Thursday, December 2, 2010

Arsenic-Based Biochemistry: Turning Poison Into Wine

Being an evolutionist means there is no bad news. If new species appear abruptly in the fossil record, that just means evolution operates in spurts. If species then persist for eons with little modification, that just means evolution takes long breaks. If clever mechanisms are discovered in biology, that just means evolution is smarter than we imagined. If strikingly similar designs are found in distant species, that just means evolution repeats itself. If significant differences are found in allied species, that just means evolution sometimes introduces new designs rapidly. If no likely mechanism can be found for the large-scale change evolution requires, that just means evolution is mysterious. If adaptation responds to environmental signals, that just means evolution has more foresight than was thought. If major predictions of evolution are found to be false, that just means evolution is more complex than we thought. So today’s falsification, though it falsifies one of evolution’s most treasured predictions, will be no different. Once again, evolutionists have great news.

According to evolutionists, one of the most powerful evidences for their notion that the world just happened to arise somehow on its own, is the underlying unity of biology’s fundamental biochemistry. From information storage in the DNA macromolecule to basic metabolism, the same designs are found across biology’s wide spectrum. As Niles Eldredge put it:

The basic notion that life has evolved passes its severest test with flying colors: the underlying chemical uniformity of life, and the myriad patterns of special similarities shared by smaller groups of more closely related organisms, all point to a grand pattern of descent with modification.

Likewise, Christian de Duve triumphantly declared:

Life is one. This fact, implicitly recognized by the use of a single word to encompass objects as different as trees, mushrooms, fish, and humans, has now been established beyond doubt. Each advance in the resolving power of our tools, from the hesitant beginnings of microscopy little more than three centuries ago to the incisive techniques of molecular biology, has further strengthened the view that all extant living organisms are constructed of the same materials, function according to the same principles, and, indeed, are actually related. All are descendants of a single ancestral form of life. This fact is now established thanks to the comparative sequencing of proteins and nucleic acids.

“The essential macromolecules of life,” explained philosopher Michael Ruse, “speak no less eloquently about the past than does any other level of the biological world.”

With these high accolades, one might think that counter indications would pose major problems for evolutionists. If an observation is such powerful evidence in favor of a theory, then isn’t its falsification a powerful argument against the theory?

Not at all, for this is no ordinary theory.

When the DNA replication apparatus—a rather fundamental biochemical process—was found to be significantly different across different species, evolutionists didn’t miss a beat. Those different versions of DNA replication, we were told, probably evolved independently. Or maybe they diverged. Anyway they evolved, that was for certain.

Next in line is the fundamental unit of energy, the ATP (adenosine triphosphate) molecule, which provides the chemical power for everything from thinking to muscle movement. Would you believe it isn’t universal as you were taught in your high school biology class?

If instead of phosphorus, what if some species turn out to use arsenic? That’s right, arsenic—the poison. It would not exactly be a minor design adjustment. In fact, it would be another major falsification of one of evolution’s most vaunted predictions.

And what would be the evolutionary spin? That’s easy: we would be told that such a monumental finding tells us more about how evolution works. In fact, does it not tell us how incredibly flexible are evolution’s designs, and therefore how much more variety we should expect in the evidence of extraterrestrial life?

That’s right. A falsification of a major evolutionary prediction would be, in a brilliant stroke, turned on its head. With ease it would be converted into evidence for extraterrestrial life. Evolution turns poison into wine.

122 comments:

  1. On the other hand Intelligent Design can easily be falsified:

    Michael Behe on Falsifying Intelligent Design - video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

    ...For a broad outline of the 'Fitness test', required to be passed to show a violation of the principle of Genetic Entropy, please see the following video:

    Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video
    http://www.metacafe.com/watch/3995248

    The Capabilities of Chaos and Complexity: David L. Abel - Null Hypothesis For Information Generation - 2009
    To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: "Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration." A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.
    http://www.mdpi.com/1422-0067/10/1/247/pdf
    Can We Falsify Any Of The Following Null Hypothesis (For Information Generation)
    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    http://mdpi.com/1422-0067/10/1/247/ag

    etc.. etc.. etc..

    ReplyDelete
  2. From the Wikipedia article on arsenic:

    Arsenic compounds resemble in some respects those of phosphorus, which occupies the same group (column) of the periodic table.

    The similarity between arsenic and phosphorus is so great that arsenic will partly substitute for phosphorus in biochemical reactions.


    Having demonstrated misunderstandings of probability theory and protein folding in the previous thread, Dr Hunter now seems to have forgotten his elementary chemistry. Time to review that periodic table, indeed.

    ReplyDelete
  3. further note:

    The GS (genetic selection) Principle – David L. Abel – 2009
    Excerpt: Stunningly, information has been shown not to increase in the coding regions of DNA with evolution. Mutations do not produce increased information. Mira et al (65) showed that the amount of coding in DNA actually decreases with evolution of bacterial genomes, not increases. This paper parallels Petrov’s papers starting with (66) showing a net DNA loss with Drosophila evolution (67). Konopka (68) found strong evidence against the contention of Subba Rao et al (69, 70) that information increases with mutations. The information content of the coding regions in DNA does not tend to increase with evolution as hypothesized. Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.”
    http://bioscience.bio-mirror.cn/2009/v14/af/3426/3426.pdf
    http://www.us.net/life/index.htm

    Dr. Don Johnson explains the difference between Shannon Information and Prescriptive Information, as well as explaining 'the cybernetic cut', in this following Podcast:

    Programming of Life - Dr. Donald Johnson interviewed by Casey Luskin - audio podcast
    http://www.idthefuture.com/2010/11/programming_of_life.html

    ReplyDelete
  4. You can't argue with a crazy man, or with an intellectually dishonest man -- and "Darwinists" *choose* to be intellectually dishonest, or crazy, or both.

    ReplyDelete
  5. Thanks Bornagain


    1) Mathematical Logic
    2) Algorithmic Optimization
    3) Cybernetic Programming
    4) Computational Halting
    5) Integrated Circuits
    6) Organization (e.g. homeostatic optimization far from equilibrium)
    7) Material Symbol Systems (e.g. genetics)
    8) Any Goal Oriented bona fide system
    9) Language
    10) Formal function of any kind
    11) Utilitarian work
    ---

    And all of the above is found in a few simple lines of symbols:

    10 a=a+1
    20 print a;
    30 goto 10

    Or its variant:

    10 print a;
    20 a=a+1
    30 goto 1


    Could't be simpler!

    Talk amongst yourselves.

    ReplyDelete
  6. Hunter:

    That’s right, arsenic—the poison.

    As someone once said: "Isn't it bizarre that some organisms would actually thrive in an atmosphere containing high concentrations of such a dangerous and corrosive gas as oxygen?"

    ReplyDelete
  7. Wait-I'm missing some steps:

    NASA has a press conference today at 2:00.
    It might be about arsenic metabolizing organisms.
    Which can't be related to the rest of life (why)?
    Which means all previously known organisms don't share common descent, and evolution is falsified, and ID wins?

    Even in there is a discovery wholly unrelated to 'conventional life,' I'm unclear how the discovery would falsify the shared biochemistry and common descent of the rest of life.

    I'll wait for the press conference.

    ReplyDelete
  8. Unfortunately the alleged unity of living organisms is not a prediction of the theory of evolution- it is merely an accomodation.

    The ToE is like the blob- it just assimilates everything....

    ReplyDelete
  9. Joe,
    Please feel free to tell us all about the predictions of ID regarding the unity (or otherwise) of living organisms.

    Oh, that's right. I forgot.....

    ReplyDelete
  10. OM,

    Please feel free tp provide positive evidence for your position.

    Oh, that's right, you can't...

    ReplyDelete
  11. This post reminds me of the Indian Weather Stone joke.

    http://www.all4humor.com/picture/funny-pictures/weather-stone.html

    ReplyDelete
  12. Joe,
    Please feel free tp provide positive evidence for your position.

    What position?

    ReplyDelete
  13. Joe
    The ToE is like the blob- it just assimilates everything....

