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

Whose afraid of Virginia Woolf?

While reading this post about Virginia Woolf,  I was reminded of an internal and eternal dialogue pondering the question of how we perceive 'alone' and 'lonely'. The problem is that the two are not synonymous, although the wide perception often is. 'Alone' is not always 'lonely'. Yet, we are conditioned to think that anyone that is alone is 'lonely'. 

Semantically, 'alone' can mean 'solitude'. A person can be literally alone: by one's self away from other people. It may feel comfortable or uncomfortable. I can be alone, the only human on a mountain top, and not lonely; I feel solitude and connected to all life round me. Likewise, a person can be 'alone' and unconnected in a crowd of people, but comfortable with it. It's usually a choice. It's less about our circumstance, but how we react to them.*

But 'loneliness' is less ambiguous: it's a feeling of being alone, unconnected, and not liking it. Both are internal states, but loneliness is less related to what is going on around us. It's a fear of solitude. 

Individually there is a wide area-under-the-curve for each on what is comfortable and what is not. Yet, the cultural definition and expectations for everyone, including children, are quite narrow and contradictory. We are expected to know ourselves, but to always be 'social', e.g. with other people. Unfortunately, too many people don't know themselves, or are uncomfortable being alone with themselves. They fear it.

So it's an illusion, created by ourselves and society. 

In the medical community and the public mindset people are expected to always be surrounded by other people. Those that prefer to be alone are almost always considered 'unwell' or 'abnormal' because, culturally, 'alone' = 'lonely'. Then comes the judgement deluge.

Those two terms don't take into consideration the time element: always, occasionally, mostly, etc. Those adverbs are important because they quantify the the amount of alone time. Or even when feeling lonely. 

Some people feel they have to be with another person, or amongst other people, all the time. I've known a few people (mostly women, but a few men, too) who almost have panic attacks when they are alone. Their loneliness is overwhelming, usually because they don't know themselves, or they fear being alone with themselves. Perhaps they even fear not knowing themselves; they lack self-esteem.

There's also a gender bias: women are expected to always be surrounded by people, and in a personal relationship with another (usually a man, but that's another topic...). Men.... not so much, if at all. In a few countries, cultural acceptance of a woman alone in public, especially without a male, is prohibitive. It's like requiring your dog on a leash when in public. 

Alternatively, because I'm a woman that prefers solitude most of the time and lives alone the all too-common perception is that I'm lonely. I've had to fend off questions and comments from others implying judgement, such as pity or concern of unwellness. Especially, 'You don't have a man so you must be lonely and helpless'. Or, 'There's something wrong with you.' That's the expectation associated with perceptions of 'alone' and 'loneliness' of many women.

'Alone' and 'lonely' are illusions we create about ourselves and others (Virginia Woolf refers to it as 'a reality', which is partly correct). And with those illusions, we place judgement and expectations on ourselves and others. We celebrate self-esteem. But we stigmatize spending time with the person we should know, and like, the best: ourselves.

Woolf's writings exemplified the strong pervasive feelings of loneliness and the illusions of it. In a diary entry she wrote of this as being a 'reality': 

"That is one of the experiences I have had...and got then to a consciousness of what I call “reality”: a thing I see before me: something abstract; but residing in the downs or sky; beside which nothing matters; in which I shall rest and continue to exist. Reality I call it."

Woolf's angst (she was bipolar) with what was 'real' for her, and the societal illusions and expectations about being alone and lonely (especially as a woman), ultimately influenced her choice to end her life. Ironically, over a century later, that societal perception still exists. 

In her post, author Maria Popova writes,

"There is a kind of loneliness that lodges itself in the psyche and never fully leaves, a loneliness most anguishing not in solitude but in companionship and amid the crowd. If solitude fertilizes the imagination, loneliness vacuums it of vitality and sands the baseboards of the spirit with the scratchy restlessness of longing — for connection, for communion, for escape. And yet it is out of this restlessness that so many great works of art are born."

