Origin-of-Life, Artificial life, and Nano-bio-thingies

jenlake · September 20, 2022, 8:51pm

“a cosmos emerges from chaos by simple rules…starting from chaos…”

I’m reposting the Emergence thread for the short video that @Stephers put in because I think it highlights the ‘license’ being given to descriptions of LIFE –or proto-life—with the support of journals like Nature magazine. What I see in this simulated “primordial particle system” is an effort to envisage a quantum field, and how perhaps entangled particles might appear or behave based on ‘pure,’ uniform, and simple rules of motion—as they admit— but applicable to any manifestation of matter from a wavelength to a rock, in my opinion. Computer simulations with rules don’t have to use actual rules, if such exist. A demonstration of creating with ‘rules’ is shown in the video “The Art of Code” which also shows the workings of the Game of Life model underpinning the design of Primordial Partlicle Systems.

The Art of Code The Art of Code - Dylan Beattie - YouTube

”The Game of Life is not your typical computer game. It is a cellular automaton, and was invented by Cambridge mathematician John Conway.” Play John Conway’s Game of Life

The transition from nonlife-to-life (abiogenesis) is usually framed as the greatest scientific Question of All Time, and has hundreds of failed experiments to show how difficult Origin-of-Life science really is. An early 20th century example of failure which seems just silly is the claimed “discovery” of organismic radiobes in this video presentation of Luis Campo’s book. @leo Radium and the Secret of Life Radium and the Secret of Life with Luis Campos - YouTube

Professor Michael J. Behe, biochemist, illustrated the faulty line of origin-of-life evidence in his 1996 book Darwin’s Black Box (updated/reprinted 2006, which is the copy I have). Behe addresses not only the abiogenesis problem, but plainly and lucidly critiques the lack of evidence for evolutionary complexity—a situation unchanged and unresolved—supporting the Intelligent Design school of thought as a matter of ruling out the impossible, as Sherlock Holmes would say. Behe has a newer argument suggesting devolution as ‘helpful’ to survival, here in Behe’s 2018 book promo for Darwin Devolves (which I haven’t read) Michael Behe Is Returning With His Latest Book, Darwin Devolves - YouTube

Stepping aside somewhat, bypassing the problems of abiogenesis, are claims to creating life in the form of viruses— however, viruses are non-living and are therefore conflated with Life as organisms. They are thought to be the proto-life missing-links described in “RNA World” theories.

“The RNA world is a hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage. Alexander Rich first proposed the concept of the RNA world in 1962,[1] and Walter Gilbert coined the term in 1986.[2] Alternative chemical paths to life have been proposed,[3] and RNA-based life may not have been the first life to exist.[2][4] Even so, the evidence for an RNA world is strong enough that the hypothesis has gained wide acceptance.[1][5][6] The concurrent formation of all four RNA building blocks further strengthened the hypothesis.[7] Regardless of its plausibility in a prebiotic scenario, the RNA world can serve as a model system for studying the origin of life” RNA world - Wikipedia

—so for the time being I’m using the word ‘virus’ as a blanket term for the various nano-bio-thingies of biochemical makeup, just as research papers do without distinction or explanation. It’s a systemic ‘quirk’ in the jargon that exploits the reader’s perception and knowledge, professional readers included, which I am not, but just interested and persnickety. In no case whatsoever is a virus a lifeform or an organism .

“Viruses (Virus particles or virions) are usually units consisting of nucleic acids and coat proteins called capsids. Viroids consist only of RNA, i.e. they contain no protein at all**. Except for a few cases, viruses are not surrounded by a membrane. If present, the membrane around a virus particle – as seen in electron microscopic images – stems usually from the host cell** (see picture). Viruses have no energy metabolism of their own. Consequently, they cannot perform syntheses and are thus unable to replicate themselves… With plant viruses, the term specificity (or host-specificity) has a very narrow meaning, since no plant virus as such exists…” Botany online: Plant Viruses and Viroids
*

J.D. Bernal, who began his rise in science as a carbon chemist and came to supervise Rosalind Franklin’s ‘virus’ group at Univ London in the ‘50s, made on the following statement on ‘Life’:

