academic freedom Intelligent Design

We can still legally refuse to drink the Kool-Aid

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In “Making Stories Visible The Task for Bioethics Commissions” (Issues in Science and Technology 27/2), Meera Lee Sethi and Adam Briggle explore claims made for science finds – under the banner, “Critical skepticism is always appropriate”: blockquote> Narrative explanations can help us understand difficult scientific issues, but they can also mislead us. Critical skepticism is always appropriate.
[ … ]

“This is the first self-replicating species we’ve had on the planet whose parent is a computer,” Venter said to a roomful of journalists. He spoke of long months spent “debugging” errors in the synthetic DNA and of “booting up” the cell into which it had been transplanted. Finally, he explained that the scientists who had created the cell, known as Mycoplasma mycoides JCVI-syn1.0, had “encoded” a series of messages into its genetic material, including the names of authors and key contributors, the URL of a Web site, and three literary quotations about the nature of discovery and creation.

By framing his work through the narrative of computer engineering, Venter was crafting a story about synthetic biology that presented it as a safe, repeatable, and controllable technology. Life, ran the story beneath his words, is essentially information. Organisms are information-processing machines. Creating life is like making a machine; if its design contains errors, we will find and fix them. And like a machine, the nature of a synthetic organism is so malleable to engineering that its DNA can be stamped with its creators’ intentions.

“What Venter’s doing,” says Rejeski, “is making use of an engineering narrative that sends a message to the policy people and the public that all this has a high degree of controllability. People tend to think, well, engineers do a fairly good job. Most of the time, bridges don’t fall down. But a cell is essentially a stochastic system, and we don’t have that kind of control over it. Venter’s got enough of a microbiology background to know better. He’s using a reassuring story that makes everything seem much simpler and less risky than it really is.” [….]

Hat tip: Pos-Darwinista

19 Replies to “We can still legally refuse to drink the Kool-Aid

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    bornagain77 says:

    Notes:

    Stephen Meyer – On Craig Venter – Complexity Of The Cell – Layered Information
    http://www.metacafe.com/watch/4798685/

    ,,,Of interest; despite the overblown hype that stemmed from Venter’s impressive technological feat, it is important to realize just exactly what Venter DID NOT accomplish in his work, Venter DID NOT create even a single novel gene or protein in his ‘creation’ of synthetic life;

    Stephen Meyer – Functional Proteins And Information For Body Plans – video
    http://www.metacafe.com/watch/4050681

    ,,,also of interest to this is the recent Herculean effort it took to ‘design’ just a single novel type of protein that would simply bind, specifically, to another preexisting protein found in life:

    Protein Binding – By Chance of By Design? – Fazale Rana
    Excerpt: When considering this study, it is remarkable to note how much effort it took to design a protein that binds to a specific location on the hemagglutinin molecule. As biochemists Bryan Der and Brian Kuhlman point out while commenting on this work, the design of these proteins required:,,, …cutting-edge software developed by ~20 groups worldwide and 100,000 hours of highly parallel computing time. It also involved using a technique known as yeast display to screen candidate proteins and select those with high binding affinities, as well as x-ray crystallography to validate designs.,,, If it takes this much work and intellectual input to create a single protein from scratch, is it really reasonable to think that undirected evolutionary processes could accomplish this task routinely?
    http://networkedblogs.com/jRdlR

    ,,, which of course agrees with the empirical research of Dr. Behe finding extreme limits to the power of neo-Darwinian evolution to ‘create’ anything of interest at all:,,,

    “The likelihood of developing two binding sites in a protein complex would be the square of the probability of developing one: a double CCC (chloroquine complexity cluster), 10^20 times 10^20, which is 10^40. There have likely been fewer than 10^40 cells in the entire world in the past 4 billion years, so the odds are against a single event of this variety (just 2 binding sites being generated by accident) in the history of life. It is biologically unreasonable.”
    Michael J. Behe PhD. (from page 146 of his book “Edge of Evolution”)

