Naturalism Origin Of Life

Chemist James Tour writes an open letter to his colleagues

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Our all-time most-read post here at Uncommon Descent was about renowned chemist James Tour: A world-famous chemist tells the truth: there’s no scientist alive today who understands macroevolution (visited 363,901 times, 66 visits today, 484 responses).

At Inference Review, he writes,

Cellular and organelle bilayers, which were once thought of as simple vesicles, are anything but. They are highly functional gatekeepers. By virtue of their glycans, lipid bilayers become enormous banks of stored, readable, and re-writable information. The sonication of a few random lipids, polysaccharides, and proteins in a lab will not yield cellular lipid bilayer membranes.

Mes frères, mes semblables, with these complexities in mind, how can we build the microsystem of a simple cell? Would we be able to build even the lipid bilayers? These diminutive cellular microsystems—which are, in turn, composed of thousands of nanosystems—are beyond our comprehension. Yet we are led to believe that 3.8 billion years ago the requisite compounds could be found in some cave, or undersea vent, and somehow or other they assembled themselves into the first cell.

Could time really have worked such magic?

Many of the molecular structures needed for life are not thermodynamically favored by their syntheses.More.

In its present state, origin of life is only a science topic out of deference to naturalism, not on account of  its research success.

See also: Biophysicist: Order can arise from nothing! I have evidence! – Rob Sheldon replies

Is origin of life really a science problem?

and

What we know and don’t know about the origin of life

22 Replies to “Chemist James Tour writes an open letter to his colleagues

  1. 1
    Mung says:

    Yes. Cell membranes are nothing like the the simple things materialists imagine them to be.

    They are not soap bubbles.

  2. 2
    DATCG says:

    Sure, over “time” anything can happen. Or can it?

    From the article…
    Coordinated systems utilizing several hundred enzymes in
    complex pathways…

    What is more, Vlatka Zoldoš, Tomislav Horvat, and Gordan Lauc observed: “A peculiarity of glycan moieties of glycoproteins is that they are not synthesized using a direct genetic template. Instead, they result from the activity of several hundreds of enzymes organized in complex pathways.”10

    Saccharides are information-rich molecules. Glycosyl transferases encode information into glycans and saccharide binding proteins decode the information stored in the glycan structures. This process is repeated according to polysaccharide branching and coupling patterns.11 Saccharides encode and transfer information long after their initial enzymatic construction.12 Polysaccharides carry more potential information than any other macromolecule, including DNA and RNA. For this reason, lipid-associated polysaccharides are proving enigmatic.13

    Cellular and organelle bilayers, which were once thought of as simple vesicles, are anything but. They are highly functional gatekeepers. By virtue of their glycans, lipid bilayers become enormous banks of stored, readable, and re-writable information. The sonication of a few random lipids, polysaccharides, and proteins in a lab will not yield cellular lipid bilayer membranes.

    the magic god of Darwinist = time…

    Mes frères, mes semblables, with these complexities in mind, how can we build the microsystem of a simple cell? Would we be able to build even the lipid bilayers? These diminutive cellular microsystems—which are, in turn, composed of thousands of nanosystems—are beyond our comprehension. Yet we are led to believe that 3.8 billion years ago the requisite compounds could be found in some cave, or undersea vent, and somehow or other they assembled themselves into the first cell.

    Could time really have worked such magic?(magic god of Darwinist)

    Answer, no, Darwinist’s god Time, is it’s own enemy

    Many of the molecular structures needed for life are not thermodynamically favored by their syntheses. Formed by the formose reaction, the saccharides undergo further condensation under the very reaction conditions in which they form. The result is polymeric material, not to mention its stereo-randomness at every stereogenic center, therefore doubly useless.14 Time is the enemy. The reaction must be stopped soon after the desired product is formed. If we run out of synthetic intermediates in the laboratory, we have to go back to the beginning. Nature does not keep a laboratory notebook. How does she bring up more material from the rear?

    according to some physicist(England)…

    If one understands the second law of thermodynamics, according to some physicists,15* “You [can] start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant.”16 The interactions of light with small molecules is well understood. The experiment has been performed. The outcome is known. Regardless of the wavelength of the light, no plant ever forms.