Below is a repost from my blog, Making and Faking Viruses | Jennifer Lake's Blog

Eckard Wimmer, the elderly researcher who created poliovirus from scratch, makes this statement [edited as a distillation from the video]: …”My favorite virus is poliovirus… and in 2002 we published a paper that we had recreated the virus from information on the internet and no virus was necessary…. This was an enormous shock…[because] the parent of this virus…was the computer.”
––the effect was to halt the ‘millenium’ debate in the WHO over stopping the poliovaccine mandate and recharge the argument of ‘bioterror.’

(9 minute youtube)

“Originally trained as an organic chemist, Wimmer developed a deep understanding and fascination for viruses as replicating (living) biological entities as well as (non-living) aggregates of organic compounds, or, “as chemicals with a life cycle”.[2][3] After working on the structure of tRNAs and the structure of a plant RNA virus (satellite tobacco necrosis virus), Wimmer chose to study poliovirus in 1968. Poliovirus is the cause of the horrific disease poliomyelitis, which can cause irreversible flaccid paralysis and even death. Neither the molecular biology of poliovirus proliferation nor the mechanism of its pathogenesis was understood in the nineteen sixties… Using the nucleotide sequence of the genome deciphered in 1981, Wimmer followed up on the work published in 1991 by synthesizing chemically the genome in the form of double stranded DNA (“cDNA”), which was then transcribed enzymatically[16] into genome RNA and “booted to life” in the cell free system.[3] This work, published in 2002 by Cello, Paul and Wimmer, was the first test-tube synthesis of an organism in the absence of a natural template achieved outside living cells.[3] The poliovirus synthesis caught global attention, high praise, ridicule and fierce condemnation…” Eckard Wimmer - Wikipedia

jenlake · September 21, 2022, 3:00pm

Life From Clay theory, or Clay Crystal theory

“Chemist Graham Cairns-Smith has spent his entire scientific career pushing a simple, radical idea: life did not begin with fiddly organic molecules like DNA, but with simple crystals. It is now 50 years since Cairns-Smith [1931–2016] first put forward his ideas about the origin of life. Some scientists have ridiculed them; others have, cautiously or wholeheartedly, embraced them.” Clay crystals theory of life 50 years old – Uncommon Descent

“Alexander Graham Cairns-Smith FRSE (24 November 1931 – 26 August 2016) was an organic chemist and molecular biologist at the University of Glasgow.[1] He studied at the University of Edinburgh, where he gained a Ph.D. in Chemistry (1957).[2] He was most famous for his controversial 1985 book Seven Clues to the Origin of Life. The book popularized a hypothesis he began to develop in the mid-1960s—that self-replication of clay crystals in solution might provide a simple intermediate step between biologically inert matter and organic life. He [was] inspired [by] other ideas about chemical evolution, including the Miller–Urey experiment and the RNA World, all of which are hypotheses that have played important roles in attempts to understand the origin of life. Cairns-Smith also published on the evolution of consciousness, in Evolving the Mind (1996), favoring a role for quantum mechanics in human thought.[3] He died on 26 August 2016…” Graham Cairns-Smith - Wikipedia

“The Miller–Urey experiment [1] (or Miller experiment [2]) was a chemical experiment that simulated the conditions thought at the time (1952) to be present on the early, prebiotic Earth and tested the chemical origin of life under those conditions. The experiment at the time supported Alexander Oparin’s and J. B. S. Haldane’s hypothesis that putative conditions on the primitive Earth favored chemical reactions that synthesized more complex organic compounds from simpler inorganic precursors. Considered to be the classic experiment investigating abiogenesis, it was performed in 1952 by Stanley Miller, supervised by Harold Urey at the University of Chicago, and published the following year… In a 1996 interview, Stanley Miller recollected his lifelong experiments following his original work and stated: “Just turning on the spark in a basic pre-biotic experiment will yield 11 out of 20 amino acids.”[8]

The original experiment remained in 2017 under the care of Miller and Urey’s former student Jeffrey Bada, a professor at the UCSD, Scripps Institution of Oceanography.[9] As of 2013, the apparatus used to conduct the experiment was on display at the Denver Museum of Nature and Science. Miller–Urey experiment - Wikipedia

—in a further post, I’ll provide Michael Behe’s critique of Stanley Miller’s famous experiment.