On the other hand, solitude lacks an illusion, or sense of loneliness, and it also feeds imagination and creativity. Journalist and Buddhist Zat Rana writes, 

"When you surround yourself with moments of solitude and stillness, you become intimately familiar with your environment in a way that forced stimulation doesn’t allow.

The world becomes richer, the layers start to peel back, and you see things for what they really are, in all their wholeness, in all their contradictions, and in all their unfamiliarity. You learn that there are other things you are capable of paying attention to than just what makes the most noise on the surface."

Being alone does not always have to mean 'loneliness'. Not all of us are afraid of Virginia Woolf, of living life free of illusion.

* Some people like feeling lonely, but that is more of a pathological issue and I'm not delving into that except for my reference to Virginia Woolf. 

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! 

Being inside out

Modern biotechnology is wonderful. It reveals wonders that we can't see without it. It tells us more about ourselves and about each other, about living things that surround us. Ironically we can see inside our bodies, but still scratch our heads on the outside wondering how we tick inside our brains.

Many years ago, while spending days [1] extracting DNA from large quantities of white blood cells from cows' blood, I added a small tube of my own WBCs. There was room in the centrifuge; why not? The feeling of seeing thin threads of your own DNA floating in solution inside a gently rocking test tube is inexplicable. 

Those fine threads were a history catalog of generations before me, before my mother and father, before them. They were strings of time more ancient that any of us can fathom, carrying the instructions on what makes me human. And how similar yet different I am from each of you. Ironically, even similar to the thick ropes of cow DNA rocking alongside in their own test tubes.

Trypanosoma theirleri and red blood cells

[1] I collaborated with a colleague to develop a sensitive assay (PCR) for detection of microscopic single-celled parasites (Trypanosomes) in the blood of cows. They literally beat up blood (red and white) cells with their 'tails' (flagellum) and weaken the animal's immune system. The process entailed extracting DNA from the fraction of liters of blood containing the WBC; in that fraction were the parasites and their DNA. A close 'cousin' of the same parasite causes Sleeping Sickness in humans.

An American Mutt (revised 12.2022)

Like most Americans I'm a 'mutt': a combination of different nationalities, rather than one identifiable national identity. Maybe I'm the only one that admits it, and proud of it. Also fitting, considering my inexplicable interest, both scientifically and personally, in canids. All canids, not just dogs and wolves.

I'm a mutt through and through. So my loyalties extend to all people and almost all real canids (those tiny dogs just aren't real canids; they're genetic mistakes).

I grew up not fitting in anywhere. And not really understanding that until I spent a summer in the Middle East and Europe. Then I realized I'm simply a member of the human race. That's all I needed to know.

We're all human.

There are no sub-species for Homo sapiens. Yet we act like there are. Our species is a very tribal one. We look for anything to belong to and separate our selves from others, pledging loyalty to this and that, and resenting any group that doesn't match our criteria. Our species is in a perpetual identity crisis.

I blame it on taxonomy. Anyone in biological sciences is bottle fed systematics: the classification of every life form. Taxonomy is a scheme of classification, usually in a hierarchical approach in which living things are organized into groups or types. People classify themselves the same way.

People born in Greece are Greeks; in Mexico, Mexicans; in America, Americans. People born in the Britain are Brits. However, if I were born in Scotland, a member of Britain, I'd be both a Brit and a Scot.

I was born in the United States of America and legally, I am an American. But I really don't feel like one. At least, not compared to how many of my fellow American citizens feel 'American'. I don't share the tribal loyalty (often blind) that many do.

So what am I?

I'm what??

My last name comes from Germany and my first name is a corrupted form of the German/Scottish/English 'Elspet/Elspeth/Elizabeth'. (Even my name is a mutt.) American names aren't original; they are fragments from many countries strung together to label a person accompanied by a unique social security number. The latter is what makes us American.

Because my parents rarely talked about their family history, my sister and I researched our family genealogy after they passed on. The patriarchal tree is relatively simple: married immigrants from Bavaria arrive at Ellis Island in 1861 with their five children, settle in Buffalo, NY, and birth six more children. Most of the male offspring married Irish or Scottish women, who also had up to 12 children, and so on. Ironically, many of the female offspring are dead ends: once they marry, their adopted husband's last names render them lost in history.