    If only there was some theory out there that could make predictions that could be tested and by virtue of testing those predictions that new theory could be differentiated from other theory's in order to see which theory best fits observed reality.

    Anybody have such a theory?

    ReplyDelete
  14. Please feel free tp provide positive evidence for your position.

    OM
    What position?

    I forgot, intellectual cowards don't make claims and don't have any stance other than to badger others who have made claims.


    OM:
    If only there was some theory out there that could make predictions that could be tested and by virtue of testing those predictions that new theory could be differentiated from other theory's in order to see which theory best fits observed reality.

    Sounds just like Intelligent Design.

    ReplyDelete
  15. Cornelius Hunter said...

    If instead of phosphorus, what if some species turn out to use arsenic? That’s right, arsenic—the poison. It would not exactly be a minor design adjustment. In fact, it would be another major falsification of one of evolution’s most vaunted predictions.


    Poor CH. Way behind the times as usual.

    Arsenic(III) Fuels Anoxygenic Photosynthesis in Hot Spring Biofilms from Mono Lake, California
    Kulp et al
    Science 15 August 2008: Vol. 321 no. 5891 pp. 967-970

    "Abstract: Phylogenetic analysis indicates that microbial arsenic metabolism is ancient and probably extends back to the primordial Earth. In microbial biofilms growing on the rock surfaces of anoxic brine pools fed by hot springs containing arsenite and sulfide at high concentrations, we discovered light-dependent oxidation of arsenite [As(III)] to arsenate [As(V)] occurring under anoxic conditions. The communities were composed primarily of Ectothiorhodospira-like purple bacteria or Oscillatoria-like cyanobacteria. A pure culture of a photosynthetic bacterium grew as a photoautotroph when As(III) was used as the sole photosynthetic electron donor. The strain contained genes encoding a putative As(V) reductase but no detectable homologs of the As(III) oxidase genes of aerobic chemolithotrophs, suggesting a reverse functionality for the reductase. Production of As(V) by anoxygenic photosynthesis probably opened niches for primordial Earth's first As(V)-respiring prokaryotes."

    link

    YAWN at this week's "EVOLUTION IS DESTROYED!" Creationist claim.

    ReplyDelete
  16. Umm thortard you are missing Dr Hunter's CONTEXT.

    Do you know what DNA is made out of?

    Replace the phosphate with arsenic and you will have a clue of the context.

    ReplyDelete
  17. I'm totally with Robert C here.
    Ignoring the fact that the press conference hasn't happened yet so these NASA findings are yet to be announced, even if it turns out we do have bacteria totally unrelated to the rest of life on Earth, how does that undermine the relatedness and common ancestry of the rest of life?

    ReplyDelete
  18. "Replace the phosphate with arsenic and you will have a clue of the context."

    Um, speaking of having a clue, phosphate in DNA is a compound containing the element phosphorus (P) bound to 4 oxygen (O) atoms, while arsenic (As) is an element. Joe, what would happen if PO4 were replaced by As?

    Besides, the press conference will take place in about an hour. We don't know that they will report that P has been replaced by As in the biochemistry of a bacteria.

    ReplyDelete
  19. Looks like the embargo is lifted, with some pretty reliable outlets reporting.

    A member of the Oceanospirillales was discovered to be able to (partially?) replace phosphate with arsenate in DNA, lipids, and ATP. No second tree of life.

    So, arsenic has a 0.1 angstrom larger radius, and largely the same chemistry as phosphate. In other life, arsenate will be used by a lot of pathways, but tends to inhibit them, or hydrolyse at some steps. Next big question is how these guys keep the molecules intact, or if they just have massive turnover, or what. Radically different biochemistry, or nifty evolutionary adaptation?

    And a falsification of evolutionary predictions? nah.

    http://blogs.discovermagazine.com/notrocketscience/2010/12/02/mono-lake-bacteria-build-their-dna-using-arsenic-and-no-this-isnt-about-aliens/

    ReplyDelete
  20. Oh dear.

    So bacteria that live in Mono lake, an environment with an extremely high arsenic content, have evolved to replace some phosphates with arsenic in their molecules. Still pretty cool, but no "Waterloo" for evolution.

    Sorry Creationists, looks like ToE is safe for another day.

    ReplyDelete
  21. Joe
    Sounds just like Intelligent Design.,

    Please then provide the predictions of ID, when and how they were tested and the results thereof.

    ReplyDelete
  22. Joe
    I forgot, intellectual cowards don't make claims and don't have any stance other than to badger others who have made claims.

    Whenever you are asked to support a claim you instead ask others to support the claim which you say they are making.

    A disinterested observer would conclude that your behaviour is designed to distract from the fact that you can't actually support your own claims.

    But I'm sure that's not the case.

    ReplyDelete
  23. So, can anybody tell me if Intelligent Design predicts anything one way or the other about biochemistry?

    Is this unexpected according to ID or expected?

    And will any ID supporter come out and say these bacteria are designed? Or not designed?

    Oh how easy it is to be an ID supporter!

    ReplyDelete
  24. OM:

    Is this unexpected according to ID or expected?

    As Cornelius Hunter has explained previously, the true empiricist considers hypotheses and theories to be metaphysical/religious, which is not science. Therefore, the true empiricist is neither able nor obliged to expect anything.

    ReplyDelete
  25. Let's see:

    We've got extremeophile bacteria that live off of arsenic.

    We've got extremeophile bacteria that live off of sulfur.

    We've got extremeophile bacteria that live in temperatures below -20C and above +120C

    We've got extremeophile bacteria that live in solutions with pH below 3 and above 9.

    So much for needing the 'privileged planet'. Looks like life is a lot more robust that the IDCers claim.

    I'd still love to hear the ID explanation for these new bacteria. How about it Joe - was the original designed bacteria 'front loaded' to exist on arsenic?

    ReplyDelete
  26. He is talking about the FUNDAMENTAL parts of life (DNA) , not some metabolite or protein which includes arsenic as a building part.

    It's even not a major design change, but a live-as-we-know-it changing design change.

    Reading is an art for few people, but a virtue for fools...

    I wonder how a poisonous arsenic became a part of the DNA in the course of evolution...

    ReplyDelete
  27. Waterloo Postponed:
    The discovery is amazing, but it’s easy to go overboard with it. For example, this breathlessly hyperbolic piece, published last year, suggests that finding such bacteria would be “one of the most significant scientific discoveries of all time”. It would imply that “Mono Lake was home to a form of life biologically distinct from all other known life on Earth” and “strongly suggest that life got started on our planet not once, but at least twice”.

    The results do nothing of the sort. For a start, the bacteria – a strain known as GFAJ-1 – don’t depend on arsenic. They still contain detectable levels of phosphorus in their molecules and they actually grow better on phosphorus if given the chance. It’s just that they might be able to do without this typically essential element – an extreme and impressive ability in itself.

    ReplyDelete
  28. Miykayah
    I wonder how a poisonous arsenic became a part of the DNA in the course of evolution...,

    That could be the first step on a very interesting journey for you.

    Are you sufficient brave to follow the evidence where it leads?

    ReplyDelete
  29. At any rate, here's how to conduct a controversy: make claims and counterclaims that lead to research.

    Still further evidence came from the use of a technique known as micro extended X-ray absorption fine structure spectroscopy (µEXAFS). µEXAFS can provide information about the structure of molecules by probing how its internal chemical bonds respond when stimulated by a beam of light. Within the DNA extracted from GFAJ-1 cells starved of phosphorus, it showed arsenic bonded to oxygen and carbon in the same way phosphorus bonds to oxygen and carbon in normal DNA.

    In other words, every experiment Wolfe-Simon performed pointed to the same conclusion: GFAJ-1 can substitute arsenic for phosphorus in its DNA. “I really have no idea what another explanation would be,” Wolfe-Simon says.

