8/2/2024

https://www.washingtonpost.com/obituaries/2024/07/31/robin-warren-nobel-ulcers-dies/

7/25/2024

https://www.cnn.com/2024/07/22/science/dark-oxygen-discovery-deep-sea-mining/index.html

3/11/2024

The reason I decided to write Freeman Dyson in 2008 or 9 was because he mentioned something about the rivalry between academics and the business class in the British class system. I found it interesting at the time, and not entirely unlike the situation in the U.S. However, I think today the reverse is true- it's not just business and academia in rivalries, but politics and business has moved into academia, and academia has moved into business and other sectors (Gale Boetticher in Breaking Bad quoting Walt Whitman:

"When I heard the learn'd astronomer;

When the proofs, the figures, were ranged in columns before me;

When I was shown the charts and the diagrams, to add, divide, and measure them;

When I, sitting, heard the astronomer, where he lectured with much applause in the lecture-room,

How soon, unaccountable, I became tired and sick;

Till rising and gliding out, I wander'd off by myself,

In the mystical moist night-air, and from time to time,

Look'd up in perfect silence at the stars.")

From "Snobbery and the class system" https://www.webofstories.com/play/freeman.dyson/18 https://www.youtube.com/watch?v=AKu5-05VCxw :

"TRANSCRIPT: I was really very lucky. Of course I hated the class, well, the snobbery of the place. It was a very, very intensely intellectual place and there was in an intense intellectual snobbery there and a social snobbery as well. I mean we were all essentially middle class kids and we looked down not only at the working class, we looked down at the business class as well. In England the antagonism has always been very strong between the intellectual middle class and the business middle class. That's one of the causes of social problems in England. It's why Margaret Thatcher was always so down on the universities, because she came from the business middle class. But in any case, so we were in this very narrow intellectually snobbish surroundings, and surrounded with high medieval walls, literally, and so I always felt an intense hatred for the system, although I loved a lot of the people and I loved the life in the college, but nevertheless I had a very bad conscience about it and wanted to tear it down and let in some daylight from outside. So I always had this very ambivalent feeling about it. I hated a great deal of this sort of "old school tie" atmosphere that surrounded it, and I found only about fifty years later I've started to lose this hatred for it because, I mean, I've just become mellowed with time." (emphasis added)

Another transcript can be found here: https://www.youtube.com/watch?v=DzC1IRYN_Ps :

"Freeman Dyson (1923-2020), who was born in England, moved to Cornell University after graduating from Cambridge University with a BA in Mathematics. He subsequently became a professor and worked on nuclear reactors, solid state physics, ferromagnetism, astrophysics and biology. He published several books and, among other honours, was awarded the Heineman Prize and the Royal Society's Hughes Medal. [Listener: Sam Schweber; date recorded: 1998]

(Youtube's Autoplay skipped to the next video, and I pasted a different, but related transcript from the same interview. Thanks to Autoplay- it can be hard to keep track of the videos in my Chrome Tabs. Its also a waste of bandwidth- should be disabled by default)

In one of the handful of emails I wrote to Carl Woese in the late 00's, one* of his replies started with "Thank you for your synthesis."

It should be observed that in today's hyper-partisan, post-truth world, dialectic is rare, and online interactions are often eristic. It is important not to view everything as critical or negative, and not just a thesis, but a synthesis. Revisionism often tries to selectively filter out what is fact.

Today, the word "synthesis" is often correlated with biochemistry or the pharmaceutical industry. The primary definition, historically, viewed synthesis primarily of ideas, theories, and systems, rather than reductionist compounds. Woese railed against fundamental reductionism in "A New Biology for a New Century", 2004.