Nanobiotechnology growing crystals in a cup

(image, How to grow a cup of quick crystal needles How to Grow a Cup of Quick Crystal Needles )

Clay Crystals, Origin of Life 1, video provided by wikipedia Clay Crystals ~ The Origin of Life 1 - YouTube ; mentions the 1960s idea of Alexander Graham Cairns-Smith and features the present work of Rebecca Schulman:

“Rebecca Schulman is an associate professor in the Department of Chemical and Biomolecular Engineering, with secondary appointments in chemistry and computer science. She is a member of the Institute for Nanobiotechnology, the Hopkins Extreme Materials Institute, the Chemistry-Biology Interface Program, the Center for Cell Dynamics, and the Laboratory for Computational Sensing and Robotics at Johns Hopkins University

“Schulman and her research group develop intelligent and adaptive biomolecular materials and nanostructures by combining ideas from materials science, biochemistry, circuit design, soft matter physics, and cell-free synthetic biology. DNA nanotechnology enables the design of complex molecular self-assembly processes involving hundreds of different species that produce structures with virtually arbitrary features at the nanoscale. Synthetic biology now allows the design of molecular “circuits” that integrate chemical information. Schulman’s group develops these techniques and uses them to produce dynamic biomaterials and smart sensors. These platform technologies can be applied to develop new assays and therapeutics for biologists, smart materials for cell culture and drug delivery, and self-assembling molecular circuits and autonomous soft micro-robots powered and controlled by biochemical reactions.

…”Schulman has developed new classes of soft materials called “hydrogels” that can change form in response to specific biomolecular sequences (or codes), paving the way for new classes of biomedical devices, robots, and materials.”

Rebecca Schulman - Johns Hopkins Whiting School of Engineering [edu MIT, Caltech, UCBerkeley]

Schulman works at Johns Hopkins HEMI, the Hopkins Extreme Materials Institute https://hemi.jhu.edu/home/about-hemi/

What Does Extreme Mean? (1 minute video) What Does Extreme Mean? - YouTube

jenlake · October 9, 2022, 7:10pm

[Darwin’s Black Box]

“The experiment that Stanley Miller reported in 1952 stunned the world. As Miller has readily explained, however, that experiment was not the first such one he tried. Earlier he had set up his apparatus in a somewhat different manner and found that some oil was formed, but no amino acids. Since he thought amino acids would be the most interesting chemicals to find, he jiggled the apparatus around in hopes of producing them. Of course, if conditions on the ancient earth actually resembled Miller’s unsuccessful attempts, then in reality no amino acids would have been produced.

“Moreover, joining many amino acids together to form a protein with a useful biological activity is a much more difficult chemical problem then forming amino acids in the first place. The major problem in hooking amino acids together is that, chemically, it involves the removal of a molecule of water for each amino acid joined to the growing protein chain. Conversely, the presence of water strongly inhibits amino acids from forming proteins. Because water is so abundant on the earth, and because amino acids dissolve readily in water, origin-of-life researchers have been forced to propose unusual scenarios to get around the water problem. For example, a scientist named Sidney Fox proposed that perhaps some amino acids got washed up from the primordial ocean onto a very hot surface, such as the rim of an active volcano. There, the story goes, they would be heated above the boiling point of water; with the water gone, the amino acids could join together. Unfortunately, other workers had earlier shown that heating dry amino acids gives a smelly dark brown tar, but no detectable proteins. Fox, however, demonstrated that if an extra-large protein of one of three different amino acids is added to the mix of purified amino acids and heated in a laboratory oven, then the amino acids do join. But even then they do not join to give proteins—the structure they form is chemically different. So Fox and collaborators called the structures ‘proteinoids,’ then went on to show that the proteinoids had some interesting properties, including modest catalytic abilities that were reminiscent of real proteins.