I'm fourth generation American-German.

The matriarchal tree is even simpler: my maternal grandmother was born in Sweden. Her parents were born in Sweden. That was easy. That makes me second generation American-Swedish.

I did what many people are doing now: ancestry DNA. I discovered that human DNA is much more complicated than the bacterial and viral DNA I was used to be. Like any genetics project, genetic information is dependent on data derived from a population of samples. If that sample pool is small, the data is also limited and may not represent the larger population. Also, as gene sequencing technology changes, so does the size and confidence of the data. Consequently, as more genetic data from people around the world are added to central databases, the more precise the genetic information of ancestors. It also adds to the histories of human migration over thousands of years.

One genealogy autosomal DNA analysis reported that I am 68% Scottish/Irish, 19% Scandinavian, and......13% German*?? Another analysis reported 44% German, 19% British Isles, 14% Slavic**, 11% Italian, and the small balance Scandanavian (2%), French, and 2%.... Peruvian??

Oh, what the hell.....  I'm a mutt. And proud of it.

*It's more complicated than that. What DNA companies don't explain (except for CRI Genetics) is that a person's DNA does not give a crap about labels and borders. The reason many people with known German ancestry are pinned to the United Kingdom, or other modern countries, is because Germany was not a unified country with a common border until 1871. Before then, the region was occupied by many ethnic groups: Romans, Germanic tribes, Celts, and, going back to the Bronze Age, the Yamnaya (originally from the steppes of western Russia). For example: Bavaria was a 'hot spot' of migration mixing.

** Preliminary online research into Scandanavian DNA projects, the Finnish DNA Project (Finnish DNA Reference Group) shed some insight into the Slavic connections. Although mtDNA (DNA from female mitochondria) provides more exact information (especially, haplotypes), "Overall, as we know from autosomal studies, Finnish ancestry derives primarily from Europe, especially the Baltic region". Many Finns migrated and settled in Norway and Sweden. That explains the Slavic connection. 

We are all mutts.

For those interested in the seven-year 1000 Genomes Project, this link leads to a summary of the project (published 2015 in Nature journal).  Data from diverse human populations, such as the Finnish Project mentioned, continue to be added. This and other smaller genome projects (e.g. link to overview of UK genome projects) serve as a basis for genetic genealogy data sources used by commercial DNA/genealogy analyses. The current expansion of this effort can be found at The International Genome Sample Resource. 

"1000 Genomes Project publishes its final two papers, which analyze 2,504 genomes from 26 populations and provide the most comprehensive view of global human variation so far."

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. 

“Hell hath no terror than a woman’s fury.”

That was my answer when a friend asked me how I was. First, I looked at her and asked myself, ‘Should I show my fake smile and lie like a robot?’. Then I decided to be honest. 

The response to my reply was an up-tick of the eyebrows and peering over her glasses, with a loud silent ‘Ohh?’. 

The many inner dialogues have been argumentative, unsure, illogical, but all too human. I’m sure I’m not the only one panicking, sometimes a bit unsettling, other times trying to put a cork in the volcano. Keep physically busy to calm the mind, and the moment you let your guard down, the fury screams through the gate. But it goes nowhere. Because you bite your tongue and clamp your mouth shut. Instead you see the silent scream when you look in the mirror. 

I don’t want to be the biting dog barking all the time; we have too much of that already from the pulpits, the streets, and the White House. But I don’t want to be the Pollyanna, either. Sometimes I want to rub the faces of the Pollyannas in the shit that is being thrown around from all directions. “Here, take your joy-joy and your little dog, too. And get out of the way!”

In the past it all used to flow through my fingertips, but something broke, snapped, in 2013 and there’s no smooth conduit anymore. I’m not a writer,  although writing was always my cathersis. And I have asked myself since then why it doesn’t work anymore. I always jokingly tell myself I need a flash drive to insert in my brain. The monologues and stories are still there, but they always trip over the door sill and never make it out. Except the stupid juvenile ones that sprint past the door and spew fury. 