"Dictionary Definitions from Oxford Languages · Learn more syn·the·sis /ˈsinTHəsəs/ noun

1. the combination of ideas to form a theory or system. "the synthesis of intellect and emotion in his work"

2. the production of chemical compounds by reaction from simpler materials. "the synthesis of methanol from carbon monoxide and hydrogen"

*In another one of his replies, I recall he employed the use of anastrophe:

I do not recall if he was consciously channelling an inner Yoda, but there was something funny about the way he wrote it (and his Yoda-like sagacity)

2/21/2024

Freeman Dyson and Entropy https://newsteve.substack.com/p/the-sunny-side-of-entropy

1/8/2024

Topological scaling laws and statistical mechanics of evolution (12/20/2023) https://www.youtube.com/watch?v=l11VDjUXEJI

11/3/2023

https://newsteve.substack.com/p/most-ideas-come-from-previous-ideas An article originally written about Steve Jobs but with tangents into Biology's technological advancements as analogized.

10/30/2023

From A New Biology for a New Century (2004, link below)

"One needs look no further than the “doctrine of common descent” to find a candidate; common descent is something that essentially all modern biologists have taken for granted. Where did this doctrine come from? Why, Darwin, of course: didn't he say that all life stems from a single primordial form? Indeed he did. But look at the context and way in which Darwin addresses the issue in Origin of Species. Herein we read (12): “… [we may infer] that all the organic beings which have ever lived on this earth may be descended from some one primordial form. But this inference is chiefly grounded on analogy and it is immaterial whether or not it be accepted. No doubt it is possible, as Mr. G. H. Lewes has urged, that at the first commencement of life many different forms were evolved; but if so we may conclude that only a very few have left modified descendants.”

That doesn't sound like doctrine to me! Darwin was merely speculating about ultimate origins—a great gap in our knowledge and something to be defined and resolved when the time came. For Darwin, common descent was an open question, an invitation to discussion. What elevated common descent to doctrinal status almost certainly was the much later discovery of the universality of biochemistry, which was seemingly impossible to explain otherwise (49). But that was before horizontal gene transfer (HGT), which could offer an alternative explanation for the universality of biochemistry, was recognized as a major part of the evolutionary dynamic."

This careful analysis by Woese shows that Darwin was only standing on the shoulders of his forebears, and that Woese could see further than Darwin, because he was acting on his tip, like his periscope. I didn't say standing on Darwin's shoulders, even though he was, because Darwin built a submarine, and in the 20th century, Sanger sequencing is more analogous to a periscope or a spot light designed for Mariana Trench PSI outside the DeepSea Challenger- a fine "optical" instrument, rather than a the practicality of scuba diving miles under the sea.

10/25/2023

When visiting a mall, those maps that show "You are Here" are quite informative:

Note: the estimates of 2.4 Billion years ago are approximate. In other estimates, 3 billion is quoted and 1 billion for a single phase (see May 2022 Youtube link below)

https://pubmed.ncbi.nlm.nih.gov/15187180/ (2nd link doesn't appear to be working anymore) https://journals.asm.org/doi/10.1128/mmbr.68.2.173-186.2004 "A New Biology for a New Century"

"If they are not machines, then what are organisms? A metaphor far more to my liking is this. Imagine a child playing in a woodland stream, poking a stick into an eddy in the flowing current, thereby disrupting it. But the eddy quickly reforms. The child disperses it again. Again it reforms, and the fascinating game goes on. There you have it! Organisms are resilient patterns in a turbulent flow—patterns in an energy flow. A simple flow metaphor, of course, fails to capture much of what the organism is. None of our representations of organism capture it in its entirety. But the flow metaphor does begin to show us the organism's (and biology's) essence. And it is becoming increasingly clear that to understand living systems in any deep sense, we must come to see them not materialistically, as machines, but as (stable) complex, dynamic organization."

