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.

Sobering thoughts for a Sunday morning

"We have become the United States of Spite, and we are in this condition because it serves the interests of the plutocrats to have us at each others throats as our quality of life disappears upstream.

This new administration has set about undoing every good thing government has done for us, one vile rescission after another. And they do it with a righteous glee that sickens me. They do it with a logic that is not logic, using facts that are not facts. And they're cheered on by people who are likely to be among their worst victims.
 

It's hellish."

This is your reality now, and mine.

"....By the time I was 19 years old, I came to view awareness not as a gift, but as a curse." - Guy McPherson, ecologist and revolutionist.

The theme of this blog over the more-than a decade existence is reality; the realities that exist, that overlap, and those realities in which we choose to exist.

Reality is like multiverses; there are many. One of the past, one of the future, and the combination of these which is the present. Is there one reality? Yes and no (the typical biologist's response to questions).

A reality exists that is outside of our body and minds. Some may call this the 'truth', but that's not exactly accurate. Some may call this 'nature' or 'science', but those are just names we apply to what we really may not know. Or what we think we know.

"Get your facts first, and then you can distort them as much as you please.”- Mark Twain

Hey, but Reality is all that is factual, right? Sometimes, sometimes not. Mark Twain understood what facts really are. Yes, facts are schizophrenic. There are facts whether or not anyone can prove they’re true. Facts do not generally depend on our beliefs or desires. They exist whether or not anyone thinks about them, proves they’re true, and so on.

The law of gravity exists whether or not anyone knows about it, thinks about it, proves it, or believes it. We know this because the fact about gravity is a testable statement, and it has been tested multiple times, over and over. We experience it every day. Thus, as a society, we have labeled it a 'fact'. Evidence we have collected by rigorous testing as a society has been put forth to a collection of people that has accepted it as a 'fact'. However, there are many 'facts' we don't know about. Yet.

Facts, including the word, are used loosely in our language. They can be considered and used in several forms of realism: physical, scientific, epistemic, and moral. In the latter, some facts depend on thoughts, beliefs, and proofs (to some extent). Those are facts about what people think, believe, or prove. Some may not exist in any of the other forms of realism. It is here where Mark Twain saw humankind.

As a scientist, my beliefs center on facts, as they exist in all facets of realism. Often, especially in recent times, this has not been an easy process to reconcile between conflicting evidence and reporting. In the realm of moral realism, sometimes evidence and facts are presented as statements that align with prevailing or personal beliefs. It is the explosion of this type of realism that challenges myself, and everyone of us, to think more critically in what we acknowledge as being factual, despite that it exists or does not.

"Sometimes people just dispute the validity of specific facts. But we find that people sometimes go one step further and... they reframe an issue in untestable ways."- Troy Campbell and Justin Friesen, Why People Fly From Facts. 

The increasing numbers of people choosing to disbelieve, or ignore, evidential and tested factual information continues to astound me. When challenged with tested facts, and providing evidence, people choose (consciously or subconsciously) to accept or not accept both the evidence and the fact. Observations of discussions with people have made me aware that, even when presented with tested or testable facts, they will not change their beliefs, which are tied into their desires. This has been tested and studied, with the same conclusions. Personal bias is the strongest realism that sometimes will trump any that is substantiated by physical, scientific, and epistemic processes.

"Unfortunately, we’ve also learned that facts can only do so much. To avoid coming to undesirable conclusions, people can fly from the facts and use other tools in their deep belief protecting toolbox." - Campbell and Friesen.

 The predominant collective reality is based not on science, not the physical, and not epistemic processes, but personal bias. It is the new disease. And this is what prompted me to run away from 'The Empire' (coined by Guy McPherson) and embark on a life of simplicity, and a mission to help preserve and conserve the environment and wildlife. This is what has kept me awake at night off and on for the past six years, but recently more pronounced. And it is this which I try to reconcile my hope in our species, and the reality of what is happening at the national and global scales.

A comment appeared on social media in response to a column in the New York Times, "The Death of Compassion". Author Charles Blow traces the beginning and sanctions of this country's rampant loss of compassion, from Ronald Regan and now to the Trump administration.  The comment to this reminds me of our choices of reality; "Cultural anthropologists say that empathy is "programmed in" to the human consciousness, or we would not have evolved or be here as a species today. A lack of it may end the long journey..."

