Friday, May 28, 2010

DNA Rules of the Road and Incredulity

Every biology student learns of two massive machines that operate on the DNA molecule. There is the transcription machine that makes a single-stranded copy of a gene, and there is the replication machine that makes a double-stranded copy of the DNA double helix. The former is the first step in the protein synthesis process while the latter is part of the cell division process. But what happens when these different machines meet as they operate on the same stretch of DNA? What are the rules of the DNA road?

New research suggests that the highly intricate replication process is not destabilized by head-on collisions wth the transcription machine, but merely pauses while it displaces the intruder. To do this it uses a protein that otherwise helps with transcription repair. As the paper explains:

These findings demonstrate the intrinsic stability of the replication apparatus and a previously unknown role for the transcription-coupled repair pathway in promoting replication past a RNAP [replisome and RNA polymerase] block.

It is research that is both important and interesting. And, as with any new finding, it may be relevant to the question of evolution. For instance, perhaps the theory of evolution had led us to predict this finding. Or, almost as good, perhaps the finding is reasonably inferred from the theory.

In this case a such a retrodiction would go something like this: If evolution is true then we would expect the replication machine to oust the transcription machine because random mutations could lead to such a design, but not to other conceivable designs.

But what if, on the other hand, evolution did not favor such a design? What if there was no such prediction, or retrodiction? Then it would be more difficult to enlist the design as support for evolution. In fact, what if evolution has no plausible explanation for the design?

In this case, perhaps the replication and transcription machines successfully negotiating their way in the crowded environment, resolving head-on collisions, and having an established “rules-of-the-road” is not likely given evolution’s random biological variation under the winnowing hand of natural selection. Here we would have a finding which does not fit evolutionary explanation, and the evidence shifts over from the plus column to the minus column.

What is interesting is how evolutionists routinely react to such findings. When presented with such designs, evolutionists almost invariably erect a series of fallacious roadblocks. You can see these same roadblocks used repeatedly, and they speak volumes about evolutionary thought.

One such fallacious roadblock is that placing such evidence in the minus column amounts to an argument from incredulity. “You can’t imagine how evolution could possibly have created such a design,” say evolutionists, “and so you think it is evidence against evolution.” It is a strange argument that places the burden on the one evaluating a theory also to defend the theory.

In fact anyone can “imagine” how evolution might have constructed the design, but what is needed is a plausible explanation. Evolutionists want us simply to accept an empty narrative. The problem is not incredulity on the part of the evaluator but credulity on the part of the evolutionist. “Don’t worry, it evolved” is not a plausible explanation.

This fallacious complaint of evolutionists also is another sign of the protectionism that runs through evolutionary thought. If findings that a theory does not explain are not allowed in the minus column, then what could possibly harm the theory? It is the ultimate form of unfalsifiability. Evidences that the theory explains make it a fact and DNA rules-of-the-road don’t count because that would be an argument from incredulity.

81 comments:

  1. That argument from incredulity card is badly frayed at the edges. But the difficult part is that all their cards are badly frayed at the edges. Nifty way to keep you guessing, huh.

    What is also interesting to say the least is their insistence that their 'mountains' of evidence for evolution does not amount to an argument from incredulity.


    Judge: "Well sir, what hard evidence do you have to prove evolution is true?"

    Coyne: "Well, first of all your honor, science doesn't seek to 'prove' anything but to find the best explanation based on the evidence. Science is always open to correction. Anyway, we have lots of pieces of information that allows us to make a reasonable inference as to what happened."

    Judge: "Translation, you don't have any hard evidence but lots and lots of circumstantial evidence".

    Coyne: "Well, I wouldn't quite put it that way, but in essence ye."

    Judge: "Very well. [turns to the Meyer]. And you sir, what direct evidence do you have to prove your position that life is designed and cannot be explained in natural terms only as Mr. Coyne contents?"

    Meyer: 'Well, first of all your honor, science doesn't seek to 'prove' anything but to find the best explanation based on the evidence. Science is always open to correction. Anyway, I too have lots of evidence that allows us to make a reasonable inference (i believe the best inference)that life is designed.

    Judge: "Translation, you don't have any hard evidence either but lots and lots of circumstantial evidence, right?".

    Meyer: "Yes, er that right, your honor. I wish to constrast my inference to best explanation against Mr. Coyne's inference to best explanation, since neither of us have any direct evidence.

    Judge: "Alight, here are the ground rules. Points for logical, well reasoned arguments, and demerits for any just-so-stories. At the end of the day, I will tally them up and the one with the most points wins the case.

    ReplyDelete
  2. Steve: "Judge: "Alight, here are the ground rules. Points for logical, well reasoned arguments, and demerits for any just-so-stories. At the end of the day, I will tally them up and the one with the most points wins the case."

    Yep, that's exactly what happened in Kitzmiller vs. Dover. The IDCer had every chance to make their case in front of the world, and they did a complete face plant. Dembski chickened out and made a lame excuse for not testifying. Behe did testify and made himself look like a total fool over his lack of knowledge about current scientific research. The rest of the IDCers did their best impersonation of clowns piling out of their teeny circus car. Had it been a football match, the final score was something like 137-0, IDC lost. "Breathtaking inanity" indeed.

    Ever since then IDC has pretty much fallen off the radar. There are a few isolated web sites like Uncommonly Dense and this one, populated by a remaining handful of woefully scientifically ignorant true believers. Kinda like the few poor Japanese soldiers on isolated desert islands who fought on for years after 1945, not knowing WW2 had ended.

    Oh well, it's still good entertainment watching them figure out new and different ways to embarrass themselves.

    ReplyDelete
  3. "In fact anyone can “imagine” how evolution might have constructed the design, but what is needed is a plausible explanation."

    Well, here's a working hypothesis:

    Head-to-head collisions are disastrous without machinery to resolve them. However, it is clear from other studies head-to-tail collisions cause no stalling of the replication fork.

    So I hypothesize primitive genomes were organized with origins and promoters in the same orientation. Interestingly, modern bacterial genomes have 80-98% of their rRNA genes, and significantly greater than 50% of their genes co-oriented with the origin of replication. Some viruses (and I think mitochondria) have entirely the same orientation.

    http://www.ncbi.nlm.nih.gov/pubmed/9847411

    Later, MFD1 evolves-it has similarity to helicases, and works to help RNA polymerase detach in a number of broken DNA contexts. It also works on head to head collisions.

    This allows a more dynamic genome, recombination without respecting orientation...beneficial. Bacteria start to put genes on either strand, with more complex regulation.

    Now, as a test, I could synthesize test genomes with and without co-orientation, and query the essentially of such a protein in each.

    I could also do detailed phylogeny on Mfd-how ancient is it, what is it most related to. Do any organisms lack it, and how do they deal with collisions?

    I could even invert some rRNA genes in E. coli, test for ill effect, and see if Mfd overexpression works to compensate.

    I'm sure there is much more to tidy up such a story, but it isn't my field, and it is late. Nevertheless, I hope this shows how a plausible hypothesis can be established and tested. You could have thought of something (probably better) but chose not to. That is what design suggests you do-stop thinking about how-stop inquiring. Why ask how, when that is already answered?

    "Evolutionists want us simply to accept an empty narrative"

    Nope, we want to do detailed empirical research, and not have you represent evolutionary biology as a field empty of process and progress, that throws its hands up in the air when it sees 'complexity.'

    ReplyDelete
  4. "Ever since then IDC has pretty much fallen off the radar. "

    ROTFLMAO!!

    You should be a comedian.
    Your logic and your pseudo science are very humorous indeed.

    Amazing how Darwinists cannot see that they are the ones that can't figure out what probabilities mean and why it matters in biology.

    You brain dead Darwinian fundamentalists should call your weak and ignoramus reasonings "The Worrell Family Science Emporium".

    ReplyDelete
  5. Rob said, "...I'm sure there is much more to tidy up such a story"

    Here we go again, yet another story passing for a plausible mechanism.

    You never learn that science is not story telling and that conjecture and speculation are not facts.

