Adult Onset Atheist

Monday, October 27, 2014

Ebola II

Many people have been asking me about Ebola lately. The following are some of my personal views on the subject. They do not necessarily represent the views of any organization with which I may be affiliated, and should not be interpreted as any official communication by anyone.

Boatloads -literally- of money has now been spent responding to the wildly out-of-control Ebola epidemic in Western Africa, and it appears to be having a measurable impact on the progression of the epidemic. Both case levels and number of deaths continue to trend significantly less than the simple exponential model would suggest. The number of cases ending in death also appears to be decreasing. It is much too early to tell if this very positive development will be enough to stop the epidemic, but it is appears to be very promising.

Because of the striking symptomology, and relatively ease with which the infected can be contained, it is not surprising that large-scale active intervention could reverse the horrible trends the epidemic was following. It is possible that simple intervention could wipe out this epidemic, but a vaccine still remains the best hope for completely stopping it with the least number of casualties.

In the following graph I’ve tried to re-create the graphic from my last post. Instead of a simple exponential regression curve I have created a curve that mimics what we would have expected if the epidemic continued to increase exponentially. As of October 23rd we would have seen 3,779 more cases, and 1,191 more deaths if the severity of the epidemic had continued to increase exponentially.

This shows the trend of EVD cases and mortality for the 2014 Western Africa epidemic (as of October 23rd).  The red and green lines show WHO reported cases and deaths respectively.  The blue and purple lines are exponential models drawn from a regression analysis of WHO data from the first 100 days I followed this. 

It is not overly jaded to suggest that it took exporting Ebola patients to more developed nations to mobilize the effort that appears to be yielding results. However, this reduces recognizing the amazing efforts of those men and women who are making a difference to some kind of moral-political statement about the collective conscience of developed nations. These men and women have earned recognition, and we should provide it.

Unfortunately blog posts like this one do a much better job of making moral-political statements about the collective conscience of developed nations.

Before we began exporting the wholesale help that appears to be making a difference we had been exporting a commodity we make way too much of: stupidity. Before the antivaxers began mobilizing against the fantastical mind-control purpose behind the Ebola vaccines now in trial. Before the teabaggers began clutching at any possibility of the Obama administration being in any way associated with the possibility of misstep in any response to Ebola patients in the US. Before the xenophobic isolationists began demanding a shutdown of any movement of people of African descent. Before any of this we had begun exporting the “real” reasons for the epidemic, and a host of “effective cures [they] don’t want you to know about”.

This type of foolishness might sound like nothing more than the discardable musings of internet trolls, and from the perspective of most of the readers of this blog it is. However, to people using limited resources to combat an impossibly expanding horror it could be more; it could provide much needed hope and blame.

“The US Department of Defense (DoD) is funding Ebola trials on humans, trials which started just weeks before the Ebola outbreak in Guinea and Sierra Leone. The reports continue and state that the DoD gave a contract worth $140 million dollars to Tekmira, a Canadian pharmaceutical company, to conduct Ebola research. This research work involved injecting and infusing healthy humans with the deadly Ebola virus. Hence, the DoD is listed as a collaborator in a “First in Human” Ebola clinical trial (NCT02041715, which started in January 2014 shortly before an Ebola epidemic was declared in West Africa in March.” -- Cyril Broderick, A Liberian scientist and a former professor of Plant Pathology at the University of Liberia’s College of Agriculture and Forestry.

A major Liberian newspaper published an article blaming the US department of defense of creating the epidemic. A patent created in the pre-supreme court decision on patenting existing life forms rush to patent everything was found for a strain of Ebola; this proved Ebola is a GMO. Motives were fielded for why an Ebola epidemic would be profitable; arguments for the potential validity of the motives became arguments for the validity of the conspiracy theories themselves.

Response in West Africa took a turn for the worst when quarantines upset important food distribution networks. Ebola patients reportedly escaped “treatment” facilities in search of food because they knew Ebola only killed 50% of its victims, while starvation killed 100%. People hid their sick friends and relatives because the state was not going to provide the “effective cures [they] don’t want you to know about”. Tracking people exposed to the virus was replaced by trying to keep track of those who died. Eventually it became impossible to provide accurate information. Bodies were being cremated before relatives knew the patient was sick.

In mid September eight aid workers were killed, and their bodies shoved into a latrine. It was thought that the disinfectant they were spraying was actually the Ebola virus.

I could pontificate about the dangers of rampant stupidity, but what good does that do? I doubt readers of this blog are even aware of even half of these Ebola conspiracies; unless they are ferreting them out for enjoyment.

It is not as if good information was unavailable. It is not even a situation where good information was hard to find. It is just that the extreme blame and hope of the fringe spokespeople in the US is much more compelling.

Possibly more important than compelling is the fact that people who got good information are doing stuff, and it appears to be working. Homeopaths Without Borders did not swoop in and cure everyone with distilled water. The citizens of West Africa did not simply cut gluten out of their diet. The drones spraying Ebola were not shot out of the sky. No.   Real people did real stuff.... and sometimes that works.

Thursday, October 9, 2014


Many people have been asking me about Ebola lately. The following are some of my personal views on the subject. They do not necessarily represent the views of any organization with which I may be affiliated, and should not be interpreted as any official communication by anyone.

Ebola Virus causes a nasty disease. The current Ebola Virus Disease (EVD) epidemic in Western Africa is running almost unchecked through a population ill-prepared to counter it.