Paired with the above map, one can speculate where this eddy can be observed in today's world. If testing in a laboratory setting, one can observe the mechanistic replication of bacteria in a petri dish, given enough nutrients, etc. If testing an early evolutionary era, prior to the formation of archaea, eukaryota, one might need to account for the anaerobic or oxygen-poor atmosphere of the Pre-Cambrian era. If testing prior to the formation of earth (the theory whereby symmetry breaking and molecule formation arose sometime after supposedly spinning off from a neutron star, then the conditions to test this theory require laboratory instruments capable of withstanding hotter temperatures (e.g.. fusion reactor such as a Tokomak). But if the quantities observed/formed cannot be produced in sizeable enough quantities (i.e the way PCR- Polymerase Chain Reaction thermocycling amplified copies of DNA), then a different math model may be needed before a laboratory test can be devise to observe any pattern formation or interaction of them that resembles the early biophysical formation of matter (CHONS), prior to geochemistry. Something like a Mass Spectrometer for a particle accelerator capable of producing sizeable quanities of precursor molecules that led to the production of life would be needed. Perhaps a thermocycler for elementary particles- quarks, gluons, those sort of things. How, when, and why symmetry is broken to create the first L-enantiomers (or any other pre-biotic precursor molecule, not assuming D was first) may be explained by Collider experiments: https://en.wikipedia.org/wiki/Parity_(physics)#Parity_violation

"In 2010, it was reported that physicists working with the Relativistic Heavy Ion Collider had created a short-lived parity symmetry-breaking bubble in quark–gluon plasmas. An experiment conducted by several physicists in the STAR collaboration, suggested that parity may also be violated in the strong interaction.[16] It is predicted that this local parity violation, which would be analogous to the effect that is induced by fluctuation of the axion field, manifest itself by chiral magnetic effect.[23][24]"

https://phys.org/news/2010-03-tiny-instant-physicists-broken-law.html

10/24/2023

I recall reading in a few articles that Dr. Woese recommended Evolution be taught after advanced Math- in college, and not in high school. The reasoning for this is that Biological Evolution as understood from its early formation, before the DNA polymerase, before the RNA polymerase, requires a mathematical formula(s) to trace historical markers. My conversation with Dr. (Stephen) Farrand during an impromptu office hour visit inquiring of graduate school pre-requisites also confirmed this- that you need to know math. It's not the answer one wants to hear, but the answer one needs to hear. Thus any reference to later stage aspects of evolution, such as genetic selection, are referring to an era far later than what scientists seeking a pre-biotic unification theory between physics, chemistry and biology are trying to elucidate. While physical laws may have carried over, the information storage mechanisms might not all have. It reminds me of a conversation E.O. Wilson had on the relationship between evangelists and evolutionists: there is not a constructive dialogue that can be mixed to derive any meaningful frameworks for any phase in evolution. One cannot imply intelligent design in any era of life's formation (separate from what is called a "physical forward dynamic process" because all of ribosomal evolution (16S rRNA) preceded neurodevelopmental (eukaryotic) development. Thus whenever I see these arguments, I realize the eras being discussed are many, many lightyears apart. I'm not very strong in the math department, so I realize even I have my limits at comprehending some models. Though I sometimes get motivated to learn some new math.

Some papers: https://guava.physics.uiuc.edu/~nigel/courses/569/Essays_Spring2006/files/Butler1.pdf "Horizontal Gene Transfer and the Emergence of Darwinian Evolution" (05/2006)

p.8:

"Optimality Properties of a Proposed Precursor to the Genetic Code" https://arxiv.org/pdf/0905.2932.pdf (5/2009)

p.2

10/23/2023

After randomly browsing* some articles, I came across this reecnt Nature paper published around 3 weeks ago: https://www.nature.com/articles/s41586-023-06600-9 It is [Edit: NOT^1] one of those "theory of everything" papers, but applied to Biology, rather than the physics portrayed on the History Channel (just outer space and "Aliens"). The paper goes further than many in that, it adds a convenient layer of abstraction by, "redefines the concept of an ‘object’ on which these laws act." This is to help understand some of the early forces of physics that led to the first biochemistry, rather than add a layer of abstraction for arbitrary or obfuscatory purposes. This is done by making fewer assumptions about what kinds of chemical bonds led to the original precursors. Bonds themselves as those "objects" make even fewer assumptions than the atoms that may be modeled in an experiment. The rebuttal in one of the comments by Sara Walker, is phenomenal.

