metaprogramming and DNA

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.

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54 Responses to Metaprogramming and DNA

  1. Michael Denton describes the cell as “wheels of complexity within wheels of complexity,” and what is already known about the cell puts it so far beyond the reach of Darwinian mechanisms that it’s laughable. I have a feeling we’ve only scratched the surface of the cell’s technology, so the situation will become ever-increasingly worse for the chance-and-necessity crowd.

    I’ve had a thought somewhat along the lines of the OP. Much of what has been proposed as junk DNA involves redundant or repetitive nucleotide sequences. Computer programs often use repetitive or iterative code (for example, for(), do(), and while() loops), the number of iterations of which are either specified or controlled by other code.

  2. Thank you, niwrad, for sharing this.

    I had read something similar before (on bio-steganography) and came to the conclusion that metaprogramming (perhaps in “junk” DNA) may have played a role in the sudden appearance of novel biological forms as seen in the fossil record. It would not be surprising since novel information is a requirement for morphological change. This can turn out to be a very sophisticated research project for the ID community. After all, the Darwinian mechanism could not be responsible for latent information if the selective advantage is also hidden from the reach of evolution.

    Great post!

  3. Meta information in DNA is already a fact.

    I haven’t read or heard of any discoveries of “meta-programming” per se yet, but it seems to me that such is necessary to explain the proteome.

    Darwinism has utterly failed at providing an explanation of any kind for the origin of information in the cell, how can it possibly explain meta-information!?

    But if meta-programs are discovered in the cell that will be Darwinisms death knell – but my prediction is that they will never admit it.

    That’s because it has nothing to do with evidence – never has.

    It is, for them, a psychological insecurity that obliges persistent denial of realities – similar to that encountered in psychiatric ward patients.

    Until they give up their utter dependence on a materialist world view and the lie that only science can explain reality, they will never be free from such bondage to denials.

  4. Astute observation! Indeed, metaprogramming techniques do appear to be utilized by DNA. In particular, the discovery of what is now referred to as microRNA occurred over a decade ago.

    If you are unfamiliar with microRNA, as the content of this posts suggests, then I suggest reading up on it, as it’s all the rage in both genetics and evolutionary theory at the moment. The basic gist is that small strands of DNA located in what were previously thought to be “junk DNA” regions of genome do not actually code for any proteins, but are actually responsible for the manipulation of certain gene expressions. Simplistically, in some cases this manifests as a ‘switch’ (if the microRNA is one way, the gene is transcribed into a protein, the other it’s not), while others have a more analog effect.

    In particular, a recent paper ( http://www.dartmouth.edu/~diet.....onetal.pdf , and subsequent discussion http://scienceblogs.com/pharyn....._explo.php ) suggests the existence of microRNA strands that regulate mutation rate. Subsequent simulations of this meta-evolution in various genetic algorithms produced some very interesting results, although I know of no publications on the subject.

    However, I disagree with your interpretation that this is evidence of a designer. While I agree that if there were a designer, it is likely that this entity would make extensive use of metaprogramming techniques, I do not believe design necessary to accomplish this. In “The Origins of Sex” by Lynn Margulis, it is postulated that the similarities observed between the proteins that ‘fix’ mutations in DNA when a cell undergoes meiosis, the transformation into a zygote, and the proteins which fixed damage to DNA caused by ultraviolet light (namely adjacent Thymines bonding together), are evidence that meiosis is an evolutionary development spurred on by organisms moving towards the surface of ancient oceans. Because these proteins work by essentially throwing themselves at the genome, the fewer there are the more likely a mutation is to occur in the offspring. This makes them ideal candidates for being manipulated by the ‘metaprogramming’ afforded by microRNA. Given the high mutation rate of organisms at the time, in particular that afforded by the predominant reproduction method of fission, it seems entirely plausible that a random mutation could have produced a very simple mechanism of metaprogramming through microRNA, which was then intensely selected towards for its benefit of allowing the much more fine-tuned metaprogramming of controlling mutation rates.