    The obvious, materialist claims make no scientific sense…

    We synthetic chemists should state the obvious. The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense.

    15* See Jeremy England, “Statistical Physics of Self-Replication,” Journal of Chemical Physics 139 (2013), doi:10.1063/1.4818538; Paul Rosenberg, “God is on the Ropes: The Brilliant New Science That Has Creationists and the Christian Right terrified,” Salon January 3, 2015

    Salon’s article is definitely a puff piece.

    Dr Tour brings reality back to science.

  3. 3
    DATCG says:

    found Dr. Tour’s other article.

    Animadversions of a Synthetic Chemist… and the many steps and lessons of building nano vehicles

    LIFE REQUIRES carbohydrates, nucleic acids, lipids, and proteins. What is the chemistry behind their origin? Biologists seem to think(more assumptions?) that there are well-understood(more assumptions?) prebiotic molecular mechanisms for their synthesis. They have been grossly misinformed. And no wonder: few biologists have ever synthesized a complex molecule ab initio. If they need a molecule, they purchase molecular synthesis kits, which are, of course, designed by synthetic chemists(intelligent designers), and which feature simplistic protocols.

    Polysaccharides? Their origin?

    The synthetic chemists do not have a pathway.

    The biologists do not have a clue.

    (assumptions)emphasis mine

    “Nature does not perform retrosynthetic analyses.”

    This is just the beginning.

    Once a target is selected, retrosynthesis is next, whether on paper or on a computer screen. Placing the target at the top, the chemist draws an inverted tree (or graph), one step down at a time, into multiple branch points, until he reaches a level where starting materials are at hand.2

    The decision tree is then pruned. Certain branches lead to dead ends. They are lopped off. Further refinement of various routes leads to a set of desired paths; these are the routes that can be attempted in the laboratory.

    Why the retrosynthetic approach to complex molecules? It is because finding a direct path to a target is far too complicated. Dead ends are everywhere; dead products accumulate massively; and, between the dead ends and the dead products, precious starting materials tend to become exhausted.

    There are no targets in evolution. Nature does not perform retrosynthetic analyses.

    It’s fascinating reading by Dr. Tour. After listing just a small overview of steps getting to certain point building nano vehicles, he ask important questions…

    Each product needed a different purification protocol.

    Chance may favor the prepared mind, but good things rarely happen only by chance.

    How does nature do it? Are the biologists sure that they know the answer?

    Are they very sure?

    no slam dunk in nature…

    Fast Motor Nanocars

    OUR PLAN TO synthesize nanocar 31 (Figure 7f) involved a modular approach in which the coupling of the axles and the stator represented the last step. According to Scheme 4, heating ketone 32 to reflux in an ethanol and hydrazine solution produced the rotor, hydrazone 33. The conversion of ketone 34 into thione 35 was improved by decreasing both the concentration and the reaction time from those in the published procedure. The generation of the sterically hindered double bond between the rotor and the stator utilized Barton–Kellogg coupling. Hydrazone 33 was oxidized to the unstable diazo intermediate 36 using manganese dioxide by careful temperature control. The inorganic residue was removed by filtration in a Schlenk set-up that enforced the strict exclusion of air, oxygen and moisture. Thione 35 was added to the deep purple filtrate. A [2+3] cycloaddition occurred and evolution of nitrogen gas indicated the formation of episulfide 37. The white solid episulfide 37 was then treated with trimethyl phosphite in a screw-capped tube at 130°C to yield the molecular motor 38 as a mixture of isomers. We planned all along to investigate individual molecules on surfaces. It was unnecessary to resolve the enantiomers.

    Nature would never have had this convenient luxury.

