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)

Precambrian on the brain

Spent a few hours living in the past during visit to Museum of the Earth (Ithaca, NY).

Did a sketch on the progression of the Precambrian period which is rarely represented to any extent in museums.

Which is weird because that is when life first appeared. Sure, it didn't have the fantastic creatures that started appearing in the Cambrian Radiation (I don't use the more common 'Explosion' because it implies all life magically happened in an instant). But to me it is more intriguing. Partly because we know less about it.

Yet, we do know that what we consider life first began before oxygen filled our atmosphere. Life then was anaerobic: without oxygen. And appeared only in water, not surprising since the planet was mostly covered with water back then. Water is H2O (hydrogen dioxide), but the two hydrogen atoms are tightly held on to the oxygen. So there was little oxygen in our atmosphere (which was then water vapor, methane, and ammonia).

Bacteria, and their appearance, is commonly called the 'first 'life'1. The cog in the wheel is that it depends on how we define 'life', but that's another long topic (which is embroiled in debate within the scientific community). Finding fossils of bacteria have been difficult: partly because they are so small, and partly that most of the rocks from that time period are also rare.

Our planet formed 4.6 billion years ago (Hadean era); a ball of gas, water vapor and hot molten minerals. The planet cooled enough ~4.4 bya for water to appear and cover the planet. A mineral crust began forming ~4.04 bya and the earliest fossils found are dated 3.5 bya.

Between that time (4.2-3.5 bya) the first single cells formed. The Last Universal Common Ancestral (LUCA) cell population from which all subsequent life forms descended is estimated to be 3.5 bya. This is estimated from genome compilation (which implies that genes had to be present!).

But! Before then was a first universal common ancestor (FUCA). A non-cellular entity is proposed to be the earliest organism with a genetic code capable of performing biological translation of RNA molecules to protein formation through peptides synthesis. In other words, it had to contain enough information to copy itself and evolve. Well, how did that come about?

And that is where my keen fascination is ignited. Hence, my interest in the Precambrian period. But much of this is absent from museums. Several hypotheses are tossed around and debated on the process of how life originated. Yet, if we restrict 'life' to the conventional definition (more a perspective) of life, it excludes possible candidates that were integral in that process.

I'm following two scientists active in this search: biochemist Nick Lane and astrophysicist Sara Imari Walker. They think outside the box. But more on that later. 

1. Some scientists posit that progenotes are the 'first life' or the First Universal Ancestor (FUCA) of all life. Philosophically, it depends on one's definition of 'life', which is still debated. There are at least 9 definitions of life, so choose your favorite. A problem associated with defining life in the scientific context of possible origins of life is constraints (top-down) in investigating and understanding the processes from when the planet formed (Hadean eon,) to the FUCA. 

The never-ending questions

The running theme in this blog, perhaps in my entire life, has been on reality, or what we think may be reality. What is reality?  Is that a valid question?

As author, literary agent, and 'thinker' John Brockman once proclaimed, he has had a lifelong obsession with asking questions, especially "the" question: "What is the last question?". 

Brockman's first book on pondering questions was By The Late John Brockman, published in 1969. In his own words, it was "about the idea of interrogating reality". Most would respond by declaring this is useless philosophy, thereby concluding it all meaningless. Yet each and every one of us plays apart in it, and without it. (As suggested in the movie, "The Matrix") Most of us just aren't aware of it. 

"Reality as a whole is unmeasurable except through effect. The unity is in the methodology, in the writing, reading, in the navigation. This system cannot provide us with ultimate answers, nor does it present the ultimate questions. There are none."*

This also precipitated his vision of the 'Third culture' consisting of "those scientists and other thinkers in the empirical world who, through their work and expository writing, are taking the place of the traditional intellectual in rendering visible the deeper meanings of our lives, redefining who and what we are." 

In 1988 Brockman and others created The Edge Foundation, an association of science and technology intellectuals. It was also an outgrowth of The Reality Club, a gathering (historically called a 'salon') of intellectuals based in NYC and held by a host. From 1981 through 1996 many well known scientists, authors, artists, technologists, and entrepreneurs met for presentations, 'round-table' discussions, seminars, etc. It retired to a virtual  presence on The Edge website in 1996. (A link on the sidebar has been posted when I created this blog in 2005.)

Despite frequently following the website after I first discovered The Edge (~1998), life became complicated and I lost track of it. An academic career sometimes consume the only existence in one's life, especially in LAC (Life After Children). I was busy "interrogating" small subsets of reality. 

It was with sadness (on my part) that Brockman ran out of questions and announced in 2018 the finale to The Edge project with the question, "WHAT IS THE LAST QUESTION?". 

"Ask 'The Last Question,' your last question, the question for which you will be remembered."

Possibly the best tribute to The Edge was in a ''moratorium'' by lecturer and writer Kenan Malik in The Guardian. The excerpt below gave me some private satisfaction in that I have always relayed similarly to students, children, colleagues, lab members, friends, relatives, and, many times, here on this blog: ask questions. (despite the frustrations of many).

"Asking questions is relatively easy. Asking good questions is surprisingly difficult. A bad question searches for an answer that confirms what we already know. A good question helps to reset our intellectual horizons. It has an answer that we can reach, yet unsettles what we already know."

 One response on the webpage, which may not really qualify as an answer for some, is one of my favorites. As we often say in the scientific fields, answers to a question may only be more questions.

"The final elegance: assuming, asking the question. No answers. No explanations. Why do you demand explanations? If they are given, you will once more be facing a terminus. They cannot get you any further than you are at present. The solution: not an explanation: a description and knowing how to consider it."**

Many people are unsettled by that, but it is the reality. Perhaps it is a very simple single question with no explanation. Just like reality.

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 * John Brockman, By The Late John Brockman, 1969, Macmillon. The Kindle format can be accessed on Amazon.com. Hard copies are >$70.

** Ludwig Wittgenstein, Zettel, eds. G. E. M. Anscombe and G. H. von Wright, trans. G. E.

AI R Us

This should not be surprising.* AI models are a mirror to human behavior. So shit that goes in results in exporting shit. 

AI models are trained to learn, consolidate, collate, and regurgitate. We don't like what we get, so we change it afterwards. But that doesn't change the mirror effect. It's a Band-Aid approach: Cover the abscess so we don't have to see it. Or, as Nikhil Garg, a computer scientist, eloquently puts it, “simply paper over the rot”.