    In your analysis of your recent IEEE paper, you suggest that the environment contains no inherent information to select towards, and thus cannot effectively be used as the endpoint of a search algorithm. To this, I would like to respond with the following quote, taken from Wikipedia, describing an interaction between Gerald Sussman and Marvin Minsky of the MIT AI lab:

    In the days when Sussman was a novice, Minsky once came to him as he sat hacking at the PDP-6.

    “What are you doing?”, asked Minsky.
    “I am training a randomly wired neural net to play Tic-tac-toe”, Sussman replied.
    “Why is the net wired randomly?”, asked Minsky.
    “I do not want it to have any preconceptions of how to play”, Sussman said.

    Minsky then shut his eyes.
    “Why do you close your eyes?” Sussman asked his teacher.
    “So that the room will be empty.”
    At that moment, Sussman was enlightened.

    What I actually said was, “If you wire it randomly, it will still have preconceptions of how to play. But you just won’t know what those preconceptions are.” –Marvin Minsky

  5. Maybe stem cells do metaprograming…

  6. 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.

    What ‘double layer of abstraction superimposed on matter’ are we talking about? Looking at a typical pc CPU, we find a primitive device capable only of executing the most basic, binary operations, expressed in the CPU’s instruction set. Iterative processes then make this into something useful, like adding two decimal numbers – and maybe even repeat-and-shift that process to create the impression of being able to multiply.

    (CPU’s have evolved, they may have some more sophisticated circuits as well, but afaik, computer technology still rely on the simplest of logical elements: and, or, and exor gates, and inverters. From such humble devices, the most complex cpu’s are built.)

    Sophistication is nothing but a lot of stacked primitives. In computing, as in DNA.

    Metaprogramming applied to biology? I’d like to see an example of that.

  7. “[...] a random mutation could have produced a very simple mechanism of metaprogramming through microRNA, which was then intensely selected [...]”

    Come on guys, come on…

  8. Borne wrote: “But if meta-programs are discovered in the cell that will be Darwinisms death knell – but my prediction is that they will never admit it.”

    30 minutes later bunny wrote:

    “I disagree with your interpretation that this is evidence of a designer. While I agree that if there were a designer, it is likely that this entity would make extensive use of metaprogramming techniques…”

    Too funny. Ever think of going into prophecy Borne? Lol! :)

  9. “Sophistication is nothing but a lot of stacked primitives. In computing, as in DNA.”

    That’s not true. Sofistication in computer programming consist in the very INTELLIGENT way you use/develop ALGORYTHMS with “the primitives”, to achieve some higly developed features/functions.

    And probably the same is in DNA… ;)

    And that’s something the Evo people refuse to understand…

  10. Sophistication is nothing but a lot of stacked primitives. In computing, as in DNA.”

    I am talking about DNA, there isn’t any CPU in the cell decoding DNA sequentially. The computer analogy simply is not relevant.

    To better understand a little about how DNA really works, this might be useful:

    http://pandasthumb.org/archive.....ies-h.html

    How do you think DNA functions in the development of a multi-celled organism, say a centipede – a fruit fly – or a human being?

    From the very first cell to the full grown animal: Each cell on its own! Each cell communicating with its neighbors; it is like a huge orchestra playing – without a conductor. And yet, each member of the orchestra doing exactly what he should, nothing more, nothing less.

    It is marvelous!

  11. Sorry, this is the quote I intended responding to:

    That’s not true. Sofistication in computer programming consist in the very INTELLIGENT way you use/develop ALGORYTHMS

  12. 12

    Cabal,

    To better understand a little about how DNA really works, this might be useful:

    Define the circumstances in which chemicals organize set of symbols that represent other checmicals/processes/outcomes.

  13. Cabal,

    To better understand a little about how DNA really works, this might be useful:

    Define the circumstances in which chemicals organize set of symbols that represent other checmicals/processes/outcomes.

