Origin Of Life

James Tour on what is wrong with origin of life research – at Inference Review

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It’s an impossible exercise if you leave out design:

The same shortcomings and omissions that plague current OOL research can also be found in the paper under review. Indeed, these issues are so routinely ignored by researchers that the field appears to have become numbed to their absence from the literature. OOL researchers are prepared to assume that an ever-increasing list of obstacles were overcome on the prebiotic earth, but do not consider these hurdles as problems to be solved in their own work. The following five shortcomings in the research presented by Krishnamurthy et al., are emblematic of broader issues that need to be addressed.

James Tour, “Much Ado About Nothing” at Inference Review (January 2022)

23 Replies to “James Tour on what is wrong with origin of life research – at Inference Review

  1. 1
    Joe Schooner says:

    Just to let you know that the link in the first sentence, “ It’s an impossible exercise if you leave out design:”, is a dead link.

  2. 2
    bornagain77 says:

    Of related interest, Dr. Tour put his entire lecture series on the impossibility of abiogenesis in this one 9 hour video:

    Abiogenesis Theory and Professor Dave Explains ULTRA Pack! Free Course from Rice University Chemist – video
    https://www.youtube.com/watch?v=WKLgQzWhO4Q
    0:00 Reasons for this Series
    26:39 Episode 1 – Introduction to Abiogenesis
    50:45 Epsode 2 – Primordial Soup
    1:03:53 Episode 3 – Hype
    1:53:25 Episode 4 – Homochirality
    2:19:51 Episode 5 – Carbohydrates
    3:05:17 Episode 6 – The Building Blocks of the Building Blocks
    3:22:20 Episode 7 – Peptides
    4:14:08 Episode 8 – Nucleotides, DNA, and RNA
    5:05:57 Episode 9 – Intermediate Summary
    5:15:37 Episode 10 – Lipids and the Cell Membrane
    6:01:00 Episode 11 – Chiral-induced Spin Selectivity
    6:33:12 Episode 12.1 – Cell Construction and the Assembly Problem
    7:46:54 Episode 12.2 – Cell Construction and the Assembly Problem
    8:34:55 Episode 13 – Summary & Projections

    Become a more educated Youtube viewer as Dr. James Tour tackles the problems of the theory of abiogenesis. This is the previously published 14 part series combined in one massive course.

    Or for a short “CliffNotes” version you can just watch these short animated videos:

    August 2021 – The Basic Building Blocks & the Origin of Life (Long Story Short, Ep. 4) – video
    https://www.youtube.com/watch?v=MFtnwriQRi8

    Nov. 2021 – Challenge to Origin of Life: Biopolymers (Long Story Short, Ep. 5) – video
    https://www.youtube.com/watch?v=Qxm3yVTcZ4E

    Long Story Short — A Strikingly Unnatural Property of Biopolymers
    Rob Stadler December 1, 2021
    Excerpt: The essential presence of long, homochiral, homolinked biopolymers in a water solution, for all known life forms, is astoundingly unnatural. It has been seventy years since the Miller-Urey experiment produced amino acids. At that time, we didn’t even know the structure of DNA. Since then, we have learned a great deal about the extremely unnatural properties of biopolymers, which explains why almost no discernable progress has been made toward producing biopolymers via prebiotic processes in laboratories.
    https://evolutionnews.org/2021/12/long-story-short-a-strikingly-unnatural-property-of-biopolymers/

  3. 3
    jerry says:

    Is anything that uses DNA alone destined to fail? Something additional organizes all this stuff into an entity that is constantly on the move. Life is never stationary. Something is causing all the proteins to move about to the right places.

    Maybe a study of Apoptosis will give a clue?

    dead link

    Essentially the same link. Both point to same article.

  4. 4
    ram says:

    Poll: what do you hope to gain by your participation on this site?

    Thanks

    –Ram

  5. 5
    anthropic says:

    What do I hope to gain from this site?

    Fame, fortune, and female adulation. Hasn’t happened yet, but I’m betting it’s just a matter of time.

  6. 6
    zweston says:

    I would like to know Ram’s answer to his question, and also what he thinks the answer is for everyone else.

  7. 7
    jerry says:

    what do you hope to gain by your participation on this site?

    Knowledge.

    First monitoring of this site in 2005 when Dembski was moderator. Great site for learning new ideas about science and thinking. Often test ideas that appear elsewhere to see what reaction/short comings are.