    But Steven Benner, a distinguished fellow at the Foundation for Applied Molecular Evolution in Gainesville, FL, remains skeptical. If you “replace all the phosphates by arsenates,” in the backbone of DNA, he says, “every bond in that chain is going to hydrolyze [react with water and fall apart] with a half-life on the order of minutes, say 10 minutes.” So “if there is an arsenate equivalent of DNA in that bug, it has to be seriously stabilized” by some as-yet-unknown mechanism.


    http://www.astrobio.net/exclusive/3698/thriving-on-arsenic

    ReplyDelete
  30. It's a derived species of Halomonadaceae, a type of Proteobacteria. It's not an alien or on its own tree.

    Felisa Wolfe-Simon et al., A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus, Science 2010.

    ReplyDelete
  31. And so, special creation of life forms dies.

    Not with a bang, but with a whimper...

    ReplyDelete
  32. OM:
    Please then provide the predictions of ID, when and how they were tested and the results thereof.

    Already have- as have others.

    OM:
    Whenever you are asked to support a claim you instead ask others to support the claim which you say they are making.

    That way I know what they will accept and they cannot run around with the goalposts.

    Ya see people who won't support their position are intellectual cowards and get nothing. So I have to ask to find out.

    As for how this fits with ID- well organisms are designed to adapt. This population has found that in the absence of phosphorus and in the presence of arsenic that arsenioc can substitute for phosphorus.

    ReplyDelete
  33. thortard:
    So much for needing the 'privileged planet'.

    Except these organisms are on this privileged planet.

    Duh...

    ReplyDelete
  34. Dr Lewis Dartnell, an astrobiologist at the Centre for Planetary Sciences in London, said: "If these organisms use arsenic in their metabolism, it demonstrates that there are other forms of life to those we knew of.

    "They're aliens, but aliens that share the same home as us."


    They're aliens but they live here?
    Maybe he should get a dictionary and learn to read or something better like learning to "think".

    Darwinists need their bloody brains examined.
    These atheists are so incredibly gullible its a wonder they can find their own butts.

    Who was it that said, "A disbelief in God does not result in a belief in nothing; disbelief in God usually results in a belief in anything."?

    Man, he wasn't kidding!

    ReplyDelete
  35. Gary! The mean little lap dog!

    Amazing you got the courage to do two drive-bys in the same week.

    yip yip yip yip yip yip!

    Sic' em Gary puppy!

    ReplyDelete
  36. Cornelius Hunter:

    "Evolution turns poison into wine."
    =====

    Perhaps what they really did was turn the poison into Kool-Aid (in the religious sense of course) ???

    While the subject is interesting, it really shouldn't be a surprise since bacteria are the grand recyclers of the Earth, especially with cleaning up after the ignorance, greed, selfishnes and stupidity of humans for which alot of irresponsible science has led the way.

    The one thing most commonly avoided are the lack of more important questions in most of the literature now days like "What is it's(bacteria's) purpose and function as an important componant found in nature ??? and How can we use and apply it ???" I see this all the time in global warming studies where instead of finding solutions to the supposed potential catastrophy of Climate Change, the Evo-shills instead are jumping up and down celebrating because they think they've discovered an imaginary example of some creature trading it's scales in for a fur coat in order to survive. Kind of like this past years experience of the "Swine Flu" Pandemic scam where instead of condemnation of the unhealthy human error which caused the conditions which set up a perfect storm of an environment for this supposed mutating beast with the supposed potential for killing millions around the world, Evo-Shills were celebrating that this was yet another example of proof that their god was alive and well. Screw the victims, we've proved Evo-World exists after all.

    Consider other amazing examples over in Chernobyl of bacteria which colonized the roots of sunflowers which decontaminated the ground of the lethal type of radiation(invention of men) and how a robot sent into the still-highly-radioactive Chernobyl reactor had returned with samples of black, melanin-rich fungi that were growing on the ruined reactor's walls. My My, bacteria/fungus eating man made deadly engineered radiation ??? No one should ever be surprized by what the amazing recyclers can do and what we'll find in the future if there is one left if they get their way.

    ReplyDelete
  37. Joe
    As for how this fits with ID- well organisms are designed to adapt.

    And you know that how exactly?

    And this "designed to adapt" idea, is there a limit to the amount of adaptation that an organism can do to adapt to it's environment?

    Are there organisms out there that are not "designed to adapt"? What about "living fossils", they cannot be "designed to adapt" as they are, well, living fossils.

    So, Joe, unless you can come up with some actual before the fact predictions about "designed to adapt" it seems it's just a label you can apply to everything and claim it supports ID.

    Ya see, IOW evolution is the ultimate example of "designed to adapt" and the more you claim that a given thing was "designed to adapt" you are in fact undermining the case for ID.

    IOW Joe "designed to adapt" describes evolution perfected. Ya see, if the designer was all that it would not need to "design to adapt", it'd just "design".

    So, I think Joe, you have already simply become a theistic evolutionist. You ascribe mechanisms such as "designed to adapt" to your designer, but can't point to any specific DNA sequence or actual evidence to prove that point. You are making the claim that these new organisms are "designed to adapt" without seeing their DNA sequence, so on what basis are you making that claim? As you have no rational basis for making that claim (on what evidence?) it's clear that upon seeing event X you'll always say "designed to adapt" and so it's essentially meaningless. Much like you.

    ReplyDelete
  38. Joe
    Ya see people who won't support their position are intellectual cowards and get nothing.

    But that's you Joe! You've never supported your position, except with threats of violence.

    ReplyDelete
  39. Joe,
    You said With that said to measure biological information, ie biological specification, all you have to do is count the coding nucleotides of the genes involved for that functioning system and then multiply by 2 (four possible nucleotides = 2^2).

    Now consider this
    Now randomize the coding nucleotides so they do nothing and specify nothing - neither "viability" nor "minimal function" nor "specific effects." Count them, and multiply by two, and arrive at precisely the same value.

    So, Joe, tell us again how your procedure measures specified information?

    Now do it backward:

    Start with the randomized sequence of nucleotides. Bring in your designer of choice - supernatural, extraterrestrial, human, whatever. Have your designer carefully tweeze thousands of entries in this nucleotide sequence such that it specifies a wonderfully complex metabolic pathway capable of minimal function, viability, and specific effects.

    Count 'em up and multiply by 2 to arrive at - well, to arrive at exactly the same number.

    So, Joe, given that neither the careful actions of the designer nor randomization of those actions change your value by jot or tittle, in what way is specification reflected in your calculation?

    http://tinyurl.com/3ycu7vv

    Anything to add? Perhaps "designed to adapt"? Or perhaps a invitation to a fist fight?

    ReplyDelete
  40. Joe,
    And finally, what is the mechanism driving "designed to adapt"?

    I suspect it would sound exactly like the mechanisms describing evolution, were you to attempt to describe them (which you won't). As, after all as you say, ID is not anti-evolution.

    IOW It's just anti the bit's you don't like.

    ReplyDelete
  41. Good one, OM.

    Or how about taking the original sequence, count the number of A's, G's, C's and T's, and shuffle such that the sequence becomes AAA...AGGG...GTTT...TCCC...C, i.e. first all A's then all G's then all T's then all C's.

    Same amount of "biological information, ie biological specification", right Joe?

    Yet almost zero Kolmogorov and Shannon information.

    Joe's stupidity is truly astonishing.

    Back to the OP: can someone explain why the Designer gave the bacteria this amazing ability to live on As?

    ReplyDelete
  42. Ya see people who won't support their position are intellectual cowards and get nothing.

    OM:
    You've never supported your position, except with threats of violence.

    All evidence to the contrary you liar.

    I have supported ID with many blog entries. OTOH you have done absolutely nothing.

    ReplyDelete
  43. OM:
    You said With that said to measure biological information, ie biological specification, all you have to do is count the coding nucleotides of the genes involved for that functioning system and then multiply by 2 (four possible nucleotides = 2^2).

    Yes I did- on my blog.

    If you have something to say about bring it there.

    ReplyDelete
  44. OM:
    And finally, what is the mechanism driving "designed to adapt"?

    Design is a mechanism.