    The stereochemical hypothesis for the origin of the genetic code is a start. It states that certain amino acids have sterochemical affinities for tRNA’s with specific anticodons that correspnd to the genetic code.:

    Yarus M, JG Caporaso & R Knight (2005). Origins of the genetic code: the escaped triplet theory. Annu. Rev. Biochem 74: 179-198.

    From the abstract:

    There is very significant evidence that cognate codons and/or anticodons are unexpectedly frequent in RNA-binding sites for seven of eight biological amino acids that have been tested. This suggests that a substantial fraction of the genetic code has a stereochemical basis, the triplets having escaped from their original function in amino acid–binding sites to become modern codons and anticodons.We explicitly show that this stereochemical basis is consistent with subsequent optimization of the code to minimize the effect of coding mistakes on protein structure. These data also strengthen the argument for invention of the genetic code in an RNA world and for the RNA world itself.

  14. Well, I don’t know about metaprogramming, but metainformation in DNA is already an established fact, and like metaprogramming, it points clearly towards a Designer. Botanist Alex Williams explains why in his article, Astonishing DNA complexity demolishes neo-Darwinism :

    The astonishing complexity of the dynamic information storage capacity of the DNA/chromosome system is, in itself, a marvel of engineering design. Such a magnificent solution to such a monster logistics problem could surely only come from a Master Designer. But the nature of the majority of this information poses an impossible conundrum for neo-Darwinists.

    Proteins are the work-horse molecules of biology. But protein-coding genes make up only a tiny proportion of all the information that we have been describing above. The vast majority of information in the human genome is not primary code for proteins, but meta-information – information about information – the instructions that a cell needs for using the proteins to make, maintain and reproduce functional human beings.

    Neo-Darwinists say that all this information arose by random mutations, but this is not possible. Random events are, by definition, independent of one another. But meta-information is, by definition, totally dependent upon the information to which it relates. It would be quite nonsensical to take the cooking instructions for making a cake and apply them to the assembly of, say, a child’s plastic toy (if nothing else, the baking stage would reduce the toy to a mangled mess). Cake-cooking instructions only have meaning when applied to cake-making ingredients. So too, the logistics solution to the cell division problem is only relevant to the problem of cell division. If we applied the logistics solution to the problem of mate attraction via pheromones (scent) in moths it would not work. All the vast amount of meta-information in the human genome only has meaning when applied to the problem of using the human genome to make, maintain and reproduce human beings.

    Even if we granted that the first biological information came into existence by a random process in an ‘RNA-world’ scenario, the meta-information needed to use that information could not possibly come into existence by the same random (independent) process because metainformation is inextricably dependent upon the information that it relates to.

    There is thus no possible random (mutation) solution to this conundrum. Can natural selection save the day? No. There are at least 100 (and probably many more) bits of meta-information in the human genome for every one bit of primary (protein-coding gene) information. An organism that has to manufacture, maintain and drag around with it a mountain of useless mutations while waiting for a chance correlation of relevance to occur so that something useful can happen, is an organism that natural selection is going to select against, not favour! Moreover, an organism that can survive long enough to accumulate a mountain of useless mutations is an organism that does not need useless mutations — it must already have all the information it needs to survive!

    What kind organism already has all the information it needs to survive? There is only one answer – an organism that was created in the beginning with all that it needs to survive. (In Journal of Creation, 21(3) 2007, p. 115.)

    From an ID perspective, I would just like to add that “created” does not have to mean “created ex nihilo, in the blink of an eye.” A Creator can work just as surely through a gradual, natural process as through a supernatural one. What Williams’ argument demonstrates, however, is that the process whereby meta-information arose in the cell must have been an intelligent one. If the meta-information in cells did indeed evolve gradually, then the evolutionary process itself must have been rigged by the Designer to allow it to generate and preserve meta-information. Making a process like that would have required just as much intelligence on the Designer’s part as ex nihilo creation, if not more so.

  15. vjtorley – “A Creator can work just as surely through a gradual, natural process as through a supernatural one.”

    Indeed. Pro-creation is one such method. It is my belief that God did indeed create things in an instant as one reads in Genesis.