This brings to mind a sci-fi series I'm watching on TV, "Beacon 23". AI, a common component of most sci-fi, is represented as two important components in the series, and are almost complete opposites: "Bart" and "Harmony". The latter is a logical Spock attached to an individual human and created by a major company that controls almost everything.

Bart is an AI developed hundreds of years prior to the primary time event of the series and serves the structure, Beacon 23, in space (it's a 'lighthouse' stationed near a flux of dark matter.  The Beacons guide space craft away from detected nearby dark matter 'clusters', like a lighthouse.) 

Bart learns and adopts human nature/behavior from all the beacon "keepers" and those who visit. He also controls all the communication and mechanics of the Beacon station. As such, Bart is just like a human, with all the messiness, assumptions, errors, etc: he lies, whines, plots, complains, quotes Shakespeare, and often acts like a child.  But Bart also significantly sets the course for what occurs on the Beacon. Whereas Harmony is logical and attuned only to her individual human, but also capable of Beacon control, including Bart (she scolds Bard many times).

Humans created AI, and in its current state in our world is like a young Bart. That we can't see that is human blindness. AI is not, and won't be our savior. We can't even save ourselves. 

"Even though human feedback seems to be able to effectively steer the model away from overt stereotypes, the fact that the base model was trained on Internet data that includes highly racist text means that models will continue to exhibit such patterns."

* "Chatbot AI makes racist judgements on the basis of dialect," Elizabeth Gibney. Nature, March 13, 2024.

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.
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[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).

Life as a human chameleon

Two common words used amongst autistics (and in the autism literature) are 'masking' and 'camouflaging'.  As a late-diagnosed adult Asperger's (on the autism spectrum), I had no idea what they meant except for their literal meaning. At the time of my (unofficially official) diagnosis in 2007 it was referred to as 'coping'. That superficially described it and I left it at that, continuing on in my own uninformed default way: coping. 

In my post of 'coming out' as an older woman on the autism spectrum (Asperger's), I explained why I hid my diagnosis for 16 years. I spent five decades coping as a stranger in a strange land, constantly asking myself "Why am I so different?", and feeling very alone in my version of reality. But I had learned to cope for the most part. As I mentioned elsewhere, I felt fine most of the time. But don't know if that's because I've dealt with it, or if I've buried it. Now I know it was both.

I interpret masking as intentionally 'wearing a mask' to hide my weirdness (which I heard frequently). Camouflage to me was interpreted as subconsciously chosen or learned behavior. As a teen and early adult I used to call the former 'games' or 'playing games'. I learned the rules (expectations) and would intentionally pretend, or not, to follow the rules. Only in retrospect did I realize that in the past I was subconsciously learning and developing strategies to interact within the neurotypical world. It was somewhat Pavlovian.

The latter was pointed out to me during my diagnosis inquiry after I mentioned two key personal accounts: my father was also Asperger's (undiagnosed; there wasn't such a thing back then), as was my closest (ever) adult friend (also Asperger's). 

I realized consciously by observation that my father was very different from other male adults/fathers: he had no social skills, no common sense, didn't like close contact, didn't talk much, had exceptional memory, and was a polymath. And I was aware of the consequences of his weirdness, such as coping with alcohol abuse and being ostracized. It was suggested that I learned some coping skills from that awareness without consciously understanding. My mother, on the other hand, picked up on it, confirmed by her frequent exasperations of "You're just like your father!!"

Decades later, a very close adult friend, 15 years younger than I, was Asperger's. We shared many personal 'secrets' about ourselves, during which I realized he was similar to my father's behavior. I recommended that he learn the same coping skills I had learned: observe and mimic neurotypical people. Unaware that I myself had done the same.

It was pointed out to me that I was sharing the same 'coping' mechanisms (masking and camouflaging) that I intentionally and subconsciously used for all those years. Because I was also Asperger's, which is highly inheritable. 

Meeting a few other Autistics late in life has finally made me feel comfortable in my own skin. I've also been researching the biology, genetics, psychology, and sociology of being Asperger's.[1] One common trait in most (if not all) neurodiverse people is to  'mask' and 'camouflage.' They are common coping mechanisms to navigate in the dominant reality of neurotypical people. Or, the "process[es] of changing or concealing one’s natural personality in order to 'fit in', or perhaps more specifically in order to be perceived as neurotypical".[2] 

But the terms still confused me. 

Masking and Camouflaging

As a biologist, I understand camouflage in the context of other animals, such as the chameleon, cuttlefish, and many butterfly species. Not so much Homo sapeins, which is primarily social camouflage. Masking and camouflaging are used interchangeably in popular books and even some of the research on autism. I wasn't happy with the ambiguous usage so developed definitions as mentioned above based on my own experiences. Until I found a webpage discussion regarding more precise and technical definitions. 

The CAT-Q 

Recent research on autism and other neurodivergent behavior has developed distinct subsets of camouflage, in which masking is one. Eva Silvertant's webpage  explains with detail and comments the subcategories -compensation, masking and assimilation- of camouflaging by neurodiverse people. 

Based on conversations with family members and fellow autistics, the how and why of camouflaging is different based on individual perception. Several have pointed out that nearly everyone does it in some degree and fashion. Yes, that is true. But the degree and consequences are different for neurodiverse people. (I often use the colloquial "conforming to the norm." (But, you may ask, 'what is normal?', which is a long topic of itself.)

As Silvertant explains, 

"Some extent of camouflaging is probably inherent to human interaction; we learn social skills to improve social interaction, we adhere to social conventions that may not make complete sense to us, and we adjust our behavior as the situation demands. For example, we tend to behave differently at work than at home. But for some people, the need to camouflage is a lot less superficial. Of course, the need to camouflage is proportional to how strange your behavior is perceived to be by your surroundings. And since autism is generally not very well understood by non-professionals—and even many professionals, honestly—it is us autistic people who find we often have a greater need to camouflage.

For other people camouflaging might mean acting, talking, and/or dressing a certain way in order to fit in with a social group of their preference. And while this probably pertains to autistic people as well, our need to camouflage tends to go deeper; because autistic people often have to camouflage their autistic behaviors, so as to minimize the visibility of one’s autism in social situations."

Silverton then discusses the how and why, and some of the consequences of camouflage for autistics. For example, when trying to explain to my family members why I can not handle hugs from people (other than my family) without suffering anxiety and emotional and physical recoiling, I realized they could not understand. What they did finally understand was why I apologetically make excuses to not attend big extended family gatherings and linger on the edges in social groups to avoid hugs. I now have decided to stop 'playing the game' and just politely tell people "I don't do hugs".