This statement sums up many events and struggles occurring in our country and around the globe. Yes, there are still small pockets of compassion and altruism. But they are shrinking fast.

We are seeing today an acceleration of a collapsing civilization, similar to the process in overpopulated groups of animals faced with increasingly limited resources (population dynamics). Animal species and groups have their own inherent checks and balances, but when that fails, they fight and kill each other. Mice will even eat their babies. Observing that as a child was my first lesson in population dynamics.

A few historians and sociologists recognized this, speaking out and publishing in academic and public media on societal collapse as far back as 2009: "....we now live in an era when multiple, large-scale, interconnected structural crises have pushed the global system to the threshold of catastrophic collapse" (Kuecker and Hall, 2011). In his book, The Population Bomb, biologist Paul Erlich warned of the consequences of overpopulation and limited resources. Like most of the general public, even some scientists called Erlich a "Doomsayer".

Some sociologists predict that small communities are the most resilient and most likely to survive (Kuecker and Hall, 2011). We have seen this cycle before throughout human civilization, but not on this scale around the world (Childs, 2012). Several biologists and ecologists increasingly join the conversation and offer evidence of collapse (McPherson, 2011).
 
It seems that only those people that are aware of this speak out. Several predicted our current situation and dysfunction. Many of these people are educated. But they have been discredited as Doom and Gloom Sayers. And ignored. I, too, discounted them. But no more. 

 "The world looked insane to me, but nobody else seemed to notice, so I buried my thoughts, and muddled on. Deep inside, this was tearing me to pieces."  - Tim Bennett

Most people are too caught up in the developing chaos to be aware and acknowledge it, and thereby contribute to the process. Many scientists are torn between taboo emotion or gagged by their institutions. The Empire is falling and the power struggle is on full-bore.

"The unwise man is awake all night, worries over and again. When morning rises he is restless still." - Unknown

America is no longer the "land of the free". It is playing 'the game', internally and abroad. We are not immune, and we have ourselves to blame for allowing this to happen here.

"With the disease of bias, then, societal immunity is better achieved when we encourage people to accept ambiguity, engage in critical thinking, and reject strict ideology. We will never eradicate bias—not from others, not from ourselves, and not from society. But we can become a people more free of ideology and less free of facts."  -  Campbell and Friesen.

Now is the time to be a Warrior. The facts, the realism -the physical, scientific, epistemic, and moral- have all coalesced into one Reality. This is our world now, and we must shape it otherwise. Or someone else will shape it for us.

For many scientists and activists, gloom is building. We have "stopped believing the stories our civilization tells itself." (Dark Mountain Manifesto, Paul Kingsnorth, longtime climate activist and novelist). If we don't act, we can add the Gloom to the Doom. Time is overdue to act.

"Trump is a cancer on this country and resistance is the remedy. The Trump phenomenon is devoid of compassion, and we must be closed to compromise. No one need try to convince me otherwise. The effort is futile; my conviction is absolute. This is a culture war in which truth is the weapon, righteousness the flag and passion the fuel." - Charles Blow.

•  Bennett, Tim. What a Way to Go: Life at the End of Empire, movie by VisionQuest Pictures.
• Blow, Charles. 2017. "The Death of Compassion," The New York Times,  Feb. 23, 2017.
• Campbell, Tony and Justin Friesen. 2015. "Why People "Fly from Facts"", Scientific American. March 2, 2015.
• Childs, Craig. 2012. Apocalyptic Planet, Pantheon Press.
• Kingsnorth, Paul and Dougald Hine. 2009. Uncivilization: The Dark Mountain Manifesto, self-published. 
  
• Kuecker, Glen David, and Tomas D, Hall. 2011. Resilience and Community in the Age of World-system Collapse. Nature and Culture, 6:18-40
• McPherson, Guy. 2011. Walking Away from Empire: A Personal Journey. PublishAmerica, Baltimore, Maryland.PublishAmerica, Baltimore, Maryland 

This is becoming your reality

It has begun........

 

Those people that struggle will be struggling more. The inequality will grow wider.