    OM:
    I suspect it would sound exactly like the mechanisms describing evolution,

    According to the ToE all its mechanisms are blind, undirected chemical processes.

    Yet no one can tell us how that was determined. There isn't any way to test that metaphysical claim.

    ReplyDelete
  45. troy:
    Back to the OP: can someone explain why the Designer gave the bacteria this amazing ability to live on As?

    As and P are very, very similar.

    Also the bateria are short-lived meaning all harmful effects taht As will cause will not come about in that time.

    ReplyDelete
  46. denture free-

    Focus on your position.

    Ya see if you could produce POSITIVE evidence for yout position ID would fall.

    ReplyDelete
  47. With that said to measure biological information, ie biological specification, all you have to do is count the coding nucleotides of the genes involved for that functioning system and then multiply by 2 (four possible nucleotides = 2^2).

    OM?:
    Now consider this
    Now randomize the coding nucleotides so they do nothing and specify nothing - neither "viability" nor "minimal function" nor "specific effects." Count them, and multiply by two, and arrive at precisely the same value.


    That is false and basically dishoest and/ or ignorant.

    If there isn't any biological function then there isn't any biological specification and therefor no SI.

    IOW the person who wrote that piece of pap has serious reading comprehension issues.

    Why do evos think their ignorance is a refutation?

    ReplyDelete
  48. OM

    Ya see, IOW evolution is the ultimate example of "designed to adapt
    ---

    Word evolution and design in one sentence. That’s not good OM. You'll piss off your evo friends.



    Pedantskiiiiii

    ReplyDelete
  49. Joe
    I have supported ID with many blog entries.

    Ever seen the timecube website? That's you, that is.

    Wake me up when you publish in a peer reviewed venue.

    ReplyDelete
  50. Joe
    If you have something to say about bring it there.

    You don't publish my comments on your blog remember Joe? So while your offer on the surface seems fair, in fact it's simply a dodge to avoid having to respond to the point. So, observers, beware Joe's apparently fair offer, its not quite what it seems.

    ReplyDelete
  51. Joe
    According to the ToE all its mechanisms are blind, undirected chemical processes.

    Yet no one can tell us how that was determined. There isn't any way to test that metaphysical claim.,


    We could test it by testing your idea that those processes are directed. If that proves to be the case then there would be no need to determine that they are blind in operation as you'll have proven that they are not already.

    So, go for it!

    ReplyDelete
  52. As for how this fits with ID- well organisms are designed to adapt.

    OM:
    And you know that how exactly?

    Observations and experiences.

    OM:
    And this "designed to adapt" idea, is there a limit to the amount of adaptation that an organism can do to adapt to it's environment?

    That is what science is for- to help us make that determination.

    OM:
    Are there organisms out there that are not "designed to adapt"?

    That is what science is for- to help us make that determination.

    OM:
    What about "living fossils", they cannot be "designed to adapt" as they are, well, living fossils.

    No it means they have adapted and don't need any more adapting.

    OM:
    So, Joe, unless you can come up with some actual before the fact predictions about "designed to adapt" it seems it's just a label you can apply to everything and claim it supports ID.

    That is false as we have already said what would falsify/ refute the design inference.

    OM:
    Ya see, IOW evolution is the ultimate example of "designed to adapt"

    Nice equivocation- what "evolution" are you talking about?

    OM:
    IOW Joe "designed to adapt" describes evolution perfected.

    More equivocation- what evolution are you talking about?

    There isn't any evidence taht blind, undirected chemical processes can construct a functional multi-part system.

    OM:
    You are making the claim that these new organisms are "designed to adapt" without seeing their DNA sequence, so on what basis are you making that claim?

    Observations and experiences. I am an engineer who has designed things to be able to adapt.

    ReplyDelete
  53. According to the ToE all its mechanisms are blind, undirected chemical processes.

    Yet no one can tell us how that was determined. There isn't any way to test that metaphysical claim.


    OM:
    We could test it by testing your idea that those processes are directed.

    Explain how you would go about that.

    And then go for it!

    ReplyDelete
  54. If you have something to say about bring it there.

    OM:
    You don't publish my comments on your blog remember Joe?

    Liar- I have published all of your comments.

    All I said was that I would give you ONE round of comments per day.

    IOW you are an imbecile and apparently proud of it.

    ReplyDelete
  55. OM:
    Wake me up when you publish in a peer reviewed venue.

    Wake me up when your position has something published in a peer-reviewed venue.

    ReplyDelete
  56. OM:
    So while your offer on the surface seems fair, in fact it's simply a dodge to avoid having to respond to the point.

    Except I HAVE responded- in this thread and on my blog.

    IOW you are a liar- as usual.

    ReplyDelete
  57. Joe

    That is false and basically dishoest and/ or ignorant.

    Oh, it's false. Is that it? No counter point?

    If there isn't any biological function then there isn't any biological specification and therefor no SI.

    Perhaps you could clarify this with a worked example? It seems to be that your mechanism for calculating biological information is fatally flawed if it comes up with the same value for a random set of nucleotides as for a set known to have function.

    And your method is by definition not much use for determining the biological information in a set of nucleotides with unknown function.

    So, given a set of nucleotides with unknown function you can't determine the biological information, i.e. biological specification, without knowing in advance what the biological function is? So your method cannot be used to determine if a set of nucleotides has a function, i.e. specification?

    Seems like a catch 22 situation to me. Perhaps you could clarify with a worked example?

    IOW the person who wrote that piece of pap has serious reading comprehension issues.


    Why don't you respond to the points raised in that piece of pap then? A worked example would be good.

    Why do evos think their ignorance is a refutation?

    Why do you think simply dismissing something is a refutation?

    Think you are convincing the observers? Think again...

    So, Joe, IOW you've struck out on this. Try again...

    ReplyDelete
  58. Joe
    Observations and experiences.

    Ah, lab work I presume. Please go into details.

    That is what science is for- to help us make that determination.


    But you are acting as if that determination has already been made. Not assuming your conclusion before evidence has been produced are you Joe?

    No it means they have adapted and don't need any more adapting.

    And you know this because.....

    There isn't any evidence taht blind, undirected chemical processes can construct a functional multi-part system.

    Yes there is. Auto catalytic networks.

    Observations and experiences. I am an engineer who has designed things to be able to adapt.

    Please give an example of such then. As you've done it already that won't be a problem will it?

    ReplyDelete
  59. Joe
    All I said was that I would give you ONE round of comments per day.

    What are you afraid of Joe? Why be scared of an open and free exchange of ideas?

    Oh, that's right....

    ReplyDelete
  60. Joe
    Except I HAVE responded- in this thread and on my blog.

    Then I must have missed when you explained how it does not matter that your "method" for calculating "biological specification" comes up with the same value for a random string and a string with known function.

    Logically any string is likely to have some redundancy or junk in place. Your method does not seem to take that into account either. Do you have a workaround for that?

    ReplyDelete
  61. Joe,
    So please tell us what to look for so we can tell if your "designed to adapt" idea has some merit? There are plenty of organisms out there that have been fully sequenced. Perhaps you can point out the sequences that control the "designed to adapt" module?

    Perhaps you can ask the guys at Telic Thoughts to help you out? But you'll have to get them to acknowledge your presence first...

    ReplyDelete
  62. Joe
    Explain how you would go about that.

    And then go for it!


    Your idea, you go test it. Typical IDer, always waiting for somebody else to do the work, just another ID armchair scientist who thinks they know better the people at the sharp edge actually doing the research.

    You keep sitting in that armchair Joe, just look where it's got you in the last 5 years! Still saying the same old tired catchphrases again and again.

    Just man up and realise that you are a TE, be honest with yourself for once.

    ReplyDelete
  63. On his blog Joe says, with regard to the biological information issue:

    Well Bill, if you could read you would have read that what I said only apllies to sequences with a biological function. So I wouldn't arrive at the same value.

    Joe, some questions:

    Does the entire sequence have to have a biological function?

    If some part does not, do you remove that from the calculation? How do you know what to remove and how much? Perhaps a worked example would illustrate your idea better then this frankly tedious exchange.