    Far more complex than what is taught to the public…

    Nature uses a procedure far more complicated than anything illustrated here.

    Designing nanoncars is child’s play in comparison to the complexity involved in the synthesis of proteins, enzymes, DNA, RNA, and polysaccharides, let alone their assembly into complex functional macroscopic systems.

    what really happens?

    Chemistry does not happen that way. Even the oxidative expulsion of SO2 from ketone 43 by the Ramberg–Bäcklund method would not work, since the sulfur is bound aromatically.

    We could have left ketone 43 in a flask for millions of years and it would not form ketone 32 by any known or rational thermal, reductive, photochemical, or enzymatic method. This is not unusual when related compounds have clearly different starting points in organic chemistry. It is typical.

    That nature has a select set of molecules that can be transformed into related structures using very precise enzymes (catalysts) is a phenomenon unknown in any other field of organic chemistry.

    A key point: parts are not always easily interchangeable without severe and unexpected consequences.

    When working environments change, drastic changes in molecular structure are often required to retain the system’s functions.

    Life Lessons for the Prebiotic Chemist

    CARBOHYDRATES ARE the backbones of nucleotides, which in turn are needed for DNA and RNA. Carbohydrates also serve as recognition sites for cells to communicate with each other, and as food sources for living systems. The difficulties involved in carrying out carbohydrate synthesis in a prebiotic environment parallel those found in making nanovehicles.

    Blind synthetic pathways lead to a host of products that are unwanted because they are unneeded; and, yet, acting as blindly as Louis Braille, nature somehow found the requisite five-carbon sugar. How?

    So far as life goes, as Teacher’s is the great Scotch, water is the great solvent. Nature depends on variations in pH and salinity. Organic synthesis is very hard to do in water. Highly oxygenated organic compounds are needed. The synthetic chemist must project the oxygenated groups out toward the water domain, and project the non-oxygenated groups in toward each other, thus generating a hydrophobic domain. It is very hard to do.

    By doing our nanocar organic synthesis in organic solvents rather than in water, we markedly lessened the difficulty; it is a luxury that nature did not (and does not) enjoy. Starting from scratch, she would have had to redesign her structures, discarding the inevitable false starts as they occurred. Whatever else she may have been doing in the prebiotic era, nature was not consulting the modern chemical literature.

    Any prebiotic system is destined, at least some of the time, to crash and burn. How does nature know how to stop, or why?

    As for the yields of chemical reactions, we design the reactions to minimize diastereomeric mixtures that can be nearly impossible to separate. We try our best to avoid the undesired diastereomers because their separation is too time-consuming and expensive. They waste a huge amount of starting material; they generate unwanted products. Enantiomeric separations are all the more difficult. We avoided that by building a system with only one motor which functioned regardless of whether it turned clockwise or counterclockwise.

    Nature has chosen a far harder route, using predominantly one enantiomer (homochiral) in a system with multiple stereogenic centers.

    Tough for us, easy for her, strange all around.

  4. 4
    johnnyb says:

    James Tour is always awesome. In everything he does – in the lab, in his public remarks, in his popular articles. I hope I get to meet him someday, because he is truly remarkable in his depth of knowledge and his ability to apply it.

  5. 5
    Belfast says:

    His formidable disdain for “simple” tricks is something else that convinces me he is right. His attitude dares you to contradict him.

  6. 6
    Dionisio says:

    BTW, where did the politely dissenting interlocutors go?
    Don’t they have any counterargument?
    They seem so loud in the philosophical discussion threads, but what about the scientific chats like this?
    Don’t they support science?
    I don’t think it can get more scientific than Dr. Tour’s open letter.

  7. 7
    Dionisio says:

    Dr. Tour wrote:

    The appearance of life on earth is a mystery. We are nowhere near solving this problem. The proposals offered thus far to explain life’s origin make no scientific sense.

