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EA’s 101 on some of the challenges of OOL Chemistry

One of the great things about UD is the commenters. In this case Eric Anderson has put up a summary — some days back — on an aspect of the blind- chance- and/or- necessity- in- a- chemical- stew- in- a- pond (or the like) OOL challenges that is well worth headlining:

___________

>> biological structures are not simply an aggregation of smaller units that naturally come about through the processes of physics and chemistry.

We first need to clarify which building blocks we are talking about. If we are just talking about chemical elements (atoms with their constituent protons, electrons, neutrons) then, yes, everyone agrees that those exist naturally. In addition, if we are talking about some simple molecules, yes, some of those too exist naturally. From there things get more dicey. Specifically, it is not the case, as you suggest, that molecules simply come together as part of a natural chemical process to form amino acids, and subsequently, proteins.

Formation of the amino acids required for life under primitive earth conditions continues to be an active area of research. To be sure, there is evidence that some amino acids can form under primitive earth conditions, and some amino acids have been found in meteorite fragments and in space. However, it is far from certain that all of the necessary amino acids could have existed on the primitive earth at the same time and under the same conditions. (And we are completely setting aside issues such as relative abundance, chirality [NB: --> mirror-image handedness of molecules that affects the possibility of folding etc], cross reactions, and so on.) So the formation/arrival of the amino acids necessary for life to form continues to be an area of interest for the chemical synthesis (to use Davies’ term) origin of life paradigm. Those building blocks are still being studied.

Nevertheless, I am willing to concede for the moment — just for sake of discussion and to help focus us on the real issues — that all the amino acids were readily available at the right time and place. What next?

You [another commenter] mention:

Ditto for amino acids–so long as you line them all up in the right order they just click together and start folding and there you have your protein.

Not really. It turns out that amino acid chains often do not have a single folding pattern. An analogy I like to use is my child’s toy of magnets and rods. In order to make a particular shape it is true that I need to have the magnets and rods in the right order. But while that is necessary, it is not sufficient. This is because the various magnets and rods can cross interact with each other, depending on how the chain is folded. And indeed, we are learning that systems within the cell help to fold the amino acid chain into the right form for the particular protein needed.

Although the formation of proteins has long been portrayed as a simple ‘amino-acid-chain-folds-automatically-into-protein’ situation, that is actually not correct. Given a chain, say 300 amino acids long, there can be many possible folding patterns — most of which constitute a jumbled mess, a few of which constitute functional structures, and perhaps only a couple of which constitute the relevant protein needed for the particular function.

Moreover, even if we were to concede that a chain of amino acids will automatically fold to the correct protein, that still leaves unanswered the $64,000 question that you gloss over with “. . . so long as you line them all up in the right order . . . .” This ordering is precisely the issue that cannot be solved by natural means within the resources of the known universe.

Beyond proteins, we have protein complexes, then larger molecular structures (for example, the molecular machines often discussed), organelles, cells, organs, larger systems, and the entire physical organism itself. All of this can, in the sense Davies is discussing, be termed “hardware.”

My point is that current chemical synthesis efforts don’t even scratch the surface of dealing with all the hardware. Right now they are still stuck back at the amino acids and proteins — what are often referred to as the “building blocks” of life.>>

____________

This brings down to 101 level, several of the key challenges for OOL (that, unfortunately, are too often glossed over in the classroom, as well as in popular science documentaries and on “science” web sites), and for the onward production of novel types of proteins as well.

Well worth pondering. END

 

 

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12 Responses to EA’s 101 on some of the challenges of OOL Chemistry

  1. Brian Cox (http://sciencefocus.com/news/brian-cox-alien-life) on his new BBC TV series:

    I came to the view with the advisors on the [Wonders of Life] series that if you have the right conditions – water, some organic compounds, a bit of rock and some pH gradients – then life will appear spontaneously.

    I wonder which OOL specialists were advising him? And how many times they’ve done it in the lab so far? Maybe he should stick to physics.

  2. JG:

    I’se be shakin’ me poor haid, mon.

    It seems that the sheer, integrated, digitally coded functionally specific complexity of life forms has not soaked into the mindset of too many who produce these pop sci programmes.

    But, in the grips of Lewontinian materialist a prioris, it SEEMS so simple and logical that that is how it must have happened, and besides we have the Miller-Urey spark in a bottle experiments! (Those still appear in textbooks as though the many gaps to realistic atmospheres, and to moving from a few AAs to complex organised life forms, can be bridged with a few breezy just so stories.)

    Beyond a certain point, we are talking creation of negligent false narratives here, failing in duties of care to accurately and fairly inform the public. Hence, why Icons of Evolution was so necessary.

