Evolution

Metagenomics

Preface

Metagenomics Definition: The study of metagenomes – genetic material obtained directly from envronmental sample.

Traditionally, a scientist would isolate one species to culture enough DNA for sequencing resulting in the loss of the true biodiversity that existed in the sample.

Shotgun Sequencing (SS)

SS randomly shears DNA, sequences the short fragments, then reassembles these sequences into the correct order – called consensus sequence.

Eukaryotic DNA can be identified and removed, leaving the microbial DNA behind for analysis.

Studies Using Metagenomics

…does each type of mammal have its own community of (gut) microbes?

…the diet of mammals, not the specfic species of that mammal, determines what microorgansms live in the gut.

Metagenomics can also be used as a diagnostic tool to discover causative agents of diseases.

Questions to Consider

  1. Why is metagnomics used versus traditional genomic techniques?

Traditional science isolated and cultured only the most abundant species, resulting in the loss of the true biodiversity that actually existed in the collected sample, metagenomics allows for determining evolutionary interactions in a particular environment by revealing the hidden biodiversity of microscopic life.

2. Why is shotgun sequencing used in the field of study?

In order to gain knowledge on the true biodiversity of all species in a given environmental sample:

SS takes pieces of DNA and sequences the short fragments into the correct order.

The result is defined as a consensus sequence.

3. Why is metagenomics closely tied to evolutionary biology?

When used as a diagnostic tool, it can be used to discover causative agents of disease, such viral evolution, by filtering out DNA of a healthy species to reveal the disease in a sick subject.

Comment:

I don’t get the explanation of Shotgun Sequencing provided by the author.  SS got its name from the broad trajectory of buckshot a shotgun blast produces.  Then, SS is likened to putting ten copies of the textbook in a shredder, taking those pieces out and reassembling a complete book.

Without going further, two consecutive metaphors (1 metaphor, 1 simile) leaves a cub-metagenomicist with a rapidly spinning propeller.  I think I would try to reconcile the two metaphors before giving an explanation that doesn’t seem to address either.  There must be a better definition of Shotgun Sequencing out there.

 

TV Cable

True Detective Season 2 Episode 3

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A lot has been said about the “I want to stay angry” scene:
Ray Velcoro (Colin Ferrell): Now, are you gonna tell me what Caspere was doing with you or do I wait to walk into another dark room, this time with real bullets?
Frank Semyon (Vince Vaugh): There’s a certain stridency at work here.  I’m gonna put it off to you getting blasted.
Ray: Oh, frankly, I’m apoplectic.
Frank: I’m feeling a little apoplectic myself.  What’s with the water?
Ray: Booze tends to take the edge off.  I want to stay angry.

One columnist referred to the scene as awkward, others feel the vocabulary is inappropriate to the characters.  Ok, here’s the thing: this verbal cockfighting is recurrent and gives Frank’s character believeability by having unbelievable dialogue in stereotype scenes.  There can no dozing through these scenes when the vocabulary demands full attention and adds to the entertainment, much like Tarintino did with playful dialogue but without the endearing high talk.

Check the other episodes where this feature was missed by the pundits:

Episode 1:

Frank Semyon (Vince Vaugh): You seeing anybody?  A woman?

Ray Velcoro (Colin Ferrell):  There something else I’d be seeing?  Nah, not interested in anything like that anymore.

Frank: Need to get back on that horse, my friend.    A good woman mitigates our baser tendencies.

Episode 2:

Episode 4:

Frank: You got this Roger Moore thing, huh?  Johnny Unflappable.

Blake Churchman (Christopher James Baker): Must be my predilection for virtue.

Frank: You know the word louche?   Somebody’s pulling me
out on the streets and you’re louche.

 

 

Activity

What a Registered Veterinary Technician’s profession Entails

The Registered Veterinary Technician profession acts in a support role to the Veterinary clinic.  The Veteranarian, the clinic, the animal owners and the animals benefit directly and indirectly from the functions and tasks performed by this licensed or certified individual.  Like a hospital nurse, the Vet Tech makes sure that the needs of the veterinarian, animal owner, and subject animal are met with high standards and thorough results.

At intake, the Tech may have to restrain or stabilize the animal.  An accurate history will be taken from the owner.  These results will have to be properly documented into the clinic system.  In support of the veterinarian, this professional may additionally be take X-Rays and samples, and prepare animals and instruments for surgery.

Customers need to be questioned, advised and trained with accuracy and consideration.  Routine procedures such as trimming nails, expressing glands and removing sutures occur regularly.  Administering prescribed medications and supervising veterinary assitants are also in the Tech’s remit.  The Vet Tech wears many hats in the support of his professional duties.