    But the thousands of years thereafter (especially the flood) have muddied the waters of that event. (Pun intended). :)

    The first created people came about in a radically different way than their progeny.

  16. 16

    Dave,

    We have been here before. Stereochemistry explains nothing about the sequencing of nucleotides within DNA. Absolutely nothing.

    The fact that (downstream from the information) the parts that are encoded to do the job, can in fact do the job, is of little consequence to the origin of the information upstream.

    No matter how you stack it, no matter what timeline you want to attribute to it, no matter in what order you see the events unfolding, you still come to a point where you have chemicals assigning representative symbolic meaning to other chemicals.

    Why? Because that is the way we find it today.

  17. .Dave,

    We have been here before. Stereochemistry explains nothing about the sequencing of nucleotides within DNA. Absolutely nothing.

    Stereochemistry establishes the relationship (i.e., the ‘meaning’) between amino acid, anticodon and codon. That has quite a bit to do with the “sequencing of nucleotides within DNA”.

    The fact that (downstream from the information) the parts that are encoded to do the job, can in fact do the job, is of little consequence to the origin of the information upstream.

    The whole concept of a ‘code’ to begin with is based on the association of amino acid, anticodon and codon. The association is the information, and the stereochemical affinities explain its origin.

  18. From Mr. Williams article re: ENCODE and certain findings…

    “We reported previously that the transcripts overlap the gene regions, but the overlaps are huge compared to the size of the genes. On average, the transcripts are 10 to 50 times the size of the gene region, overlapping on both sides. And as many as 20% of transcripts range up to more than 100 times the size of the gene region.”

    Botanist? Pffft! “Silly creationist” what does he know?

    The moment I learned about meta-information transcription process of overlapping, as any informed programmer will tell you, there must be pointers and/or keyed codes for such a Read/Write recogniztion system. It is one thing to do this as a programmer. The CPU/Storage and OS is already setup. Unless you are a developer in machine language, you are fairly oblivious to how memory swapping, “Overlapping and shared memory is utilized and compressed.

    There is still much more Meta-Information I think to be fully understood on a detailed level about how these features work. Much less any meta-programming aspects.

    Especially for dynamic systems.

    This is why I doubt the story telling devices used so often by Darwinist. Saying “it could have” “happened” does not make it so. We can easily say, a Designer “could have” designed it this way. At this point no one wins the argument.

    So, lets drop that line of reasoning from the Darwinist. That simply does not work anymore. The “anything can happen” psuedo-logic statement of perceived macro changes over time is history.

    “This would be like photocopying a page in a book and having to get information from 10, 50 or even 100 other pages in order to use the information on that page.”

    I challenge any Darwinist to build a system based upon their actual theory that matches what we observe today in genetics of the cell.

    First, they cannot utilize stored blueprints of existing DNA. They must start from scratch. Second they cannot utilize Intelligent Regulators(i.e. formerly Junk DNA) and third, they cannot start with any Coordinate Control System that
    helps all independent systems to work simultaneously together for replication while defending against any threat to survival.

    When they have completed this project they will have discovered how to Design a living system from scratch, much like they say “it happened” a billion years ago.

    Funny, even if they were to pull this off, they’d still be “designing” it from the start with a goal in mind for animated life to appear.

    If this was not so serious a fight for truth, I’d be laughing all the time at such parody of foolish concepts by the Darwinist.

    I didn’t even mention the necessary FirmWare/OS systems environment: Physics laws, Constants, Energy, atomic forces, electron orbits, etc., etc., required to keep a stable environment. Otherewise, none of us can play with our ideas in the first place. Darwinist or IDist. Manipulating On/Off switches, Boolean Gates, and signalling structures so that the symbolic codes align or not. To play with such toys in a Designer Lab is only available to any of us due to the hardware around us.

    But, as VJTorley stated, I’m not sure about the meta-programming aspects at this point, but the meta-information clearly has shed light on the foolishness of Darwinism in light of information from ENCODE and even from the past several decades.