    ReplyDelete
  6. Gary,

    You're very fond of parroting these supposed 'probabilities.' Care to give us an example and apply some mathematics to this system?

    ReplyDelete
  7. Thorton, so what's your answer to the article? I think you know that the Dover case was basically meaningless since the Judge copied vast portions of the ACLU script verbatim in his ruling. ID certainly does have the best explanation for the evidence. Evolutionists are forced to rely on countless miracles to save their theory. We all know that meaningful or specified information does not simply emerge from a magic hat. Complex body plans do not emerge in a geological blink of an eye.(Cambrian Explosion) Relying on the multiverse just so story cannot rescue stellar evolutionary ideas. Exquisitely designed machines do not simply pop into being by chance. Protectionism wouldn't be necessary if there really was good evidence to silence the opposition. If it weren't for your worldview that has blinded you to the truth, you might have great insight. Better get used to ID ideas. It's only going to get worse from here on out. If it is good entertainment for you, then you are in luck, but one of these days, I have a feeling it will stop being so funny and become a serious matter. Already many people wonder if it isn't the evolutionists who are embarrassing themselves because of their staunch seemingly immovable faith in Father Charlie.

    ReplyDelete
  8. "Specified information does not simply emerge from a magic hat"

    How much specified information does Mfd contain? How many units of specified information is it from its nearest relative?

    ReplyDelete
  9. LOL! I just love the IDC mouthbreathers who come out of the woodwork to spout the same old empty boasts. "ID is taking over science!! Evolution is on its deathbed!! Oh God it's SO complex, it just HAS TO be designed!!"

    WATERLOO!! WATERLOO!!

    When you guys stop beating your gums and produce some actual positive evidence through your research, maybe mainstream science will stop laughing.

    Here's the sum total of ID 'theory' to date:

    "An unknown Designer at an unknown place and unknown time using unknown materials with an unknown process and for unknown reasons manufactured something".

    Feel free to provide more details, anytime.

    ReplyDelete
  10. Here's the big thing you IDCers still haven't figured out:

    Just because science hasn't discovered all the details of everything that has gone on in evolutionary processes in the last 3.3 billion years doesn't mean that ID wins by default.

    Science is perfectly OK with saying "I don't know, so I'll research it more" for areas like abiogenesis or the origin of DNA replication. IDCers think that "I don't know yet" equates to "MY Intelligent Designer must have done it!!" It's the same stupid false dichotomy that ID has been living on for years. IDers like to pretend there are only two categories

    1) Natural processes did it
    2) ID did it.

    In reality there are three categories

    1) Natural processes we currently understand did it.
    2) Natural processes we currently don't understand did it
    3) ID did it.

    Just because some data isn't in category 1) doesn't mean it automatically falls into 3) That's why science require positive evidence for a position, not just "ToE can't explain this so ID wins. And positive evidence for ID is something you have ZERO of.

    It really is that simple.

    ReplyDelete
  11. RobertC:

    “You could have thought of something (probably better)”

    Rather than “primitive genomes were organized with origins and promoters in the same orientation” I would have them randomly oriented from the beginning, thereby avoiding any suggestion of teleology or design, and keeping with the evolutionary theme of randomness. Next I would have the consequence of head-on encounters be that transcription fails. This, it could be argued, was only mildly serendipitous, if we avoid the (probably more likely) consequence that both fail, and present it as a 50/50 case. With replication persisting you (i) avoid the fatal problem of reproduction not working and (ii) have a nice segue to the extant design.

    And with transcription failing you simply have more useless DNA. How did functioning gene sequences arise in the first place? Who knows, but surely there were plenty of useless segments. So what if you have some more useless segments as a consequence of head-on encounters. Also, one could argue that in such primitive forms these head-on encounters were not so frequent because … transcription was not as common, or replication was not as common, or both, or … whatever.

    Later MFD1 evolved because it helped RNA polymerase do its job. But its function was somewhat flexible, or sloppy, such that it could actually perform multiple tasks sometimes. These were refined, and thus you had a divergence of functionality, as multiple, well developed, functions arose. In the case of the head-on encounter functionality, MFD1 helped to oust RNA polymerase in a more orderly fashion, thus enhancing the probability of a successful restart. This opened up about half the genome to successful transcription, which by the way was becoming increasingly important as transcription and replication frequencies were probably increasing significantly.

    Of course much of the newly transcribed genome was junk, but there could have been some useful sequences. And in any case this would have increased the selection pressure on that half.

    There you have it, evolution happens.

    Unfortunately this scenario, or yours if you like, is not a plausible explanation. There is substantial detail missing which shows no sign of being easy (which is why it is missing). What is even more unfortunate is that evolutionists seem to be oblivious to this problem. Aside from making occasional charges of “just-so stories” against sub hypotheses they don’t favor, evolutionists routinely construct their own just-so stories. But it is easy to be oblivious to such problems when the overarching idea is a fact. The problem of explaining designs, such as the DNA rules of the road, is not to justify evolution’s plausibility, but rather to elucidate a process that, one way or another, must have occurred. It is question of *how* it worked, not *whether* it worked, and the bar is lowered ever so low. For evolutionists, what passes as “plausible” is amazing.

    ReplyDelete
  12. "One such fallacious roadblock is that placing such evidence in the minus column amounts to an argument from incredulity. “You can’t imagine how evolution could possibly have created such a design,” say evolutionists, “and so you think it is evidence against evolution.” It is a strange argument that places the burden on the one evaluating a theory also to defend the theory."

    It is a passing strange (ahem!) argument, isn't it? And, at the same time, it exposes the curious credulity of Darwinists, does it not?

    ReplyDelete
  13. "But what happens when these different machines meet as they operate on the same stretch of DNA? What are the rules of the DNA road?

    New research suggests that the highly intricate replication process is not destabilized by head-on collisions wth the transcription machine, but merely pauses while it displaces the intruder."

    I don't know whether my understanding of this is correct, as I'm not a biologist.

    I am, however, a computer developer, and what is described here, sounds pretty much like thread management.

    Suppose you have two users accessing the same variable. The two users run code in different threads, but the two threads use the same variable. How do you prevent all kinds of weird anomalies when different threads want to change the same variable? You add a lock on the code section: This means that when the first thread enters the lock, it has exclusive rights to execute it. The second thread needs to wait for the first thread to exit the lock, before the second thread can continue.

    It is absolutely remarkable how simmilar DNA is to computer programming. Not just in the simplistic, such as syntax, but also in the more advanced areas.

    I would not be surprised if we were to discover Object Orientated programming in DNA, where logic is encapsulated in functions, which gets called from other areas of the DNA, rather than to have the same logic duplicated where ever it is needed.

    Oh, and I would dare any Darwinists to show me a natural process capable of producing computer code. I think Darwinism is intellectually bankrupt, and its entire foundation is baseless assertions.

    ReplyDelete
  14. Hanno ,
    you may get "hurricane" answer like I did few days ago when asked similar question.

    ReplyDelete
  15. Hanno: "Oh, and I would dare any Darwinists to show me a natural process capable of producing computer code. I think Darwinism is intellectually bankrupt, and its entire foundation is baseless assertions. "

    LOL! another computer science guy who doesn't understand the difference between analogies and reality. Too funny.

    When scientists speak of DNA 'code', they are using a broad definition of code as 'any process that maps a specific input to a specific output'. Computer code falls under a different definition of 'code': 'a system of using abstract symbols to pass a message over a medium.' IDCers love to equivocate over the two definitions.

    Computer code is used as an analogy for DNA function, but like all analogies it breaks down when examined closely. In the fundamental mechanics the two operate completely differently. Computer code uses abstract symbols to pass information to the machine doing the work. The symbols are independent of the medium and needs to be interpreted at a different time in order to perform operations. DNA on the other hand is not abstract at all. It is a physical molecule that is part of a self- sustaining chemical reaction (granted an amazingly complicated one). A reaction that merely follows the laws of chemistry and physics to proceed. It is completely dependent on its physical structure. A model of DNA created out of sticks and clay and won't code for a protein no matter how hard you pray.