Cuba

The Campesino-to-Campesino agroecology movement

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The journal of peasant studies published this article in 2011.

Quoting from the article:

“Agroecology has played a key role in helping Cuba survive the crisis caused by the collapse of the soviet bloc in Europe (1989) and the tightening of the US trade embargo (1996).  Cuban peasants have been able to boost food production without scarce and expensive imported agricultural chemicals by first substituting more ecological inputs for the no longer available imports, and then by making a transition to more agroecologically integrated and diverse farming systems.”

The article concludes that:

“Our key findings are:

  1. the spread of agroecology was rapid and successful largely due to the social process methodology and social movement dynamics (of Campesino-to-Campesino Agroecology Movement (MACAC))
  2. farming practices evolved over time and contributed to significantly increased relative and absolute production by the peasant sector
  3. those practices resulted in additional benefits including resilience to climate change.

My post will explore the article for the practical details which support these three findings.

1. MACAC

2. Peasant Sector Production

3. Resilience to Climate Change

A concise definition of what agroecology is given:

  • Increase biomass recycling & balance nutrient flows
  • Assuring favorable soil conditions
    • cover soil with mulch or cover crops
    • high soil organic matter
    • active soil biology
  • Minimize nutrient losses
  • Promote biodiversity
  • Promote biological synergisms

Several simple methods are suggested for promoting agroecology with the following combinations:

  • worm composting of crop residues
  • constant incorporation of organic matter into the soil
  • pasturing animals on crop residues
  • the promotion and maintenance of an active soil biology

A high level of agroecological integration is described as:

…a complex peasant agroforestry system with multiple annual crops and trees, animals, rotational schemes, and perhaps even a fish pond where pond mud is collected to be used as an additional crop fertilizer.

Alternative agriculture in wealthier countries fails to out-yield conventional agriculture because they use conventional industrial inputs instead of agroecological inputs.

The paragraph on page 165 of this article provides some interesting terms, among them, food sovereignty and re-peasantization. Food sovereignty is the governing of a countries food supply through the support of the domestic family farm and securing of the country’s food stores.  Only the family farm can maintain food production sustainability and without the support of massive outside inputs.  Only domestic vigilance in maintaining home food stores can protect a country from international nutritional blackmail.

Re-peasantization is a term coined to describe the transition to agroecology.  This term and trend is the emancipation of a country from the dependence and doom of attachment to monopoly corporations that control policy and population through dominating the food industry inputs and outputs.  Modern agriculture is dependent on their supplying of animal feed, breeding stock, seeds, pesticides, and their outlet to food trading, processing and retail.

After the 1959 revolution, the initial policy was directed at diversifying away from sugar but evolved policy ended up strengthening the export mono-crop emphasis.

The soviet era provided temporary food security but not food sovereignty, it provided high yields but unsustainable, and key crop production declines resulted.

Cuba

Cuba & the Taino Escape

Their pathetic inability to resist the Spanish invaders made their eventual submission in the hands of the conquistadores an inevitability.  But it wouldn’t be today.  Maybe tomorrow they would start to fall, one by one, to disease, suicide and the sword.  Today they glided away from harm, knowing that their continued life in paradise was only an indulgence.  A luxury such as this verdenture could only be afforded to them for so long in these devolving times.   For perhaps the first time they stole quick glances of one another and saw a cherished for the last time.

To these indigeness people, the pain of living incorporated death.  For their pursuers death was usually a destiny for the conquered.  Because these gentle people were not even considered human, there was no atrocity too great, no slaughter too grand.  The reports of wealth and the unloading it at the Royal docks far off were the only objectives.  A ledger of body count to booty bound would sicken the hardest of hearts, if only there were one among the violators, including the accompanying padres,

The Deluge, Vignettes

The Difficulties of Genuine Friendship

The promise made to the friend concerned when the depression could be lifted and the relationship resumed.  The conditions were out of everyone’s’ hands.  The moroseness allegedly surfaced when the rains drowned the old man’s hopes.  His hopes floated on the notion that work and tasks brought satisfaction and happiness, but that was not all.  Most of all the buildings, barns and beasts existed so approval could be had.  With approval came fleeting happiness. Fleeting happiness brought relationship.

The rains continued to wash the dirty banks and erode the synthesized sanity.  Normally this weather didn’t stay that long but she remained collapsed on this segment of country as if to prove a point or bring the fragile farmer to his senses and to admit that his outer show differed from his inner truth.  That until he admitted to his lie, she would continue her onslaught, indifferent to his pain and fading hope.

