Dancing molecules

 "It's all about chemistry."

"No, it's all about physics. It makes chemistry happen."

"But I love chemistry and hate physics!"

"Chemistry is protons, neutrons and electrons dancing around each other on a crowded floor. To understand chemistry, you must learn about physics."

"But...."

"There is no 'but'."

"*sigh*"

"Start with water. It's a chameleon. It's the only natural chemical substance that exists in three states: a liquid, solid, and gas. Water changes from one phase to another at specific temperatures and pressures. This is all physics and the basis of interactions with other molecules, what you call chemistry."

"Umm...."

"You can't think of chemistry without physics. 'It is the Way.'"

(based on an actual conversation between me and my late father when I was an undergrad)

Which Reality is Real?

What is 'reality'? Ask 10 people that question and you'll likely hear 10 different answers, including "I don't know." The question may be as old as human consciousness. However, it may not be a realized 'thing' [1] that all humans ponder. 

A quick summary in the online encyclopedia Wikipedia present reality as..

"Reality is the sum or aggregate of all that is real or existent within the universe, as opposed to that which is only imaginary, nonexistent or nonactual. The term is also used to refer to the ontological status of things, indicating their existence. In physical terms, reality is the totality of a system, known and unknown."

Is reality a thing? Or is a way of looking at 'things'? 

Reality may be both. No one may have understood this more than physicist Erwin Schrödinger, famously known for his thought experiment (1935) in quantum mechanics, Schrödinger's cat, . It was as an argumentum ad absurdum (reductive argument to absurdity) intended for questioning the then proposed behavior of atoms and larger manifestations as being one or the other, as in "dead or alive", and which depends on the observer. Or, simply put, it suggests that reality is relative to the organism that observes or experiences it in one way or another.

Recalling an old platitude: If a tree falls in the forest and no one is looking or hearing it, did it really fall?

 Yet, Schrödinger's paradox legitimately questioned, 

"When does a quantum system stop existing as a superposition of states and become one or the other?" (More technically, when does the actual quantum state stop being a non-trivial linear combination of states, each of which resembles different classical states, and instead begin to have a unique classical description?"[2]

More simply put, 

"Our intuition says that no observer can be in more than one state simultaneously—yet the cat, it seems from the thought experiment, can be in such a condition. Is the cat required to be an observer, or does its existence in a single well-defined classical state require another external observer?" [2]

This may bring to mind Einstein's "Theory of Relativity," which is associated with quantum mechanics. Indeed, Einstein considered each alternative as absurd. He wrote to Schrödinger,

"You are the only contemporary physicist, besides Laue, who sees that one cannot get around the assumption of reality, if only one is honest. Most of them simply do not see what sort of risky game they are playing with reality—reality as something independent of what is experimentally established. Their interpretation is, however, refuted most elegantly by your system of radioactive atom + amplifier + charge of gun powder + cat in a box, in which the psi-function of the system contains both the cat alive and blown to bits. Nobody really doubts that the presence or absence of the cat is something independent of the act of observation."[3]

Many interpretations, both technical and popularized,  provide explanations and answers to Schrödinger's paradox. However, the quantum world is full of counterintuitive ideas, which was strongly implied in Schrödinger's thought experiment. Several physicists contemporary with Schrödinger and after his passing proposed their own perspectives. 

Of note, American physicist, Hugh Everett who  proposed (in his 1957 PhD thesis) what is now known as the many-worlds interpretation of quantum mechanics. I'm sure most readers here are familiar with the popular "multi-verse' of science fiction genre and even modern physics. Everett's idea of quantum mechanics does not single out observation as a special process. His many-worlds interpretation of Schrödinger's paradox explains that, 

"...both alive and dead states of the cat persist after the box is opened, but are decoherent[4] from each other. In other words, when the box is opened, the observer and the possibly-dead cat split into an observer looking at a box with a dead cat and an observer looking at a box with a live cat. But since the dead and alive states are decoherent, there is no effective communication or interaction between them. 