    That Darwinist still rule intellectually today in the classroom is not due to being correct, but merely their old beards have not yet faded away. Their ridicule worked for a long time. Their mocking and scoffing. But they have no where to turn now. The evidence is overwhelming against their theory now. And their future is certain failure. Because they will never “design” a random system such as they believe in.

    1) They need hardware – Life Support
    2) They need an end goal – Life.

    One is meaningless without two and two cannot exist without one.

  19. @Cabal, post #10

    Unfortunately I wasn’t able to access the link you posted, but I’ll try again later. I’m sure it’s interesting.

    Are you absolutely sure there isn’t any “CPU” in the cell?… Because there are a lot of processes in the cell that work exactly as computer programming, decoding and copying information. More, there are sensor built in, that help identify modifications in the cell environment, send signals, signals that are interpreted and functional execution is started right away.

    I cannot think of inside cell structure example for the above, but first thing that pops up into my mind is the functioning of the immune system – it decodes the information (presence) of the “invaders” and reacts in a pre-programmed way. The digestive system in vertebrates is similar – generates enzymes according to the ingested food type, and many more examples can be listed.

    What I want to point out is that – as you said (“orchestra playing”) – an organism is a HIGHLY AUTOMATED “DEVICE” that works in a pre-programmed way. All the functions of the organs are very specific and NOT RANDOM! Important to be understood… I have a master degree in Automation and Computer Science and I can tell you/assure you that a living organism is simply an excellent example of FULLY AUTOMATIC MACHINERY, pre-programmed to take care of itself and multiply itself. It can react to environment changes, trough sophisticated sensors “on board”, it can feed itself, it can move, it can communicate, it can even heal itself in some degree.

    I am challenging you to explain how an decision making (IF – THEN – ELSE) structure, that is present also in the DNA, can arise by random, fully materialistic, non-conscious, unguided, unintelligent processes.

    BR,
    Sladjo.

  20. An organism that has to manufacture, maintain and drag around with it a mountain of useless mutations while waiting for a chance correlation of relevance to occur so that something useful can happen, is an organism that natural selection is going to select against, not favour! Moreover, an organism that can survive long enough to accumulate a mountain of useless mutations is an organism that does not need useless mutations — it must already have all the information it needs to survive!

    It has already been established that organisms carry loads of seemingly inactive, superfluous DNA. They survive. At any given opportunity it may be put to use… By the designer?

  21. Define the circumstances in which chemicals organize set of symbols that represent other checmicals/processes/outcomes.

    I know nothing about that. What I think I know is that the processes taking place at the most basic level are unaware about the existence of any higher levels.

    Chemistry doesn’t recognize symbols.

  22. I guess I should make it clear that my primary objection is directed at the tendency to compare activity in the cell with a computer program. Metaprogramming? I say no.

    It may be fun, but is it relevant?

    I am challenging you to explain how an decision making (IF – THEN – ELSE) structure, that is present also in the DNA, can arise by random, fully materialistic, non-conscious, unguided, unintelligent processes.

    How it (whatever it is) got there is one question, another is where is it?

    Aren’t we reading our abstractions into what actually is going on at the basic level? The way I understand genetics is that there isn’t any master plan for an organism.

    I don’t see any if-then-else in DNA so I can’t say anything about it.

    I think developmental biology, i.e. evo-devo is the part of biology most relevant for understanding DNA. Not only does it explain how DNA works, it also is very relevant wrt the question about origins that fuels this debate.

  23. Cabal,

    Please read stuff (on Wiki, for instance) about DNA replication and cell cycle. You will find that there are a lot of CONTROL MECHANISMS that overlooks the DNA replication and cell division.