    KF

  3. Rabbi M.Averick, had a recent article on the origin of life ‘problem’:

    Atheistic Science is Rapidly Sinking in the Quicksand – January 28, 2013 – Rabbi Moshe Averick
    Excerpt: As Nobel Prize winner, Dr. Jacque Monod explains in his classic work, Chance and Necessity, there are no chemical or physical laws that determine any particular order of amino acids to build the first proteins (all amino acids can link together equally well) and similarly there are no chemical or physical laws that would determine the sequences of nucleotides that code for these proteins in DNA. The only option left for him is chance. He acknowledges that the random probability of such a system coming into being is “virtually zero.”
    http://www.algemeiner.com/2013.....quicksand/

    Or perhaps this article from a few months back will help get the point across:

    The Humpty-Dumpty Effect: A Revolutionary Paper with Far-Reaching Implications – Paul Nelson – October 23, 2012
    Excerpt: Tompa and Rose calculate the “total number of possible distinct patterns of interactions,” using yeast, a unicellular eukaryote, as their model system; this “total number” is the size of the space that must be searched. With approximately 4,500 proteins in yeast, the interactome search space “is on the order of 10^7200, an unimaginably large number,” they write — but “more realistic” estimates, they continue, are “yet more complicated.” Proteins present many possible surfaces for chemical interaction. “In all,” argue Tompa and Rose, “an average protein would have approximately 3540 distinguishable interfaces,” and if one uses this number for the interactome space calculation, the result is 10 followed by the exponent 7.9 x 10^10.,,, the numbers preclude formation of a functional interactome (of ‘simple’ life) by trial and error,, within any meaningful span of time. This numerical exercise…is tantamount to a proof that the cell does not organize by random collisions of its interacting constituents.
    http://www.evolutionnews.org/2.....65521.html

    Though these obscenely large numbers, that defy any meaningful comprehension, are certainly impressive as to showing the absurd levels of blind faith that Darwinists cling to, in the ‘hope’ that ‘random’ processes will ever produce biological life from lifeless molecules, the Theist has, as far as science itself is concerned, a recourse to a far greater proof than these obscenely large numbers. This far greater proof, as far as science itself is concerned, comes from recent breakthroughs in our understanding as to what is actually holding the cell together,,, what is holding the cell to be so far out of thermodynamic equilibrium. What is now found to be ‘holding the cell together’, to be so far out of thermodynamic equilibrium, is found to be non-local, beyond space and time, quantum entanglement. This ‘spooky’ ‘beyond space and time’ quantum entanglement is now found in every DNA and protein molecule of a cell,,,

    Quantum Information/Entanglement In DNA – Elisabeth Rieper – short video
    http://www.metacafe.com/watch/5936605/

    DNA Can Discern Between Two Quantum States, Research Shows – June 2011
    Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property.
    http://www.sciencedaily.com/re.....104014.htm

    Testing quantum entanglement in protein
    Excerpt: The authors remark that this reverses the previous orthodoxy, which held that quantum effects could not exist in biological systems because of the amount of noise in these systems.,,, Environmental noise here drives a persistent and cyclic generation of new entanglement.,,, In summary, the authors say that they have demonstrated that entanglement can recur even in a hot noisy environment. In biological systems this can be related to changes in the conformation of macromolecules.
    http://www.quantum-mind.co.uk/.....-c288.html

    And although materialists try to imagine all sorts of bizarre scenarios to try to ‘explain away’ quantum entanglement, such as infinite parallel universes (i.e. Many Worlds), the fact of the matter is that, ever since Einstein derided this ‘spooky action a distance’ to Neils Bohr last century,,,

    Quantum Entanglement – (Neils Bohr and Einstein debate) – Materialism – Alain Aspect – video
    http://www.metacafe.com/w/4744145

    ,,,the experimental science itself, despite the objections of materialists, has consistently indicated that quantum actions are indeed instantaneous and cannot be reduced to any conceivable within space-time causation by materialists:

    Looking Beyond Space and Time to Cope With Quantum Theory – (Oct. 28, 2012)
    Excerpt: The remaining option is to accept that (quantum) influences must be infinitely fast,,,
    “Our result gives weight to the idea that quantum correlations somehow arise from outside spacetime, in the sense that no story in space and time can describe them,” says Nicolas Gisin, Professor at the University of Geneva, Switzerland,,,
    http://www.sciencedaily.com/re.....142217.htm

    The materialist simply has no coherent cause to appeal to to answer the enigma of quantum entaglement, whereas the Theist has always maintained that God, who is beyond space and time, is the source for all life. Thus it is not surprising at all for the Theist to find non-local’, beyond space and time, quantum entanglement in molecular biology on a massive scale:

    Perhaps, it would be wise for materialists, in their futile search to understand how life came to be from non-life, to pause for a moment and soberly consider the implications of the One who defeated death on the cross?:

    Verse and music:

    John 1:4
    In Him was life, and the life was the Light of men.