Censorship and propaganda will proliferate. You will know only what the Dictator wants you to know. The federal government will have no transparency.

This is what you voted for. Be prepared to shoulder your responsibility in this.

"Soon after Donald Trump was sworn in as president, his administration undid one of Barack Obama’s last-minute economic-policy actions: a mortgage-fee cut under a government program that’s popular with first-time home buyers and low-income borrowers. The new administration on Friday said it’s canceling a reduction in the Federal Housing Administration’s annual fee for most borrowers. The cut would have reduced the annual premium for someone borrowing $200,000 by $500 in the first year."

and

"Within hours of the presidential transition, the White House, now under the control of President Donald Trump, took down the Native Americans web page that was part of the Obama White House website for the past eight years.

Also gone from the Trump White House website are web pages on civil rights, people with disabilities and climate change.

New to the White House website is First Lady Melania Trump biography, which is normal when a presidential transition occurs. What is not generally done though is promoting a First Lady’s product, as is now the case. The new web page mentions her  jewelry line sold on QVC."

and

 "‘‘All bureaus and the department have been directed by incoming administration to shut down Twitter platforms immediately until further notice,’’ said an email circulated to Park Service employees Friday afternoon."

and

"Shortly after President Donald Trump raised his right hand and took the Oath of Office, the Joining Forces page on WhiteHouse.gov went dark."


This is only the beginning. To be silent, is to be complicit.

Modern stressful life and depression

"While being physically ill causes inflammation, it is far from being the only cause. Modern life itself seems to be a state which our body responds to negatively."

An article, Depression Is Only Partly a Psychological Condition, links depression, physical illness, and inflammation. But it is more complex than the process explained by the author.

"While the symptoms of depression are marked by changes in the brain, the cause of the disease may ultimately lie in the body, specifically in a family of proteins called cytokines that set off inflammation."

 One component missing here, but alluded to, is stress. Chronic stress sets off a cascade of inflammatory responses, which affects physical and mental health. For a review of the complex links of chronic stress, depression and many physical illnesses, I recommend a review by G. Slavich and M. Irwin, From Stress to Inflammation and Major Depressive Disorder: A Social Signal Transduction Theory of Depression.

"This highly conserved biological response to adversity is critical for survival during times of actual physical threat or injury. However, this response can also be activated by modern-day social, symbolic, or imagined threats, leading to an increasingly proinflammatory phenotype that may be a key phenomenon driving depression pathogenesis and recurrence, as well as the overlap of depression with several somatic conditions including asthma, rheumatoid arthritis, chronic pain, metabolic syndrome, cardiovascular disease, obesity, and neurodegeneration."

 A complex environment of chronic stress, poor eating habits, and lack of exercise is probably responsible for more of our modern health (physical and mental) issues than most people realize, and it seems to be an acceptable state of normality in our modern world. No wonder that depression is at an all-time high.

We've been here before.......

Here we go again.
"I feel like 
I've been here before, 
and you know, 
it makes me wonder, 
what's goin' on, 
under the ground."*
Déjà vu.


But this time, those that rose to protest and civil disobedience in the 1960's are silent or a whisper. Instead, the soma of a privileged class is complacent like walking zombies hooked into a global information stream that has made them numb and elite.

How is it that many of those same protesters of the 60's are silent now? Many that I know personally are talking heads that spew drivel and blindly continue on their indignant paths of privilege.

Some are so full of anger that their mouths and fingers waggle at everyone but themselves as they claim that anarchy is the only way to righteousness. Without admitting that those they voted into office are responsible, or denying they support the tyrants and bullies. Compassion is no longer an option, they cry. "It's all your own fault!", they sigh. And go back to their handwringing while mouthing on and on.

Too many hide behind religion as their flag to change the rules. The old power that whispers behind hands and shouted with self-righteous justification for their own ends to control and bully. Power is their deity that hides their quest for control in the name of a God that vindicates all their words and deeds. While the ghosts of the Spanish Inquisition urge them on and laugh at our ignorance and division.

Do they not realize they are the same as those they label as terrorists, 'unholy', and destroyers? Is spreading their own version of terror their personal salvation?