    I would dare any IDCer to show that DNA relies on abstract symbols that must be interpreted, independent of the medium of transmission like computer code does.

    ReplyDelete
  16. Try the other way around :
    computer processor just moves electrons around because some other electrons were presented to processor electron storage matrix so it forces them against each other.Of forced bunches of electrons some squeeze others and emerge into some other paterns of electrons blah blah
    Electron bunches just move acording to natural laws

    ReplyDelete
  17. This reply from the evolutionist speaks volumes.

    ====
    LOL! another computer science guy who doesn't understand the difference between analogies and reality. Too funny.

    When scientists speak of DNA 'code', they are using a broad definition of code as 'any process that maps a specific input to a specific output'. Computer code falls under a different definition of 'code': 'a system of using abstract symbols to pass a message over a medium.' IDCers love to equivocate over the two definitions.

    Computer code is used as an analogy for DNA function, but like all analogies it breaks down when examined closely. In the fundamental mechanics the two operate completely differently. Computer code uses abstract symbols to pass information to the machine doing the work. The symbols are independent of the medium and needs to be interpreted at a different time in order to perform operations. DNA on the other hand is not abstract at all. It is a physical molecule that is part of a self- sustaining chemical reaction (granted an amazingly complicated one). A reaction that merely follows the laws of chemistry and physics to proceed. It is completely dependent on its physical structure. A model of DNA created out of sticks and clay and won't code for a protein no matter how hard you pray.
    ====

    This is what evolution is about. Having just enough knowledge to be dangerous, mandating their theory must be a fact because their religion demands it, injecting their religion into their science, accusing others of doing just that when they never did any such thing, ignoring massive problems, ridiculing the question, and when they do give an answer it fails to address the problem. In this case it simply raises yet more profound problems.

    Indeed, a profound difference between biology and engineering is that in biology the feedback loops, signals, information, and so forth, are very much part of the plant. This makes it profoundly more complex, something evolutionists seem to take for granted without having a clue about.

    Religious certainty based on ignorance, coupled with hypocrisy and demonization. It sounds like incredible hyperbole, but all one need do is read the literature (or the comments).

    ReplyDelete
  18. Dr. Hunter's comment:

    "Rather than “primitive genomes were organized with origins and promoters in the same orientation” I would have them randomly oriented from the beginning, thereby avoiding any suggestion of teleology or design, and keeping with the evolutionary theme of randomness."

    Summarizes why ID (as a science) is doomed-it started with a pre-falsified premise:

    Anything non-random is teleological!

    And proceeds from there...

    The genetic variation going in to evolution is the product of random processes, but selection produces anything but random results. Take my hypothetical example-if ancient replicators ligated genes together in the wrong direction, they are doomed. So a simple selective process can produce a result where all gene promoters are ordered in the same direction. We see the remnants of this system today. This organization LOOKS designed to Cornelius, and he immediately screams designer, but is just the product of necessity.

    Moving to less hypothetical examples, we know in directed evolution, genetic algorithms, and direct observations that information can increase in evolution.

    Until you soundly refute this point, you have interesting but irrelevant observations.

    And arguing that evolutionary biology hasn't solved every detail of every last system doesn't argue for ID as a replacement. It is a testament to its success that you have to keep moving to smaller and smaller systems, and more recent discoveries to find what science doesn't know yet/

    I provide a pathway to study the evolution of this system above. What ID-based path would you take to understanding? Oh, right, there is non, because you presume the answer at the onset. Even your silly counter-example presumes evolution.

    "Religious certainty based on ignorance, coupled with hypocrisy and demonization. It sounds like incredible hyperbole, but all one need do is read the literature (or the comments)."

    Projecting?

    ReplyDelete
  19. Oh, and just for fun, some gain-of-function from selection acting on random input. Yeah, the empirical falsification of ID:

    Btw, these are natural gain-of-function mutations:

    http://www.plantcell.org/cgi/content/short/14/12/3149

    http://cancerres.aacrjournals.org/cgi/content/full/68/21/8928

    http://www.sciencemag.org/cgi/content/abstract/281/5377/710

    http://www.newscientist.com/article/dn13673-evolution-myths-mutations-can-only-destroy-information.html

    http://genesdev.cshlp.org/content/20/19/2728.full
    http://atvb.ahajournals.org/cgi/content/full/25/10/2018

    http://www.jstor.org/stable/20205905

    http://atvb.ahajournals.org/cgi/content/full/26/6/1236

    Ok, so those are all natural, but here's a cool directed evolution type experiment-random domain shuffling yields new interesting phenotypes following selection:

    Rapid diversification of cell signaling phenotypes by modular domain recombination.
    Peisajovich SG, Garbarino Science. 2010 Apr 16;328(5976):368-72.JE, Wei P, Lim WA.

    If you are interested, google 'directed evolution' for a ton more along these lines-where human made random variation + selction -> new function.

    "Information" from randomness if you will.

    ReplyDelete
  20. "...what is needed is a plausible explanation." No, what is needed is the scientific method applied to the theory of evolution. A scientific method consists of the collection of data through observation and experimentation, and the formulation and testing of hypotheses. "Plausible explanation" is not science unless backed by a scientific method. By accepting a "plausible explanation" you set the bar so low that evolution becomes believable.

    ReplyDelete
  21. Cornelius: "This is what evolution is about. Having just enough knowledge to be dangerous, mandating their theory must be a fact because their religion demands it, injecting their religion into their science, accusing others of doing just that when they never did any such thing, ignoring massive problems, ridiculing the question, and when they do give an answer it fails to address the problem. In this case it simply raises yet more profound problems.

    Indeed, a profound difference between biology and engineering is that in biology the feedback loops, signals, information, and so forth, are very much part of the plant. This makes it profoundly more complex, something evolutionists seem to take for granted without having a clue about.

    Religious certainty based on ignorance, coupled with hypocrisy and demonization. It sounds like incredible hyperbole, but all one need do is read the literature (or the comments)."


    LOL! CH, I notice you trotted out the same tired old creationist canards we've all heard for years but didn't address a single point I raised in any of my posts.

    Just another epic FAIL for the science-free IDCers.

    ReplyDelete
  22. One such fallacious roadblock is that placing such evidence in the minus column amounts to an argument from incredulity. “You can’t imagine how evolution could possibly have created such a design,” say evolutionists, “and so you think it is evidence against evolution.”

    And yet the same evolutionist who uses this argument then proceeds to tell us that evolution must be true because God wouldn't have created things the way they are. So they can use the argument of incredulity against the existence of a creator but we can't use the same argument against the viability of evolution?

    Me thinks I smell a double standard here.

    ReplyDelete
  23. I've read some of the replies to my comments. It appears that to Darwinists, Evolution IS the scientific method. When observations is made in other sciences that contradict some aspect of Darwinian theory, Darwinists are quick to dismiss it as "Oh, but because its not biology, it does not count." Evolution sits on its own little island, untouchable by other sciences.

    Also, Darwinists seems to have difficulty understanding simple arguments. So, I am to understand that DNA is not like computer code, because, physically, they are quite different? So what? I already know that! No one is making an argument that they are physically identical. When we say DNA is like computer code, we are refering to their INFORMATIONAL properties. And the INFORMATIONAL PROPERTIES are identical, as far as structure, as well as being a NON-PHYSICAL, ABSTRACT ATTRIBUTE. Chemistry CAN NOT EXPLAIN the Information needed to produce a self replicating cycle because physically, there is nothing ordered in information, it is completely irregular. Information is significant, because it is irregular and it is specified, a highly unlikely combination. The problem with Darwinists is that they are ignorant: They study Darwinism only and know nothing of what other scientific fields have to say about it.