    For example, within cell cycle process, there are CHECKPOINTS CONTROL MECHANISMS that assures the correct completion of a particular cell replication phase.

    http://en.wikipedia.org/wiki/Cell_cycle

    Any CONTROL MECHANISM contains, in one way or another, decision making structures or functions. Controlling something means that you must HAVE INFORMATION about the process you need to control, and you MUST HAVE (already available!) an CONTROL ALGORITHM. Controlling the cell cycle means that there must be a way the cell KNOWS what is the status of the replication phase process – that implies some sensors or pattern recognition ability that will generate an output (PASS/FAIL). Also “the cell” needs to know HOW TO PROCEED FURTHER, and so on and so forth.

    My understanding of the cell (division) cycle is that inside the cell there are computing capabilities – there is no question about that, capabilities able to understand if the process of the particular division phase completed successfully. And IF yes (if current phase completed successfully), THEN go further with the next phase, ELSE do something else.

    IF-THEN-ELSE is the the abstract of decision making.

    Ok, maybe I have failed to give examples of decision making structures within the DNA, but within the cell, there are plenty of them. And neither supports evolution theory.

    Bonus – two paragraphs from above link, that (IMHO) heavily supports ID:

    “Regulation of the cell cycle involves processes crucial to the survival of a cell, including the detection and repair of genetic damage as well as the prevention of uncontrolled cell division. The molecular events that control the cell cycle are ordered and directional; that is, each process occurs in a sequential fashion and it is impossible to “reverse” the cycle.”

    “Cell cycle checkpoints are used by the cell to monitor and regulate the progress of the cell cycle. Checkpoints prevent cell cycle progression at specific points, allowing verification of necessary phase processes and repair of DNA damage. The cell cannot proceed to the next phase until checkpoint requirements have been met. Several checkpoints are designed to ensure that damaged or incomplete DNA is not passed on to daughter cells.”

    Keywords: regulation, detection, repair, prevention, control, ordered, monitor, verification, designed (sic!).
    All of these in deep contrast with: chance, random, purposeless, unguided, uncontrolled, blind…

  24. Bunny,

    “In “The Origins of Sex” by Lynn Margulis, it is postulated that the similarities observed between the proteins that ‘fix’ mutations in DNA when a cell undergoes meiosis, the transformation into a zygote, and the proteins which fixed damage to DNA caused by ultraviolet light (namely adjacent Thymines bonding together), are evidence that meiosis is an evolutionary development spurred on by organisms moving towards the surface of ancient oceans.”

    No. Similarities are convincing evidence of similarities. They are at best weak circumstancial evidence of evolution. There are many similar biological functions in nature. To postulate an evolutionary pathway amid a myriad of possible choices is at best quesswork. Take for example Darwin’s constantly changing tree of life.

    There is only one way to prove evolution. Scientists can map genomes. To prove evolution a) the dna from one species like a chimpanzee must be altered to produce a completely new species such as a gorilla, b) the mechanism for this change in nature must be verified. It is not enough for a scientist to design life. The scientist is an intelligent agent afterall. And c) it must be show how this mutation can occur and succeed in a large enough population to sustain a new species.

    If this can be done then you may convince some intelligent people of the fact of evolution. But until this is done, considering the complexity of life and the limited time, geological evidence, etc. evolution is unconvincing.

  25. 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.

  26. 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.

  27. 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?

  28. 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.

  29. 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 TKI

  30. 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.

  31. 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?

  32. 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

  33. 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?

  34. 34

    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.

  35. 35

    Cabal, have you ever heard of any code reassignment studies?

  36. 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.

  37. 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.

  38. 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.

  39. 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.

  40. DW and Cabal:

    Looks like UB adn Joseph have done a good enough job of addressing your talking points.

    GEM of TKI

  41. 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.

  42. 42

    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.

  43. Dave Wisker,

    You may have missed my comment up above at #38 but could you lay out the attractions and how they work. Thanks.

  44. 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.

  45. 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: 4537-4542

  46. 46

    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.

  47. 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.

  48. 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.

  49. 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.

  50. 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.

  51. “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.

  52. jerry,

    Modern tRNA attaches itself to the amino acid differently than its ancestor did, but close to the original binding site.

    Is that clearer?

  53. 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.

  54. 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.

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