Some have struggled through darkness and wrestled with their conscience, dropping out of the Rat Empire to advocate awareness, truth and change. A few even campaign for radical change, while feeling mostly alone in a sea of hypocrisy and hopelessness.

And there are those of us that see the ghosts of people in the streets wearing arm bands, waving banners. Some put fingers to keyboards to call attention to the hell that is breaking loose around us. Some thrust mirrors in our faces and point to the public horrors and plights. Others try to pull heads out of the sand and hands away from deaf ears.

But where are the songs? Where are the Pete Seeger's, and Dylan's, and Joan Baez's? Where are the marchers, chanters, and changers?

We drown in words that flash across the TVs and smart phone screens until we are desensitized, dazed and confused. They mean nothing anymore. And we drown in all the noise.

We need the songs and feet on the ground.
'Bang the drum slowly' while we drag our feet.
Take up the voices while moving the beat.
Because we are at war here.
And it may implode.
But the only ones that we can blame,
Are ourselves
In hidden shame.


*Crosby, Stills and Nash, Déjà Vu. 1970.

The Rule of Seven. Happy New Year, Self!!

I hate the number seven. It seems that every seven years, my humanity is tested. Sometimes the trial is tough, challenging, and sometimes I fail. Trip and fall. Hit my head and have a headache for a year. But I always get up, put myself back together and carry on. The Survivor mentality. 

Or, as my father used to say, "What doesn't kill you makes you stronger."

“By knowing things that exist, you can know that which does not exist. That is the void.” - Miyamoto Musashi

This time was another test of my humanity. It wasn't as devastating as it was back in 2006. But, then again, I'm not as young as I was either. And betrayals never get any easier to bear. Again, this was partly my own fault for forgiving an earlier transgression that I should have not have. 'Another chance,' I convinced myself. And it bit me a few years later.

"I feel like 
I've been here before, 
and you know, 
it makes me wonder, 
what's goin' on, 
under the ground."
Déjà vu.

Lesson hammered home. The Void.

Yet..... if this past trial had not happened, I would not be where I am now. I am strong, happy, productive, and full of life. Living what exists now, I also know what no longer exists. And I am grateful for that. Rising from the ashes and flying with flames of rebirth. "In my pockets, I carry new-found fruits and seeds that nourish my journeys. And scatter some along my way."

Happy First Anniversary, Phoenix. Welcome back, you old wolf. 
Let's go, brother Coyote. We have an adventurous road of discovery ahead of us.

“The truth is that strength lies in the interior of the Warrior: in his heart, his mind and his spirit… The heart is essential in helping the intellect to understand the spirit.” - Miyamoto Musashi, Book of Five Rings

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."

Why Academics' Writing Stinks - The Chronicle Review - The Chronicle of Higher Education

Why Academics' Writing Stinks - The Chronicle Review - The Chronicle of Higher Education



"Why should a profession that trades in words and dedicates itself to the
transmission of knowledge so often turn out prose that is turgid,
soggy, wooden, bloated, clumsy, obscure, unpleasant to read, and
impossible to understand?"



Uh huh. 

Science in the hands of the beholder

My ex-partner and I had an ongoing argument on university-based scientific research. He adamantly opposed publicly-funded research. His stance was that science research should be privately funded at private institutions and companies.

My primary argument against his assertions was that profit drives private and business-based science. Research is funded by these entities only if they result in a marketable product that nets them capital gain. Public research is motivated by basic, transitional and applicable science. And human compassion.

Additionally, discoveries originating at public institutions are supposed to be free to the public and commercial development. They are shared. Discoveries from commercial research are not shared; they are sold.

The current danger of global antibiotic resistance is an example. The Soviet Union had developed and relied upon using bacteriophages as an alternative to antibiotics for decades. They were forced to because Russians were denied access to some of the best antibiotics developed on the rest of the world. Many countries of the former Union still use phage therapy today.

Faced with the looming disaster of antibiotic resistance, many Western researchers and institutions are now collaborating with former Soviet Union scientists to investigate and develop phage therapies. New projects are funded by governments and non-government and non-profit organizations. They hope to quickly determine which phages target disease-causing bacteria. Because a phage is specific to a bacteria species, phage therapy will not only reduce the risk of resistance but also avoid wiping out the beneficial bacteria.