Researcher Laura Hall, et. al.[3] designed a questionnaire, the "Camouflaging Autistic Traits Questionnaire (CAT-Q)," that helped them develop a model of camouflaging with three categories:

1. Compensation — Strategies used to actively compensate for difficulties in social situations.
2. Masking — Strategies used to hide autistic characteristics or portray a non-autistic persona.
3. Assimilation — Strategies used to try to fit in with others in social situations.

The 25 items of the social camouflaging model are diagrammatically explained on Silverton's webpage and in the original published paper.[3] 

The CAT-Q questionnaire was validated  by others and it is purported by the researchers to be a "reliable self-report measure of adults’ social camouflaging behaviors, suitable for use in autistic and non-autistic male and female populations. It can be used in research settings to quantify camouflaging behaviors and compare between groups; in clinical settings as a potential screening tool for individuals who may be missed under current autism diagnostic criteria because they camouflage; and by autistic and non-autistic people to aid identification of beneficial or harmful behaviors they use in social situations." [3]

However important technical terms are in science communication, they can be confusing to the lay public. I can understand why using the two terms masking and camouflaging, rather than the three categories from the CAT-Q would be most efficient.  Regardless, the CAT-Q terminology should be a standard in autism research and professional publications.

In common use, it may be helpful to define masking and camouflaging more narrowly than to be used interchangeably. Thus far, the only book I have read that distinguishes between the two is Unmasking Autism: The Power of Embracing Our Hidden Neurodiversity, by Devon Price, PhD, autistic and a social psychologist.

Learning that many of my inherent differences and quirks in social communications and interactions are common amongst other neurodiverse people has more than explained my responses and behavior in the past. I regret my unwillingness to learn this earlier when I was in academia and where I experienced the most stigma about my neurodiversity. Now that I am retired and meeting more neurodiverse people on the autism spectrum and others, like ADHD, I feel more free to be who and what I really am; a lot less masking and camouflaging, but also more relaxed when 'light masking'.  
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1.  That's part of my Asperger's: extremely focused on specific topics, mostly the living sciences. Which is why I became a scientist.

2. Silvertant, Eva, 2020/2023. Autism & camouflaging (pulled from the Internet 02/24/2024)

3. Hull, L, et al., 2018. Development and Validation of the Camouflaging Autistic Traits Questionnaire (CAT-Q),  Journal of Autism and Developmental Disorders.

Air Pollution is Us

The dangers of air pollution seem obvious and of concern to some, but apparently only a minority. How much of the apathy is attributed to "I don't care" or "I don't believe it", or both, is unknown. Yet, I see it on a daily basis. 

The most striking is the number of people that leave their gas-powered vehicles running while at stores or other business. On my walk to and from the gym, I pass cars parked on the sides of the street and in the post-office parking lot. It's more common than not to notice that most vehicle engines are on and running with no occupants in them. 

Out of curiosity, I timed 4 empty vehicles independently with engines running (1 at post office, 2 at a barber shop, 1 store parking lot). Vacancy time was 12-32 minutes. The other day 5 running vehicles parked at the post-office were backed into the lot with rear ends butting the sidewalk. Another time I walked passed an engaged car with a passenger in a store parking lot. ~Twenty-five minutes later when I exited the store, the car was still running with it's passenger. I see this year-round, not just seasonal.

I see this ALL the time! Imagine how much emissions are exhausted into the air. I notice during my walks on cold and gray days that the exhaust stays closer to the ground, not dissipating into the air above, and worse on windless days. What that means is that I'm breathing it the entire time I walk along the streets. I can smell and taste it. 

All this in a small rural town. Now, consider the expansion of this in cities and along major highways. This is why I don't like living in urban areas (as well as my hypersensitivity to noise). And it affects more than just us humans; it impacts all life forms. 

Here is an important factoid: a scientist discovered by stringent experiments that lead in the environment was almost nil until the beginning of the Industrial Revolution and increased every year. By sampling the permafrost in Greenland he found that the levels significantly increased in the 1950's, coinciding when lead was added to gasoline. Lead in gas was (is) volatilized in engines and emitted from tailpipes. Therefore, lead was deposited along streets and highways for decades. 

The dangers of lead were known decades before unleaded gas was introduced for on-road vehicles in the 1950's. Yet it took another 20 years for unleaded gas to be phased out completely. Lead use in gasoline was prohibited in the US in 1986.

The problems are: 

1. Lead is a heavy metal and stays in living tissues for some time, depending on how much and long an organism was exposed. High exposure (time and amount) can lead to the metal deposited and stored  in bones and teeth (the two common sources for sampling of lead contamination).

2. Bioaccumulation: lead from air pollution, etc can accumulate in soil and plants, and the organisms that use plants for food source. And lead can persist for hundreds of years.

"Lead shares about 10% of total pollution produced by heavy metals. The uptake of lead by the primary producers (plants) is found to affect their metabolic functions, growth, and photosynthetic activity. The accumulation of lead in excess can cause up to a 42% reduction in the growth of the roots."

Also, lead arsenate and other lead compounds were used as pesticides for food crops,  such as fruit orchards and on other crops, until the 1950s. But that lead in the soil is still there and being absorbed by plant roots. Sampling of plants along highways and streets demonstrate that plants absorb, and some sequester, lead from the air. (Avoid planting edible plants next to roads and highways.)

Pollution particles are not just lead, as this recent science article points out. Yet no one seems to care, considering the amount of pollution generated, knowingly and unknowingly, on a daily basis. Right under our noses.

"The damage that air pollution can do is wide-ranging and well-known: The chemicals produced by human activities can trap heat in the atmosphere, change the chemistry of the oceans and harm human health in myriad ways.

Now, a new study suggests that air pollution might also make flowers less attractive to pollinating insects. Compounds called nitrate radicals, which can be abundant in nighttime urban air, severely degrade the scent emitted by the pale evening primrose, reducing visits from pollinating hawk moths." ("Polluted Flowers Smell Less Sweet to Pollinators, Study Finds," Emily Anthes, New York Times, 2/08/2024)

 

Speaking Out

What convinces me that our species is 'doomed' (I wish I could avoid using that term, but can no longer deny the applicability) is the global pathological denial of the train wreck. Additionally, human civilization has already dragged down other species, and continues to do so at alarming rates.