“The scientific community has remained deeply skeptical of these experiments. As with our imaginary baker, a heavy odor of investigator involvement hangs over proteinoids…” –pp169-170, Darwin’s Black Box, by Michael J. Behe

AMcD · October 9, 2022, 9:22pm

I had never heard of this campus of Columbia University. It is across the Hudson on the Palisades - the former summer estate of the board chair of JP Morgan back in the day. Has been set aside as an earth science / climate science campus since 1948 - atoms for peace era. Was looking for a back-up site visit as it turns out Tuxedo Park / Loomis Labs site is a no-go due to 24/7 gated security.

In any event this seems interesting in light of your line of thinking - origins of live. Deep ocean seismic activity, bio-geo chemistry.

Allan Bé, micropaleontologist who worked at the lab

AMcD · October 10, 2022, 12:26am

Who in god’s name regulates this shit. Is it already outside the lab?

Stephers · October 10, 2022, 12:50am

@AMcD @jenlake I bumped up against Schulman’s entity today (I can’t recall at the moment why it popped up for me):

A few of the partners are not labs . . . This stuff could be in play . . .

https://hemi.jhu.edu/home/about-hemi/partners/

AMcD · October 10, 2022, 1:03am

Pretty intimidating list - I see Drexel and Rutgers among them.

Stephers · October 10, 2022, 5:33pm

@jenlake

I get the sense that the following two videos (clips from the same interview with some overlap between the two) may relate well here . . . Please forgive me if they do not, or if you have already covered this material elsewhere. Also, I hope you will excuse my tardiness in exploring your post and thread here. Life has thrown me many curve balls of late. I am doing my best to play some catch up today.

Only 6 minutes long:

8 minutes long (a bit redundant from clip #1, but I think it is helpful):

https://www.edge.org/memberbio/stuart_a_kauffman

STUART A. KAUFFMAN is a professor at the University of Calgary with a shared appointment between biological sciences and physics and astronomy. He is also the leader of the Institute for Biocomplexity and Informatics (IBI) which conducts leading-edge interdisciplinary research in systems biology.

Dr. Kauffman is also an emeritus professor of biochemistry at the University of Pennsylvania, a MacArthur Fellow and an external professor at the Santa Fe Institute.

Originally a medical doctor, Dr. Kauffman’s primary work has been as a theoretical biologist studying the origin of life and molecular organization. Thirty-five years ago, he developed the Kauffman models, which are random networks exhibiting a kind of self-organization that he terms “order for free.”

Dr. Kauffman was the founding general partner and chief scientific officer of The Bios Group, a company (acquired in 2003 by NuTech Solutions) that applies the science of complexity to business management problems. He is the author of The Origins of Order, At Home in the Universe: The Search for the Laws of Self-Organization, Investigations and Reinventing the Sacred: A New View of Science, Reason, and Religion.

Note: I purchased Kauffman’s Reinventing the Sacred back in 2020. If you are interested, and feel it is appropriate for this thread, I am happy to report back with a brief synopsis on it (after I re-read it). If not, no worries.

Some supporting/supplemental material (related to Kauffman):

He served as the Chairman of the Technical Committee on Evolutionary Computation and also as the Executive Vice-President of the Institute of Electrical and Electronics Engineers Neural Network Council. He was the general chair of the First IEEE Congress on Evolutionary Computation held in Orlando in June 1994.[8]

jenlake · October 11, 2022, 1:07pm

@Stephers You have no need to apologize or seek excuses for anything, dear lady, as a principal workhorse on this forum. I posted it initially to explore some valuable details—like the scientific experimental record– which apply to subjects already raised. Your contributions throughout are immense.