Most Pharmaceutical companies, on the other hand, have not only discontinued their antibiotic R&D, but are also reluctant to get on board with the phage development. They would not likely be able to claim treatments as intellectual property or patent any phages isolated from nature because of last year's US  Supreme Court ruling against patenting natural genes. In other words, they would not be able to make a profit.

Case made.

A-X Challenge: Y. Yodel?

Due to an accident and injury, the last two days of this Challenge were postponed.

Music is language. Not necessarily in word, but in tone, mode, and forms. Yodeling, and its various forms, probably originated not in music but as a form of communicating information by sound. Later it was incorporated into ethnic songs and music.

Most are familiar with the yodel of the commercial for menthol cough drops in the Alps, or in older country and western singers, such as Jimmie Rogers. But few are aware that the 'yodel' is only one expression of a wider form and expression of voice.

According to Wikipedia, yodeling is a "form of singing which involves repeated changes of pitch during a single note. The singer quickly switches between the low-pitch chest register (or "chest voice") and the high-pitch head register or falsetto." The most familiar to American listeners is the yodel from the Alps, where the yodel was used by herders to call their livestock or to locate their location to others. Yodeling and whistles were also used by some indigenous African hunters to communicate location of game and themselves. In almost all cases, this form of communication became embedded in their traditional music, especially during rituals.

Other forms of yodeling are found in many ethnic folk music: Persian, Bulgarian, Arabic, Flamenco, Georgian, and African. The differences can be profound or subtle. In contrast to the wide variation in scale and tone of yodel of the Alps, another form is common in the former Persian countries. Any person that has listened to the morning or evening Islamic call to prayer never forgets the eerie yet entrancing trills that float on the air.

"In Persian classical music, singers frequently use tahrir ("tremolo" in English), a yodeling technique that oscillates on neighbor tones. It is similar to the Swiss yodel, and is used as an ornament or trill in phrases which have long syllables, and usually falls at the end of a phrase. Tahrir is also prevalent in Azerbaijani, Bulgarian, Macedonian, Turkish, Armenian, Afghan, and Central Asian musical traditions, and to a lesser extent in Pakistani and some Indian music."- Wikipedia

Voices using micro-intervals and polyphony can still be heard in ethnic and folk music of some European countries. Microtonal music can refer to all music which contains intervals smaller than the conventional contemporary Western semitone. Think of mini-yodeling.

My personal favorite is flamenco, which is rooted in the Andalusian gypsies and ancient Moorish influence. The cante flamenco, or 'flamenco song', often uses micro-intervals and polyphony to express passion. 'Cante jondo' is considered the purist form, the heart and soul, of flamenco voice; it is the 'deep song', expressing death, anguish, despair, or religious sentiments. Cante jondo is often accompanied by flamenco guitar, but also sung to the percussion of hand claps and stamping feet or a cappella (without instrumental accompaniment). 

Flamenco singer Camaron De La Isla championed the traditional style of cante jondo, as did others that followed him (such as Enrique Morente, who passed away in 2010). You can hear a podcast examining Camaron's career and flamenco voice by following this link (Camaron De La Isla: The Voice Of Flamenco).

Variations of a yodel my be heard in other traditional music.  Mugham is a style of music and voice of the Azerbaijani people in the Caucus mountains and nearby. This, too, has roots in old Persian music style.

"The full throated yodeling technique of the Kavkaz Azerbaijani ashikh lends an extraordinary power to the elegant and folksy melodies they employ while accompanying themselves on the saz, a long neck lute. When these two great and ancient musical traditions met and mixed, they gave birth to an extraordinary style of music that is evolving. To best appreciate mugham, it should be understood as a modern development of an ancient practice, which is the use of sound to induce a transformation of consciousness. Today this might be called trance music, but it would not be a good translation, because the word ’trance’ is associated with the hypnotic trance, whereas mugham offers an enhancement of consciousness, not a loss of consciousness of any degree.