  8. 8
    Fasteddious says:

    Ram @4: I gain insights and updates into ID and related topics. I also gain insights into how non-ID people think about ID and related topics. I also try to sharpen my posting and commenting skills – or lack of same. I can do all these things at this ID-friendly site.

  9. 9
    Joe Schooner says:

    Poll: what do you hope to gain by your participation on this site?

    An interesting, honest and non-confrontational discussion with people who disagree with my views. So far, my goals have not been met.

  10. 10
    Belfast says:

    Sorry to hear that, Joe.
    Any idea how long you will stay before you give it up as a bad job?

  11. 11
    Joe Schooner says:

    Sorry to hear that, Joe.
    Any idea how long you will stay before you give it up as a bad job?

    Could be a while. There have been a few people who are capable of a good debate. As long as they stick around, I will as well.

  12. 12
    Belfast says:

    “ So far, my goals have not been met.”
    “ There have been a few people who are capable of a good debate.”

    That sound mighty like the opening of a ‘Glenties,’ Joe.
    ‘Glenties:- Series of small steps by which someone who has made a tactical error in a conversation moves from complete disagreement to wholehearted agreement.’

  13. 13
    Joe Schooner says:

    That sound mighty like the opening of a ‘Glenties,’ Joe.

    No. So far, most of the people who give a good and fair debate are the ones who’s views I generally share. The only exceptions, so far, have been WJM and EDTA. I am hopeful for a couple more.

  14. 14
    jerry says:

    So far, most of the people who give a good and fair debate are the ones who’s views I generally share

    Not interested in debate because I find it rarely adds anything here. That doesn’t mean disagreeing is out.

    But I will put propositions out to see if it generates anything that contradicts it. Not to debate it but to learn if anything is wrong with idea.

    For example, above I suggested that apoptosis may have a clue as to what the process of life is about. Have no idea if this will or will not be useful. But obviously so far neither does anyone else here.

    Have recommended Stephen Blume as one of the best people with insight into Evolution/life issue. Only one other person since I first recommended him has bothered to comment on his ideas.

    Aside: Kf is one of the best sources of interesting ideas on this site. That doesn’t mean I always agree with him but he certainly is knowledgeable. I actually believe most of his long and convoluted posts are counterproductive but not because they are wrong. (hope this does not start a long back and forth over his ideas)

    PS – William Briggs is much better at logic and truth then anyone I have seen.

  15. 15
    johnnyb says:

    Just to note – I’ve gained many friends and insights on this board, as well as got the opportunity to be sharpened and improved by feedback and criticism.

  16. 16
    Truth Will Set You Free says:

    BA77@2: Thank you for sharing that.

    Ram@4: I visit UD to stay current on all matters involving the intelligent design movement. This site is a blessing!

  17. 17
    bornagain77 says:

    Darwin’s “Death as the Creator”

    How Has Darwinism Negatively Impacted Society? – John G. West – January 11, 2022
    Excerpt: Death as the Creator
    A third big idea fueled by Darwin’s theory is that the engine of progress in the history of life is mass death. Instead of believing that the remarkable features of humans and other living things reflect the intelligent design of a master artist, Darwin portrayed death and destruction as our ultimate creator. As he wrote at the end of his most famous work: “Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of the higher animals, directly follows.”13
    https://evolutionnews.org/2022/01/how-has-darwinism-negatively-impacted-society/

    And in unison Hitler, Mao, and Stalin all said amen.

    Chairman MAO: Genocide Master (Black Book of Communism)
    “…Many scholars and commentators have referenced my total of 174,000,000 for the democide (genocide and mass murder) of the last century. I’m now trying to get word out that I’ve had to make a major revision in my total due to two books. I’m now convinced that Stalin exceeded Hitler in monstrous evil, and Mao beat out Stalin….”
    http://wadias.in/site/arzan/bl.....de-master/

    Hitler, Marx, Lenin, Stalin, Mao – quotes – Foundational Darwinian influence in their political ideologies
    July 2020
    https://uncommondescent.com/intelligent-design/michael-egnor-on-the-relationship-between-darwinism-and-totalitarianism/#comment-707831

    Verse:

    John 10:10
    The thief cometh not but to steal and to kill and to destroy. I am come that they might have life, and that they might have it more abundantly.