^1 "Despite the media marketing on this matter, it is not a theory of everything and it cannot be because of its focused design: establish to which extent a product (like a complex molecule) is the result of evolutionary forces."

Supplemental Information: https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-023-06600-9/MediaObjects/41586_2023_6600_MOESM1_ESM.pdf

"""The purpose of abstraction is not to be vague, but to create a new semantic level in which one can be absolutely precise"—Edsger Dijkstra" from https://c4.santafe.edu/

It appears that Evolution borrowed a concept from Computer Science, which borrowed from Evolution. This was the type of abstraction I was thinking about when I referred to extra "layer," but nonetheless facilitates the discussion on irreducible components during symmetry breaking and making (chemical bonds, but can refer to other objects as well).

In Between 2006 and 2010, Carl Woese and Nigel Goldenfeld collaborated on some papers that discussed evolution as a physical phenomena:

https://arxiv.org/pdf/1011.4125.pdf "Life is physics: evolution as a collective phenomenon far from equilibrium" (2010)

p.5: "Implicit in this approach is the assumption that the evolutionary time-scale is different from the time-scale of the ecosystem. The crucial question of the timescale of the evolutionary process, even taking at face value the perspective of the modern synthesis (which we do not) remains a thorny issue[61], and indeed it is fair to say that the theory’s conceptual framework is so poorly quantified that one cannot confidently make sensible and realistic estimates of timescales (for an excellent pedagogical discussion of this point, see [62])."

https://arxiv.org/pdf/0712.3332.pdf "Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement" (2008)

https://arxiv.org/pdf/q-bio/0605036.pdf "Collective evolution and the genetic code" (2006) Kalin Vetsigian, Nigel Goldenfeld, and Carl Woese

These papers were very interesting then. I remember Carl Woese mentioning the polar requirement in class in 2006 and his research that he was working on at the time.

He also first wrote about the polar requirement way back in 1965-66 while many were deciphering the codon table (including the likes of Francis Crick): https://youtu.be/6KUazEyqGbo?t=2526

In one of those papers, he references the phrase "statistical protein." This concept is very similar to the "combinatorial" aspects of Assembly Theory, and assembly theory may be most applicable to a pre-Darwinian phase or threshold. There is also mention of chirality, which in chemistry differentiates between non-superimposable molecules.

In a lot of ways, I have been waiting for a paper like this. It suggests a paper that was ahead of its time is just starting to get noticed in its relevance to discoveries that hint to a chronological continuum. Woese refers to the cell (and by that logic, DNA) as a "historical document":

A paper that causes so much controversy is sure to reveal certain assumptions about biology that have less testable hypotheses[Edit: I used the phrase "less testable" because I did not know whether the Assembly Theory (AT) paper used methods that can be experimentally tested outside of mathematical modeling; e.g.

"An object that exists in multiple copies allows the signatures describing the set of constraints that built it to be measured experimentally. For example, mass spectrometry can be used to measure assembly for molecules, because it can measure how molecules are built by making bonds." )

, but are nonetheless valid hypotheses that have not garnered significant consideration. More opportune would be that this discovery is from an adjacent [eon], allowing a "missing link" to be made of evolutionary timeframe. More likely than not, some analytical methods can lead to not-so-coincidental deductions that place a discovery adjacent another. In other words, the pre-ribosomal era may have existed billions of years ago, but an era not so distant before that could also be deduced based on mathematical modeling of pre-cursor molecules, that, while not resembling universal amino acids or ribosomal RNA, could still retain a universal biochemical mechanism that the early geologic era's atmosphere did not preclude.

