Friday, February 28, 2014

Desperately Seeking.... Part IV

Have you ever been sick and dragged yourself to work anyway?  You figured being able to put in 80% was better then 0%

You were sitting in your cube or working the line.  You hacked.  You sneezed.  You blew your nose like a trumpeting elephant.  You were miserable.

Your co-worker looked over the cubical partition, or across the line and said, "Joe, you ain't worth a broke popsicle stick.  You take your butt home before you make the rest of us as miserable as you are."

Therein lay the salvation of hypovirulence.

Two Masses Orbiting

The script for two actors was discussed in Part III.  The dynamics of two actors leaves little room for improv.

As humans, we have a vision of a chestnut orchard or a forest dominated by oak.  The script in Part III has that orchard or forest living on borrowed time.  The increasing density of the hosts changes the selection pressure from "host discovery" to "rapid host exploitation".

Unlike animals, plants do not have an active immune system that develops a portfolio of antibodies with exposure to pathogens.  Being exposed to a hypovirulent strain of a disease does not harden the plant against a future exposure to a virulent strain.  Increasing density of potential hosts makes catastrophe inevitable and the timing is completely unpredictable.

Economists, planners and bank loan officers do not respond well to unpredictability.  It is also emotionally harrowing.

The Third Actor

The trajectories of two masses that are mutually orbiting is mathematically predetermined and offers little drama and little opportunity for human intervention.

Adding a third actor opens up a multitude of potential outcomes because the range of "solutions"

One of my hobbies is homebrewing and home wine making.  In the course of pursuing this hobby I stumbled across "Killer Yeast".

From Wikipedia

In Saccharomyces cerevisiae are toxins encoded by a double-stranded RNA virus, translated to a precursor protein, cleaved and secreted outside of the cells, where they may affect susceptible yeast. There are other killer systems in S. cerevisiae, such as KHR [6] and KHS [7] genes encoded on chromosome.
The L-A dsRNA virus of S. cerevisiae...encodes a secreted protein toxin (the killer toxin) and immunity to that toxin. L-A and M are transmitted from cell to cell by the cytoplasmic mixing that occurs in the process of mating. Neither is naturally released from the cell or enters cells by other mechanisms, but the high frequency of yeast mating in nature results in the wide distribution of these viruses in natural isolates.

 Picnic Bugs

Picture from HERE

Picnic bugs (aka, sap beetles) are the natural vector of Oak Wilt.  Picnic bugs are attracted to rotting fruit, presumably by the volatile esters.  The fruiting body of the Oak Wilt produces those kinds of attractants.  After becoming a carrier of the fungi, the picnic bug feeds on the sap of an open wound, presumably attracted by the byproducts of fermentation.  In the event that the open wound is on an oak tree, there is a high probability that wounded tree will become infected.

Picnic bugs are "Bill's" vultures.

At this point, it is speculative to presume that an existing strain of Killer Yeast virus could pass from a yeast bearing culture to a picnic beetle, thence to an infected tree...and debilitating the virulent form of Oak Wilt to where it "ain't worth a broke popsicle stick."

It is entertaining to speculate about.  Also, given viruses sloppy replication and rapid mutation, I believe it could be made to happen.


A table of strains of yeast.  Column 10, "Competitive Factor"  active indicates a "killer yeast".

A trap for capturing picnic bugs can be easily constructed from a two liter soda bottle.  Fruit juice that has been inoculated with yeast makes excellent bait.  Warm fermentation temperature favors production of esters.  It is rumored that cans of beer with two swallows left in them are also effective picnic bug traps.  I cannot vouch for that, never having left any beer in a can.

Attempting to inoculate the picnic bug with killer yeast would involve feeding them with a yeast culture via a sponge sitting in a bowl.  It should be in a warm place but out of the sun.

Thursday, February 27, 2014

Desperately Seeking..... Part III

Desperately seeking hypovirulence

A contagious pathogen that kills its host too quickly is a failure.

Even though hypovirulence may be in the long-term best interest of the species, hypovirulence is usually not in the short-term interest of a given strain of that pathogen.

It is one of the classic contradictions to Adam Smith's Invisible Guiding Hand theory which holds that autonomous actors will always arrive at a global optima as an unerring side effect of seeking their own, personal optimum.

The pathogen may end up at that place but the path is messy and strewn with wreckage.

Hypovirulent strains cannot compete with the speed and totality that the hypervirulent strains exhibit when exploiting the nutrient resources of the host.