  18. 18
    martin_r says:

    ok guys, lets get back to the topic…

    some of you may already know, that i have a degree in mechanical engineering,
    so i am not very qualified to talk about chemistry… but

    … i am following Dr. Tour’s lectures from the beginning, since he appeared on Youtube for the first time with his “The origin of life: an inside story”-lecture (2016)

    I watched all his online lectures so far, including his latest 13 parts series on OOL issues.

    Despite i am not a chemist, one thing is pretty easy to understand even for a mechanical engineer…actually, anybody can understand it, even Seversky, Chuck, JVL & Co.

    IF nature wants to create those basic building blocks of life, AMONG MANY OTHER LUCKY ACCIDENTS IN THE RIGHT ORDER, one very important thing is TO HAVE A NATURAL ENVIROMENT WITH HIGH CONCENTRATIONS OF ‘NATURAL’ CHEMICALS…

    The problem is, nowhere on Earth is such a place… that’s why Darwinian OOL-researchers cheat with purchased chemicals to achieve such a high/required concentration …

    From Dr. Tour’s article:

    OOL research is often beset with concentration problems. How might starting materials become available in sufficiently high yields and undiluted by the oceans, for example, so that the chemistry can occur at any usable rate? How can synthesis outpace decomposition at ultralow concentrations? Krishnamurthy et al. claim to have solved this problem by using an ultrahigh concentration paste of the 2?-deoxynucleosides. This is a convenient way to resolve the issue—in effect, solving the high dilution problem by assuming that there were so many homochiral 2?-deoxyribonucleosides present that they could form agglomerates too concentrated to dissolve. And where do the researchers suggest finding such a high concentration of nucleosides in the prebiotic environment? This question is left unanswered; it is a problem for the early earth, but not for the modern researcher . Assuming that, by some stroke of good fortune, high concentrations of homochiral 2?-deoxyribonucleosides were found in a paste, this would still not be enough.

  19. 19
    bornagain77 says:

    Hi Martin_r, you stated,

    “some of you may already know, that i have a degree in mechanical engineering,
    so i am not very qualified to talk about chemistry… but”

    I happened to listen to a podcast last night that you may be very interested in. It turns out that engineers, via some of their, (fairly technical), models for understanding engineered systems, have a lot to say about biology, particularly about correctly understanding biological adaptations, (directed mutations, etc..).

    Engineers Crash the Evolution Party, Rethink Biological Variation
    https://idthefuture.com/1549/
    On today’s ID the Future, physicist and engineer Brian Miller sits down with host Casey Luskin to survey exciting developments in intelligent design research that are driven by an engineering model for understanding and studying variations in species. ID researchers are pushing this work, but so too are systems biology researchers outside the intelligent design community. Tune in to hear Miller and Luskin discuss everything from fruit flies, finch beaks, and stickleback fish to mutational hotspots, phenotypic plasticity, and the gravity well model of biological adaptation.

    Further notes:

    How the Burgeoning Field of Systems Biology Supports Intelligent Design – July 2014
    Excerpt: Snoke lists various features in biology that have been found to function like goal-directed, top-down engineered systems:
    *”Negative feedback for stable operation.”
    *”Frequency filtering” for extracting a signal from a noisy system.
    *Control and signaling to induce a response.
    *”Information storage” where information is stored for later use. In fact, Snoke observes:
    “This paradigm [of systems biology] is advancing the view that biology is essentially an information science with information operating on multiple hierarchical levels and in complex networks [13]. ”
    *”Timing and synchronization,” where organisms maintain clocks to ensure that different processes and events happen in the right order.
    *”Addressing,” where signaling molecules are tagged with an address to help them arrive at their intended target.
    *”Hierarchies of function,” where organisms maintain clocks to ensure that cellular processes and events happen at the right times and in the right order.
    *”Redundancy,” as organisms contain backup systems or “fail-safes” if primary essential systems fail.
    *”Adaptation,” where organisms are pre-engineered to be able to undergo small-scale adaptations to their environments. As Snoke explains, “These systems use randomization controlled by supersystems, just as the immune system uses randomization in a very controlled way,” and “Only part of the system is allowed to vary randomly, while the rest is highly conserved.”,,,
    Snoke observes that systems biology assumes that biological features are optimized, meaning, in part, that “just about everything in the cell does indeed have a role, i.e., that there is very little ‘junk.'” He explains, “Some systems biologists go further than just assuming that every little thing has a purpose. Some argue that each item is fulfilling its purpose as well as is physically possible,” and quotes additional authorities who assume that biological systems are optimized.,,,
    http://www.evolutionnews.org/2.....87871.html