There could have been five evolutionary eons (not necessarily overlapping with geological epochs). There could have been seven epochs. Or seventy. My point is that it is unclear or not easily determinable, as the connection above made between the phases of astrophysical superconductivity and geochemistry is "obscure". Some of these epochs/eons may have been much shorter than others. Some amount of punctuated*** equilibrium must have occured, and some phases could have happened within a day (not metaphorically referring to years or millenia). But it's very possible that between early atoms** (Hydrogen, Helium and so on,- a grad student TA once said that some astronomers studying the early universe only study H and He, for the most part) and the later universe that led to carbon-based life comprised of a number of epochs, are a number of phases that cannot be experimentally deduced (+deduced and abductively hypothesized) from the early Big Bang, but by working backwards from the Ribosome.

"They made this claim by sequencing a single, highly-conserved gene across many organisms: Ribosomal RNA. This is the catalytic part of ribosomes, the protein-making machines inside of cells. By studying how rRNAs had mutated over eons and eons, Woese and Fox inferred the evolutionary connections between cells.

Many well-regarded microbiologists at the time believed that the relationships between microbes could not be determined without a fossil record. This sounds hilarious in hindsight. But it was a real, mainstream belief."

*** The AT paper cites in #10 Biblio: "Elena, S. F., Cooper, V. S. & Lenski, R. E. Punctuated evolution caused by selection of rare beneficial mutations. Science 272, 1802–1804 (1996)" [check relationship b/t Gould]

postscript: Life really is physics in a way that requires focus on the physical aspects of nature. But on a day to day basis, this fact is not simply grasped or known.

1987: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC373105/pdf/microrev00049-0051.pdf Woese wrote a 51 page paper on Bacterial Evolution, and was aware of the missing connection that microbes had to the modern genetic code (addition: In the MAINSTREAM Molecular Biology "consensus"). I haven't read the entire paper, but the first page already resembles his later treatises in the mid 2000s.

• (asterisk) The phrase "randomly" is often a misnomer. An early description of Twitter circa 2008 was, that social networks form and borrow from the metaphorical flock of birds (hence the name of Twitter, from tweeting birds). It would appear that Twitter is more or less an experiment that tests the phrase "birds of a feather flock together." Twitter is a way to efficiently interact with many parties in a sky of birds, like an Alfred Hitchcock flick. To say something has been randomly found on Twitter is more or less suggesting it was located in a flock of temporal similar interests, some which may even be diametrically opposed (or merely observing). Thus "randomly" is a misnomer because it is referring to the chaotic extraction of new information from a flock of birds, some of which may be realigning themselves according to the flock's trajectory, and others forming independent thoughts. As this repository (and all of them) seeks to practice open methodology, it is occasionally necessary to clarify this point.

**

(this image should be a demonstration of why Chat-GPT can't be trusted)

https://www.nature.com/articles/s41559-024-02361-4 - Primitive purine biosynthesis connects ancient geochemistry to modern metabolism, 2024

Miscellaneous bio blog posts

A Tale of Woese, 1998 https://www.scribd.com/document/16300262/A-Tale-of-Woese

"All the junk written about Beethoven's irascible personality does not add at all to the appreciation of his music."

One of the articles that Woese distributed to the 2006 class: https://www.science.org/doi/10.1126/science.1082968

"Woese says part of the skeptical stance to the 1977 report could be traced back to classical microbiology's quiet divorce from the decade's evolutionary thinking. “There was a disconnect between Darwinists, who had taken over evolution, and microbiologists, who had no use for Darwinian natural selection,” he says. To make matters worse, molecular biology's application-oriented approach, he adds, smothered evolutionary considerations of life. “There was a tacit agreement between evolutionists and molecular biologists—en entente curieuse—that neither group would criticize the other.” Add to these reasons microbiologists’ reluctance to abandon the existing classification of life into eukaryotes and prokaryotes, and Woese's phylogenetic classification met with widespread resistance. “By then, the concept of prokaryotes had become firmly entrenched. When the phylogenetic classification was proposed, it was as if a crutch had been taken away,” he recalls."