Then I found a perfect explanation by writer Jeremy Wade, “Tr*mp has traumatized so many of us to such an extent that attaching any positive descriptors to his name is infuriating. You don’t need me to tell you that’s a valid response. He is fascist garbage, and he’s responsible for some real heinous shit. I’m sorry for all the ways it’s affected you and the people you care about.” I feel partly vindicated, despite that it’s more than that ‘T Name I Cannot Speak.’

It’s not the virus, the pandemic, the social distancing, or wearing a face mask. I’m a biologist; I know the virus, what it is, how it works, what it does, and what I, we, need to do. I’m fine with that. It’s the politics, the history, and the humans. They are illogical, unreasonable, unintelligent, memory impaired, and blind to long-term consequences beyond their noses. And they would all rather fight against each other than try to work together to make this unfunny universe more a joy to live in. They are always right and everyone else is always wrong.

It’s also all the collateral damage. Everything we hear and read about the environment is unavoidable doomsday-esque. It’s hot, it’s on fire, polluted, becoming scarce, radioactive, dead and extinct animals, no more butterflies and bees, oil-covered ducks, fish with mercury, children drinking lead, calamitous storms, and not one acre on the planet without a human footprint. Instead we shove the flag of Planet Plastic waving over a scorched earth. I try to do more than recycle and reuse, but it’s like taking one grain of sand from the Saharan desert. Meanwhile, I’m surrounded by frenzied shoppers on their cell phones and their loud cars.

Then I found the perfect descriptor from the book, “Who Will Run the Frog Hospital?” (By Lorrie Moore): “The bad news of the world, like most of bad news, has no place to go. You take it to the bulletin board part of your heart. You say, ‘Look’. You say, ‘See’. That is all.”

This has been the bulletin board, translated and deciphered.  But there’s still a pin hole in my heart.

The obese 'horse' and the diabetic cart

The link leads to an interesting article by a biology scientist. I especially appreciate his discussion of models for obesity. However, he shifts from criticism of the standard model, mouse, to using that of bear. Which may or may not be more useful.

Regardless, he, too, falls into the same pit as so many others: the 'bandaid' approach. Putting the cart (solution) before the horse (cause). Or, putting a bandaid over the wound without addressing the causes (which are multifactorial).

Universally neglected is how to educate, encourage and motivate humans to eat less and increase activity. The solutions, such as behavior modification and choices, could solve many of the associated issues with obesity and diabetes: weight gain, dysfunction of insulin sensitivity and glucose regulation, concomitant and/or subsequent metabolic illnesses (inflammation, cardiac dysfunction, etc).

Why does the medical and scientific communities ignore the psychology of eating and sedentary lifestyles? No drugs or animal models will magically solve these dysfunctions. Let's start with healing the horse first, then we can address the cart. 

Image by Rachel Sumpter

We construct or deconstruct our future

“Many crucial issues need to be handled globally, and involve long-term planning. In contrast, the governmental focus is on the short-term and the national or local. Moreover, the actions of large corporations are less and less easy to regulate by any government.

In tackling climate change, for instance, we are asked to make short-term sacrifices for the benefit of people in remote parts of the world 50 years (or more) into the future — to pay an insurance premium now, as it were, to reduce the probability of a worst-case climatic disaster during the lifetime of a child born today. Politicians are influenced by the press and by their inboxes. So these actions will slip down the agenda unless there’s public pressure. Governments will only prioritize these actions if pressured by a popular crusade. But that’s how all big social changes happen: abolition of slavery, black power, gay rights, etc.”. - excerpt from interview with Martin Rees, astrophysicist

What separates children from adults, and humans from non-human primates, is the ability to think about time over long-term. That includes predictions, actions, consequences, and planning. Unfortunately, the tendency is to think short-term and even disregard long-term. I call it the “Me Now” mentality. Most profit-driven interests are short-term, and governmental actions have been following suit.