As a scientist, I intellectually understand that denial is a defense mechanism to help cope with anxiety (coupled with explaining away problems and blaming others). Denial enables ignoring or refusing to believe an unpleasant reality, protecting psychological well-being in any situation that produces anxiety or conflict including challenges to one's standard of living or power status quo. But when one is looking into the jaws of a lion ready to bite off your head, or staring at the giant wall looming before the speeding train, denial no longer serves as a defense mechanism. Here I lose understanding, and I blame my science colleagues as much as the politicians and financiers that perpetuate the fuel of denial.

Most of the scientific community, including medical, is either in denial, or running to look for technological solutions rather than evaluate the root origins of our problems and address 'how we got from there to here.' Our politics, economics, policy, and, many times science are based on 'bandaid' cures. Put a bandaid on it, cover it up, and it will go away. Ignore the festering wound underneath; its origins, the process and interrelated changes of its development. Ignore the peripheral interacting relationships and far-reaching impacts. "Let's amp up production; don't pay any attention to consumption." "Give them a pill; who cares about prevention?" "Collect the species DNA and we can ignore life extinction."

At this rate, our civilization will collapse. As history teaches us, it will also arise again like the Phoenix. But perhaps a Phoenix with a limp. My sympathies and grief are for the non-human species on this planet. Their collapse and extinction is finite. And they have no concept of denial. The ubiquitous law of supply and demand is a part of population dynamics. The changing supply of resources -water, food, shelter- will trigger changes in population. I suspect that without modern industrial sustainment of large scale food production, water collection and long-distance distribution, human population everywhere will decline, possibly quickly collapse. Earlier civilizations, even other species, have experienced these cycles; we are not immune.

Sometimes I have to look beyond the doom and gloom and find specks of hope that we can change this trajectory. But my brain isn't convinced.

Pangea gone wild

Pangea and the diversity of life. 

Most everyone knows what Pangea was: the largest supercontinent in Earth's history. All land masses united in a large group gathered together for a conference. They also shared all organisms on their surfaces before splitting into individual continents. 

This split didn't magically happen like many people think. It was a very long process. Pangea split into unequal halves forming two supercontinents: Laurasia and Gondwana. Additionally, these two landmasses continued sharing some flora and fauna over a long period of time.

Over millions of years further tectonic activity caused Laurasia and Gonwana to split into smaller landmasses gradually forming the continents we are familiar with today. This long process was a key impact on early evolution of both flora and fauna. 

The expanding distance between continents reduced exchanges of flora and fauna, eventually isolating many groups of life. Some fauna continued dispersal from continent to continent by rafts of islands or ice. Others migrated by air (e.g.seed and flying animals). Our knowledge of the degree of and when continental shifting impacted evolution of flora and fauna is continually evolving (pun intended) in the field of biogeography. There are two theories:

"Do new species come from animals populating new territory (called dispersal), or did populations get separated during Earth’s breakup (called vicariance)?"

We know that both dispersal and vicariance played roles in early evolution of nearly all flora and fauna. And we need to consider that distribution of life occurred over a long periods of time, even during different stages in the evolution of flora and fauna. Local, regional and continental changes in topography or climate can influence dispersal of isolated populations. It can also expand habitats for others enabling mixing of populations where isolation barriers once existed. 

Several approaches can help elucidate the contribution of vicariance or dispersal at different points of an organism's evolution. The most valuable is phylogenic trees, structural diagrams that represent evolutionary relationships among organisms. The pattern of branching in these trees reflects how groups and individuals of  organisms evolved from a series of common ancestors and their predicted evolutionary timing. They are evolutionary 'trees'. 

A group of scientists used the data within a set called the Timetree of Life. It is a phylogenic tree of life scaled to time. Using data for major freshwater and terrestrial vertebrate groups (animals with backbones: fish, amphibians, reptiles, birds and mammals) that were descended from common ancestors and represented on at least two continents, they examined when they diverged. 

Dates of divergence of those groups separated by continents lined up with the continents geographically separating. This supports the theory of vicariance over dispersal as the major cause for speciation. However, this may change as the data sets change. 

There are considerations that may impact this theory. One is the contribution of moving pieces of land, such as land bridges. Another is narrow bodies of water separating the shifting continents and facilitating both flora and land dispersal. 

As the author of the article highlighting the study commented, "this paper is swinging the pendulum between two competing ideas". And, as science is sometimes fraught with binary thinking, the two theories don't have to be a "competition", or mutually exclusive. Life isn't A or B; it is a dynamic collection of events that can happen together or seamlessly flow from one to the other. Generalizations don't always pan(gea) out. 

Humans are not islands

"Pathosystem" 

I like that term. It encompasses a systems perspective -both pathogen and host- rather than focusing on just a single component of a system. It is an ecosystems perspective with emphasis on pathogen-host-environment. 

My academic career spanned plant, animal and human pathology (except for the last several years in physiology). A systems perspective is always inherent in the first two, less so in human pathology. It's as if Descartes binary philosophy (separation of mind and body) extended to separation of body and the environment in which bodies exist. As medical specialization demonstrates, even separation of organs from the rest of the body. 

I have wondered if this might be a contributing factor in some of the failures of modern medicine. An example is the lack of translational research of human psychology and medicine. 

The prime example is diabetes: lot of research in physiology and pharmacology, but little research and application of how/what to inform and impact people to change and adopt behaviors that prevent and reduce diabetes. This extends also to social systems: education, policy, connecting the production, supply and access of nutritious food. 

We know how this works and how to achieve these goals with plants and animals. And we practice it, most of the time. The question is why can't we do it for ourselves, and other people? 

This is what we really need to focus on. It's that part of the 'ecosystem' that is dysfunctional. Science should be the leader in this. 

Why isn't it? Has that failed us, too?

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? 

History of obesity. In Denmark.

“The origins of the obesity epidemic may be further back than we thought”

A recently published paper concluded that the rise of obesity began earlier than conventionally assumed. (See article summarizing study: The Origins of Obesity in Science.)

"This study revealed that continuous steady increases since the interwar period in the upper percentiles of the BMI distribution preceded the obesity epidemic, with an almost similar pattern in the children and the young men." (published paper)

I agree with some of the criticisms of the study and conclusions, such as population sample=1 (Denmark). Is this trend replicated in other countries? 

Another comment from a biostatistician that “slow and steady increases in obesity don’t necessarily indicate an earlier onset of the epidemic [of obesity]”. A proper data pool for that would require data before 1930’s. 