https://www.pnas.org/doi/10.1073/pnas.1120749109

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3973382/

"Dyson won numerous scientific awards, but never a Nobel Prize. Nobel physics laureate Steven Weinberg said that the Nobel committee "fleeced" Dyson, but Dyson remarked in 2009, "I think it's almost true without exception if you want to win a Nobel Prize, you should have a long attention span, get hold of some deep and important problem and stay with it for ten years. That wasn't my style."[11]'

[11] https://www.nytimes.com/2009/03/29/magazine/29Dyson-t.html https://en.wikipedia.org/wiki/Freeman_Dyson

It's true that in order to be considered an expert, one typically has to have worked in a field for a number of years. Yet, generalists are a rarer breed, and, are just as resourceful at "solving" or "working" on academic problems/issues than those in highly specialized fields. In fact, while many question the value of tenure in a world where industry dominates the employment sector, a defense of tenured generalists should gain new support, should academia seek to remain relevant and maintain its "editorial independence" on the direction of applied sciences.

"Although adaptation to changing circumstances is easier with a diverse knowledge base, “Renaissance people” or polymaths are rare, because specialization is rewarded more generously in the short term. By crediting focused accomplishments, the existing reward system of grants, awards and promotions creates silos of knowledge with suppressed cross fertilization. This unfortunate backdrop only highlights the essential role played by generalists. Those who cross boundaries of disciplines act as butterflies that pollinate flowers unintentionally by carrying pollen stuck to their bellies. Occasional random winds can accomplish the same outcome but with a reduced efficiency and vigor."

"A classic example is Richard Feynman’s own investigation as an independent member of the Rogers Commission in 1986, which revealed the misunderstandings between NASA’s engineers and executives regarding the O-rings safety factor in the Space Shuttle Challenger disaster, using elementary physical reasoning."

from: https://blogs.scientificamerican.com/observations/advice-for-young-scientists-be-a-generalist/

And the decline of SciAm: https://www.city-journal.org/article/unscientific-american

Be the O-ring investigator you want to see in the world.

https://distill.pub/2017/research-debt/

While peer-reviewed research papers in academia do now typically include disclaimers on whether any of the researchers claim a conflict of interest, there remains a strong influence of corporate-funded research in higher education, which results in a very uncritical, pro-industry academic track for many scientific degrees. In fact, some degrees appear to be no more than a conveyor belt for positions for dense IP trolls and non-practicing patent entities (NPEs).

If one were to follow the trajectory of the brain drain after the Manhattan Project, one can see that the physicists who did not want to develop weapons of war, left to study Biology in the late 1940s- early 60s (e.g. Pasteur Institute) after Hershey and Chase's experiment on DNA. Other scientists later went on to develop the internet.

With the popularity of the Christopher Nolan film, Oppenheimer, being released this weekend, I have been reading some memoranda from other post-WWII periods that underscore the dangers of nuclear warfare: https://archive.org/details/The1958TaiwanStraitsCrisisADocumentedHistory_201712

Abridged supplement (not a substitute): https://www.rand.org/pubs/research_memoranda/RM4900.html (Some margins are more legible in this version, even though it is missing 46+ pages)

While not as publicized as the Cuban Missile Crisis, the 1958 Taiwan Straits crisis details (and posted by the late Daniel Ellsberg in 2021) the near-miscalculations of Chinese Communist and Chinese Nationalist forces in the vicinity of present-day Kinmen islands.

https://www.nytimes.com/2021/05/22/us/politics/nuclear-war-risk-1958-us-china.html

Article about a Biologist that was originally in my post-scarcity repository, but added here as well: https://www.theguardian.com/world/2019/jun/20/donna-haraway-interview-cyborg-manifesto-post-truth

"In the struggles around climate change, for example, you have to join with your allies to block the cynical, well-funded, exterminationist machine that is rampant on the Earth. I think my colleagues and I are doing that. We have not shut up, or given up on the apparatus that we developed. But one can foreground and background what is most salient depending on the historical conjuncture."

https://www.thefactsite.com/charles-darwin-eating-habits/