    Nature Paper,, Finds Darwinian Processes Lacking – Michael Behe – Oct. 2009
    Excerpt: Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function (of a protein to its supposed ancestral form) are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought. (which was 1 in 10^40 for just 2 binding sites)
    http://www.evolutionnews.org/2.....hes_t.html

    ===================

    f/n

    Stability effects of mutations and protein evolvability. October 2009
    Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,,
    http://www.ncbi.nlm.nih.gov/pubmed/19765975

    When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe
    Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied.
    http://biologicinstitute.org/2.....t-collide/

    =========================

    Here is a song for our resident ‘cyberstalker’,

    “Revelation Song” by Phillips,Craig and Dean – music video
    http://www.youtube.com/watch?v=gYTDI8QOoMY

    ,,,Jesus Loves You!!!

  3. 3
    Mung says:

    …it is important to realize just exactly what Venter DID NOT accomplish in his work, Venter DID NOT create even a single novel gene or protein in his ‘creation’ of synthetic life;

    I’m not sure how relevant that is, really. I don’t think Venter was trying to create novel genes and proteins.

    But I think others have. See the above referenced book in my first post.

  4. 4
    bornagain77 says:

    Mung, you state;

    ‘But I think others have.’

    Please do tell.

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    bornagain77 says:

    Perhaps you are thinking of this mung;

    ‘Another interesting section of Creating Life in the Lab is one on artificial enzymes. Biological enzymes catalyze chemical reactions, often increasing the spontaneous reaction rate by a billion times or more. Scientists have set out to produce artificial enzymes that catalyze chemical reactions not used in biological organisms. Comparing the structure of biological enzymes, scientists used super-computers to calculate the sequences of amino acids in their enzymes that might catalyze the reaction they were interested in. After testing dozens of candidates,, the best ones were chosen and subjected to “in vitro evolution,” which increased the reaction rate up to 200-fold. Despite all this “intelligent design,” the artificial enzymes were 10,000 to 1,000,000,000 times less efficient than their biological counterparts. Dr. Rana asks the question, “is it reasonable to think that undirected evolutionary processes routinely accomplished this task?” ‘

    Mung, the ‘relevance’ of my post is, besides letting the air out of the hype of Venter’s work, to show that not only is ‘design’ required for life but that the design that is required to explain life is vastly superior to the ‘design’ we can accomplish using our most sophisticated technology!

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    bornagain77 says:

    And mung, what is your point???

    The first two papers are on the same thing;

    ‘We reasoned that the rigidity and defined geometry of an alpha-helical domain linker would make it effective as a conduit for allosteric signals. To test this idea, we rationally designed 12 fusions between the naturally photoactive LOV2 domain from Avena sativa phototropin 1 and the Escherichia coli trp repressor’

    To which I say ‘So What???”, they copied it exactly from preexisting proteins in life!!!

    The last ‘artificial enzyme’ paper you listed is, I believe, the same exact one that Dr. Rana focused on in his book that was 10,000 to 1,000,000,000 times slower than the enzyme found in life!

    Of interest:

    Fazale (Fuz) Rana Cell’s Design MP3 podcast series
    http://manawatu.christian-apol.....st-series/

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    pvoce says:

    Off topic to be sure, but we now have an “Evolution Machine.” Of course, no directions are necessary, its all random chance:)

    http://www.newscientist.com/ar.....?full=true

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    bornagain77 says:

    pvoce, that article is a gem for this one quote alone:

    ‘Yet changing even a handful of genes takes huge amounts of time and money. For instance, a yeast engineered to churn out the antimalarial drug artemisinin has been hailed as one of the great success stories of synthetic biology. However, it took 150 person-years and cost $25 million to add or tweak around a dozen genes – and commercial production has yet to begin.’

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    Mung says:

    BA77: it is important to realize just exactly what Venter DID NOT accomplish in his work, Venter DID NOT create even a single novel gene or protein in his ‘creation’ of synthetic life

    Mung: I don’t think Venter was trying to create novel genes and proteins. But I think others have. See the above referenced book in my first post.

    BA77: Please do tell.

    Mung: provides links

    BA77: And mung, what is your point???

    ???

    If you’re already aware of the fact why are you asking me for references?