Kauffman, though, is outside my scope here. His opinions are familiar to me, enough to regard his presentations as tortured tautology. “Radical Emergence,” as I see it, is a pseudoreligious scientismic substitute for Intelligent Design because of the ‘fundamental’ baggage associated with Creationism—something to be feared being his point. Intelligent Design is a term used by scientists, not believers who are fine with ‘God’, so ultimately ‘Designer’ is a wrong idea. There are no ‘designers’ in creation, if I get his drift. It justifies tinkering (if you get mine). Anyway, persona-wise, he’s not the guy I care to hear it from nor have the Sacred Reinvented by-- If you like, give this video about 10 minutes and it will set up the scope of complications regarding Stuart Kauffman (1:08 hr) lecture, 2016: Stuart Kauffman | Full Lecture | KLI - YouTube

On the other hand, here’s some background on Kauffman’s interviewer in the clips:

Robert Lawrence Kuhn [1] (born November 6, 1944) is a public intellectual, international corporate strategist and investment banker. He has a doctorate in neuroscience and is the author and editor of over 25 books. He is a recipient of the China Reform Friendship Medal, China’s highest award; he is a long-time adviser to China’s leaders and the Chinese government, to multinational corporations on China strategies and transactions, and is a frequent commentator on the politics, economics, business, finance, philosophy and science of China. He is a columnist for China Daily and South China Morning Post and appears on the BBC , CNN , China Central Television (CCTV), Bloomberg and other major media. Kuhn is the creator, writer and host of the show Closer to China with R.L. Kuhn[2] and The Watcher[3] and Xi’s Deep Message[4] commentaries. Kuhn is the creator, writer and host of the public television series Closer to Truth , which presents scientists and philosophers discussing fundamental issues (cosmos, consciousness, philosophy/religion).[5] His presentation, Asking Ultimate Questions,[6] is the foundation of Closer To Truth . Kuhn received a bachelor’s degree in human biology from Johns Hopkins University (Phi Beta Kappa) in 1964, a PhD in anatomy and brain research from the University of California, Los Angeles’ Brain Research Institute in 1968 and a Master of Science in management as a Sloan fellow from the MIT Sloan School of Management in 1980

Kuhn appears to have made a fortune integrating middle market U.S. companies into China and lauding the Chinese CCP ‘reform’ (and world-directed ‘friendship’) in doing so. His books about China’s leadership are criticized thusly: In Forbes , Gordon G. Chang wrote that How China’s Leaders Think: the Inside Story of China’s Reform and What This Means for the Future was difficult to even read to completion, saying, “Kuhn stated–on the fifth page of the introduction–that Chinese leaders are not authoritarians. That’s demonstrably untrue, but I struggled on for another hundred pages before finally realizing there was no point in reading a work of propaganda.”

Geneva Companies

[Sept 2000]—“Geneva Group Inc., a broker for sales of small and mid-size companies, agreed Wednesday to be acquired by Citigroup Inc. for a reported $200 million in stock. Geneva, based in Irvine [CA] since its founding as a mergers-and-acquisition firm in 1977, will become a separately operated part of Citigroup’s Salomon Smith Barney, a major provider of services for wealthy individuals. Having helped thousands of mostly family-owned businesses sell themselves to larger concerns, Geneva now becomes part of a consolidation trend itself, this one in financial services. The deal with the New York financial services giant is expected to close by year-end… Neither Geneva nor Citigroup disclosed financial terms. Geneva has been owned for nine years by Troob, Chief Operating Officer Robert Kuhn and Loeb Holdings, a New York banking company… Since Troob and his partners bought Geneva from Chemical Bank, the staff has grown from about 200 to 350, half of whom work in Irvine. Troob said he and Kuhn will stay on for at least three years as Geneva accelerates its growth through Salomon.” Citigroup to Acquire Irvine-Based Geneva Group for $200 Million

—anytime “Kuhn” and “Loeb” appear close together in the same sentence, I pay attention. “UCLA” and “neuroscience” too.

Stephers · October 12, 2022, 4:40pm

@jenlake

Excellent breakdown (takedown) of these individuals (and sincere gratitude for your sentiments).