    Many ID proponents have noted that there is no such thing as "Junk DNA" therefore there are no sequences without function, only function that we are not aware of. Does your method take that into account? Do you disagree then with mainstream ID that some sequences do not have function? You must do, as you've already stated as such.

    But if ID predicts that junk DNA has a function then you cannot be an IDer can you? As you predict that some does not...

    Please clarify these issues Joe, I'm sure your method works but a few examples that encompass the points I raised will go a long way towards making your idea practical.

    And if you ever do get out of your armchair and write a paper, as opposed to a blog post, then critical review of your work is part of that process. And my questions are nothing to what you'd get from people who know this stuff inside out.

    So if you can't respond to me rationally then...

    ReplyDelete
  64. OM

    man you are all over the place.

    Its like throwing jabs at a big guy and he is just looking at you and saying :are you done yet?
    Pick one thing and talk about it either with Joe or somebody else.

    ReplyDelete
  65. Eugen said...

    Pick one thing and talk about it either with Joe or somebody else.


    You need to understand that Joe G has severe mental health issues. He's been all over the web the last few years posting his same content free anti-science dreck, lying about his background, tossing insults, making physical threats against folks. He almost got fired a few years back for doing it from a work computer.

    Most people just ignore him, except the few who get entertainment by poking him to make him dance. Like now.

    ReplyDelete
  66. Thorton

    Ok, it looked like OM was all over the place but instead he was teasing.

    Something like this:

    Pedantskiiii

    ReplyDelete
  67. CH:

    Being an IDist means there is no bad news. If new species appear abruptly in the fossil record, that just means that an intelligent designer did it. If species then persist for eons with little modification, then an intelligent designer did it. If clever mechanisms are discovered in biology, then an intelligent designer did it. If strikingly similar designs are found in distant species, then an intelligent designer did it.


    So today’s falsification, though it falsifies one of evolution’s most treasured predictions, will be no different.

    If it had been copper instead of arsenic, you might have been closer to being on to something. As it is, you do realise that arsenic is poisonus just because it is so similar to phosphorus? Enzymes recognise it because it is so similar to phosphorus. The chemical bonds arsenic can form are very similar to those of phosphorus.

    ReplyDelete
  68. Does the bacteria need special adaptations to live with arsenic? If so, how did it live with arsenic before the adaptations evolved? And if it wasn't living in arsenic, then why would they evole, because they weren't needed in a an environment without arsenic?

    ReplyDelete
  69. natschuster:

    "If so, how did it live with arsenic before the adaptations evolved? And if it wasn't living in arsenic, then why would they evole, because they weren't needed in a an environment without arsenic?"

    A good start would be to search for free articles in pubmed using keywords like: arsenic resistant bacteria.

    A bacteria can survive in an environment with arsenic without having to use it directly.

    ReplyDelete
  70. natschuster:
    Does the bacteria need special adaptations to live with arsenic?

    Compare the situation to the human situation. We're living with toxins never before seen in nature. No possibility to adapt to them in a single generation, which would have been the case on day 1. Yet we're still here.

    If so, how did it live with arsenic before the adaptations evolved?

    Perhaps he same way we're living with those new toxins. Some effects to be sure, none good more then likely, but unless those effects are lethal...

    And if it wasn't living in arsenic, then why would they evole, because they weren't needed in a an environment without arsenic?

    See Lenski et al.

    ReplyDelete
  71. The larger question is if life was found on earth (as this one was) but this life did not possess the universal genetic code, would this falsify evolution?

    Enough said.

    ReplyDelete
  72. Neil:

    The larger question is if life was found on earth (as this one was) but this life did not possess the universal genetic code, would this falsify evolution?

    If it was radically different, then perhaps all of life could not be traced back to a single ancestor. Would that mean that all we think we know about evolution was wrong? Hardly.

    Enough said?

    ReplyDelete
  73. Neal,

    The reason question is would that falsify ID?

    Would it? Common design and all that....

    Or would it mean, to you, that there was more then one designer?

    ReplyDelete
  74. Design theory is based on identifying known patterns of specified complex information and is not dependent on how many codes there are... it's the fact that specified and complex code exists. Not how many there are.

    Evolutionists, however, use the Universal Genetic Code (See Theobald's 29 Evidences, etc) as evidence for evolution. Would finding more codes falsify evolution?

    How would more codes be viewed?

    1. The additional code falsifies major evidence for evolution and brings serious questions to the validity of common descent theory itself?

    or

    2. The additional code was unexpected and shows that we don't know as much about evolution as we thought, but evolutionary theory is still well established.

    The Universal code is soft evidence. It is based on current findings and then the story simply accommodates it. Such is the stuff that mountains of evolutionary evidence is made of. Evolution lives on with it or without it.

    ReplyDelete
  75. Neal
    Design theory is based on identifying known patterns of specified complex information

    Is it? Could you give a few examples of successful identifications of specified complex information indicating a designing intelligence, other them humans of course.

    it's the fact that specified and complex code exists.

    Of course.

    Not how many there are.

    No, I suppose if we were to find really different codes on a different planet that would not falsify ID either. Would anything falsify ID in this regard?

    Would finding more codes falsify evolution?

    "evolution" is a somewhat broad term. But does "evolution" predict that all life everywhere is based upon the say "code" as it is here on earth? Of course not? Does "evolution" predict that even on earth there could not be a totally distinct brand of life independent from what we know now? No, of course not, but it does predict that it would have to be isolated from our version otherwise they'd simply compete. And of course it's unlikely that life would happen to evolve twice on the same planet in totally different ways and remain isolated from each other.

    How would more codes be viewed?

    How would ID view more codes? You've already said, it makes no predictions one way or the other. Funny that.

    The Universal code is soft evidence. It is based on current findings and then the story simply accommodates it.

    Basing your story on "current findings" is called science. How else would you expect it to be?

    If you instead kept "the story" the same despite "current findings" then that'd be like religion wouldn't it?

    Such is the stuff that mountains of evolutionary evidence is made of. Evolution lives on with it or without it.

    That's right. It's because "evolution" is a field of vast depth, the deeps of which you are not capable of perceiving. It's not a single thing, it's made up of mountains of consiliant evidence. But that evidence can never be allowed to change your story can it?

    ReplyDelete
  76. Neal,
    Do you agree or disagree with Joe's method of calculating CSI?

    all you have to do is count the coding nucleotides of the genes involved for that functioning system and then multiply by 2 (four possible nucleotides = 2^2).

    ReplyDelete
  77. Joe,

    Are human beings the underlying analogy for intelligent design?

    ReplyDelete
  78. Charles:

    Does the bacteria need special adaptations to survive in an arsenic environment? If that is the case, then my question still applies, even if they don't use the arsenic.

    ReplyDelete
  79. natschuster,
    Does the bacteria need special adaptations to survive in an arsenic environment?

    Let's consider a thought experiment. This "arsenic environment" is presumably an environment with a gradient of arsenic concentration going from "none" to "lots".

    Like the sea. You go from "all water" to "beach - some water" to "no water".

    So your question can be summarised like so: "why would tolerance to arsenic evolve if there was no arsenic (as if there was it would kill the bacteria), and if there was arsenic present how could the bacteria survive to evolve the required adaptations it needs to survive?"

    That about right?

    It's catch 22 when you put it like that. Which I suspect is the point.

    But consider the gradient. We could imagine this "arsenic environment" to be a circle a foot in radius. From the centre of the circle to the outside of the circle there is more then less arsenic. Outside the circle, none at all.

    Bacteria will grow and surround the circle of arsenic. When bacteria reach the concentration of arsenic that makes it impossible to survive, they will die.

    So we have around the edge of the circle bacteria that can just about survive with a tiny amount of the "poison". Now, widen that circle massively. It's actually a fractal edge really, so a has very high volume and so can support a correspondingly high population of bacteria.