    And then there is the argument that I, as a lay man, could not possible know enough to understand the complexities of Darwinian theory. Well guess what, Darwin's theory is as simple as it is stupid. And I WILL question "scientists" who blurt out just-so stories as valid scientific theories, who are unable to accurately portray ID before "refuting" is, and who set themselfs up as "THE HEROIC DEFENDERS OF SCIENCE", while having a blind eye for the fraudulent proofs that is presented to school children as evidence for Darwinism.... such as Heacle's Embryo drawings. (This has been known for over a 100 years!!!) Funny also how Darwinists insist that "theories should make predictions" and how every prediction Darwinism has made BEFORE THE FACT has turned out to be false: From the "simple protoplasm idea of the cell" in Darwins time, to Eugenics, to Junk DNA, to Evolutionary phycology that says self awareness is an illusion. You must have self awareness to have an illusion of anything, so how can selfawareness be an illusion itself? So, being alive is just an illusion, where really just as dead as my laptop??? I know of no other scientific fields where scienitists are so often "surprised" by new discoveries as in Darwinism. Maybe that says something about your paradigm!

    ID has made a strong case, using empirical evidence, and combining various scientific dissiplines, while Darwinists only reinforce their case by destroying their own reputations with pathetic "refutations". You have a better chance to see a blind man hit a bulls eye, than to see a Darwinist making a case against what ID ACTUALLY states, rather than against their own imagination.

    ReplyDelete
  24. "And yet the same evolutionist who uses this argument then proceeds to tell us that evolution must be true because God wouldn't have created things the way they are. So they can use the argument of incredulity against the existence of a creator but we can't use the same argument against the viability of evolution?

    Me thinks I smell a double standard here."

    Oh Oh, I have another one!

    When we say there is no natural process in the known universe that can produce specified irregularity, apart from ID, they say it's an argument from ignorance. But they themselves have no problem with using vestigial structures as evidence for evolution. Yet, just because we don't know why something is constructed a certain way, does not necessarily mean that it is evolutionary junk. Remember junk DNA? Arguments from ignorance are used all the time to defend evolution.

    Then there is the claim that Irreducible Complexity is unfalsifiable. I will grant the Darwinists this one, it is a bit fuzzy, and it is easy to circumvent with the creative imagination of Darwinists. But Darwin wrote Evolution can be falsified by showing that structures exists which could not possibly be formed in a slow and gradual process, in other words, that IC exists. If IC is unfalsifiable, then so is Darwinism, because IC is the criteria with which to falsify Darwinism.

    ReplyDelete
  25. Thorton:

    "Computer code is used as an analogy for DNA function, but like all analogies it breaks down when examined closely. In the fundamental mechanics the two operate completely differently. Computer code uses abstract symbols to pass information to the machine doing the work. The symbols are independent of the medium and needs to be interpreted at a different time in order to perform operations. DNA on the other hand is not abstract at all. It is a physical molecule that is part of a self- sustaining chemical reaction (granted an amazingly complicated one). A reaction that merely follows the laws of chemistry and physics to proceed. It is completely dependent on its physical structure. A model of DNA created out of sticks and clay and won't code for a protein no matter how hard you pray.

    I would dare any IDCer to show that DNA relies on abstract symbols that must be interpreted, independent of the medium of transmission like computer code does."

    The Genetic Code IS abstract, and is described by tRNA. tRNA is a molecule that associate a particular amino acid with a particular triplet of RNA codons. This code is completely arbitrary, as there are nothing in the chemical properties of the codon that determine that they should associate with any particular amino acid. In fact, the code does differ in some species.

    Also, the DNA specifications get translated into an amino acid string that just happen to fold into a workable protein. There is no physical reason why the sequence of DNA bases should specify anything beyond its own chemical makeup. It is this specification, which have no chemical explanation, that begs the informational question. Yes, chemistry dictate what DNA looks like, and chemistry control the translation of DNA, but it DOES NOT explain why DNA the translated molecule from DNA should have any meaningful function at all. In fact, without this information, you can not even build the molecules that does the translation, as they themselves are incoded into the DNA.

    Pointing out the physical properties of DNA does not take away its informational attributes, which is completely abstract.

    ReplyDelete
  26. "I would dare any IDCer to show that DNA relies on abstract symbols that must be interpreted, independent of the medium of transmission like computer code does."

    The fact that the genetic code is *not* universal, the fact that there is no chemical necessity that *this* codon triplet translate to *that* amino acid shows that the DNA medium is not the message.

    But, of course, one knows better than to ever expect the DarwinDefenders to admit to such a truth.

    ReplyDelete
  27. Hanno:

    There is no physical reason why the sequence of DNA bases should specify anything beyond its own chemical makeup. It is this specification, which have no chemical explanation, that begs the informational question.

    On the contrary, see:

    RNA–Amino Acid Binding: A Stereochemical Era for the Genetic
    Code


    http://mcdb.colorado.edu/labs/yarus/JME_239_2009_9270_OnlinePDF.pdf/

    From the Introduction:

    I am particularly struck by the difficulty of getting [the genetic code] started unless there is some basis in the specificity of interaction between nucleic acids and amino acids or polypeptide to build upon. (Woese 1967)

    Nonetheless, it is clear that at some early stage in the evolution of life the direct association of amino acids with polynucleotides, which was later to evolve into the genetic code, must have begun. (Orgel 1968)

    Part I: The Observed Mechanism of RNA–Amino Acid
    Interaction

    Just above, Carl Woese and Leslie Orgel, writing at the dawn of molecular biology and coding, suppose that chemical interactions between nucleotide sequences and amino acids are an indispensable basis for the genetic code. It is the conclusion of the present narrative that such interactions are easily demonstrated, utilize plausible, simple chemistry, and can indeed be shown to echo part of the genetic code.

    ReplyDelete
  28. Hanno:

    Pointing out the physical properties of DNA does not take away its informational attributes, which is completely abstract.

    Abstraction is a mental activity. Don’t confuse pattern recognition by the human mind for the operation of stereochemical processes :: Don’t confuse the map with the territory.

    ReplyDelete
  29. Hanno: "The Genetic Code IS abstract, and is described by tRNA. tRNA is a molecule that associate a particular amino acid with a particular triplet of RNA codons. This code is completely arbitrary, as there are nothing in the chemical properties of the codon that determine that they should associate with any particular amino acid."

    LOL! Of course it's not an abstract code, any more that the chemical reaction for forming sulfuric acid from sulfur trioxide and water

    SO3 + H2O --> H2SO4

    is abstract.

    The human description of the reaction uses abstract symbols, but not the reaction itself. HUGE difference.

    Here's an experiment you can do Hanno. Trot on down to your local ID lab. Build a replica tRNA molecule from Tinkertoys. See how long it takes that molecule to create a Tinkertoy amino acid. Get back to us with the results.

    ReplyDelete
  30. "LOL! Of course it's not an abstract code, any more that the chemical reaction for forming sulfuric acid from sulfur trioxide and water
    .
    SO3 + H2O --> H2SO4
    .
    is abstract.
    "

    These people are fools; it's not that they're ignorant, it's not that they're stupid, it's that they are intellectually dishonest. It's that they intentionally assert falsehoods and intentionally engage in faulty reasoning ... all in a hopeless effort to protect Darwinism (and atheism) from rational scrutiny.

    ReplyDelete
  31. Thorton:

    "LOL! Of course it's not an abstract code, any more that the chemical reaction for forming sulfuric acid from sulfur trioxide and water

    SO3 + H2O --> H2SO4

    is abstract."

    You are either ignorant of how DNA translate into amino acid strings, or you are dishonest.

    There is no chemical reason why one DNA base pair should be followed by another particular base pair. In fact, if there were, DNA would've been a crystal, unable to carry any information. Its message would be reduced to something like ATGCATGCATGCATGC...

    The sequence of the DNA base pairs are NOT determined by their chemical properties, but by the ABSTRACT genetic code. Seen from a purely physical perspective, the base pairs are irregular and chaotic. It is the abstract meaning of the code that makes it significant. Information is recognized when there's specification, without any physical attachment with the object being specified. Nature does not create specifications, it simply follows laws of physics wherever they lead. Specification is always a product of mind.

    No one is arguing the physical mechanism to read and interpret the data. Computers read their data via physical processes as well. Without it, the data would be meaningless. No one is disputing the physical processes involved in reading the data. That is not the issue, the issue is the data itself.

    ReplyDelete
  32. "You are either ignorant of how DNA translate into amino acid strings, or you are dishonest."