It is the compound interest problem, again.  If aggressive exploitation (which kills the host) gives the hypervirulent strain a 2X advantage, the hypervirulent strain will outnumber the hypovirulent strain by a factor of one million-to-one after 20 generations.

The pathogen lays vast populations to waste.  Tiny, isolated pockets of the host remain and pump seed out into the void.  The pockets grow until they encounter a smoldering ember of the pathogen and the process repeats.

Hypothetically, one of those smoldering embers will be less virulent than the first wave.  Its victims will be able to survive the infection and the pathogen will be able to undergo multiple generations of spoor release without killing the host.  That multigeneration spoor release and the sparse distribution of the host is the basis for the hypovirulence's competitive advantage over the hypervirulent strains.

Another way to say the above is that hypervirulent strains will dominate when the hosts are close together and speed of exploitation (invasion, extraction) is the bottleneck in reproduction.  Hypovirulent strains will have a slight selection advantage when discovery of new hosts is the primary bottleneck in reproduction.  This state may oscillate back and forth as population density changes and climatic factors vary---either favoring or suppressing the ability of the pathogen to "find" new hosts.

So, where might one look for hypovirulence?

The hypothesis presented here suggests one might find hypovirulence in two, very different places.


One place to look is the pathogen's epicenter where, presumably, the host and the pathogen have had the longest amount of time to oscillate their way to an equilibrium.  This is where the host population was first decimated and where the selection pressure first shifted to "host discovery".

When the Varroa Mite started devastating honey bee hives, researches went to the Amur region of Siberia (north of Korea) to collect resistant strains of honey bees.  Their focus was on finding resistance in the host rather than finding friendlier pathogens.  But the same principle applies.

The fringe

The second place to look are at the fringes of the host's natural range where the pathogen is petering out due to the scarcity of the host.  The primary selection pressure on the pathogen is "host discovery" and hypovirulent strains should become relatively more abundant.

Presume that the host's range covers an area large enough to show climactic variation.  Also presume that one side of the range favors the spread of the pathogen.  It follows that the pathogen will spread on the less friendly side only in those rare years when the weather favors the pathogen.  That amounts to an extreme penalty against the one-and-done, hypervirulent strains and creates a relative bias for the hypovirulent strain.

Therefore, if a pathogen favored cool, humid conditions then one might be well advised to look for hypovirulent strains along the southwestern (hotter, drier) fringe of the host's distribution.

Desperately Seeking, Part IV

Wednesday, February 26, 2014

Desperately Seeking... Part II

A contagious pathogen that kills its host too quickly is a failure.

Consider two pathogens.  One of them kills its host in two weeks.  It is a disease that telegraphs its presence with visible markers. It incapacitates the host for much of those two weeks.  Contrast that with a second pathogen that does not kill its host for years or even decades.  This second pathogen is communicable during the entire time. Further, consider that the pathogen does not present any distinctive symptoms so it is impossible to identify potential sources of infection.


It is widely known that the European explorers and colonists brought many contagious diseases to the New World.  Measles, smallpox, typhoid, scarlet fever, influenza and cholera mowed down the indigenous populations.  There are many documented cases of European conquerors entering hostile territories and being hard pressed to find any living natives to conquer.

It is less widely known that some diseases were carried from the New World back to Europe.  Syphilis was one of those diseases.

Pretty hard to hang onto that romantic feeling looking at these.

Voltaire's book Candide is accurate in its portrayal of syphilis.  People died within two weeks of being infected.  People had fingers, arms, legs, ears and noses fall off.  Voltaire included syphilis in Candide because sexual promiscuity was a prominent self-identifier of upper class Europe, much like doing lines of cocaine were part of being an "authentic" 1980s Rock Star. 

Some of the virulence was due to the complete absence of antibodies against syphilis.  Much of it was due to the extremely virulent form of syphilis that Europe was first exposed to.

Over time the most virulent strains of syphilis self-extinguished.  That is, in aggregate, they killed off their carriers before they had a chance to spread the disease.

Compound interest

It is a compound interest effect.  The (aggregate infectivity) raised to the generation.  That is, (AI)^ (Number of Generations).

So a disease that has a 80% aggregate chance of infecting another victim before killing off the carrier will diminish to (0.80)^10 (about 11% of base population) in ten generations and to 1% in twenty generations.

Looking at the flip side, suppose a disease has an aggregate chance of infecting two new victims before killing off the carrier.  The twentieth generation will be (2.0)^20 which is a little bit over one million new infections in that generation alone.