However, most successful businesses are those that plan for the long-term, while also considering short-term. Most financial planners, historians, and ecologists are trained to think in terms of many timelines: past, present and future. But our culture and society tend to nurture short-term goals and ignore or deny long-term predictions and consequences. We are experiencing the effects of that now; especially in the current economic and political arenas.

It’s time to change that. We are not children, and we are not monkey or apes.

Or, are we?

Don’t wait until it’s too late.

Why shine a light on my own past, 30 years later? Why speak about this so publicly? I have had a good career and achieved most of the things I had hoped to. Why rake up the past? Why not stay silent as I have for three decades? 

If a person who has reached the highest point in their specialty still feels ashamed of events 30 years ago, and is reluctant to admit it, how must those who are going through things and feeling disempowered now feel? I am determined to use my own example to point out that mental health problems are nothing to be ashamed of.*

This is sobering. Depression and suicide are not limited to just medical practitioners. It’s more common than many suspect, but it remains mostly invisible. It is a silent killer. It’s like a leprosy that no one wants to be visible or share. Relationships, families, jobs, and lives can crumble. Uneedlessly.

Anyone that has or had a friend or family member with depression knows. Many times too late.

Please. Don’t let this happen to a friend or family member. No one is an island.

*  Dr. and Professor Steve Robson, President of the Royal Australian and New Zealand College of Obstitricians and Gynecologists, in “Learn from me: speak out, seek help, get treatment.”

Academia is failing and everyone is responsible

I chose to retire early because the academic environment I was in had become toxic. And not just for me.

In addition to working 9-10 hours, sometimes more, and having a four-hour daily commute, the academic environment had become dysfunctional. In addition to experiencing discrimination, increasing (often unreasonable) demands, incompetence at all levels of administration, support and guidance was not only lacking, but often there was no accountability. Many PIs lacked people and group management skills, department heads often overlooked bad behavior and management, and too many times the university Human Resources either overlooked or refused to intervene when valid complaints were reported. This lack of accountability only enabled poor lab environments at the expense of productivity, quality research, and satisfaction by all lab members. Education also suffered collateral damage.

In the capacity of most of the strata of that hierarchy (except as department head and institutional office) over several decades, I have seen many bright and capable students, staff, and even PIs, leave academia. I (and a colleague) left one university because of discrimination, harassment and a very dysfunctional department. I finally retired from another university after ten years with similar experiences. During that time I worked with a few colleagues that had exceptional people and management skills, and who also left for other positions and institutions. With sadness, and some anger, I have also seen productive graduate students with excellent potential also leave. Most eventually found a favorable position and institution, but a few left science completely because of their bad experiences.

The culture and system is deteriorating at all nodes and needs attention. I am encouraged to see some attention to these matters in the last several months in a few reputable journals and on social media, especially blogs. However, the focus has been on graduate students, especially post-docs. But that attention and concern needs to broaden out to include PIs, department heads, and institutional management.

Yes, the fault is spread everywhere in the system. So let’s include every participant.


The group at the journal Nature recently posted a poll on their FaceBook group page, Nature News and Comment.

The following was my comment to this poll about people management training in academia:

“I chose “Additional training for PIs” because:

1. I could choose only one.

2. The established hierarchy of the academic unit is PIs at the top. A PI with good skills with people and work management, especially communication, will potentially already establish and maintain a healthy and productive lab environment. That includes training of lab assistants and students.

Additionally, students (and other lab staff) often feel powerless when department heads and even Human Resources do not provide guidance or intervention when complaints are reported. In those cases, the PIs weld complete authority.

3. After perusing the articles in Nature and other journals on this topic, most of the attention is on graduate students. Lacking is focus on improving skills for PIs and the overall members of the culture (including department heads and administration). Glaringly absent is recognition of lab assistants, especially lab managers, who often are the surrogate lab nanny and educator.