    A DarwinDefender will do or say just about anything, including emulating a stultifying and irreversible ignorance, in order to keep from seeing that not only is his evolutionism false, but that it can't even be true.

    ReplyDelete
  33. Hanno: "The sequence of the DNA base pairs are NOT determined by their chemical properties, but by the ABSTRACT genetic code."

    That's just plain stupid. Maybe you should go look up the definition of 'abstract' and 'abstract symbol' before you stick that other foot in your mouth.

    BTW, how's that experiment with the Tinkertoys coming? Have the 'abstract' toy molecules produced any amino acids yet?

    ReplyDelete
  34. Hanno:

    Specification is always a product of mind.

    Prove it.

    ReplyDelete
  35. There is no chemical reason why one DNA base pair should be followed by another particular base pair.

    Did you read the reference I gave you?

    RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

    http://mcdb.colorado.edu/labs/yarus/JME_239_2009_9270_OnlinePDF.pdf/

    There's plenty of reason, apparently.

    ReplyDelete
  36. Hanno: "Specification is always a product of mind."

    David: "Prove it."

    Translation: "Make me admit the self-evident truth that I *will not* admit."

    ReplyDelete
  37. Ilion,

    That's OK, he can still prove it. Or you might try.

    ReplyDelete
  38. Hanno,

    Is the Rydberg formula

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

    abstract or an abstraction?

    If the former, did a "mind" design it?

    ReplyDelete
  39. "In the 1880s, Rydberg worked on a formula describing the relation between the wavelengths in spectral lines of alkali metals"

    Ofcause a mind designed it. The Rydberg formula is not the actual relation between the wavelengths in spectral lines of alkali metals, it describes the relation between the wavelengths in spectral lines of alkali metals.

    The formula itself has no physical relationship with the thing it describes, and yet it specifies it.


    Also, isn't always Darwinists who complain that you "can't proof a negative?". Specification IS ALWAYS the product of mind, and we know this from everyday experience. If you feel that undirected natural processes are capable of producing specification, then the burden of proof is on you.

    Lastly, I admin I have not read your article. I have very limited time, and I'm growing quite weary of Darwinists who constantly waste my time by referring me to articles that simply assumes evolution occurred, and then back it up with just so stories. I don't know what exactly that is suppose to prove. I do not refer you to Signature of the Cell. Though it would be great if you could read it yourself, I know you are probably to biased to bother, so I describe the argument as best I can in a post short enough for you to read.

    Rather than bombarding me with links (Which I noticed is a favorite tactic of Darwinists) Why don't you just give me a summarized version of the argument, and if it isn't just another case of "We know evolution has occurred, so maybe this is how it could've happened", I'll read it. At least show me that you've read and understood the argument yourself, by explaining it in your own words, before referring me there. Otherwise, we might just as well stop talking to each other, and just start posting links.

    ReplyDelete
  40. David.

    So you expect me to read a 24 page, highly technical article on RNA evolution, and then simply comment on it here?

    As impressive as this all seems, I have only one question, one which David Berlinski has asked as well: "Can the results of Powner et al be reproduced without Powner et al?" - or in this case "Can the results of Yarus et al be reproduced without Yarus et al?"

    All these abiogenesis experiments achieve is to underline how critical intelligent interference is in order to produce these molecules. Without an intelligent agent that filter out impurities, protect the molecule from degradation, and guide the molecule's development by playing the role of selection (selection for future advantage, I might add, which is basically what design is), all the abiogenesis scenario's fall apart.

    ReplyDelete
  41. @Thorton

    Oh no? So what PHYSICAL property DOES dictate the sequence of DNA nucleotides? Enlighten me.

    BTW, I don't exactly know what your point is with the tinker toys. No one ever argued that chemistry played no role in biochemistry. That would just be stupid.

    ReplyDelete
  42. Of cause a mind designed it. The Rydberg formula is not the actual relation between the wavelengths in spectral lines of alkali metals, it describes the relation between the wavelengths in spectral lines of alkali metals.

    Hanno, thanks for your comment, but you seem to be contradicting yourself. What mind designed the Rydberg formula? God's or Rydberg's? When ID persons use the word "design" referring to biology, it means "create." And then you say the formula does not describe the "actual" relation between the wavelengths, but it yet describes the relation between them. What is the function of the word "actual" in your sentence?

    Who did the specifying in this specification? God or Rydberg?

    By the same token, who specified the "actual" genetic code, chemical evolution, God, or human beings? Can you see that the code is a description conceived by humans of chemical processes that developed naturally, just as Rydberg's formula is a description of physical properties that matter displays?

    ReplyDelete
  43. Hanno.

    So you expect me to read a 24 page, highly technical article on RNA evolution, and then simply comment on it here?

    Granted, the paper is technical, but since it refutes your reiterated claim that the genetic code has no chemical basis, you might at least have said something about it.

    Surely the excerpt from the introduction that I posted earlier would have explained the issue well enough.

    At some point, doesn't a science skeptic need to understand the science?

    ReplyDelete
  44. David

    Regarding your first post, you seem to be making a category mistake.

    The formula describing some feature in nature is distinct from nature itself. All formula's are derived from mind. E=mc2 is the formula and is a product of Einstein's mind. The atom bomb is physical effect. The formula IS NOT the natural effect, it DESCRIBES the natural effect. The particles themselves only react to chemical and nuclear forces, while the formula describes how they react. Formula's are forms of information, and like all information, it is the product of mind.

    Likewise, there is no chemical necessity that DNA code should specify functioning proteins. You can mix the DNA code in any order you want, and, thanks to the machinery of the cell, is will produce a amino acid string, but that string will not necessarily fold into a stable protein. The SEQUENCE of DNA nucleotides constitute information, as it has no physical relation to the final product.

    Secondly, regarding your paper, I will have to admit that you have me at a disadvantage. I did admit to being a layman in science, which means that I have SOME scientific knowledge, but not enough to comment on a highly technical paper. However, I do not think this disqualifies my position out of hand.

    Firstly, there ARE ID scientists that DO understand these technical papers, and who are NOT convinced. (Scientists with all kinds of different religious backgrounds) According to them, all these papers assume evolution occurred, rather than concluding it. All abiogenesis experiments involve some form of human intervention, and always simulates conditions in a idealistic way rather than a realistic one. If abiogenesis is possible, one would expect a scientist to be able to set up the initial (realistic) conditions, and then sit back to see chemistry do its thing.

    Secondly, ID Scientists make very strong arguments based on empirical evidence. One hardly ever see a calm reasoned response from Darwinists, rather it their replies involve name calling, and misrepresentations of the argument itself. If Darwinism is true, why can't they just answer the question, rather than avoiding it?

    Thirdly, while Darwinists appear VERY concerned about the effect ID would have on science, one hardly ever hear any concern from them about inaccuracies on the Darwinian side. To the contrary, if you point them out, you're a "creationist".

    Fourthly, there is a very clear double standard applied between ID and Darwinism. For Darwinism, just so stories are acceptable theories, while no amount of empirical evidence and reasoning seems to be enough for ID.

    If ID made anything clear, it is that the Darwinian scientists are *NOT* honest in their motivations, and *DOES* exclude certain possibilities for purely philosophical reasons. Under these conditions, I feel perfectly comfortable attacking Darwinian theory.

    Also, in Signature of the Cell, Stephen C Meyer outline his own study of the various theories on origin of live since Darwin to the RNA world. All these theories treat the origin of live as a purely chemical problem and either ignores or displaces the problem of informational origin. Though I can not do so myself, ID scientists like Meyer can understand your paper, and will criticize it. Moreover, I have a general idea of what his criticism would be: most probably displacing the origin of information out of view, rather than explaining it.

    Now, I'm completely open to an explanation on how undirected natural processes can form information. I'm also not afraid of technical terms, as long as I can find an explanation for them. But to shoot above my head and then to call it quits is not fair play. Lacking knowledge is not the same as being stupid.

    Lastly, I'm not a science critic, I'm a Darwin critic.

    ReplyDelete
  45. May I point out an example.