Rumors abound that HIV was "invented" by malign, human agents.  Much of that speculation originates because of the malevolent perfection of the HIV virus.
  • HIV circulates at the highest levels in historically stigmatized groups: Drug Users, Prostitutes, Alternative Lifestyle Choice Practioners, Minority populations.
  • HIV is symptom free for most of its life cycle
  • Untreated HIV is a virtual, though delayed, death sentence
  • HIV does not have a clear progenitor "in-the-wild"
  • HIV originated in Africa, a continent free from health monitoring
  • HIV has proven extremely resistant to efforts to produce a viable vaccine.
There is some debate whether viruses are life forms or simple large molecular catalysts that replicate.

For the purpose of this essay, we will consider them life forms.

The Gossip by Norman Rockwell.  What are the odds that the message mutated a little bit with each telling?

A defining characteristic of viruses is they lack the ability to edit their replication.  Think of the process of a zipper (a strand of DNA) unzipping with the virus being the slider.  The virus grabs long strings of pre-sequenced amino acids when it thinks it has identified the start of a string it will need.

Mutations occur frequently.  Sometimes the virus makes a mistake in identification.  Different individuals of the same species have slight differences in DNA.  Sometimes the virus jumped from its native species and is ad libbing, making the best guesses it can, in the new host species.  Unlike higher animals, viruses do not have a fidelity checker for its creation.  It just keeps going.

Most of these mutation probably offer little advantage to the virus.  Sometimes, however, the mutation becomes a complete game changer.

One of those times is when the surface of the virus is sufficiently different from its progenitor that the host's immune system does not recognize it.

HIV mutates rapidly, even for a virus.  That made developing a viable HIV vaccine a problem.

Another issue in controlling HIV difficult is that it primarily attacks certain cells in the immune system.  That results in the disease manifesting in many, many different ways.  Basically, it opened the door to a host of opportunistic disorders.  It is impossible to know if a potential partner has HIV without resorting to a blood test.  The lack of ability to self-diagnose means that those populations with either no access, or no desire to access healthcare are at highest risk.

Desperately Seeking, Part III

Desperately Seeking..... Part I

You may have noticed that I failed to meet my goal of one-post-per-week.  There is a reason for that.

I have been grappling with how to handle this next topic.  I decided to treat it as fiction.  Yes.  That is right.  Fiction.

There comes a point where ideas, no matter how intriguing to the author, are too speculative to be treated as fact.

The other dimension is the blog format.  The blog format does not lend itself to long expositions.  Breaking "plot development" down into manageable pieces fragments the flow.  More to the point for this blog, the next two or three posts will seem VERY off-topic.

I beg your patience as I try my hand at crafting "fiction".

Desperately seeking anthrax.  Part I of ?

Guillermo ("Call me Bill") Peña was a graduate student in Biology at Midwestern State University in Wichita Falls, Texas.

He posed a dilemma.  More precisely, choosing a thesis for him was tying his major professor into knots.

Kindly stated, Bill was not the strongest student academically.  Lab work was not his strength.  His major professor briefly considered a "topic-counting" thesis.  That kind of thesis was typically assigned to part time, working students.  It involved performing a literature search and tallying "fer-it" and "against-it" papers.  It was an exercise in clerical work.

His professor rejected the topic-counting as a waste of Bill's talent.  While Bill struggled in the class room Bill was incredible out in the field.  He got along with everybody and he had a unique ability to think with both his hands and his brain.  Most important, he got stuff done.

Bill was from Del Rio, Texas, a seven hour drive from Wichita Falls.  Del Rio was on the Rio Grande River and near the western edge of the Texas Hill Country.  Both were which are biologically very interesting areas.

Due to financial considerations, it would be a kindness to find a topic that would allow Bill to operate from his parent's home.

The Topic

In the end, the professor decided to finesse the dilemma by giving Bill a monitoring project where failure was the null hypothesis.  That is, Bill was assigned the task of monitoring the west end of the Texas Hill Country for anthrax.

Monitoring anything in the Texas Hill Country is a huge challenge.  The topography is treacherous.  The ground cover is thorny brush.  And the people are the yin to Austin's cosmopolitan yang.

Picture from HERE

Finally, the violence of the drug trade flickers in and about all of the counties near the Rio Grande.  Like the Comanche of 1830s and 1840s, one never knows who might show up on your door step.  Strangers are viewed with the strongest of prejudice, regardless of how they dressed.  Loaded firearms are kept close to hand.

The anthrax monitoring project solved a couple of problems for the professor.  He did not expected Bill to not find any anthrax.  Failures to find it would confirm the existing belief.  That gave Bill the option to fall on his face and still produce a thesis that met the standards of Midwestern State University.