    The bacteria never make it past the "death" level concentration on the gradient. Until one day, when a bacteria has a random mutation that allows it to survive a little better and so grow a bit closer to the centre of the circle. It now occupies a niche that other bacteria cannot occupy. If it's adaptation allows it to continue to replicate, it does so.

    Repeat and Rinse. One day there are bacteria that occupy the entire circle.

    What's that, it's a "just so" story? Sure. But there's more plausibility in it then "one day a designer made is so and *poof* it was so".

    natschuster, why don't you try and spin a similar "just so story" using your preferred origin of such adaptations? We can then compare tales....

    ReplyDelete
  80. natschuster:

    By doing a quick pubmed search using "arsenic resistance genes" keywords, I found this free article (among many others):

    Genes involved in arsenic transformation and resistance associated with different levels of arsenic-contaminated soils.

    Basically, bacteria develop resistance to arsenic by using resistance mechanisms similar to the one used against other toxic compounds:
    oxidation and efflux mechanisms.

    ReplyDelete
  81. See a good critique from an evolutionist skeptical of NASA's findings:

    RRResearch: Arsenic-associated bacteria (NASA's claims)

    http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html

    ReplyDelete
  82. See a good critique

    Sure, NASA is over-blowing their claims somewhat. They are over-blowing them somewhat less the the media is however...

    But what I find odd is how similar critiques of ID claims are simply ignored by ID proponents.

    Why is it when a scientific critique is made by "evolutionists" to other "evolutionists" claims it's held up by ID supporters as some kind of proof that "evolution" is failing, but when similar critiques are made of ID claims they are typically ignored or made out to be not that significant, even if it totally destroys the ID claim. For reference see Behe and his claims that have been destroyed over and over again but he repeats the same old canards in his talks to this very day.

    Why is ID apparently immune from similar scientific criticism?

    What's good for the goose....

    And it's how science works. You make a claim, people will try and pick it apart.

    So far not a single ID claim has survived that process.

    ReplyDelete
  83. pos-darwinista,
    In your blog you say (translated) with regard to the NASA finding:
    I recommend reading the book Darwin's Black Box , Michael Behe , which shows the inability of natural selection at this level.

    As natural selection could not, according to you, have caused the bacteria to evolve a way to survive, please tell me how your explain it from an Intelligent Design point of view?

    ReplyDelete
  84. The point I made there was about the frailty of origins science trying to explain the OoL, which I labelled as Mysterium tremendum = something science knows nothing about. So, this Mysterium tremendum remains Mysterium tremendum despite all the Baconian efforts of doing science: go and ask nature questions.

    OM: Thus far, and this is a very Kantian, nature has been so meager in giving us answers about this noumena. QED: the Mysterium tremendum remains Mysterium tremendum.

    ID, if you have read any books about IDT, has no OoL theory, but only that signs of intelligence are empirically detected in nature.

    And, boy, my blog is going beyond the Brazilian borders...

    ReplyDelete
  85. pos,
    16,000 papers about OOL published this year:

    http://scholar.google.co.uk/scholar?hl=en&q=origin+of+life&as_sdt=2001&as_ylo=2010&as_vis=0

    Yes, frail indeed. If that makes origins science frail, what does it make ID?

    ReplyDelete
  86. Have they established scientifically the OoL or are they still just-so stories? As far as I know, and I am History of Science researcher on theories of evolution and OoL, thus far the area remains in terra incognita as per ISSOL late conferences:

    http://issol.org/

    The Mysterium tremendum still remains a Mysterium tremendum, and science has just a flickering candle to light our knowledge in this area. I tremble and fear as I write this, but scientists are almost totally ignorant on the OoL issue.

    ReplyDelete
  87. pos
    Have they established scientifically the OoL or are they still just-so stories?,

    I think if a definitive origin of life had been discovered we'd all know about it by know.

    As far as I know, and I am History of Science researcher on theories of evolution and OoL, thus far the area remains in terra incognita as per ISSOL late conferences:

    Yes indeed. A empty land with nothing but thousands of scientists working hard and discovering new things every day.

    Compared to current OOL research's unknown land, ID is a hard vacuum the like of which does not exist except in the empty expanses between galaxies.

    It's obvious you never speak to any people at issol or any other scientific organisation, and that you are not a scientist yourself. If you did so speak or were a scientist or even knew anything about the scientific enterprise or mindset you would know that calling somebody's life work a "just so story" might be a little insulting, even demeaning. It might even cause them to remark hic puer est stultissimus omnium!. Or even tace atque abi.

    So, as you are a researcher on theories of evolution and OOL, what is the best scientific, peer reviewed evidence for a designer?

    The Mysterium tremendum still remains a Mysterium tremendum, and science has just a flickering candle to light our knowledge in this area.

    Yeah, but the thing is you are recommending that people actually read Darwin's Black Box as if it has not been totally discredited. So if you continue with your current reading habits, then your knowledge will indeed remain little.
    I tremble and fear as I write this, but scientists are almost totally ignorant on the OoL issue.

    Don't be afraid. 16,000 papers about OOL published this year:

    http://scholar.google.co.uk/scholar?hl=en&q=origin+of+life&as_sdt=2001&as_ylo=2010&as_vis=0

    Almost totally ignorant? Perhaps not.

    And again, what does that make ID? Yet you support ID despite rather then because of the evidence.

    If you really followed the evidence where it led you'd not be an ID supporter.

    And one last thing. Do you agree or disagree with Joe's method of calculating CSI?

    all you have to do is count the coding nucleotides of the genes involved for that functioning system and then multiply by 2 (four possible nucleotides = 2^2).

    Start identifying those patterns in nature!

    ReplyDelete
  88. Pos darwinista

    Thanks for link to blog exposing problems with science work done regarding arsenic based life. There are other expert blogs reporting the same issues. Expert language is hard to follow but I get the idea.
    More and more it seems it was attention grabbing media show by NASA.
    I like your use of Latin words. It is old fashioned in a good way. Scientists-philosophers of old times always used Latin in their works. I still remember some of that beautiful language from my father who was Latin and Greek language teacher.

    ReplyDelete
  89. It's amazing that people are so astounded that one scientist has problems with another scientist's work and says so. It's how it's supposed to work people!

    Review by your peers!

    I suppose it's news to some people because in the ID world no ID "scientist" will criticize another ID "scientist" because they are all working against a common enemy - reality.

    So there's room for all sorts in the ID big tent, even people like Joe/ID Guy who knows nothing and believes nothing unless it comes directly from Behe or Dembski.


    Eugen, do you agree or disagree with Joe's "method" to calculate CSI?

    all you have to do is count the coding nucleotides of the genes involved for that functioning system and then multiply by 2 (four possible nucleotides = 2^2).

    See what I mean? Nobody dares take a stand and say "that's simply nonsense".

    ReplyDelete
  90. It's amazing that persons who claim to be rational (and claim to be the epitome of rationality) are so astounded that persons who are rational -- and who know that 'Science!' does not, and cannot, deliver truth -- would dare to raise rational questions about the claims of scientists (much less of scientistes).

    ReplyDelete
  91. Hi OM,

    There are actually more links to other expert blogs from the one pos provided. I will agree that criticizing is a part of peer review process but you will have to agree these critiques will not get any attention.That's part of media manipulation.

    ---
    unless it comes directly from Behe or Dembski.
    ---

    I do wear ID ( or IDiot like some called me) glasses but not to extreme level. Few years ago,after reading books by above scientists it did make me think "could it really be"?

    ReplyDelete
  92. Eugen,
    I will agree that criticizing is a part of peer review process but you will have to agree these critiques will not get any attention.

    But we're talking about them! :P And anything that gets the general public talking about science has to be a good thing, even if it's somewhat over-hyped. From what I've read so far the critiques do make salient points. Obviously the debate will continue.

    Few years ago,after reading books by above scientists it did make me think "could it really be"?

    Sure, fair point. But the problem is that in those intervening years, what have those authors done? Any actual science? It seems the preference of ID's leading lights is to write books, not to get their hands dirty in a lab and push forwards the boundaries of knowledge. It's almost as if they know their ideas will fail if tested...