    In a debate between Stephen Meyer and prof Atkins, prof Atkins, world renowned chemist, made the claim that "Information and structures" are effectively the same thing. Now, I'm pretty sure prof Atkins can blow my mind with chemistry, but it does not take a rocket scientist to know that information is NOT the same as structures. Structures form due to the interplay of forces on the individual parts. The physical processes define the structure. Information, from a physical point of view, is completely chaotic. Without the abstract specification that underlies the arrangement of the characters, it would have no significance what so ever.

    ReplyDelete
  46. Hanno: "Lastly, I admin I have not read your article. I have very limited time, and I'm growing quite weary of Darwinists who constantly waste my time by referring me to articles that simply assumes evolution occurred, and then back it up with just so stories"

    Shorter Hanno: "I already know everything. I don't need to read or study any scientific research, or do anything to cure my ignorance. I'll just loudly proclaim that I'm right and declare victory."

    Ignorance plus arrogance - the tried and true creationist formula.

    ReplyDelete
  47. ^^ As I keep pointing out, it is logically impossible to engage in rational discussion with DarwinDefenders on any subject which may touch upon the inadequacy of Darwinism ... or of question-begging and/or special-pleading as a basis for reasoning.

    ReplyDelete
  48. Thorton:"I already know everything. I don't need to read or study any scientific research, or do anything to cure my ignorance. I'll just loudly proclaim that I'm right and declare victory."

    Funny, coming from someone who does not even understand the basics of transcription and translation. (At least, so far you've given every indication for me to think that.) So, look who is calling the kettle black.

    ReplyDelete
  49. Say Thorton.

    Since you are way more scientifically literate than I am, why not read the article yourself, and give us an overview of what it says.

    ReplyDelete
  50. Hanno: "Without the abstract specification that underlies the arrangement of the characters, it would have no significance what so ever."

    You still haven't figured out the difference between the physical object and the human produced abstract description of the physical object I see.

    ReplyDelete
  51. http://www.eurekalert.org/pub_releases/2006-04/ir-nms042406.php

    Please read this and use molecular machines in your head to think about it.

    ReplyDelete
  52. Ok Thorton. Let me try to explain it to you. DNA consist of a long string of nucleotides. There are 4 different types nucleotides, which are refered to A,T,G and C. The chemical bonds between these letters ARE EXACTLY THE SAME. This means that ANY character can follow ANY character. THERE IS NO CHEMICAL PREFERENCE. That means you CAN NOT EXPLAIN the sequence of DNA nucleotides with underlying chemistry. The chemistry DOES NOT dictate the sequence.

    These character functions EXACTLY like letters in the alphabet. The simplest of its functions is protein synthesis. In a process called Transcription, a section of DNA is opened up so a molecular machine can make a copy of the DNA. This single stranded copy is called messenger RNA, or "mRNA". This mRNA is then transported to the ribosome to start a process called translation. tRNA facilitates this function: On the one side, there is a 3 anticodons, which will match 3 codons in the mRNA. On the other side, there is an amino acid. Nothing in the chemistry of tRNA determine what amino acid gets associated with what anticodon triplet: The amino acid are assosiated with the correct tRNA by enzimes.

    As the tRNA bonds to the mRNA, the corrosponding amino acids bond together to form an amino acid string. Link nucleutides, the chemical bonds between different kind of amino acids are exactly the same. Each kind of amino acid have a different side chain. These side chains will play a crittical role when the amino acid string is folded into a functional form, called a protein. They will ensure that the string folds into the correct shape, so the protein can perform its function.

    So, as you can see, when scientists say that the DNA code is abstract, that it's "like" computer code, or language, they mean exactly that. You can not have just any sequence of DNA nucleotides, it has to specify an aminoacid string that will fold into a functioning protein. And these proteins are also responsible for transcription and translation. So, you have a chicken and egg scenario right down to molecular level.

    Even in the RNA world scenario, you need specifisity in the sequence of the RNA molecule in order for it to self replicate. Where are you going to get this information from?

    Get it? Probably not.

    ReplyDelete
  53. Hanno writes:

    "Nothing in the chemistry of tRNA determine what amino acid gets associated with what anticodon triplet: The amino acid are assosiated with the correct tRNA by enzimes."

    It is a shame that you found the paper suggested for you too technical. It empirically contradicts your assertion above.

    Dave Wisker

    ReplyDelete
  54. Hanno: "Ok Thorton. Let me try to explain it to you. DNA consist of a long string of nucleotides. There are 4 different types nucleotides, which are refered to A,T,G and C. The chemical bonds between these letters ARE EXACTLY THE SAME. This means that ANY character can follow ANY character. THERE IS NO CHEMICAL PREFERENCE. That means you CAN NOT EXPLAIN the sequence of DNA nucleotides with underlying chemistry. The chemistry DOES NOT dictate the sequence."

    But the chemistry dictates exactly how the reaction will proceed and what the final product will be. That's because the molecules are NOT abstract symbols, they are physical entities that can only behave a certain way.

    How the DNA sequence for a particular stretch of genome came to be is a completely different question. The answer, of course, is that they evolved from simpler precursors through the process of naturally occurring genetic variation filtered by selection.

    "These character functions EXACTLY like letters in the alphabet."

    No, they don't. You still can't grasp the difference between the physical molecules in the chemical reaction and the human produced abstract notation used to describe the molecules in the chemical reaction.

    "So, as you can see, when scientists say that the DNA code is abstract, that it's "like" computer code, or language, they mean exactly that.

    Reference please. I don't know of any scientist anywhere saying that physical DNA molecules represent abstract symbols. BTW, the "like" part means they are using computer code as an analogy.

    The only 'specification' involved in DNA is the after-the-fact human produced one created by determining the existing molecular composition.

    It's just like I found a rock and decided to measure/weigh/assay it to gather every last bit of info about the rock that I could. I now have an after-the-fact specification that I could use to build a replica rock if I so desired. That doesn't mean the original rock had or required a before-the-fact specification to be created.

    ReplyDelete
  55. @Thorton

    Thought so.

    There is non so blind than those who refuse to see. Either you don't understand who DNA works, or you don't understand what information is.

    I'm growing bored with you.


    allopatrik

    Behind every technical term is a logical and understandable concept. Given enough time, I'm sure I'll be able to google every single technical term used in the paper, and figure out what it says. However, by that time, the discussion has moved on, and my insights would no longer be relevant.

    That is why I'm so annoyed with Darwinists posting links to make their case for them. It is a catch 22 situation: If you ask them to explain the paper to you, they go "AHA, you don't understand science, and therefore you loose. Case closed". If you take the time to study it, well, by the time you come back and comment on it, he has long forgotten that he participated on that forum. Frankly, I find the tactic dishonest. If you can't explain in simple terms what the main point of the article is, like I've explained DNA, then you probably don't even understand it yourself. Or, you understand it, but you don't want your opponent to understand it, so he can't fault it.

    Take Micheal Behe's Darwin's Black Box, for example. You can not understand the ID argument if you know nothing about Biochemistry. Therefore, he spends most of his book explaining some biochemistry in such a way that a lay person, taking some effort, can understand it. (This contrast sharply with Darwinists that just bombard you with highly technical papers and then declare you are to stupid to understand science) While Darwinists do their best obscure and mystify science in order to protect their theory, ID people explain and clarify it. Unfortunately, there will always be someone who knows more than you, and who'll use that knowledge to overpower you, rather than to inform you. Fortunately, some of those people, like Behe, use the same knowledge to inform the public. Before Behe wrote his book, he did a thorough study of technical biochemical evolutionary papers. He found that all of them simply assert that evolution occurred, without providing a testable hypothesis of how this could've occured. Or, when they do explore the evolutionary details, the environment they work with is not realistic, and there is constant human intervention to ensure that the chemistry does what they want it to do.

    So, on the basis of the scientists who have read these technical papers, and explained why they find them insufficient, I am not intimidated by this link bombardment tactic. I am willing to discuss it, if they are willing to explain it. I do not pretend to know everything, but I know enough to know that Darwinism can not explain biochemistry, and that more knowledge will only worsen the problem for Darwinism.