    Systems Biology as a Research Program for Intelligent Design – David Snoke – 2014
    Abstract: Opponents of the intelligent design (ID) approach to biology have sometimes argued that the ID perspective discourages scientific investigation. To the contrary, it can be argued that the most productive new paradigm in systems biology is actually much more compatible with a belief in the intelligent design of life than with a belief in neo-Darwinian evolution. This new paradigm in system biology, which has arisen in the past ten years or so, analyzes living systems in terms of systems engineering concepts such as design, information processing, optimization, and other explicitly teleological concepts. This new paradigm offers a successful, quantitative, predictive theory for biology.,,
    http://bio-complexity.org/ojs/.....O-C.2014.3

    Can biological complexity be reverse engineered? – Sara Green – 2015
    Excerpt: “But many biologists agree that there is a connection between the robustness of biological networks and their non-random connectivity distribution and hierarchical structure (Steinacher & Soyer, 2012). Other examples of design principles are bi-stable switches (Tyson et al. 2003) and overabundant sub-circuits in gene regulatory networks, called network motifs (Alon, 2007a, see below). To some researchers, such findings provide optimism that there is simplicity in the apparent complexity of biological systems (Csete and Doyle, 2002; Alon, 2007c).
    The quest for design principles reflects a hope that key properties of biological systems can be understood without knowing all the lower-level causal details. This is not only a point about practical convenience but also about the relevant level of analysis. The cancer biologist Lazebnik (2002) provocatively compared biomedical research strategies to the attempt to fix a radio by atomizing the system into component parts and studying these in isolation. If the malfunction of the system is connected to the orchestrated organization of parts and processes, searching for broken molecular components is bound to fail. Lazebnik therefore proposes an engineering approach to investigate how the components are wired together as a functional whole.”
    http://philsci-archive.pitt.ed.....neered.pdf

  20. 20
    Lieutenant Commander Data says:

    Martin_r
    ok guys, lets get back to the topic…

    some of you may already know, that i have a degree in mechanical engineering,
    so i am not very qualified to talk about chemistry… but

    but anything in chemistry of life is about engineering. 🙂

  21. 21
    martin_r says:

    BA77
    let me add to your list the following

    from a Darwinian paper!!!!

    Do cells use passwords in cell-state transitions? Is cell signaling sometimes encrypted?

    Organisms must maintain proper regulation including defense and healing. Life-threatening problems may be caused by pathogens or by a multicellular organism’s own cells through cancer or autoimmune disorders. Life evolved solutions to these problems that can be conceptualized through the lens of information security, which is a well-developed field in computer science. Here I argue that taking an information security view of cells is not merely semantics, but useful to explain features of signaling, regulation, and defense. An information security perspective also offers a conduit for cross-fertilization of advanced ideas from computer science and the potential for biology to inform computer science. First, I consider whether cells use passwords, i.e., initiation sequences that are required for subsequent signals to have effects, by analyzing the concept of pioneer transcription factors in chromatin regulation and cellular reprogramming. Second, I consider whether cells may encrypt signal transduction cascades. Encryption could benefit cells by making it more difficult for pathogens or oncogenes to hijack cell networks. By using numerous molecules, cells may gain a security advantage in particular against viruses, whose genome sizes are typically under selection pressure. I provide a simple conceptual argument for how cells may perform encryption through posttranslational modifications, complex formation, and chromatin accessibility. I invoke information theory to provide a criterion of an entropy spike to assess whether a signaling cascade has encryption-like features. I discuss how the frequently invoked concept of context dependency may oversimplify more advanced features of cell signaling networks, such as encryption. Therefore, by considering that biochemical networks may be even more complex than commonly realized we may be better able to understand defenses against pathogens and pathologies.

    https://pubmed.ncbi.nlm.nih.gov/31175621/

    P.S.1: How can a rational well educated person even suggest that blind unguided process encrypts something in order to protect it ? What is wrong with 21st century Darwinists ?

    P.S.2: by the way, i said i am not qualified to talk about chemistry, but as an engineer, i am qualified to talk about design in biology, so i can only agree with the list you posted above …

  22. 22
    martin_r says:

    LCD

    what i meant was, i am not qualified to talk about particular chemical reactions, whether they will occur or not …

  23. 23
    bornagain77 says:

    Thanks Martin_r,

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