When opening the box, the observer becomes entangled with the cat, so "observer states" corresponding to the cat's being alive and dead are formed; each observer state is entangled, or linked, with the cat so that the observation of the cat's state and the cat's state correspond with each other. Quantum decoherence ensures that the different outcomes have no interaction with each other. The same mechanism of quantum decoherence is also important for the interpretation in terms of consistent histories. Only the "dead cat" or the "live cat" can be a part of a consistent history in this interpretation. Decoherence is generally considered to prevent simultaneous observation of multiple states."[5]

Quantum mechanics is often used in contextual explanations of reality. One could possibly, and loosely, refer to Everett's hypothesis as 'alternate' realities. Is this a real 'thing'? Or just another thought experiment or interpretation of reality?

This all begs the question, is there just one reality? If so, then what is it? Afterall, a 'real' reality could exist for non-living things (we know they exist, but the non-living have no consciousness), and another for living things (because we have consciousness and are aware). Which suggests that an infinite number of personal realities may exist. A shared reality may be then be overlapping personal realities like many flexing Venn 4-dimensional boxes that overlap, constantly shifting, temporally and spatially. 

As mentioned earlier, reality is the the totality of a system with known and unknown existences.

Or perhaps reality is like the smile of the Cheshire cat: it remains even when the cat becomes invisible.
_______________________________________________

[1] I'm compelled to explain my use of 'thing' as in it's most recent etymological context: used colloquially since 1600 AD, as a word to substitute for what a person cannot think of it's meaningful name. However, this ubiquitous word 'thing' has an interesting history back to the Vikings. 
[2] "Schrödinger's cat," Wikipedia
[3] Letter to Schrödinger in 1950.
[4] In quantum physics, decoherence is the process in which a system's behavior changes from that which can be explained by quantum mechanics to that which can be explained by classical mechanics.
[5] Hugh Everette III, Wikipedia. As an aside, both Hugh and his son, Mark Oliver Everett, are thought by many to be Asperger's (on the autism spectrum).

Theories and uncertainty

I love this quote. Wish I had it on a rubber stamp. 

"Being unable to accurately measure the thing on which a theory is based is a fairly fundamental uncertainty." - John Kennedy, climate scientist and physicist

 Heisenberg's uncertainty principle in measurement, anybody? 

What do you complain about the most?

 What do you complain about the most?

Noise, the unpleasant energy sound waves that reach my ears, disrupt the waves in my brain leading to physical and mental unsettlement. It’s like nasty hands that pull part of my brain and pound nails into it, making my whole mind and body flinch.

                                                                    Me

 

Quantum evolution

To fully understand evolution, and life itself, one must be able to grasp quantum theory (quantum mechanics is mostly mathematical equations at the microscopic level and not at all required to conceptually understand quantum systems). General relativity is also a quantum system. 

Seeing time only through clocks and calendars will never give us any kind of appreciation of time on a larger scale. Those are metrics, but are not really time itself. Same with evolution: it exists at many points and flows back and forth. It really can't fit into what we consider as 'time'.  

Biophysicist Werner Loewenstein succinctly presents evolution as a quantum system of information.*  Rather than thinking of evolution following a linear path in time, it is information in the quantum realm, constantly shifting places like tiny sand particles on an ocean beach. 

Thus, evolution is chunks of information existing in the future and the past. What we see is how it manifests only at any point within that realm. There is no moment of 'creation' just as there is no moment of 'end'. Species don't magically appear; they evolve, and devolve. 

"It is difficult to even talk about an instant of time, because we can’t even say with certainty which “chunks” of space-time lie in the future and which in the past." -physicist Jonathan Oppenheim 

Evolution requires us to jump off that restrictive scale and think in terms of shifting sands.

* The Touchstone of Life. Werner Loewenstein, 1998.

Quantum time, quantum people

It's unnerving, and rather irritating, when someone you reconnect with after 4+ decades tries to pin you to a point on a linear time scale, expecting you not to move from that point.

Change is the only certainty in life, perhaps in all reality. Some people box their memories of another on a point in time and expect them to permanently reside there, existing only within the two points on a timeline, their timeline. Then ask many years, timelines, later why we aren't still sitting on that stretch of time. It's worse when that stretch of time is relatively short.

Same could be said of history. History is not just one recollection or explanation of a point or stretch of time. It's multiple recollections, even interpretations. Any narrative of history should always be considered in that way. Partly because of the quantum nature of time, where past, present and future are the same (time flows back and forth, it never stands still). Even if we were present in a point of historical time, our recollection is within the frame of our own mind. And our recollections are biased.