A statement from the original published paper confirms my observation over the years traveling this country: “The acceleration of the obesity epidemic has been stronger in rural and provincial areas than in densely populated urban areas, which was seen already in the beginning of the rise of prevalence in obesity in Danish young men during the 1960s.”

And, like anything involving human behavior, the contributions are multifactorial.

The high prevalence of obesity in people of all ages in rural Ohio was a shock when I moved there in late 2001. 

During a conversation on this subject with a man (late 20’s) that I was training, he commented that as agriculture became industrialized it required less physical activity by all family members. However, the culture of food and eating amongst farm families remained the same: calorically dense food, especially fats, and large portions during meals. 

Consequently, while activity levels decreased, the energy balance became very skewed towards a positive high caloric net balance. Which, over time, results in increased body mass.  

We can see an eventual similar trend in urban areas over time, albeit slower. My hypothesis is that most rural families used to grow their own food, meat and vegetables/grains. So they had an almost guaranteed supply of food and energy. 

Urban people had to purchase all their food (and still do). Purchasing power for food was based on their incomes and other debts (rent, etc). History worldwide has shown that wealthy people always have had almost unrestricted access to food. For many centuries, being overweight was a social sign of being affluent. 

It was only during the last half century when increasingly more people began moving from rural to urban communities. Industrial agriculture and food processing caused a large shift in the nutritional content and availability of food, and the culture of food. 

As Gary said that day, “People of Ohio still love their corn and pork, and there is plenty of it here. But now everyone has desk and ‘standing still’ jobs. And the kids don’t play as much; they’re glued to their phones and video games.”

Muscles don't have memories!!

Peeve: When the scientific community can't agree on a definition consensus for a term, such as 'muscle memory'. 

Muscles don't have memories. Brains do. 

Ask anyone in a gym and you'll get four or more interpretations of what 'muscle memory' is or means. Ask scientists and you'll get one of three; each thinking they offer the only correct definition. 

This was a frequent source of amusement in our lab (neuromuscular pathology); we agreed to avoid the term unless being sarcastic. We often used the general term 'muscle plasticity': the ability of a given muscle to alter its structural and functional properties in accordance with the environmental conditions imposed. That's what muscles do. 

Then, what IS muscle memory?

According to Wikipedia (and a more summarized definition in Oxford Dictionary), 'muscle memory' is:

"...a form of procedural memory that involves consolidating a specific motor task into memory through repetition, which has been used synonymously with motor learning. When a movement is repeated over time, the brain creates a long-term muscle memory for that task, eventually allowing it to be performed with little to no conscious effort. This process decreases the need for attention and creates maximum efficiency within the motor and memory systems."

So, what is muscle plasticity? 

Phenotypic* plasticity allows single genotypes to express different phenotypes under diverse environmental conditions. Organisms, and tissues (some more than others), respond to different environments by changing how they act, look or function. Skeletal muscle is a highly plastic tissue. 

For example, exercise initiates signaling pathways that modify muscle fiber metabolic, physiological and contractile properties of skeletal muscle (sometimes referred to as 'remodeling'). That is 'muscle plasticity'. Whereas exercise can also evoke memories (conscious and subconscious) in the brain of how movements are executed. It is a back-and-forth communication between muscles and the brain via the central nervous system. That is  'muscle memory'.

In language, adjectives connote specificity. In particular, 'neuromuscular plasticity' and pathology were the focus of our research. Muscle plasticity requires the coordinated interaction between neurons and muscles, but pathology narrows the focus. Disease or injury of motor system components, including responsive proteins in muscle fibers, can lead to muscular motor dysfunction. Like all tissues, biological/molecular processes are included. 

One example is muscular dystrophy: a disease in which one or more muscle proteins are absent or dysfunctional because of genetic aberrations that interrupt the signal between the motor neurons and the ability of the muscle to respond. It has little if anything to do with procedural memories, aka 'muscle memories', in the brain. A muscle group without dystrophin won't be able to contract, irrespective of any 'muscle memory' in the brain. 

Using the correct language is imperative for science communication within the scientific community. Incorrect** and vague terms are perpetuated throughout communication and education (formal and informal) outside of that community, such as with medical professionals, trainers, social media, etc. Yet confusion remains if members of the scientific community do not consistently use correct definitions of terms. This needs fixing.

Summarily, the use of the term 'muscle memory' should be restricted to the associations of movement and 'memories' established in the brain. Better yet, these terms are better:

• Procedural memory ( or 'Kinesthetic memory'): the automatic movements involved in throwing a ball, dancing, swimming, steering a vehicle, typing, or even squats.), or
• Motor memory:  process by which animals can adopt both persistent and flexible motor behaviors. 
  
  

MUSCLES DON'T HAVE MEMORIES!
Brains do.

------------------------------------------------------------------
* Phenotypic is the observable traits of an individual resulting from the interaction of its genes (genotype) and its environment. 

** Many researchers have recently published papers in scientific journals and still use the term 'muscle memory' in the context of muscle biology/molecular biology and physiology without ANY reference to -'memories' formed and stored in the brain! 

Are we breeding for stupid dogs?

 "Little brainiacs and big dummies: Are we selecting for stupid, stout, or small dogs?"

Intriguing study. The title is catchy, so I read it. 

A general scaling quotient related to brain size, or encephalization, for all mammals is defined as the amount of brain mass exceeding that related to an animal's total body mass. Brain size non-linearly scales with body weight between species within mammals to around the 0.67 power. However, within species, this scaling exponent appears to be much smaller. An early study compares dogs with non-canid species. According to this study, we are breeding dogs to have smaller brains. 

Dogs today have smaller relative brain size than dogs 100 years ago. That may not be an intention, but we do selectively breed them for certain behavioral traits as well as well as physical appearance. The famous Russian Silver Fox experiment confirms that (6 generations of breeding and choosing individuals for tameness resulted in a domestic fox). Keep in mind that genes linked to behavior and physical appearances may be linked to brain size. 

This encephalization quotient generally estimates 'evolved intelligence' or other behavioral traits, "under the assumption that the bigger the brain per kilogram of bodyweight beyond what would be required for basic neural functions, the greater the intelligence." But have we humans also bred for lower brain function? aka 'stupid' dogs?