    Natalie Grant – Alive (Resurrection music video)
    http://www.godtube.com/watch/?v=KPYWPGNX

    Turin Shroud Hologram Reveals The Words ‘The Lamb’ – short video
    http://www.metacafe.com/watch/4041205

  4. KF

    I didn’t see the programme, but wondered if Cox might be influenced by the Bejans of this world, but thought better of it. It would surely have to be someone more mainstream. Given his interest in astrobiology, Carl Woese seems a more likely influence: cf this important article .

    On the other hand towards the end Woese criticises the hegemony of physics and chemistry over biology as, itself, a fundamental science.

    Much to think about in the article in this month following Woese’s death – most interesting is his clear rejection of the Darwinian paradigm and reductionist molecular approaches. Apart from James Shapiro and others like him, it’s hard to believe from the state of the discussion that such a key figure divided the pursuit of biology in such a fundamental way 9 years ago.

  5. I came to the view with the advisors on the [Wonders of Life] series that if you have the right conditions – water, some organic compounds, a bit of rock and some pH gradients – then life will appear spontaneously.

    And they have the gall to assail us for having “faith”!

    At least the object of our faith makes more sense rationally speaking than what they place their faith in.

  6. Very kind, KF. Thanks for reposting this.

  7. EA: Welcome, it was headlining-worthy. KF

  8. JG: I think you nailed it with:

    I wonder which OOL specialists were advising him? And how many times they’ve done it in the lab so far?

    To which we can add, in which year did they receive the Nobel Prize sure to be given out for such an achievement?

    KF

  9. 9
    sagebrush gardener

    Life is not just energy and matter. It is information. Maybe Darwin could be forgiven for not understanding information as a separate and essential entity 150 years ago, but educated people should know better by now. I myself have spent the last 25 years of my career, not manipulating matter, but skillfully arranging ones and zeros.

    In the beginning was the Word. All things were made through Him, and without Him nothing was made that was made. We still use “word” to describe a basic unit of information in computer programming.

    It’s all about the information.

  10. Hi KF

    this post should encourage readers to think. Few years ago I came across Uncommon Descent and your ID foundations series. After reading the series it made me question about what main stream science was force feeding us regarding some aspects of biology.
    About the OOL issue, it is interesting how hundreds of labs in hundreds of universities around the world, spending many millions of dollars cannot find a solution to OOL. Sure these labs sometimes produce a finely engineered chemical process and that is commendable result of a hard work. But when you think of it, how close is chemical engineering to presumed prebiotic soup of a warm little pond billions of years ago?

  11. Just a few condiments short. That’s all.

  12. Hi Eugen

    It’s been a while since I last saw you comment at UD. Good to hear from you.

    Pardon my delay in getting back to this thread.

    You will be amused to learn of the rating scale of experimenter interference put forth in the very first technical ID book, TMLO, back in 1984:

    Special constraints (conditions) as in synthesis of insulin

    Specific constraints (conditions) as in synthesis of freon or nylon
    ______
    ______

    8) Selected chemicals, isolated from other soup ingredients

    7) Selected wavelengths of UV, heat, isolated from other energy sources

    6) Spark, shock waves, isolated from other energy sources

    5) Concentrated solutions where reactions depend on concentrated conditions (e.g., HCN polymerization)

    4) Traps (–> Trapping out products, saving them from being destroyed by other processes, or contaminated through cross-reactions)

    3) Phososensitization

    Threshold of illegitimate interference
    ————————————–
    2) Concentrated solutions where law of mass action is validly extrapolated

    1) “Synthesis in the Whole”: dilute solutions mixed together

    [Fig. 6-1, p. 107, TMLO. Caption reads: "Geochemical plausibility scale for evaluating prebiotic simulation experiments. Experimental techniques (conditions) are arranged according to the degree of inves-tigator interference. At some point along the scale investigator involvement reaches a threshold, beyond which investigator interference is illegitimate. "]

    In short, the threshold of illegitimate engineering, for good reasons, is fairly low. You may want to argue that allowing light of suitable and favourable wavelengths, and absence of that of the wrong ones, to be acceptable, but surely trapping out is not right. Right from the Miller-Urey spark in gas exercises, that has been a standard. Not to mention, use of concentrated agents of the right chirality, etc etc etc.

    OOL chemistry has long been in trouble, and the issue of getting to the sort of metabolic systems — the reaction sets alone remind me strongly of a vast and complex chemical plant with very carefully co-ordinated integration. The use of special catalysts — enzymes — and ATP produced by our “motor enzyme” and more, all point to design. Strongly. Remember, ever so much of the chemistry involved is chemically uphill and the life systems use constraining nanomachines to make it go, e.g. protein synthesis.

    And on and on it goes.

    As to the vNSR that is joined tot he metabolic automaton and gives the cell self replicating funciton, that is yet another example of the same, but multiplied by stored coded information. Codes, info storage, processing algorithms embedded int eh operations of life and before the first genuine cell?

    That all reeks of design to me, for excellent reason.

    And with design sitting at the table by right at OOL, that utterly transforms everything thereafter.

    KF

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