    Beyond our planet, all the others that have been probed are lifeless, a result in accord with our chemical expectations. The laws of physics and chemistry’s Periodic Table are universal, suggesting that life based upon amino acids, nucleotides, saccharides and lipids is an anomaly. Life should not exist anywhere in our universe. Life should not even exist on the surface of the earth.

  8. 8
    Dionisio says:

    Any objections?
    🙂

  9. 9
    Dionisio says:

    DATCG,
    Thanks for the comments.

  10. 10
    Dionisio says:

    In embryonic development, the fascinating morphogenesis seems like a process where molecular signaling profiles –aka morphogen gradients– are formed following a complex choreography that guarantees the correct interpretation by the receiving cells, thus determining their individual fate. The localization/delocalization of the morphogen sources, their secretion rate, the type of morphogen, their different modes of transportation, their degradation rate, all that affects the resulting organs or tissues. Complex functionally specified informational complexity on steroids.

    When those of us who have spent years working on software development for complex engineering design projects, watch in awe the marvelous cellular and molecular choreographies orchestrated within the biological systems, we are humbled at the realization that the work we used to be so proud of suddenly looks like LEGO toys for toddlers.

  11. 11
    harry says:

    Technology is defined as the result of the application of scientific knowledge for a purpose. James Tour’s open letter to his colleagues makes clear that life is the result of the application of knowledge that modern science does not possess and may not ever be possessed by mere mortals. And if science ever does come to possess such knowledge will it then assert that life came about mindlessly and accidentally? Not if it is rational.

    The physical dimension of life is obviously technology that is light years beyond our own. It is the result of the application of whose scientific knowledge?

  12. 12
    daveS says:

    Dionisio,

    BTW, where did the politely dissenting interlocutors go?
    Don’t they have any counterargument?
    They seem so loud in the philosophical discussion threads, but what about the scientific chats like this?
    Don’t they support science?

    Assuming I count as a PDI, my answer is simply that I don’t know enough about the subject to comment. And while I would like to be less ignorant of biology, I have other interests that I like even more.

  13. 13
    Mung says:

    daveS:

    I have other interests that I like even more.

    Time travel isn’t possible.

  14. 14
    daveS says:

    Thanks for that useful information, Mung.

  15. 15
    es58 says:

    Dionisio@6:
    “They seem so loud in the philosophical discussion threads”

    which they use as a basis for accusation that this site isn’t really about the science

    “but what about the scientific chats like this?”

    Or like Gpuccio’s post about interesting proteins, while constantly complaining that ID people never do science.

  16. 16
    RodW says:

    Who specifically do you think should be contributing to this conversation?

  17. 17
    Axel says:

    ‘The physical dimension of life is obviously technology that is light years beyond our own. It is the result of the application of whose scientific knowledge?’ – Harry

    Why, the scientific knowledge of ‘nothing’, of course, Harry ; the nothing that created everything, including the digital code in DNA strands.

  18. 18
    Dionisio says:

    es58 @15:

    Exactly! Thanks.

  19. 19
    Dionisio says:

    Axel @17:

    That’s right. You’ve got it. Nothing caused everything. That’s an irrefutable scientific fact. Isn’t it? 🙂

  20. 20
    es58 says:

    Hi RodW!

    Please see gpuccio’s response to your request for clarification at post #298; thanks in advance for your reply!

    at this path:
    https://uncommondescent.com/intelligent-design/interesting-proteins-dna-binding-proteins-satb1-and-satb2/

    Thanks!

  21. 21
    Dionisio says:

    harry @11:

    …whose scientific knowledge?

    The knowledge behind creation is not scientific. It’s absolute knowledge and wisdom beyond our comprehension.

    We can’t even look at it. Just have a glimpse of it and imagine what is unimaginable.

    It’s so unbelievable, but it’s written in the Holy Scriptures so that those who have to believe it will do.

  22. 22
    Dionisio says:

    RodW @16:

    Who specifically do you think should be contributing to this conversation?

    Whoever is serious about it.
    You know what that means, don’t you?

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