My main concern/takeaway is that when reading (re-reading my highlighted markings) Kauffman’s Reinventing the Sacred, his theory of the emergence of collectively autocatalytic sets (https://www.researchgate.net/publication/359728646_Emergence_of_Autocatalytic_Sets_in_a_Simple_Model_of_Technological_Evolution) seems to be precisely depicting Laszlo’s World Homeostat System (WHS) – constructed of auto-catalytic cycles/hypercycles/cross-catalytic cycles – as seen on p. 25 – see here (c/o @AMcD):

Albeit tangential . . . I recently stumbled upon Nahum Goldmann’s Spirit of Militarism – from 1915 – which may tie into this reinventing (tinkering) concept (also directly paralleling – yet preceding – Reiser’s World Sensorium/Global Brain in 1946):

p. 37-39

The meaning and the historical mission of our time can be summed up in one: its task is to reorganize cultural mankind, to put a new social system in place of the one that has prevailed until now. One has the same in mind when one - as usual - calls our time one of transition. Transitional periods are precisely those that stand between a social order that has prevailed up to now and a new one that is to be established, and have the task of replacing the old one with the new one.

All adjustments and reordering now consist of two things: in the destruction of the old order and the reconstruction of the new. First of all, all border posts, regulatory barriers and labels of the previous system must be removed and all elements of the system that are to be reorganized must be disassembled as such, on an equal footing with one another.

Only then can the second, the reorganization of these elements, be started.

Thus, the first task of our time is destruction: all social stratifications and social formations created by the old system must be destroyed, individuals must be torn out of their ancestral milieus; no tradition may be considered sacred any longer; old age is regarded only as a sign of illness; the slogan is: what was, must go. The forces that carry out this negative task of our time are: in the economic-social field capitalism, in the political-spiritual field democracy. We all know how much they have already achieved, but we also know that their work is not yet completely finished. Capitalism is still fighting against the forms of the old, traditional economy, democracy is still fighting a hot battle against all forces of reaction. The militaristic spirit will complete the work. Its principle of uniformization will carry out the negative task of the time completely: when all members of our cultural circle are uniformed as soldiers of our cultural system, this one task will be solved.

But only then the other, greater and more difficult task arises: the construction of the new order. The links, which are now torn out of their old roots and stratifications and lie around disorderly, anarchically, must be closed into new formations and categories; if in the solution of the first task all were at first declared equal, now men must again be divided and differentiated: a new pyramidal, hierarchical system must be established. Capitalism also tried to solve this task; we know with what misfortune. It made the fundamental division into rulers and ruled according to wrong points of view: according to those of wealth, of capitalist power. This second task, too, can only be solved by the militaristic spirit by virtue of its other great guiding principle of subordination. He will bring the true aristocratic principle to rule: Let those who can rule, rule.

It is not origin and name, not fortune and power that decide, but the talent to rule. In an army organized entirely according to the demands of militarism, there would be only one criterion for promotion: ability to command and lead. In the society that the militaristic spirit will rebuild, the same point of view will prevail: whoever is capable of ruling will rule.

But when both these things have been accomplished, the old system smashed and the new order established, then a third thing has to be done, without which this whole work would be incomplete, through which only the new order will prove to be superior to the old, to be the higher one: it will be necessary now to form the new society into a uniform, closed organism. Why was it necessary to destroy the old social system and replace it with a new one? Because it had lost its organic unity over time, because its members and organs began to disintegrate and internal anarchy set in. The new social system will not be completed until it becomes an organism. We all know today that this task is the greatest and most important; we only use to call it differently: we call it the solution of the social question. The social question - what else is it than the state of inner social anarchy? The fact that the few possess too much and more and more, and the majority too little and less and less, that production and consumption do not balance each other harmoniously, that agriculture and industry do not complement each other, and all the other great partial problems of the total complex of the social question, all these are only expressions of the inner anarchy and disorganization. What force can overcome this anarchy? Only one: the idea of organization, of organism; the very idea which we have recognized as the highest, supreme idea of the militaristic spirit. From this it follows of itself: Only the militaristic spirit can accomplish this last and greatest task of our time, the solution of the social question, or what is the same, the organization of the new social system. That it alone is called to this is today already general knowledge or at least general suspicion.