Being retired has allowed me to reflect on the past 28 years serving in the capacity of all points in that hierarchy (except department head). At each node is the ability to contribute to a healthy, productive, and satisfying academic experience and culture for all.

However, it seems that the appropriate skills have deteriorated, and awareness of that has fared even worse over the last two decades. Academia and the culture, including the institutional, have generally but not universally deteriorated, with both education and research suffering. I have seen many bright graduate students and PhDs leave (myself included). And it needs “fixing” at every node in the system.

Why place the burden solely on the students?”

As you think we know........

Thetis: “Why then, child, do you lament? What sorrow has come to your heart now? Tell me, do not hide it in your mind, and we shall both know.”

Achilleus: “You know; since you know why must I tell you all this?”

The Iliad, Book I

As a writer I really have few ‘pet peeves’. If you place a comma in the wrong place, if you use quotation marks instead of apostrophes, or other slights and ambiguities of punctuation, we still get your meaning. If you weren’t raised on the Strunk and White bible, “Elements of Style”, don’t stress it. Strunk be damned and White was a hypocrite (he himself advocated ignoring his manual). As long as you use appropriate periods and spaces, you can get your message across. We really don’t have to be style Nazis.

However, a pet peeve that I do have, or it has me, is overuse of “As you know.....” or “As you already know.....”. YES WE ALREADY KNOW! Or NO, STUPID; HOW DO YOU EXPECT US TO KNOW?!

It’s a tropism used in writing fiction; a literary tool to give information or explain something to the reader that they don’t know otherwise, or have forgotten. But it has to be used carefully and not assuming that the reader (or audience) doesn’t know or does know where the lead in is going. But if the writer, or speaker, assumes that the reader or audience knows, and when that assumption has a high probability of being wrong, THEN DON’T USE IT! Recall that commonly used cliche! “‘Ass-ume’ makes an ass out of you and me.”? Well, it makes more of an ass out of the person that assumes, and it irritates the hell out of the ‘me’.

I see the use of this misplaced trope much too often on blogs and other social media, especially posts on FaceBook. “As you know, I moved across the country to this location.” I think to myself, ‘If you know we know, then why tell us that we already know?!’ It makes me want to shake the writer, or pull a Gibbs and smack the writer on the back of the head (TV series NCIS reference). Don’t use this trope unless you are writing a novel!

I have heard this trope used in some presentations, but it is placed well as a segue or to invite a question from the audience. Example: “As some of may know, not all grasses use the same photosynthetic pathway. Some species use the C3 pathway, others may use the C3 and C4 pathways.” Assumptions that all those in the audience know this is not implied, and the speaker explains a setting for the rest of his talk.

If you are writing a novel or short story, and a character needs to fill in a gap, this trope can be handy in dialogue, such as the example above of the speaker’s use, or to refresh the reader’s memory of an immediate and pertinent point. It can also be used to imply character personality, especially arrogance, such as with the famous character of Sherlock Holmes.

But if you don’t want to appear arrogant or pretentious, then DON’T USE IT!!

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.

Curses!

Long quote for the.......... (choose arbitrary time line).

This one is a keeper.

“2. I mostly don't often admit this, even to myself, but at times I can't ignore it. Movies really suck. Most books. Most music; art, architecture, civil planning, project management, military strategies and politics are awful. They are ill conceived and poorly implemented. We've gone to the trouble to document the hard earned learnings of our lengthy civilization only to set them aside, all over again, every generation. 

It can be awful to sit in a restaurant alone and overhear random people chatting. Many are self-centered and infantile, focused on all the wrong things, misunderstanding what matters and how things work. They scar their own children unaware and make choices that can only harm themselves in the future. Meanwhile, outside the window, the cumulative cost of a huge and powerful society of mental middle-schoolers is baring down on us. Our society not only denies truth, it acts to suppress it; to rewrite it, but that only insures we will lose eventually.