What I eventually realized was that person has pinned his or herself to that point in time, and thus the image of another person occupying that same point never moves on. And neither does the image of his or herself. Those people are prisoners of their own minds, stuck on a small point or stretch of time, refusing (or afraid) to move forward. And expecting other people to be the same. 

                                    Henrik Sorensen/Getty

Oh, Phosphorus. How art thou?

I'm bored with spinning, TV and reading my books. It's cold and raining outside. So I'm reading a few papers on how phosphates evolved to facilitate biological life. Physics, chemistry and information theory. 

The word phosphorus derives from the Greek phōsphoros: phōs ‘light’ + -phoros ‘-bringing’. Perhaps the Greeks knew more than we do.

I asked this question of my graduate biochemistry instructor: "How did phosphorus evolve to be the key element of life?". She just shook her head and answered, "You just have to sometimes accept that we don't have the answers, that we just don't know."

"Nah. I bet we do, or will soon."

That was in the mid-1980's. Westheimer published a paper, "Why nature chose phosphates", in 1987 proposing a theory (partly) answering my question. His theory was refined in 2013 by Kamerlin, et al: "Why nature really chose phosphates." Then, Liu et al took it to a different level with "How Prebiotic Chemistry and Early Life Chose Phosphate". 

Goldford, et al. commented in the introduction of their paper ("Remnants of an Ancient Metabolism without Phosphate," 2017), "Phosphate is essential for all living systems, serving as a building block of genetic and metabolic machinery. However, it is unclear how phosphate could have assumed these central roles on primordial Earth, given its poor geochemical accessibility." But we now know how phosphates assumed that essential role. 

Hess et al published earlier this year (Nature,16 March 2021) another theory,
"Lightning strikes as a major facilitator of prebiotic phosphorus reduction on early Earth". (Remember the Greeks?) It circles back to biophysicist Werner Loewenstein's 1999 book ("Touchstone of Life") in which he explains why lightening probably facilitated phosphorus being the first and basic element for life on Earth (and may be on other planets). This book is enlightening for integrating information theory, physics, chemistry, and molecular biology. (One star of the book is Maxwell's demon.)

But, wait! A treatise explores the 'phosphorus enigma' at the largest scale: the book, "The Chemical Evolution of Phosphorus: An Interdisciplinary Approach to Astrobiology" (Enrique Maci -Barber, PhD, Professor of Condensed Matter Physics in Madrid, Spain). In the forward of the book, Sun Kwok (astronomer studying the physics and chemistry of stellar evolution) wrote:

"This book beautifully traces the stellar origin of the element phosphorous, its chemical properties, and the observations of phosphorous-based molecules and minerals in the interstellar medium and in the solar system. [The author] then connects the astronomical studies with the role of phosphorous played in living organisms, presenting the biochemistry of biomolecules that incorporate phosphorous, and the roles that these molecules play in the origin of life on Earth."

Unfortunately, the book is also a hefty $150; far out of my price range. 

Branching off but parallel to the road of physics and chemistry, information theory has expanded understanding of prebiotic and current life. My first introduction into this was more like an epiphany while reading Loewenstein's book when it appeared on the shelves in 1999. It filled in the gaps for a continuing passion of concepts in cell signaling. It wasn't just about chemistry; physics was the parent. (College physics, taught only as mechanical physics, turned me off to the subject. I endearing called  it "'fysics; the other 'f' word". Despite that my father, a biophysicist/biochemist, tried to convince me to not ignore 'fysics'.)

Realistically, information theory integrates physics, chemistry, molecular biology, structural biology, geology, and more. It's like a spider web with life (and death) at its core. Whenever anyone, especially during this pandemic, mentions the spike protein and ACE2 receptor, antibodies and ligand, and, especially, the immune system, my immediate response is "Conformation is everything", a mantra I picked up  in biochemistry and incessantly repeat. (Network theory, inclusive of information theory, is now being applied to the immune system.)