    ReplyDelete
  56. Hanno,

    I'm glad you're interested in discussing the paper, and I'm more than willing to express its findings (and other findings from Yarus's lab) in less technical terms. What it says is that there is a stereochemical relationship between RNA, amino acids, and the codons and anticodons that specify those amino acids. What Yarus found was, out of a huge pool of randomly generated RNA sequences, a statistically significant number of those RNAs which bound to specific amino acids contained the correct codon or anticodon sequence (from the genetic code) for that amino acid within the binding site. Yarus uses this information to hypothesize the origin of translation starting with a core of amino acid polymers resulting from stereochemical affinity, and RNA action alone. This idea is bolstered by another paper by Yarus which points out that many of the significant reactions involved in translation can be performed by RNAs alone. No enzymes needed. This suggests the chicken-and-the-egg problem you so confidently asserted may not exist, especially when we also know that RNA can not only catalyze reactions, it can also catalyze its own replication. We even have evidence for assembly of ribonucleotides under plausible prebiotic conditions, and even polymerization as well, all without the need for enzymes.

    Dave Wisker

    ReplyDelete
  57. Hanno said...

    @Thorton

    Thought so.

    There is non so blind than those who refuse to see. Either you don't understand who DNA works, or you don't understand what information is.


    You forgot to provide your references where any scientists anywhere say that physical DNA molecules represent abstract symbols.

    So I guess you were making it up.

    That's always been one of the biggest draws to creationism for scientifically challenged folks like you - you get to make up crap as you go.

    ReplyDelete
  58. Hanno,


    Here is a very good discussion of Meyer's book in regards to the origin of the genetic code, and the work by Yarus I mentioned earlier. Art Hunt is a molecular biologist specializing in RNA, and understands the issues very well.

    http://aghunt.wordpress.com/2010/01/03/signature-in-the-cell/

    ReplyDelete
  59. Thorton.

    I haven't responded to you because you have exposed yourself as an ignorant Darwinist pomp pomp girl. If you must have a quote, here's one: "[t]he machine code of the genes is uncannily computer-like." That's by Richard Dawkins, by the way. If you knew anything about DNA, you would not have asked me for such a quote.


    allopatrik

    Thank you, that is much better. What you said is certainly interesting. Though I don't have the expertise to do so myself, I would imagine that someone like Stephen C Meyer's first question would be: Did the conditions in which the experiment took place represent a realistic prebiotic world? These experiments are obviously done in ideal conditions, but biochemical molecules in the real environment has the tendancy to break down before they can evolve in something more complex.

    Also, I do not think that Meyer's argument depends on the fact that enzymes code the tRNA. It's a minor footnote in Signature in the Cell. Rather, the question is how do you get the correct sequence of RNA nucleotides to get a self replicating cycle going. As my understanding goes, RNA does not automatically self replicate, it needs to have a particular shape, determined by its nucleotide sequence, and even then, it can only replicate part a of itself. To get to that point, abiogenesis usually selects the RNA strings for future advantage.

    Moreover, tRNA is only part of the puzzle. Without mRNA, and the Ribosome that does the translation, it is unlikely that tRNA will form amino acid chains by themselves, or even if there is some mechanism that can bypass the ribosome, it still does not guarantee that the resulting amino acid chain will fold into a stable, functioning protein. For that you need information. You need all the various parts in close proximity to each other, plus the RNA strings with the right sequence to actually produce these parts.

    So, yes, though the results are quite interesting, and since I'm not technically inclined enough to fault the paper, I'll even admit that it might give some hope for a future Darwinian explanation. However I would not consider the findings sufficient to dismiss the informational dilemma, nor is it sufficient to prove that Darwinism will ultimately explain it.

    Therefore, I would argue, that ID and Darwinian biology should be allowed to coexist for, say 50 years, and then we can determine which group of scientists made the best predictions. ID's predictions is not so much about the origin of live, rather it is about the functioning of live. Darwinism tend to dismiss our ignorance of the functions of certain features as evolutionary left overs. ID predicts that the apparent uselessness has more to do with our own ignorance than evolution. In the case of Junk DNA, ID has already scored one point, predicting before the fact that it will have function.

    ReplyDelete
  60. Hanno said...

    Thorton.

    I haven't responded to you because you have exposed yourself as an ignorant Darwinist pomp pomp girl. If you must have a quote, here's one: "[t]he machine code of the genes is uncannily computer-like." That's by Richard Dawkins, by the way. If you knew anything about DNA, you would not have asked me for such a quote.


    Yeah, silly me. Expecting you to back up your claim that scientists think DNA molecules are really abstract symbols.

    BTW, in your quote from Dawkins "[t]he machine code of the genes is uncannily computer-like."

    ..there's that work like again. That means he's using an analogy.

    Do you know what an analogy is Hanno? Do you understand that analogies aren't reality? Apparently not.

    ReplyDelete
  61. Hanno,

    "In the case of Junk DNA, ID has already scored one point, predicting before the fact that it will have function."

    I'm afraid there is evidence that the vast majority of the genome isn't transcribed. The findings where non-protein-coding DNA was found to have function involved RNA transcripts. So, discovering most of the genbome isn't even transcribed is not good news for the ID "prediction" that the non-coding DNA has function.

    Here is a great blog by biochemist Larry Moran discussing this:

    http://sandwalk.blogspot.com/2010/05/junk-rna-or-imaginary-rna.html

    Dave Wisker



    Dave Wisker

    http://sandwalk.blogspot.com/2010/05/junk-rna-or-imaginary-rna.html

    ReplyDelete
  62. Hanno,

    "Though I don't have the expertise to do so myself, I would imagine that someone like Stephen C Meyer's first question would be: Did the conditions in which the experiment took place represent a realistic prebiotic world?"

    A better question, Hanno, is why Meyer doesn't explore Yarus's work in his book. The stereochemical hypothesis is one of the most important (and empirically fertile) in the RNA world literature. I don't recall Meyer mentioning Yarus at all, though it's been awhile since I looked at Meyer's book.

    A minor quibble: Meyer is not a scientist. He is a philosopher.

    Dave Wisker

    ReplyDelete
  63. Thorton, you are setting up a straw man and you know it! You seem to think ID proponents says that DNA code is PURELY ABSTRACT. And no matter how much I try to explain that that is not the case, you keep on hammering your point.

    It is people like you that gives Darwinists a bad name: "Uh, I can't refute what they say, so I'll refute what I want them to say".

    To be fair, though, not all proponents of Darwinism is so pig-headed. I have met one of two reasonable Darwinists whom I can respect.

    ReplyDelete
  64. allopatrik

    I have to disagree:

    http://www.nature.com/news/2010/100331/full/464664a.html

    "Just one decade of post-genome biology has exploded that view. Biology's new glimpse at a universe of non-coding DNA — what used to be called 'junk' DNA — has been fascinating and befuddling. Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA2. Much non-coding DNA has a regulatory role; small RNAs of different varieties seem to control gene expression at the level of both DNA and RNA transcripts in ways that are still only beginning to become clear. "Just the sheer existence of these exotic regulators suggests that our understanding about the most basic things — such as how a cell turns on and off — is incredibly naive," says Joshua Plotkin, a mathematical biologist at the University of Pennsylvania in Philadelphia."

    ReplyDelete
  65. Hanno,

    The ENCODE project papert is addressed by Moran's blog. Th emore recent PLOS paper contradicts its findings:

    "We conclude that, while there are bona fide new intergenic transcripts, their number and abundance is generally low in comparison to known exons, and the genome is not as pervasively transcribed as previously reported."

    Dave Wisker

    ReplyDelete
  66. Hanno,

    As reported in Nature on May 18th 2010:

    "RNA 'dark matter' hinted at by previous studies of mammalian genomes may not exist after all. The mysterious matter refers to the large amounts of RNA that are copied from the DNA sequence, or transcribed, but which cannot be accounted for by the genes that have been identified so far.