    So, sure, set the movement going with a book or three but if that's all, then it's not really science at all. I mean, even Behe said that it's for others to test the claims he's making. That's just not how it's done.

    And anyway, Behe does not even allow debate on the forums he posts on, neither his Amazon nor his UD blogs allow comments. Don't you ever wonder why?

    ReplyDelete
  93. Ilíon,
    would dare to raise rational questions about the claims of scientists (much less of scientistes).

    Many rational questions have been raised about Behe's and Dembski's work, all ignored by them.

    Examine this: http://dieben.blogspot.com/2010/09/what-is-wrong-with-public-debate.html

    And tell me who's got the problem with public debate?

    ReplyDelete
  94. could it really be"?

    Sure, fair point

    -----
    Usually I get angry responses. Some people here get pissed off quickly and are very serious. Maybe they have some other problems in their lives.
    I hate to insult and be angry so I try to keep it light with silliness.

    Other than that I do have serious issues with logic of some who recently said: replicator is replicator. That's it. No further explanation needed.

    Well, I need further explanation. We have to understand why we call it a replicator. We have to try to visualize details of this replicator. Like they said ,devil is in the details.

    ReplyDelete
  95. Eugen,
    Well, I need further explanation. We have to understand why we call it a replicator. We have to try to visualize details of this replicator. Like they said ,devil is in the details.

    There's plenty of details out there. Of course, we don't know what the first replicator was and we'll probably never really know in detail.

    But does that mean we know nothing at all? Absolutely not. Does that mean that ID can fill any of those gaps? Absolutely not. You are welcome to try, of course.

    But do you require the same level of detail for your (I presume) belief in an Intelligent Designer? I expect not. So on one hand we have an option where we have some detail (OOL) and on the other we have no detail at all (ID) but you choose (I presume) to believe in the evidence free option. Why don't you demand the same level of evidence from both?

    There are also alternatives to the "replicator first" option. See "The Origins of Order: Self-Organization and Selection in Evolution" by Stuart A. Kauffman for one. I don't know how well it's aged however (1993) and it's been a long time since I read it.

    ReplyDelete
  96. As a History of Science researcher I know how hard it is to get papers and articles published in scientific journals, much more difficult to have a paper or talk aproved at ISSOL or any other scientific conference where views like mine are considered to be heretic. As a History of Science researcher on OoL and Evolutionary theories, I maintain the frailty of OoL research status.

    A much more qualified scientist than most people here (including me), Rosie Redfield has disassembled the NASA-sponsored "alien life forms" story:

    http://rrresearch.blogspot.com/2010/12/arsenic-associated-bacteria-nasas.html

    There's a difference between controls done to genuinely test your hypothesis and those done when you just want to show that your hypothesis is true. The authors have done some of the latter, but not the former. They should have mixed pregrown E. coli or other cells with the arsenate supplemented medium and then done the same purifications. They should have thoroughly washed their DNA preps (a column cleanup is ridiculously easy), and maybe incubated it with phosphate buffer to displace any associated arsenate before doing the elemental analysis. They should have mixed E. coli DNA with arsenate and then gel-purified it. They should have tested whether their arsenic-containing DNA could be used as a template by normal DNA polymerases. They should have noticed all the discrepancies in their data and done experiments to find the causes.

    The Redfield Lab
    http://www.zoology.ubc.ca/~redfield/

    QED: The OoL remains as a Mysterium tremendum for science.

    ReplyDelete
  97. "This Paper Should Not Have Been Published"

    Scientists see fatal flaws in the NASA study of arsenic-based life.

    By Carl Zimmer
    Posted Tuesday, Dec. 7, 2010, at 10:53 AM ET

    http://www.slate.com/id/2276919/pagenum/all/#p2

    ReplyDelete
  98. pos
    As a History of Science researcher I know how hard it is to get papers and articles published in scientific journals, much more difficult to have a paper or talk aproved at ISSOL or any other scientific conference where views like mine are considered to be heretic.

    What, you mean views like dismissing years worth of work as "just so story's". I'm not surprised you are not published.

    As a History of Science researcher on OoL and Evolutionary theories, I maintain the frailty of OoL research status.,

    Colour me impressed.

    A much more qualified scientist than most people here (including me), Rosie Redfield has disassembled the NASA-sponsored "alien life forms" story:

    It's how science works.

    They should have mixed pregrown E. coli or other cells with the arsenate supplemented medium and then done the same purifications.

    So write a paper explaining what they got wrong and why the got it wrong. Posting your thoughts on a creationists blog won't progress your aim, if you aim is indeed to make science more accurate.

    And in any case, the phrase "They should have thoroughly washed their DNA preps (a column cleanup is ridiculously easy)" appears 27 times in google.

    http://tinyurl.com/2wulor3

    You have just copied and pasted your criticisms.

    Scientists see fatal flaws in the NASA study of arsenic-based life.

    Funny how when fatal flaws are found in the work of Behe, Axe, Dembski etc they are ignored by ID supporters.

    ReplyDelete
  99. "Scientists see fatal flaws in the NASA study of arsenic-based life."

    wait- wasn't this whole post a gloat about how scientists have discovered a life form that uses arsenic rather than phosphate in its DNA, thereby falsifying common descent, even though evolutionists won't admit it? now another IDer is gloating how the scientists might have gotten it wrong, and there is no arsenic-based life form? i guess armchair quarterbacks don't have to be consistent..

    ReplyDelete
  100. OM said:

    Of course, we don't know what the first replicator was

    Me said:

    Thank you.

    We can agree on that. Honest evolutionist you are.

    But thing we all know is how any replicator should work if it will function as such and carry that name proudly. From there we could have a good guess about first chemical replicator.

    If we conclude that chaotic soup can not produce functioning replicator what choice do I have. I think there is the key for my coversion.

    ReplyDelete
  101. nanobot74:
    "i guess armchair quarterbacks don't have to be consistent.."

    No, it just means that you have to back up your claims with solid experimental data if you expect them to be accepted. It also helps to have independent labs confirming your results.

    By the way, there is an important difference between an arsenic based life form and an organism that is able to use arsenic as an alternative to phosphorus. The bacteria in the study copes much better in an arsenic free environment.

    ReplyDelete
  102. Eugen
    From there we could have a good guess about first chemical replicator.,

    http://www.sciencemag.org/content/323/5918/1229.abstract

    An RNA enzyme that catalyzes the RNA-templated joining of RNA was converted to a format whereby two enzymes catalyze each other's synthesis from a total of four oligonucleotide substrates. These cross-replicating RNA enzymes undergo self-sustained exponential amplification in the absence of proteins or other biological materials. Amplification occurs with a doubling time of about 1 hour and can be continued indefinitely.,

    An accessible write up can be found here, at PZ's place: http://scienceblogs.com/pharyngula/2009/01/chemical_replicators.php

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  103. Charles
    No, it just means that you have to back up your claims with solid experimental data if you expect them to be accepted. It also helps to have independent labs confirming your results.

    I could not agree more. Now, if only proponents of ID shared your clarity!

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  104. Thanks OM:

    An accessible write up can be found here, at PZ's place: http://scienceblogs.com/pharyngula/2009/01/chemical_replicators.php
    ---
    I read post and yes it's interesting. If anything, constant human input during experiment proves intelligence is needed to start such a complex event as copying or duplication.

    To be fair , I appreciate work of lots of smart scientists on an interesting experiment.

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  105. OM: "I could not agree more. Now, if only proponents of ID shared your clarity!"

    That is just too funny coming from a DarwinDefender.

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  106. Eugen
    If anything, constant human input during experiment proves intelligence is needed to start such a complex event as copying or duplication.

    Ah, of course. And I expect computer simulations of, for example, objects falling under the influence of gravity cannot tell us anything about how objects fall in reality except that intelligence is required.

    I.E. Intelligent falling.

    http://en.wikipedia.org/wiki/Intelligent_falling
    the motions which the planets now have could not spring from any natural cause alone but were impressed by an intelligent agent

    Please define "complex event". There may be some examples of naturally occurring systems which I can provide (I.E. no intelligence required) that meet your definition (once you supply it) of "complex".