    The last ‘artificial enzyme’ paper you listed is, I believe, the same exact one that Dr. Rana focused on in his book that was 10,000 to 1,000,000,000 times slower than the enzyme found in life!

    That makes it not a protein?

    Do a patent search if you want more. I’ll bet people are applying for patents on these things.

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    bornagain77 says:

    pvoce, To bad they will tell only of ‘the hype’ of ‘overexpressed genes’ that produce more of what they want and not of the ‘sheer brick wall’ they will soon discover to ‘evolvability’!

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    Mung says:

    Proteins are made by translating the genetic information which is carried in a cell’s genes. Scientists synthesized in the laboratory genes for the two insulin “A” and “B” chains. This was accomplished by chemically linking together small pieces of DNA sequence and then joining them in a specific manner to form complete genes.

    Synthetic Insulin

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

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    Mung says:

    That belongs in the “Darwinian medicine” thread, haha. NOT.

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    bornagain77 says:

    Mung, again what is your point??? It is a preexisting protein!

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    Mung says:

    “This is the first self-replicating species we’ve had on the planet whose parent is a computer,” Venter said to a roomful of journalists.

    You have to love how some people think that DNA is a self-replicating molecule, and that all you need is a self-replicating molecule and all the rest of the living world is suddenly there for the taking.

    Well, folks, it just may not be that simple.

    Checkpoints are surveillance-dependent controls on the various steps in the indescribably complex business of cell reproduction; they guarantee that the entire process does not move forward until all the preliminary steps, such as ensuring genome integrity, have been completed.

    http://www.uncommondescent.com.....ent-387878

  16. 16
    bornagain77 says:

    Mung, I don’t know what your chip on the shoulder is for me, but all the things you have listed are in agreement with the point I was making in my post, i.e that man has not designed a novel protein/gene, using all his technology, that exceeds the design of proteins in life.

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    Mung says:

    No argument about that. I thought you were saying it hadn’t been done and implying that it could not be done.

    All’s well that ends well.

  18. 18
    Mung says:

    …all the things you have listed are in agreement with the point I was making in my post, i.e that man has not designed a novel protein/gene, using all his technology, that exceeds the design of proteins in life.

    I missed that last bit.

  19. 19
    bornagain77 says:

    mung; to clarify a bit more, nor have I seen evidence for man designing any completely novel proteins/genes that even ‘matches’ the efficiency of the proteins found in life. One reason why I think man shall never ‘match’ the perfection/efficiency of the proteins we find in life is because the information in proteins is not merely sequence dependent information (classical information) but also information that extends down to the ‘non-local’ quantum information level:

    Quantum Information/Entanglement In DNA & Protein Folding – short video
    http://www.metacafe.com/watch/5936605/

    In the preceding video, ‘Gretchen’ asked if quantum entanglement/information could also somehow be measured in protein structures, besides just DNA, and it turns out that quantum entanglement/information has already been detected in protein structures. Here is one such measure;

    Proteins with cruise control provide new perspective:
    Excerpt: “A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.”
    http://www.princeton.edu/main/...../60/95O56/

    The preceding is solid confirmation that far more complex information resides in proteins than meets the eye, for the calculus equations used for ‘cruise control’, that must somehow reside within the quantum information that is ‘constraining’ the entire protein structure to its ‘normal’ state, is anything but ‘simple classical information’. For a sample of the equations that must be dealt with, to ‘engineer’ even a simple process control loop like cruise control along a entire protein structure, please see this following site:

    PID controller
    Excerpt: A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal.
    http://en.wikipedia.org/wiki/PID_controller

    further notes:

    Myosin Coherence
    Excerpt: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. Living systems have mastered the making and breaking of chemical bonds, which are quantum mechanical phenomena. Absorbance of frequency specific radiation (e.g. photosynthesis and vision), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects.
    http://www.energetic-medicine......Page1.html

    Coherent Intrachain energy migration at room temperature
    Elisabetta Collini & Gregory Scholes
    University of Toronto
    Science, 323, (2009), pp. 369-73
    The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state.
    http://www.scimednet.org/quant.....d-protein/

    etc.. etc..

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