    Using next-generation sequencing technology, researchers based in Canada have found that, in human and mouse cells, most RNA transcripts are copies of regions within or near genes that are known to code for proteins or to regulate gene expression. The finding disputes earlier work claiming that the vast majority of the mammalian genome — including the 98% or so that does not code for proteins — is transcribed into RNA."

    http://www.nature.com/news/2010/100518/full/news.2010.248.html

    Dave Wisker

    ReplyDelete
  67. "A better question, Hanno, is why Meyer doesn't explore Yarus's work in his book."

    I would say purely because ID scientists are vastly outnumbered by Darwinist scientists.

    However, Stephen C Meyer has demonstrated his willingness to debate prominent darwinists, including Dawkins (who declined) and Peter Atkins (Who believe ID=Creationism and was hugely unprepared) I measure the strength of the ID arguments not only on their own merits, but also by the strength of the counter arguments (which, I must say leaves much to be desired)

    I see no reason why Stephen would not want to debate Yarus, and if it does happen, I would love to download the podcast.

    ReplyDelete
  68. Hanno,

    Rather than debating (which, IMNSHO, is a waste of time, especially won such a large and technical subject), I'd prefer Meyer to have simply examined the stereochemical hypothesis and assessed its weakness and strengths. But he didn't. Frankly, I was disappointed that someone who is trying to present himself as a serious scholar on the subject did such a poor job.

    Dave Wisker

    ReplyDelete
  69. Hanno said...

    Thorton, you are setting up a straw man and you know it! You seem to think ID proponents says that DNA code is PURELY ABSTRACT. And no matter how much I try to explain that that is not the case, you keep on hammering your point.


    I know what you told me:

    "Hanno: The Genetic Code IS abstract, and is described by tRNA. tRNA is a molecule that associate a particular amino acid with a particular triplet of RNA codons."

    Now if you want to change your story and backpedal, I completely understand, since you're just pulling it out of your butt as you go anyway.

    You want to tell us when you have your next fantasy du jour ready? Your constant flip-flops are hard to follow.

    Have you figured out what an analogy is yet?

    ReplyDelete
  70. Hanno,

    You might enjoy Art Hunt's recent experience debating Meyer.

    http://aghunt.wordpress.com/2010/05/17/well-that-was-interesting/#more-1083

    Dave Wisker

    ReplyDelete
  71. Eugen said...
    Try the other way around :
    computer processor just moves electrons around because some other electrons were presented to processor electron storage matrix so it forces them against each other.Of forced bunches of electrons some squeeze others and emerge into some other paterns of electrons blah blah
    Electron bunches just move acording to natural laws

    C mon thorton, when electrons move are they moving acording to abstract rules or natural ones ?

    ReplyDelete
  72. This comment has been removed by the author.

    ReplyDelete
  73. Ever hear of the seven layer OSI model for computers? Moving electron are at the lowest, physical layer. Computer programs that use abstract symbols are at the top, the application layer. They need to be interpreted to run. Even lower level assembly language using abstract symbols needs to be interpreted to be translated to machine code to make electrons move at the physical level.

    DNA-->protein is a chemical reaction. All it has is the physical layer. There is no abstraction of symbols, no instruction interpreting being done. It's just a big, complicated chemical reaction at the physical layer.

    Humans use descriptions from computer software as analogies to parts of the complicated chemical reaction for ease in describing/understanding the functions, but that's all they are. Analogies.

    As far as the question "where did the information in DNA come from", the answer is it came from the environment. Naturally occurring genetic variations that happen during reproduction get filtered by natural selection. The results get passed on and the cycle happens again. The entire process creates the DNA structures we see today. All you need to create complexity is imperfect self-replicators experiencing differential reproductive success. And that just what the evidence shows we've had for the last 3.3 billion years.

    ReplyDelete
  74. allopatrik,

    Thanks for your reference to Art Hunt's explanation of the work by Yarus, and its refutation of Meyer's (and Hanno's) argument that the genetic code is arbitrary.

    Now it's clear where Hanno got his talking points. And it's also clear why he's been squirming so vigorously to escape the evidence. Armchair theorizing a la Meyer is once again blown to smithereens by empirical evidence.

    ReplyDelete
  75. David,

    Yarus's work is fascinating. Unfortunately, one of his most interesting isn't attainable online-- it describes how four predicted reactions for early translation (Activation of amino acids, formation of peptide bonds, synthesis of aminoacyl RNAs, and synthesis of effective peptide catalysts) are well within the repertoire of RNAs alone:

    Yarus, M (2003). On translation by RNAs alone. Cold Spring Harbor Symposia on Quantitative Biology LXVI: 207-215.

    Dave Wisker

    ReplyDelete
  76. thorton
    I do not want to use words program or machine for now.
    Why are there more electrons in some matrix locations than the others? They are moving by natural law but following unlikely pattern. They would not be able to do it if just left to natural laws alone.What is forcing them to follow unlikely pattern?

    ReplyDelete
  77. Eugen said...

    thorton
    I do not want to use words program or machine for now.
    Why are there more electrons in some matrix locations than the others? They are moving by natural law but following unlikely pattern. They would not be able to do it if just left to natural laws alone.What is forcing them to follow unlikely pattern?


    Humans designed and built specific hardware to cause them to move in "unlikely pattern".

    And before you make the inane claim that the chemical reactions involving DNA also follow "unlikely patterns", you've got to show why they're unlikely. Complicated or complex does not mean unlikely.

    ReplyDelete
  78. I will try not to make claims but see if there is any sense here.


    I have lots of electronic components at home and at my work desk so
    lets make computer(or something) in the bag.

    Lets fill 30% of the bag with tiny logic gates(simple rules for electron flow) and somehow keep them floating.Than attach little magnets to gates so they can self assemble ( sipmle rules ). Also,lets put small batteries in the bag and attach little magnets to them as well. Put in there tiny memory chip,too( lets not forget little magnets ).

    Slosh the bag.

    I wonder how would all this self assemble?

    I may be practical but I'm not trying this experiment.

    ReplyDelete
  79. Eugen said...

    I will try not to make claims but see if there is any sense here.


    I have lots of electronic components at home and at my work desk so
    lets make computer(or something) in the bag.

    Lets fill 30% of the bag with tiny logic gates(simple rules for electron flow) and somehow keep them floating.Than attach little magnets to gates so they can self assemble ( sipmle rules ). Also,lets put small batteries in the bag and attach little magnets to them as well. Put in there tiny memory chip,too( lets not forget little magnets ).

    Slosh the bag.

    I wonder how would all this self assemble?

    I may be practical but I'm not trying this experiment


    Let's try a different experiment. Let's set up a computer to simulate the observed evolutionary mechanisms of small random variation filtered by selection, and fed back into subsequent generations. Let's let it run for a while and see if produces a complex design with no intelligent intervention or explicit instructions.

    Well, how about that!

    NASA Evolvable Systems Group: Automated Circuit Design

    ReplyDelete
  80. Fantastic web site,thanks.

    "Let's try a different experiment. Let's set up a computer to simulate the observed evolutionary mechanisms of small ..."



    Fair idea , lets use my compuer in the bag when it self assembles.

    Enough talking,lets keep sloshing.
    I need beer!

    ReplyDelete
  81. Hanno writes:

    "In the case of Junk DNA, ID has already scored one point, predicting before the fact that it will have function."

    You might want to read this brief history of the concept of junk DNA. You'll find that ID is a latecomer to the party regarding suggesting that junk DNA had function. And ID consistently gets it wrong when it asserts that the theory of evolution requires that junk DNA have no function. Personally, I question how ID can claim to predict all or most junk DNA to have function without making a very basic assumption about the nature of the designer, something ID theorists continually insist ID doesn't do.

    The link is here:

    http://www.genomicron.evolverzone.com/2007/09/junk-dna-let-me-say-it-one-more-time/

    And a sample:

    "You can tell someone who knows very little about the science or history of “junk DNA” when they make one or more of the following claims: 1) All scientists have always thought it was all totally irrelevant to the organism. 2) New evidence is suggesting that it is all functional. 3) “Darwinism” led to the assumption that non-coding DNA is non-functional. The opposite is true in each case."

    ReplyDelete