My interest was more in how this compares to non-dog canids than within domestic dogs. A phenomenal earlier study* (1986) compared brain size and weight between all families within the carnivore order (all carnivore families, genera and most species). The study also used metrics including ecology and behavior as well as body and brain size, developing an encephalitic quotient (EQ) range. Canids placed in between the families Ursidae (bear family) and felids (cats). 

What is interesting is the EQ within domestic dogs compared to the within species of non-dog EQ. The current study found that EQ decreases with increasing body weight in dogs: "Small dogs had higher EQ than their non-dog canid counterparts of comparable size, but large dogs had lower EQ than similarly sized non-dog canids."

Encephalization quotient decreases with increasing body weight in dogs. The dashed black line represents the regression line for dogs, the dark gray solid line represents the regression line for dogs from the Richet dataset, and the light gray solid line represents the regression line for canids from the Gittleman dataset. The regression line for canids crosses the regression lines for dogs at approximately 10–15 kg.

In other words, domestic dogs have a brain-size-to-body-size relationship that markedly differs from the general rule between-species relationship (power function of 0.26 rather than 0.65–0.67). That's quite a difference. 

But this is even more impressive: modern dogs have lower relative brain sizes than dogs of a century ago. There are two possible biological explanations. First, humans purposely select for smaller heads, which includes the size of the cranium. This is unlikely. 

The second and more likely explanation is that modern dogs are fatter than their lighter counterparts from a century ago: "...plentiful evidence exists that dogs, like people, in the United States are experiencing an increasing prevalence of obesity." 

Authors in the recent study recognize an important methodological criteria related to the above explanation: "Researchers a century ago recognized the importance of examining brain-size-to-body-size relationships in animals that are in 'optimal condition,' and cautioned including data for domestic animals that often differ in body condition from their wild counterparts." Definitely true. Regardless, the prevalence of obesity in dogs (and humans) is concerning. 

What about intelligence? Are bigger dogs smarter than small dogs due to brain size, or vice versa?

Despite common beliefs we all hear, the authors conclude "no behavioral evidence exists that small breed dogs are more intelligent than large breed dogs." Most of us know that behavioral studies are fraught with discrepancies in methodology and interpretation. Additionally, several studies failed to observe a relationship between brain size and cognition. Some studies have reported that certain breeds are more "trainable" or perform better at certain skills. Similar reports are associated with horse breeds.

The authors offer a more plausible explanation; what these studies and anecdotal claims more correctly identify is a "selection of specific morphotypes for specific tasks, and certain cognitive skills that underpin those tasks, rather than selecting for or against overall intelligence." Specific physical attributes are more suited for specific tasks and skills than others, and behavior is a result of genes and learning. 

"Such a hypothesis finds support in studies that identify “trainability” with working breeds vs. non-working breeds, rather than size. Given that working breeds are generally larger than non-working breeds, size might simply be a poor surrogate for “working breed.”

I enjoy good challenges (and controversies) in biology. They force people to critically think (and they should). The authors in this study challenge existing and generalized assumptions about interpretations and conclusions relating to differences in body sizes with a subtle hint of well-deserved sarcasm. 

"This observation flies in the face of assigning an encephalization quotient to dogs—in our study, small breed dogs had a relative brain size far exceeding their “expected” brain size, while large and giant breed dogs had relative brain sizes of mental midgets. Therefore, applying an encephalization quotient to dog breeds appears nonsensical, and challenges the entire anthropocentric notion of encephalization as a measure of intelligence."

This, to me, is the coup d'état challenge for scientists that arrive at assumptions and generalizations that persist on shaky evidence. It also represents a challenge to those that choose and pick their data or facts to support their preconceived assumptions. In this case, the challenge is how we perceive intelligence in dogs, and perhaps all animals. Including our own genus, Homo spp.**

Read the last two paragraphs of the paper where the authors discuss "What makes a dog a dog?" and how selecting for smallness has a limit (which it does, so stop it). 

"....regardless of how small domestic dogs become, brain size must be conserved to accommodate sufficient neuronal complexity for the dog to maintain its “dogness.”

In all, excellent discussion and writing for a published scientific paper.  

* Gittleman J.L. Carnivore brain size, behavioral ecology, and phylogeny. J. Mammal. 1986;67:23–36.

** A recent article (sometime in March 2021) challenged our modern assumptions about the inferior intelligence, or lack of, in Neandertals and Denisovans. You'll have to do a google search for that article. 

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.

Bats and viruses co-evolved!

Bats harbor many viruses and are a source of old and new emergent viral diseases in humans. Why? 

Two papers review the unique bat immunology summarize what we know thus far, as well as some as yet untested theories. In short, a bats' immune system is competent at confusing and tricking virus biology, and we don't quite fully understand all of it. 

Given their herculean immune system, viruses have to 'work hard' to fool and evade their immune system to actually cause disease, without, of course, killing them. (A virus that kills its host quickly is a dead end for a virus. It may be able to replicate a few times, but it can't transmit all those new virions to other hosts after it dies. So, dead end.)

One way for viruses to test the the bat immunity barriers is a random process of mutations and evolving behavior of the virus to successfully infect and replicate (fitness). I'll explain some of that in another post (information theory). One of those barriers is heat: viruses don't like heat. One immunity mechanism of mammals to fight virus infection is a fever. It may not kill all viruses, but it slows their biological trajectory to infect cells and replicate. Another component of that is it buys time for the rest of the immune system to respond and bring in the artilleries: antibodies, T-cells, etc. They attach to and disable or kill virus particles, and destroy already infected cells so that the little new virions inside the cells die, too. 

This was one of two approaches I used to rid very important plants (nuclear stock) of viruses before they went to certified nurseries for mass propagation and sale to industry growers and commercial nurseries (1980's-1990's). The approach was to expose a plant to high heat in a growth chamber, the hottest temperature it could stand, then take 1mm size pieces of the apical meristem (growing point) and grow them on tissue culture media containing an anti-viral, now known as Ribavirin. (Protocol developed by me and collaborator at university in CA.)

So now that I have established some credible evidence for the relationship of heat and viruses, albeit in plants, keep that in mind in this next part. 

Five scientists from US, UK and AUS methodically detailed over five pages a hypothesis of why bats and viruses co-evolved together(1). It actually makes sense, although not good for other mammals, especially humans. 

I recall from reading a review last year that viruses must be super-evolvers, aka go through many and numerous random mutations, in order to successfully infect and evade the bat immune system. By the time some of those viruses jump from bat to another animal, especially another mammal, they are super-duper viruses and often deadly to humans. 