On the other hand, Bill had proven to be an innovative thinker.  The professor believed that anthrax might lay smoldering in the Texas Hill Country.  The professor was confident that Bill would find it if anybody could.

Channeling Mitchner

---37 pages of character development redacted for the sake of compactness---

Back to play action

Bill sat in the deer blind as the mid-morning heat rose.  His binoculars were hung on a nail beside the window.  He had video equipment already focused on the bait, just in case.  He was jamming to the tunes on his iPhone.  He had a jug of iced tea and his lunch in a cooler beside him.  He planned to stay all day.

Bill was watching a deer carcass approximately 50 yards away.  He had packed it in on the quad and placed it on the bald top of a gentle (for the area) limestone ridge.

He was waiting for vultures.

Vultures have astonishingly good eyesight.  They ride the thermals which develop as the heat of the day drives both the wind and temperature differences on the surface of the ground.

A vulture can lock his wings and ride a thermal with the energy expenditure that is the equivalent of a human taking a nap in a Laz-E-Boy recliner.  It is a very efficient way to find food.

Bill made a deal with the county highway crews.  He would pick up road kills for his project and they would not have to deal with them later.

Bill had picked up this deer on the way to his stake-out.  It was a fawn which made for easy handling.  He had selected the location for his stake out based on the friendly land owner (his Uncle Luis), the easy access and the fact there was already a deer blind in a convenient location.

His Uncle Luis had asked only one favor in return, that Bill shoot any coyotes or feral hogs that he saw.  Consequently, Bill's Savage .223 lay across his lap with the 3X9 scope dialed down to the lowest magnification.  Coyote hides were not worth a nickel this time of year and hogs were as skinny as rails but any carcasses would make fine addition to the buzzard bait pile.

Bill had put the deer out, on top of the ridge.  It would be like a drive-up window at a fast food restaurant to the vultures.  The carcass was as visible as glowing neon arches.  It was Easy in.  Easy out.

PVC Pipe

PVC pipe is also known as Redneck Tinkertoys.  (At least it is in Michigan.)

Picture from HERE

Bill had never really studied vultures before.  What he had seen from other birds, though, was that they often landed near food and then hopped over to it.  Perhaps it was because they wanted to inspect it before they committed themselves.

Bill was counting on vultures doing the same.

He had constructed a "fence" around the bait.  The fence was really a series of hurdles made of PVC pipe and fittings.  The hurdles were of various sizes.

Bill's plan was to find out the optimum height of hurdle.  Optimally, he wanted the vulture to perch on the top bar while eating but he would settle for having the birds briefly perch on the top bar before hopping onto the bait.

Old short stories

One of Bill's hidden vices was to read collections of short stories from the 1950s, the Golden Age of short stories.

A favorite author of his was Theodore Sturgeon.  Bill had gotten the idea for the data collection methodology from the last story in Sturgeon's book E Pluribus Unicorn.  The title of the story was A Way of Thinking

In that story, the villain's MO was the opposite of what most people would do.  Trying to take a propeller off of a shaft?  The villain would drive the shaft out of the propeller.  In a bar fight if a contestant threw a bottle at him (and the bottle flew through the window out into the street below), our villain would throw the contestant out the window after the bottle.

Bill decided it would be much, much easier to find anthrax if he could figure out a way to have the anthrax find him.

Enter vultures

Picture from HERE

There are thousands of vultures plying their trade in the Texas Hill Country.  The area has abundant deer, sheep and cattle.  They die for all the usual reasons.  Many of the carcasses are never found by the land owner.  None elude the vultures.

Bill figured that if there was any way to pull cultures from the beaks and/or feet of the area vultures.

The last piece had fallen into place a few days ago when his mom had yelled at him for leaving his dirty sweat socks on the floor.  He had asked how she knew they were his and she had pointed to the smudge around the ankle and said, "Your dad wears boots."

At that moment, the picture of the hurdle made of PVC pipe and sleeved with sweat socks had popped into his head.

Now, all he had to do was dial into the optimum height for the top bar.  Then he would mass produce the hurdles and set up his trap line.

This summer promised to be much easier than the other ones when he had been hoeing weeds and picking fruit down near Brownsville.

God Bless Education.

Desperately Seeking, Part II

New Species of Stone Oak found in Thailand

The following article was brought to my attention by Lucas Machias.  Thanks Lucas!

Illustrations/photos from HERE.  They may be expanded by clicking on them.

