Saturday, December 13, 2014

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 their 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."

Sunday, October 05, 2014

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. 

Tuesday, June 17, 2014

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.


Wednesday, May 07, 2014

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.



Monday, April 28, 2014

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.

Saturday, April 26, 2014

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.

Friday, April 25, 2014

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."