Think about the first SARS-1 virus pandemic: a short-lived pandemic because it was less transmissible than the current SARS-2, but it was also more deadly. Short-lived because countries quickly contained and eliminated it. Also consider MERS, another bat coronavirus that emerged after SARS-1. Very deadly, and very poorly transmissible. It, too, was quickly controlled. That it was a deadly virus contributed to that. 

A decade later a new SARS-like virus emerges: it's highly transmissible, not as deadly, but it spreads like wildfire. It has, however, been able to also evade part of our immune system if the latter is in any way compromised, including obesity, diabetes, etc. Two other important factors helping it along is the relatively poor and/or belated human response in controlling spread, and its stealth: it can infect mammals, replicate and transmit to others while not inducing any or many symptoms. A caveat to the latter is we now know that some infected people of all ages may have had little to no symptoms but still developed some tissue damage (e.g. cardio myelitis, kidney, etc) that occurred slowly enough not to elicit recognizable symptoms. l can see this as a stealthy way to evade the bat immune system, too. 

Back to co-evolution of bats and viruses. This is a good summary from their abstract: 

 "We hypothesize that flight, a factor common to all bats but to no other mammals, provides an intensive selective force for coexistence with viral parasites through a daily cycle that elevates metabolism and body temperature analogous to the febrile response in other mammals. On an evolutionary scale, this host–virus interaction might have resulted in the large diversity of zoonotic viruses in bats, possibly through bat viruses adapting to be more tolerant of the fever response and less virulent to their natural hosts."

And, 

" We hypothesize that the increased metabolism and higher body temperatures of bats during flight might serve as an evolutionary adjuvant to their immune systems, providing a powerful selective force against virulence and promoting the diversity of viruses that infect bat populations. Perhaps counter-intuitively, this would enable bats to tolerate a greater diversity of viruses that have a high potential for virulence when transmitted to other mammals.

The hypothesis also might help explain why co-evolved bat viruses cause high pathogenicity when they spill over into other mammals because the bat-derived viruses might survive well under both febrile and cooler conditions."

Pretty respectable! Actually, it's brilliant. Don't blame the bats, or their viruses. It's just another biological ecosystem that we are not meant to get involved in. So leave the bats and their habitats alone. Many of those viruses become zoonotic because we tend to invade their habitats. 

Isn't science beautiful? 😁

1. Bat Flight and Zoonotic Viruses, O’Shea, et. al. Emerging Infectious Diseases, Vol. 20, No. 5, May 2014.

Further reading on bat immunology:

Novel Insights Into Immune Systems of Bats, A. Banerje, et. al. Frontiers in Immunology, Vol. 11, No. 26, January 24, 2020.

The bat-virus detente, R. Ehrenberg, Knowable Magazine, June 19, 2020. 

Judges Playing Scientists

Superior Court Judge Elihu Berle, argued that roasters and manufacturers failed to prove that that there is no substantial risk to drinking coffee, or that the benefits of drinking the beverage outweigh the risks posed by acrylamide, a substance created naturally during the brewing process. By the standards of California’s decades-old Proposition 65 law, Berle affirmed in his final ruling last week, all coffee sold in California must come with a warning label stating: WARNING: This product contains chemicals known to the State of California to cause cancer and birth defects or other reproductive harm. *

An example of scientific ignorance and misguided judgement.

If coffee should be labeled as carcinogenic, then so should toast, grilled meat, pizza crust, and a plethora of other foods that contain a lot of carbohydrates and proteins.

BUT it is ‘okay’ to ingest foods that have been exposed to pesticides demonstrated to be neurotoxins and carcinogens, and drink water tainted with the same, without the same warnings!

The Maillard reaction that occurs during heating or breakdown of certain substrates does produce acrylamide (and free radicals). It is basic organic chemistry. Is it carcinogenic? It can be, depending on dose and the animal. This is based on experiments with mice, but not with humans. Although mice are not men (murine models have limitations for extrapolation to humans), using mice can lead to suggestive conclusions that then must be tested in humans. Pharmacology history is fraught with failures in extrapolation from mice to humans.

Should we be concerned? Possibly, if you are drinking a gallon or more of coffee every day. The greatest threat from anything involving the Maillard reaction products, including acrylamide, is smoking! And uncontrolled blood glucose levels.

The Maillard reaction that occurs from smoke inhalation and rampant metabolism of glucose and proteins in tissues causes exceedingly high free radical production and Amadori products which accelerate breakdown of connective tissue in the body (elastin and collagen in skin, tendons, ligaments, vascular tissue, eyes, etc.). That’s why smokers have accelerated aging of their skin, and it is a contribution to diabetic pathophysiology.

We shouldn’t expect judges to be scientists, but we should expect them to consult with experts in the field in which rulings are concerned.

Interesting that they don’t exert the same concern and rulings with documented toxins in our environment, other than those spurious claims.

* In Labeling Coffee a Carcinogen, California Leaps Ahead of the Science

Is life like Play-Doh?

On the tail of the silver fox.......

Despite that the field of epigenetics is often dismissed as a fad topic, that may come back to surprise us, just as the derision of ‘junk DNA’ did several decades ago. 

Similar to the silver fox domestication project, scientists in Sweden replicated domestication of red jungle fowl (ancestors of modern chickens) and selected for fear of humans tameness. After five generations, they examined changes in the genetic structure associated with certain phenotypic traits, especially behavior.

Behavioral traits are associated with many physiological and neural mechanisms. Signaling compounds in the body involved with these processes are dopamine, glucocorticoids, epinephrine, and many others. All of these signaling molecules are synthesized in tissues and organs, such as they hypothalamus. Based on prior studies, the research team examined changes in the hypothalamus of  their test subjects. They discovered that not only were DNA methylation patterns associated with cellular metabolism and neural signaling, but there were sex-specific changes.

In agreement with other similar studies of selection pressure during domestication, this study adds further evidence that changes in genetic structure are related to the driver(s) of selection for specific traits, such as egg size in a breed of domesticated chickens.

“This suggests that different selection pressures generate distinctive sets of epigenetic changes, which in turn are related to specific phenotypic traits.”

Epigenetics may have increasing importance now because of its suggestive role in phenotypic plasticity, which often precedes adaptation to environmental change. Understanding how organisms respond to selection pressure can help us better model and predict the fates of many species of concern in this age of rapid climate and anthropogenic changes. Including our own.