Melodies used to attain ’trance’ states are relatively simple and repetitive, and versions of this can be found throughout the Middle East, Africa and Central Asia among the more nomadic tribes. In the cities, the more ’classical’ styles of music evolved, such as dastgah and mugham. In this sense, mugham is modern. It is as evolved in its form as the great classics of European music are in their form." - Visions of Azerbaijani

Another example of voice that incorporates a type of yodeling is the folk music of Bulgaria, exemplified by the wonderful Bulgarian State Television Female Vocal Choir. They use diaphonic singing and distinctive timbre, as well as modal scales and dissonant harmonies, usually unaccompanied by instruments. Their voices are melodic and captivating. If you listen to the song embedded below, you can detect the micro-intervals of voice that, again, is a type of yodeling.

So now you know that yodeling is not relegated to the Alps or American country singers. You might even be enchanted by the various forms in other world music like I am.

A-Z Challenge. Xēros and xerosere.

The letter 'x' is rather lonely. Compared to other letters of the alphabet, not many words begin with this letter.

My first association with any 'x' is the female chromosome. But that's an abstract association: the shape of the female chromosome is 'X'. I suppose that might be a legitimate blog post for today's letter, but let us venture into a word that does begin with 'x': xēros. Then we will slide right into another word that descends from xēros: xerosere.

The etymology of 'xero' is from the Greek xēros, which means 'dry'. In combination with a noun or vowel , xero- indicates dryness. Now, if we add the suffix sere, we have 'xerosere'.

Sere is derived from the modern word 'series', which means a group or a number of related or similar things or events arranged or occurring in temporal, spatial, or other order or succession or sequence. The two words were combined as xerosere in the late 1920's to refer to the series of changes occurring in the ecological succession on dry soil, including bare rock.

A primary component of a xerosere is limited water availability. Deserts, rocky places, and lava beds are examples of the type of ecological succession that typifies a xerosere.

Xerosere

This begins on exposed parent rocks or dry sand. The pioneer plants in the primary succession are lichens and mosses which help in forming soil by accelerating erosion. In time, herbaceous vegetation such as grasses, etc., grow on the soils deposited on rocks and enhance weathering. As these plants die, they add nutrients and organic matter to the forming soil deposited on and around the rocky areas.

Mixed shrubs then establish the area, which attracts birds and mammals. These animals help in the succession by dispersing and depositing seed. Intermediate plants develop and form a transition community. Eventually a climax community (also called a 'biome') establishes itself where populations of plants or animals remain stable and exist in balance with each other and their environment.

The following is an example of forest xerosere on barren rock.

1. Bare rock is first colonized by lichens and bacteria.
2. Small amount of soil formed by the lichens is colonized by mosses, which do not have roots and require little soil, and ferns.
3. As the seedless plants live and die, the soil continues to develop to the point that grasses can successfully grow and a grassland community forms.
4. Over time, the soil level increases to the point that shrubs can grow in the grassland.
5. The grassland is replaced by a shrub community.
6. The shrub community may be gradually be replaced by a forest.

A desert xerosere is quite different than that in an environment with greater water availability. For those that live in the deserts, I invite you to look around you and ponder how such a progression of a stable ecosystem might proceed from bare rock or sand. Consider the time involved in these changes, and then consider your own role in this progression.

A-Z Challenge. Wonder and Wisdom

"Wisdom begins with wonder." - Socrates

"The only true wisdom is in knowing you know nothing." - Socrates

"Socrates liked to tease his interlocutors by saying that the only thing he knew was that he knew nothing. There is a deep insight in this, for the one thing that is more dangerous than true ignorance is the illusion of knowledge and understanding. Such illusion abounds, and one of the first tasks of philosophy – as wonderfully demonstrated by Socrates in Plato's "Meno" – is to explore our claims to know things about ourselves and the world, and to expose them if they are false or muddled. It does so by beginning with the questions we ask, to ensure that we understand what we are asking; and even when answers remain elusive, we at least grasp what it is that we do not know. This in itself is a huge gain. One of the most valuable things philosophy has given me is an appreciation of this fact." - Anonymous quote

To wonder is to keep alive and fresh the child's curiosity. For, indeed, there lies the beginnings of wonder and wisdom. And the beauty of life.

A-Z Challenge. V is for.... Volk?