Dr. Chris Adami, theoretical physicist and computational biologist, is the one of the few researchers using information theory to understand the physical and medical sciences and evolution. Life should not be thought in terms of chemical events. Instead, it should be thought of as information transmission. Adami comments during an interview:

"Information is the currency of life. One definition of information is the ability to make predictions with a likelihood better than chance. That’s what any living organism needs to be able to do, because if you can do that, you’re surviving at a higher rate... Think of evolution as a process where information is flowing from the environment into the genome. The genome learns more about the environment, and with this information, the genome can make predictions about the state of the environment."

When asked about the origin of life, he relates one of a few hypotheses amongst scientists for the circumstances of life origins: 

"I have heard tremendous amounts of interesting stuff about what happens in volcanic vents [under the ocean]. It seems that this kind of environment is set up to get information for free. It’s always a question in the origins of life, what came first, metabolism or replication. In this case it seems you’re getting metabolism for free. Replication needs energy; you can’t do it without energy. Where does energy come from if you don’t have metabolism? It turns out that at these vents, you get metabolism for free."

 However, nothing is free. Maxwell Demon knows that. The prime denomination of that currency of information is energy. And one of the earliest components of life that transfers energy is a phosphate group in an energy unit: adenosine triphosphate (ATP). With the origin of ATP began the synthesis of large biomolecules. The release of a phosphate group supplies energy for molecular couplings, resulting in adenosine diphosphate (ADP). Subsequent combinations release a phosphate group that reattaches to ADP, forming ATP. This is a positive feedback loop that cycles over and over. 

First there was lightening. Over millions of years of trial and error a system became more stable, and it also became more adaptive. And then life was born.

We have come closer to understanding the origins of life. And I am closer to understanding how and why phosphorus evolved as the key element of life. Did Nature choose this, or did this choose Nature as it's product? That may be an ouroboros question. 

(A comment by Adami echoes thoughts throughout my higher education and academic years: "...the more you learn about different fields, the more you realize these fields aren’t separated by the boundaries people have put upon them, but in fact share enormous commonalities."  Yes.)

Molecular Demons and Gedankenexperiments

 What caffeine does to the brain. 

This question has popped up in short ‘vacant spaces’ (periods of quiet without other junk thoughts) the past few months with all these various virus variants (couldn’t resist the redundancy) popping up. This morning I saw this Twitter thread echoing the same questions. 

Then I had a Gedankenexperiment, a thought experiment. It appeared to me that if we can determine the molecular configuration of these virus variants, we should also be able to computationally predict those with high probability of becoming thermodynamically stable or increased fitness. This is used in predicting ligand docking (protein conformational fit with target protein, aka ‘ligand’) for drug development. 

We could then do automatic searches in newly submitted virus variant genome sequences for such candidates. Why else would one mutation and consequent conformation change in the spike protein be independently popping everywhere? Because it is a top thermodynamically fit conformation. And given the vast uncontrolled landscape in which the virus can ‘choose’ a random mutational configuration that increases transmission offers evidence that the virus is winning within a relatively short time. Especially when TWO adventitious mutations come together.  (See Twitter screenshots below)

It’s the Molecular Demons in information theory. 

Now back to mundane life.

Relativity is Very Special

I have a love/hate relationship with fysiks (aka physics), that other 'f' word.

I'm a 'conceptual physics lover', 'calculated fysiks hater'. I read 'Physics for Biologists' and the 'Tao of Physics'. But I hated my physics text book.

Physicists are obsessed for finding the 'Theory of Everything'. As if there was 'one' theory for anything. To me, physics is modeling for probabilities. Not to be confused with 'anything is possible.' But probabilities are what reality is made of, each having a different weight. Many theories in physics can be modeled by mathematics but not tested in the 'real world'. Nevertheless, sometimes that's all we have.

I have followed with the interest, curiosity and amusement of a physics novice the rapidly changinng theories of late: string, relativity, origins of the universe (and it's many components), and Farscape. Okay, the latter is more for entertainment.

So now we have physicists challenging Einstien's special theory of relativity with.........
very special theory of relativity [1].

Is it clear in color? Does it require a helmet? I bet it rides a magic bus.

Time for all us Observers to get on our Neutrinos and ride!

[1] Article in New Scientist (Jan. 20, 2007; vol. 193, No. 2587).
Letter by Andrew Cohen in Physical Review Letters (97, 021601; 2006).