“Our results suggest that bidirectional selection for tameness involves epigenetic factors that can even differ in a sex-specific manner. Observation of divergent DNA methylation patterns in the hypothalamus after only five generations of artificial selection highlights the importance of epigenetic mechanisms, in addition to genetic composition, in evolutionary phenotypic variation that emerges in response to selection pressures.”

A researcher in Europe has been studying these association based on changes in gene expression in melanin, phenotype, and behavior adaptation in owls. Ironically, humans have unknowingly been experimenting in this for thousands of years by our own selection for domestication of many plant and animal species.

My Third Law: It Depends!

Should burns take place in spring
Or wait for autumn rain?
Would baiting help or hinder?
Can owl chicks live through flame?
‘I dunno,’ we had to answer.
‘Not sure, can’t really say.
Needs further replication
Might vary day-to-day.’
PhDs require devotion,
Long days with no weekends
But the ultimate conclusion seems
‘Umm, well, it depends.’
- excerpt from post, 'My Grand Conclusion', on zoologist Bron's blog, Working on the Wild Side

The two of us answered in unision..... "It depends." And looked at each other with a knowing smile.

A retired couple asked for information on where to go to see this bird and that bird. Husband asked for specific details: what species, what location, what time. He was dissatisfied with my answers, including "They were seen here yesterday morning, and there yesterday afternoon, and at this location this morning, but they may be anywhere. They don't send us memos on when or where they go."

When asking for exact details on how to get to 'Point A' from 'Point B' (a distance of 125 miles), my explanation of various options of traveling from Point A to Point B resulted in some visible upset. His wife gently reminded him that they aren't in a hurry and he might enjoy experiencing different things along the way. Her comment was met with a hand wave, pointing at a map, and listing what he expected to see, do, encounter, etc. He wanted no surprises.

"If something changes, if we stray from the map, it will be an adventure!", said his wife.

"No! No surprises, and I don't like adventures. Adventures mean poor planning," Husband responded. "How long will it take to get to 'Point B'?"

Wife and I replied simultaneously, "It depends!"

I looked at them both and then asked Husband, "Are you a mathematician?"
Eyebrows went up and he said, "Why, yes! How did you know?".

"A strong aversion of risk and uncertainty," I responded. Wife returned my smile.
"Oh my God, are you a biologist, too?!" Husband asked with raised eyebrows and looking like he was stuck in between two conspirators.  By that time, all three of us were laughing.

Third Law: It Depends!

My First Law, unapologetically borrowed from The First Law of Thermodynamics (aka 'You can't win'), states that where there's a positive, there is a negative. And this is related to My Second Law: 'Everything is relative'. 'Positive' and 'negative' are relative to the perspective of that which observes or experiences the action/reaction, which depends on time, place and being. (Note that the Second Law of Thermodynamics is 'You can't break even'. See blog post linked above.)

I think you can see where I'm going.

My Third Law is 'It Depends'. If anything I have learned in biology and ecology (and life itself) remains constant, it is: It depends. For the person who demands or insists on a life or reality of 'Yes' or 'No', you will either be disappointed or live in perpetual denial. For life is not simply black and white. A vast area of gray reside in between.

Evolution of......

As an undergraduate back in the early 1980's, and in the 'backward' state of Maine, specialization was not the norm. To specialize meant the same fate as an organism that is specific to a very narrow habitat and diet. It could mean death in a drastically changing environment. As most biologists will recognize the analogy, plasticity in lifestyle, education and thinking meant adaptability and survival.

Thrust into the rapidly evolving culture and society of rampant specialization in grad school (Oregon) was somewhat traumatic for me. But that did not deter me from learning and cultivating both professionally and in my own culture, plasticity. It has been ironically amusing to see a reverse in the trend of specialization the last six years, albeit at a slow rate in academia. Several life science disciplines still resist recognition and acceptance of integrated sciences and practice. Even in my beloved field of biology.

An exception is ecology. Perhaps because the very concept and foundation of ecology is based in dynamic and complex relationships. No longer can only one variable be 'the' determinist'. In ecology, models are not equated with 'laws', but serve as bases for probabilities and predictions. With a good dose of 'it depends'.

Evolution itself operates on 'It depends'. Nearly all phenotypic traits are based on the expression of multiple genes interacting within the context of a dynamic relationship with their environment. A trait will evolve and remain as long as it confers fitness within a set of environmental conditions.

Changing one note in a symphony is sometimes drowned out by the rest of the music. Except for rare diseases, one single gene is not responsible for obesity and/or diabetes. Ernst Mayr commented, "The idea that a few people have about the gene being the target of selection is completely impractical; a gene is never visible to natural selection, and in the genotype, it is always in the context with other genes, and the interaction with those other genes make a particular gene either more favorable or less favorable."

Frankly, I feel more comfortable with a world of 'it depends' than dictates of 'The Theory of Everything', the 'Gene for Everything', and 'Models are Laws'. A world of Venn Cubes (a more complex 3-D model of Venn Diagrams ;) makes more sense to me; it's more representative of life and reality. Perhaps I can handle the uncertainty and risk.

So, according to my Third Law, there is a caveat to my First and Second Laws. It depends.


Interview  with the late biologist, Ernst Mayr on  Edge.org:

MAYR: "One of the surprising things that I discovered in my work on the philosophy of biology is that when it comes to the physical sciences, any new theory is based on a law, on a natural law. Yet as several leading philosophers have stated, and I agree with them, there are no laws in biology like those of physics. Biologists often use the word law, but for something to be a law, it has to have no exceptions. A law must be beyond space and time, and therefore it cannot be specific. Every general truth in biology though is specific. Biological "laws" are restricted to certain parts of the living world, or certain localized situations, and they are restricted in time. So we can say that there are no laws in biology, except in functional biology which, as I claim, is much closer to the physical sciences, than the historical science of evolution."

 

EDGE: "Let's call this Mayr's Law."

Further reading:
"The typical ecological answer – it depends", blog post by oikosasa. Website: Oikos: Synthesizing Ecology.

"Which species is best for their host marsh cordgrass? Fiddler crab or mussel? The answer is – it depends"

"Ecological processes depend on …", blog post by CJA Bradshaw. Website: ConservationBytes.com.

"In real ‘ecological’ life, things are vastly different. It’s never as straightforward as ‘yes’ or ‘no’, because ecology is complex. There are times that I forget this important aspect when testing a new hypothesis with what seem like unequivocal data, but then reality always hits."