Americans have their common generic name, 'Smith'. Germans have their common name, 'Volk'. I can always recognize upon introduction a person that speaks German when they pronounce the word as 'Folk', which is the correct German pronunciation.

The etymology of the word, 'volk' is interesting because it has several derivations. The noun 'volk' is the generic German and Dutch word for 'people' in the ethnic sense. The Old English noun 'folc' was derived from the an early German term, and was used in reference to 'common people'. Hence, the modern English word 'folk' has the same meaning and pronunciation of the German 'volk'.

The German 'volk' is now used often in compound words, specifically determining 'of the common people'. The most well-known example is the popular little car Volkswagon, literally translated as 'the people's car'. Another example is the 'Volkswalk' (a common event of public walking groups).

Of course, it also is a common surname. In fact, it is my family name and I wear it proudly. And there are other Volk's in the American science community, such as a a chemist at UTHSC in Houston, TX, a biologist at SUNY-ESF (Environmental Science and Forestry, Syracuse, NY), and an anesthesiologist in Oregon (whom I met while I lay on a gurney waiting for anesthesia).

I know of three scientists in my own extended family: My father (biochemistry), Sherry (retired biology teacher), and myself (biologist). Considering the large number of siblings in past Volk generations from which I descend from (10-12 siblings recorded in several generations), there may be other distantly-related 'Volk' scientists out there we are not aware of. Maybe we are the 'common people' scientists.

Then again, 'volk' is also Slovenian for 'wolf'. That could explain many things. ;) Perhaps wolves and people have a long shared history together.

Hats off to all you 'Volk's out there!

Da bo vôlk sit in koza cela!

Wolves could be people's best friend. Volk's in kind.
"Wolves had a pre-existing capacity to learn from social partners — and that humans capitalized on that capacity more than 18,000 years ago."

A-Z Challenge. U-FOs?

Roughly 96 miles from where I live is a small remote community called Marfa (Texas). Although the town is mostly known for its density of artists (long history), it's also known for UFOs. The phenomena are called the Marfa Lights.

These lights are observed near US67 on Mitchell Flat east of Marfa. There is even a viewing 'platform' on the side of the highway. A mixture of rural legend (a sibling of 'urban' legend) and perplexed scientists, the lights are an attraction like a magnet for passersby and visitors to the Trans-Pecos area.

Paranormalists have attributed the Marfa Lights to everything from space aliens, to secret federal aerial projects, and to wandering ghosts of Spanish conquistadors. Scientific candidate explanations range from vehicle lights, mirages, glowing gases, electrical charges from surface rock, etc.

Whatever the reality behind these lights, think of a West Texas version of fireflies.

People love their legends. :)

Marfa Lights on Wikipedia.

A-Z Challenge. T is for Toponyms

Edward Abbey once wrote about the human propensity to ascribe everything with a name:

“Unless we can name things, they remain for us only half-real. A man’s name can become more important than his person. A plant, an animal, a thing without a name is no thing – nothing. No wonder we humans like to think that in the beginning was – the Word. What word? Any word at all, anything rather than the silence and terror of the nameless.”

Having shared that viewpoint all my life, I often make up names for things already named. Sometimes things remain nameless. Even people. 

I live in a place where many things clash, including names. It is the desert. 

This area of the southern Big Bend country encompasses a state and national park, a wildlife refuge, small scattered human communities, and a river. All collectively called many names, such as “The Big Empty”. Or “God’s Country”, “Paradise”, “Devil’s Playground”. I recall perusing topo maps before my first trip down there, smirking at some of the names given to landmarks: Dealer’s Gap, Mule Ears, Dog Canyon, Elephant Mountain, and more. Some quite entertaining, some named after a long-dead person, others with religious names, many with assigned descriptive names, such as ‘The Window’.

But when you are there, you sometimes invent your own personal name for a landmark. I christened a peak in Black Gap as “Randy’s Monolith” because my friend Randy was enthralled with its presence. I’m sure it probably has an accepted toponym decreed by someone long ago and propagated over time without dissent, eventually being recorded on a map and copied over and over again.

But if you are truly in the desert, and a part of it, you don’t remember or care about names. You can make up any name you want for anything there. Or see and know landmarks without a name. 