    To be fair , I appreciate work of lots of smart scientists on an interesting experiment.

    Don't you ever wonder why there are no similar experiments supporting ID?

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  107. Ilíon,
    That is just too funny coming from a DarwinDefender.,

    What aspect of "darwinism" do you think lacks solid experimental data?

    Please do tell.

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  108. OM

    I would stick with this definition:

    A function ƒ takes an input, x, and returns an output ƒ(x). One metaphor describes the function as a “machine” or “black box” that converts the input into the output.

    ( I use next few lines because of its simplicity)

    10 a=a+1
    20 print a:
    30 goto 10

    This logical unit is made of reusable components (commands) and its following rules ,protocols and conventions of the BASIC programming language.It will display incrementing string of numbers so we could give it a name according to that function.

    If we want looping f(a)=a+1 than we are not allowed to take out any of the elements(components). Every element is dependent on the other and has to be in prescribed order.

    Later we could switch from abstract, symbolic world to a material – chemical one. I think that should be acceptable because logic should follow.

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  109. Eugen,
    Please take a look at this

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

    Given a set M of molecules, chemical reactions can be roughly defined as pairs r=(A, B) of subsets from M.

    a1 + a2 + ... + an → b1 + b2 + ... + bm

    Let R be the set of allowable reactions. A pair (M, R) is a reaction system (RS).

    A molecule m ∈ A ∩ B of a reaction r is a catalyst of this reaction.

    A RS is autocatalytic, if all the catalysts for all its reactions are in M.

    The above definition is not sufficient to describe dependency on external resources or nutrients. This can be formulated by a closure over a generating subset of M.

    Formally, cl(S) denotes the smallest subset Y of M that contains S such that for each reaction (A, B)

    A ⊆ S ∪ Y ⇒ B ⊆ Y

    A RS is generated (over some resources S), if all reactants A in its reactions are in cl(S) and none of the resources is a catalyst.
    A generated autocatalytic set is an RS that is both autocatalytic and generated


    Does that comply with your definition? If not, why not. These networks naturally occur (no constant intelligent input is required), have cycles which repeat (goto 10) and sustain themselves. The "logic" is preserved.

    If you don't agree, perhaps you could give an example of a chemical system that does satisfy your definition and we can take it from there?

    Every element is dependent on the other and has to be in prescribed order.

    Sounds to me like you are exactly describing an autocatalytic set. But please do tell why you are not. And do these sets occur in nature with no intelligent input? Well, take a guess...

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  110. Thanks for the link.
    I'm not familiar with autocatalytic sets but it definitely looks interesting. Also, I'll look up Kauffman who is mentioned on the page. It will take me a day or so to get some understanding.
    OOL is the most interesting part of evolution discussions because it deals with transition from chaos to order, non living matter to living self replicating autonomous units. I try to envision this process but it's very difficult.

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  111. Eugen:

    "Thanks for the link.

    OOL is the most interesting part of evolution discussions because it deals with transition from chaos to order, non living matter to living self replicating autonomous units. I try to envision this process but it's very difficult."
    ======

    Well then perhaps you'll find these links interesting as well. Here's one which came out the same day as Cornelius Hunter's above post.

    Alien Life? by Rob Sheldon

    Then there is this article just a couple days ago in Yahoo News which referenced the criticism of Alien Panspermia Arsenic Hoax with this quote from the article:
    "But then other scientists began digging into the paper outlining NASA's research and findings, and they're now charging that the research behind it is flawed."

    Scientists poke holes in NASA’s arsenic-eating microbe discovery

    Then there is Rose Redfield's who is an Associate Professor who runs a micobiology Research Lab in British Columbia and her scathing report back on December 4th 2010 which the above Yahoo News article referenced her work.

    Arsenic-associated bacteria (NASA's claims)

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  112. Eocene

    Thanks for the links. I'll go trough them tomorrow. I'm behind schedule a bit. Too many (good) distractions.

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  113. OM
    I was quite surprised to find Kauffman turned from science to philosophy and religion. From this interview you can see he supports some kind of religion . I'll look up some videos on him soon.

    I'll give you one quote from his interview :" I wrote a whole book, The Origins of Order , and I very carefully never defined self-organization."

    I respect him for saying that. Like I said it's very difficult to imagine OOL process. I'll setup thought experiment using PLC programing principles just to examine what minimum count of components are needed to get logically unified and functional replicator - duplicator.

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  114. Eugen
    Like I said it's very difficult to imagine OOL process.

    Indeed, in fact it's so hard that many people give up and just insert (assert) a designer instead.

    Which seems to me to be the easy way out.

    From this interview you can see he supports some kind of religion .

    I don't see the relevance. Many religious people see a naturalistic origin of life as perfectly possible. One does not preclude the other.

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  115. OM: "Indeed, in fact it's so hard that many people give up and just insert (assert) a designer instead."

    Ah! OM, as is typical of DarwinDefenders (it seems to be a religious requirement), is credulous. Why, I'd just about bet you could convince him of *anything* -- so long as it's anti-reasonable.

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  116. OM:

    "Indeed, in fact it's so hard that many people give up and just insert (assert) a designer instead.

    Which seems to me to be the easy way out."
    =====

    WRONG!

    The easy way out is the laziness of disconnecting oneself from belief in a designer. It relieves one from any responsibility of being accountable for ones own actions. It excuses one from responsiblity of their own bad decision making or how their own personal actions may have negatively effected or impacted others. That's what this whole arguement is about. Science is a crutch and an excuse to lean on. It justifies actions and salves the nagging torment of the conscience. The real subject matter here is just what Pedant said it was, ideology, philosophy, politics and yes another type of religious worldview to be prosyletized worldwide.

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  117. OM

    I did homework on DNA replication. While reading I would occasionally think of a guy posting few weeks earlier how "replicator is just replicator ". My first impression was this system is incredibly complex but I don't want to use complexity as an argument for design now. All I would like to learn is if this is reducible process and if it is what its precursors were. What I mean is which sub function of this unified functional system can we remove and have lets say slower or maybe partial replication.
    Right now it seems to me there are few absolutely critical events to the point of logical necessity. If any of them would be done in wrong order or at the wrong place we would not get desired function. Assemblies like polymerase, primase , helicase already have function that could be used in some other cell process ( modularity). Further, each is assembled of discreet chemical subassemblies (folded proteins). There are pre and post replication events and I can't tell if there is proper event border to these or they all combine.
    After all I'm just shocked layman and it would be nice to have help from somebody who knows cell chemistry very well.
    PLC model is out of question after learning all this. I briefly consulted my colleagues on this and they agree its doable but thought I was crazy. It would not be nearly as simple as I originally imagined.

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  118. The author is right to be skeptical of evolution and its precepts, but the fact that evolution, as a theory, itself evolves, is not proof or even substantial evidence for its rejection.

    What makes science scientific-- and thus, useful-- is its openness to criticism; no matter how fundamental a component may be, it is known to not be invincible and may be rejected with significant evidence. If you asked a biochemist whether arsenic-based life were possible, he (if he were a good biochemist) would have said "Yes, but it has not yet been observed so we have no evidence to belief it may actually exist." P and As are chemically similar and thus it is fully believable that either could be used; really, which chemical predominates in biochemistry may be more a function of abundance than chemical character. It is conceivable that we may some day observe life based on Si instead of C for similar reasons.

    This practice is what makes science different from certain forms of religion. While science welcomes criticism, religion forbids it. While science accepts revision, religion avoids it for centuries past its due. While science is open and humble, religion is "omnipotent". Yet, unwavering as it is, this character of religion is certainly not evidence of its truth.

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  119. Well, gee, that was kind of clueless on a couple of different levels.

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  120. Ilíon:

    "Well, gee, that was kind of clueless on a couple of different levels."
    =======

    Actually I couldn't have read a more perfect explanation for blind faith that "Last Remianing Light's" Religious Sermon. LOL

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