Whiskey and women would not be the answer so the old wanna be farmer decided to give a kind of faux honesty a try.  He would look the part of goatherd with shepherd crook, and blue chambray button down, and a Quaker’s broad brimmed straw hat.  High muck boots and whiskers on the chin added to the appearance, but that was all it was.  The answer was not there for him to find.  He might as well abandon his behavior and get back to doing something.  Even something that could not possibly gain him approval.

Even then, he still found it difficult to have a genuine friend.

Tao Te Ching

Tao Te Ching Verse 8 Revisited

In R.L. Wing’s book the Tao of Power, verse 8, Noncompetitve Values, there are lines that appear in no other translation in the form Mr. Wing has presented.

The lines are:

  1. The value in a dwelling    is location.
  2. The value in a mind          is depth.
  3. The value in    relations    is benevolence.
  4. The value in a words         is sincerity.
  5. The value in    leadership  is order.
  6. The value in    work           is competence.
  7. The value in    effort          is timeliness.

Wing, in his commentary on this verse tells us how to achieve these 7 noncompetitive values:

  1. To achieve  location          one must know              the whole.
  2. To achieve  depth             one must know              its possibility.
  3. To achieve  benevolence  one must                        comprehend human nature.
  4. To achieve  sincerity        one must know              inner truth.
  5. To achieve  order              one must know              the entire structure.
  6. To achieve  competence  one must know              the results of a perfectly executed task.
  7. To achieve  timeliness     one must                        hold in mind both the past and the fututre.

I am reviewing this verse for the thousandth time and I recognize things which I never did before.  First, number 4, I couldn’t fully grasp what Wing meant by Inner Truth.  Now I completely understand that I can not be sincere in my words unless I understand the truth within myself and the motivation in my words.  It’s about those things that can only be known by me and those things are ingrediants of sincerity, not the words but the meaning.  The words, whether accurate or not, have no value unless they are directly mapped back to the truth within that no one else can know.  When one can accomplish this, one can have words of value because one speaks sincerity from the inner truth known secretly to oneself and revealed to others in simple words.

The other revelation is that of the the principles that lie at the base of Taoist thought and philosophy.  Wu Wei is very much involved in the achievement of timeliness because nonaction is the best course to take when the time is past or time has not yet arrived.  The caution on timeliness is that one must be aware of the Path: everything eventually takes the path of least resistence; Polarity: every ascent has a descent in its future and every descent has an ascent in its future;  The Pattern: each event begins in the dead season of winter when seeds lie dormant, some are planted in the spring and some come to life, some of the living grow and develop in the long harsh summer of life, some of those that live to maturity come to be harvested in the fall and the timeliness of that some can be assessed for that life’s effort at that time.

Tao Te Ching

Tao 15 Clarify by Quieting

Clarify troubled waters by slowly quieting them.

Be content, be able to mature without desire to be newly fashioned.

Be ready to adapt like ice at the point of melting.

After gaining calmness of mind by concentration, who can gradually pass from its calmness into the activities of life and always retain the same calmness of mind?

Who is able to impart unending life to that which is at rest by setting it in perpetual motion?

Be unpretentious like wood that has not been fashioned into anything…

Since one is not filled, therefore one may grow old,; without renewal he is complete.

 

Tao Te Ching

Tao 11 The value in reality is immateriality

The things of value yield no peace.

The things of no value yield peace.

Take away desire and want and receive peace and satisfaction.

Pursue satisfaction and indulgence in desire, and peace will continue to be lost to you.

Seek the utility of the neglected corner and she will serve you without complaint.

Long for notice and comfort and you can expect abandonment and self induced pain.

The path to happiness is plain and stark, do not try to add one thing or ask for more.  Find it within and unencumbered and you can keep it.  Require accoutrements and refinements and it will divorce you.

Word Episode

The Farm

Over the years, Sarah suspects, Tommy has floated to the surface of her.  They are swimmers now, far apart, on the top of the sea.

What does this mean?

At one time, Tommy was below the surface of the sea of Sarah, but over the years, he floated to the surface of the person Sarah.

At one time, neither Tommy nor Sarah were swimmers but now they are both swimmers on the surface of the sea of Sarah and they did not swim in the same direction and therefore are now far apart.

This is strange way to say they have grown apart and are getting further apart because they continue to move in different directions in their lives.

There was a time when they were together below the surface of the sea of love but they could not breathe there.  The sea turned from love to alchohol and prohibited sexual endulgence to salve the pain of living in a marriage that was no longer satisfying.  Indulgence is the cure for despair, it is yet another path to hurt and unhappiness.  Moving up and away from one’s own unhappinesss is not the right direction, it is just another direction.  Happiness is in the spot where you are, even if it is below the surface and alone, which is where you and I will all end up anyway.

 

Just Evolveu