I've always been interested in how people perceive places and how people create meaning through places. I try to listen to the voices, the versions and the scenes. I don't restrict meaning to organized tours, glossy brochures and pamphlets, but try to really find and listen to the many voices of a landscape. Even the quiet voice of the physical environment, for it is not really silent.

Learning how we ascribe symbols to places, events and other people, or names in general, reveals much about ourselves and those that came before us.  We are products of language, thus, language imparts power. Place names, or toponyms, provide valuable insight into the historical geography of a particular region.  These names attached to the physical landscape inform us of its past and present culture, including ethnic settlement patterns.  The other association with toponyms is the dominant voices in the past and the present, and those voices that have been silenced.

Place names can be quite revealing. The Native Americans sometimes gave many names to non-living things, including each other. Not uncommonly, one individual could have many names. Never were they names that Europeans use. No Native American chose to be Robert or Ester without a strong European influence, or even Anglo-American coercion. Even after death, many natives were buried the Anglo way and assigned Anglo names that were inscribed on their headstones. I witnessed this in several cemeteries, such as in Fort Sill (Oklahoma) where Geronimo was buried.

Here is no different. With reluctance I have referenced this region in south Texas as ‘Big Bend Country’. I also call it 'Occupied New Mexico'. But inside my head and heart, it is the desert and canyons, with special locations called 'Home'.

•  For those interested in toponyms, I highly recommend reading this book by Mark Monmonier: From Squaw Tit to Whorehouse Meadow:How Maps Name, Claim, and Inflame.
• Witch's Tit is a mountain in the Big Bend area. And it really does have the shape of a..... breast. 

A-Z Challenge. S. Statement for Today

Today is Earth Day. It should be every day.
It is also 'S' day. So here is my Statement for today.

I pledge allegiance to the Earth, and to the Universe in which it rotates; one planet, indivisible, with liberty and justice for all life. May all life sing on all Days of this Earth.

A-Z Challenge: Quoting a Quark.

"Quack, quack!", said the Quark. He thought he was a duck.

The neighboring Loon looked over and said, "Oh, hum. How elementary. And what is the matter now?"

"I'm not sure. I can't see where my children are! They are always together. Even if they can't be seen," replied the Quark.

"I see," nodded the Loon.

"No you don't. You can't see them!," exclaimed the Quark. "They tend to group themselves in these 'hadrons', as they call themselves. And they seem to elude me all the time."

Loon ruffled his feathers. "Sure; there is probably a very strong force between them. What are your children's names?"

Quark thought for a moment, trying to remember. "I think their names are Up, Down, Strange, Charm, Bottom, and Top. That is, if I remember correctly."

With a shake of his neck, Loon muttered in his beak, "You've got to be kidding me. And they call this 'fysics?'"

In 1963, when I assigned the name ‘quark’ to the fundamental constituents of the nucleon, I had the sound first, without the spelling, which could have been ‘kwork’. Then, in one of my occasional perusals of ‘Finnegans Wake,’ by James Joyce, I came across the word ‘quark’ in the phrase ‘Three quarks for Muster Mark.’ Since ‘quark’ (meaning, for one thing, the cry of a gull) was clearly intended to rhyme with ‘Mark,’ as well as ‘bark’ and other such words, I had to find an excuse to pronounce it as ‘kwork.’ But the book represents the dreams of a publican named Humphrey Chimpden Earwicker. Words in the text are typically drawn from several sources at once, like the ‘portmanteau words’ in ‘Through the Looking Glass.’

From time to time, phrases occur in the book that are partially determined by calls for drinks at the bar. I argued, therefore, that perhaps one of the multiple sources of the cry ‘Three quarks for Muster Mark’ might be the pronunciation for ‘Three quarts for Mister Mark,’ in which case the pronunciation ‘kwork’ would not be totally unjustified. In any case, the number three fitted perfectly the way quarks occur in nature.

—Murray Gell-Mann, in his book The Quark and the Jaguar: Adventures in the Simple and the Complex.

Murray Gell-Mann, born in 1929, is an American physicist who received the 1969 Nobel Prize in physics (or, that 'f' word, fysics) for his work on the theory of elementary particles. Including quarks.