We require money to feed ourselves, so off to work we go. You do not pick your co-workers or bosses. Diversity is important and powerful, but nature loves a bell curve, so you know some of the people you interact with will be the sports and celebrity chat show set. You soon discover that people do not pick leaders for intelligence or maturity or wisdom. You know you will be tasked with inefficient, unhelpful work. You know that when you see change coming, you cannot say so, because they hate you more for being right than for being wrong. Sometimes, you know more about a person than they know about themselves. They don't realize that the messages their subconscious sends out are perfectly clear.

So, the second point is, yes it can be seriously depressing to be ruled by corrupt children, fed on junk, surrounded by monuments to poor decisions and weak literature.”

(Really excellent post and very long but enlightening, somewhat entertaining, thread of comments.)

No Single Diet for a Big Planet

The increasing pressure for everyone to convert to a vegan diet smacks of ignorance and righteousness. Yes, that includes scientists, and shame on them.

This stated universal solution for the health of everyone on this planet and all the ills of climate change is fraught with negligence to the fact that not every person can subsist in good health on a vegan diet. Nor is it necessary (some bold scientists have published data on why).

While the public, and many scientists, claim that adopting a vegan diet is the most important way to lose weight, be healthy, reverse climate change, and treat the planet better, there are reasons to believe this isn’t always the case. Despite the prevalent binary thinking and judgement of our Western society, fad science, and culture, there is no one, universal, de facto “right” diet for everyone. Our genetics, physiology, medical history, economic status, food accessibility, and aesthetic tastes are vastly varied. Absolutisms are rarely absolute.

Many people have food sensitivities and/or allergies: allergies to peanuts, gluten-related disorders (including wheat allergy and insensitivity to fructans), intolerance to yeast and/molds (such as in leavened breads, beer and several cheeses), phytates in m,any legumes and vegetable (taboo for people prone to kidney stones), “onion intolerance” (sensitivity to ingestion, even dermal exposure, to one or more plants in the Allium family), fructose malabsorption (bad things happen when eating even a small amount of most fruits), legume (including soybeans) intolerance/allergies, and the list goes on. People with these sensitivities and allergies may be unable to commit to a vegan diet without jeopardizing their overall health.

Another topic rarely seen in the lay media, and uncommon in the scientific literature, is the nutrient efficiency of a diet containing even a small amount of animal products - meat, milk, yogurt, cheese, eggs. By comparable weight, animal food products contain more protein (especially in the context of complementary amino acid profile), bioavailable minerals, and energy than any non-animal product. 

The cautionary point here is that most of the consumed energy is in the form of lipids, aka ‘fats,’ especially cholesterol. Primates -yes, us, too- evolved to store dietary fat for emergency energy in cyclic periods of famine. However, in our modern world of convenience and accessible plenty, we no longer need as much, and eat too much of it. Also, removing excess fat and eating naturally lean meat is an alternative.

The loud proclamation that everyone should embrace a vegan diet is unwarranted and impossible for many people. Nor should the reason of significantly reducing our carbon footprint be justification for imposing guilty consciousness. Some people just can't adopt a vegan diet. Moreover, a universally adopted vegan diet will not solve the demand for food and reverse climate change. 

Research at the USDA-Agricultural Research Service found that removing animal protein from the diets of many people would increase nutrient deficiencies that have been associated with certain health risks, like cardiovascular disease. Mary Beth Hall, animal scientist and one of the study researchers  at the U.S. Dairy Forage Research Center, comments in a press release,

“Different types of carefully balanced diets — vegan, vegetarian, omnivore — can meet a person’s needs and keep them healthy, but this study examined balancing the needs of the entire nation with the foods we could produce from plants alone. There’s a difference between what’s possible when feeding one person versus feeding everyone in the U.S.”

More importantly we should put more emphasis on growing some of our own or buying locally produced food, learn to make better food choices, eat balanced meals of both vegetables and animal products, plan meals centered around seasonally available foods, and stop piling so much food on our plates. 

Oh, and spending less time on our devices, in our vehicles, and getting off our butts and moving around around would not only reduce our appetite, improve our health, and possibly shrink that carbon footprint. Add supporting informed policy change at the local, state and national levels, too.