The following passages are excerpted from the Pensoft article found HERE.
An international team of scientists from Xishuangbanna Tropical Botanical Garden (China) and the Forest Herbarium (BKF - Thailand) discovered a new species of Stone Oak in the Ton Pariwat Wildlife Sanctuary in Thailand...The wildlife sanctuary covers a region of low-lying forested mountains and is located in the middle of a fascinating transition zone that lies between the northern Indochinese and the southern Sundaland biogeographic regions.

...distribution limitation and rarity is not uncommon in tropical Oaks. Within this region alone, there are several species that are known only from one or two localities. Though not uncommon, such restricted ranges stress the possible delicate conservation status of new species and other flora and fauna present in the Ton Pariwat Wildlife Sanctuary. "The unique species composition, high diversity and relatively intact forest structure...
Currently, more than 300 species of Stone Oak have been described, occurring from eastern India to Japan and the eastern tip of Papua New Guinea.

Monday, February 17, 2014


Snow continues to clog things up.  I hoped to have a spiffy picture of many bags of acorns stratifying.  Unfortunately, my source for acorns has been virtually shut down by snow.  Many of their acorns are stored in outbuildings.  Snow drifted the buildings in.

They also have the issue receiving supplies of some of the species.  Q. texana/nuttallii drops its acorns late in the year.  Their most northern sources for Q. nuttalli acorns had not been out collecting before the rare, for them, snow storms covered up the ground.

So I don't have very many acorns stratifying....yet. Hope springs eternal. 

Q. robur bottom left, Q. phellos top left, Northern Pecan top right.

I have a great wife.  Acorns stratifying in the pantry.  Scionwood in the refrigerator.

Oak Trees around the Homestead

I have several trees around the homestead that are notoriously short lived.  It is time to start planting their replacements so I can have a smooth succession of shade.

My current plan is to move a 4' tall Burr Oak (Q. macrocarpa) from the garden to the north side of my house.  The seed for this Burr Oak came from a NAFEX member, Lucky Pittman, several years ago.  The parent tree was growing beside the First Baptist Church parking lot in Hopkinsville, Ky.  It has had no problems enduring Michigan winters. 

I also plan to move an 8' Swamp White Oak (Q. bicolor) to the south side of my house. 

I am pondering what to graft over them.  My current inclination is to graft scionwood from the McBaine Burr Oak on the Burr Oak on the north side and a Q. x byarsii (Q. macrocarpa X michauxii) on the south side of my house. 

That would mean my house was bracketed by Q. bicolor to the west, Q. macrocarpa to the north, Q. muehlenbergii to the east and Q. x byarsii to the south.

Further afield

Out back I have many seedling oaks of no distinguished parentage.  A few show slightly better form than the others.  My plan is to practice my grafting on some of them as well.  That is where any extra McBaine scionwood will go. 

Typical branching habit of Q. robur

Seedling of Q. robur with semi-fastigiate form.

Q. robur, in particular, seems to tend toward narrow crotch angles.  I suspect that it is an unintended legacy of early importation/selection for fastigiate forms.

Q. robur has its flaws (crotch angles, powdery mildew, susceptibility to borers) but it it grows fast and produced huge amounts of acorns.

Tuesday, February 4, 2014

Oak Wilt

Excerpted from Oak Wilt Home Page by David Roberts, Ph.D:

Pruning:  DO NOT PRUNE during the warm season; trimming is a major cause of oak wilt infections in Michigan today. If oaks need to be pruned, the dormant period is best - November through February. If storm damage occurs during the warm season, clean-prune the branch 1-2 feet below any visible injury and seal with a pruning paint. Repair of storm damage should occur as quickly as possible-optimally within hours or within a couple of days of the damage. 

Storm damage which has occurred during the dormant (winter) months is not of particular concern for oak wilt. Nevertheless, winter storm damage should be repaired during the winter months and not during the warm season. It is not advised to use pruning paints during winter storm repair. 

Except for emergency situations, cessation of pruning during the warm season, is probably our most effective tool for preventing oak wilt at this time. Compared to Dutch Elm Disease, in which elm bark beetles can easily transmit the fungus from diseased trees to healthy trees, the oak wilt insect vector is inefficient at transmitting the oak wilt fungus when no wounds on oaks are present.

Additionally, have enough space between oak trees, especially those in the Red Oak family, so that root grafts are unlikely will limit the speed of Oak Wilt spreading through a planting.

Oak in the Red Oak family typically die within one season.  Oaks in the White Oak family die more slowly...perhaps five years.  Oak in the Live Oak family are intermediate in resistance.