It is unlikely that EVD will cause a global pandemic. The progression of the EVD epidemic is slow, and those who are sick are easily contained. There is also an effective vaccine on the near horizon. The EVD epidemic will be stopped; my notoriously unreliable crystal ball tells me it will be fully contained by next summer. Unfortunately it is out of control now, and it is likely that tens of thousands of people will die of EVD in Western Africa before it is stopped.

It is so likely that tens of thousands will die that it is possible to assign a statistical confidence to that prediction. Simply plotting the reported numbers yields a trace that displays an uncanny adherence to an exponential growth rate. Through a statistical process known as regression analysis one can generate an average trace of the data (shown as the black lines in the following chart).

Total cases and mortality data from WHO-reports as of 5 October 2014 Click to view larger

The mechanism for generating the average trace also generates a statistic –called “R-squared”- that tells us how well the average line describes the data. An R-squared value of 0 would mean that the trace described none of the data, and an R-squared value of 1 would suggest that the average line described 100% of the variability of the data. The R-squared value I generate for the average trace of the mortality data from the last several months of the EVD epidemic is 0.9951.

An R-squared value of 0.8-or-so for an exponentially increasing average line would strongly suggest that the epidemic was out of control. An R-squared of 0.9951 suggests that none of the response measures implemented to date have had any measurable effect on the progression of the epidemic. There is no fine detail in this trace, and it may be that unexpected setbacks have perfectly offset any effective countermeasures. However you look at it these data are very “not good” in a bad way.

The trace also provides a strong reason not to worry about this EVD epidemic breaking out and creating a global pandemic. The upward “slope” of the trace is just not steep enough. Almost a hundred years ago today, peaking in October and November of 1918, the Spanish influenza epidemic swept through the world’s population. In just a few months it infected as many as half a billion people; killing as many as 60 million. By the time the Spanish influenza epidemic was over it infected as many as 800 million people and killed as many as 100 million; all between January 1918 and December 1920. EVD is not fast enough to outpace the world’s response in the way that Spanish Influenza did.

Notice, in the above description of the Spanish Influenza epidemic, my use of wishy-washy soft-data language. I use “as many as” four times. This is because we do not really know how many people died of the Spanish Influenza. In 1918 the social structure needed to even count the people dying became too overburdened to operate effectively. The lower number of people killed worldwide is half as large as the maximums I provided. There are mass graves.

The social machinery which counts the number of EVD deaths in Western Africa is showing signs that it is being pushed beyond its breaking point. There is informed speculation that as many as several EVD cases actually exist for every case reported. There have been reports of bodies left to rot in the street, or forgotten to ripen in some back bedroom of some apartment.

The World Health Organization (WHO) was, until September, providing disease outbreak news every couple of days; until some WHO healthworkers caught EVD, and died. Now they are providing Situation reports every two-to-six days; sometimes significantly revising the numbers of previous reports. Without a means of protection at least as effective as a good vaccine some of the first to succumb to an epidemic are the people needed to properly track the epidemic’s progress. With a super-rapid epidemic like Spanish Influenza in the informationally-challenged early 20th century the obstacles to effective data management must have been insurmountably huge.

To understand why EVD is less contagious, and therefore less likely to cause a global pandemic, than a disease like Spanish Influenza it is worthwhile to look at the basic biology of viruses.

Viruses are not really alive. They are essentially a sticky capsule of bad instructions. The instructions essentially say “make more virus”, and the sticky outside of the capsule cause it to attach to cells that can load and run the bad instructions. In some cases, like for HIV, the instructions say something like “make more virus slowly for a long time”; for viruses like influenza and Ebola the instructions say “make more virus as fast as you can until you explode”. The sticky capsule can be specific for certain types of cells. The tiny Polio virus capsules preferentially attach to nerve cells, and so the polio disease is characterized by paralysis. Influenza capsules attach to cells in the throat, and so the virus is shed into the phlegm that is converted into airborne droplets when someone with the Flu coughs or sneezes.

Ebola virus attaches to many different cells in the body. As it circulates through the body in the bloodstream it is presented first to capillary walls. When the thin capillary walls are weakened by the liquefaction of cells that died while furiously making new virus the capillaries themselves begin to leak.  At  this early stage of infection the body mobilizes defenses which cause the temperature of the body to rise. It is possible for a person who has been properly exposed to Ebola to fight off the disease in this early stage, before it manages to cause much damage; otherwise exploding capillary cells continue to spew more and more virus into the bloodstream, and the infection spirals out of control.

Most of the noticeable symptomology of hemorrhagic diseases like EVD occur in places where there are large concentrations of capillaries. Most EVD patients die in this intermediate stage of failures in capillary-rich internal organs, like kidneys. Given luck, or competent supportive care, an EVD patient can live into the final stages of the disease.

The fact that only about 5% of western African patients are surviving to the spectacular terminal phase of EVD probably suggests a lack of comprehensive supportive care. The first active Ebola case in the US (Thomas Eric Duncan ) received such comprehensive supportive care that relatives declined to view him via remote video (he was in an isolation unit) because it was “too disturbing”.

In the terminal stages the capillaries become completely porous, and begin leaking blood as well as fluid. The sclera of the eye fills with blood; there may be blood tears. Blood leaks through the capillary-rich intestinal linings into the digestive tract, and from there gushes out the rectum; the patient uncontrollably vomits blood. Blood begins to ooze from mucous membranes; the gums bleed, the nose bleeds, the genitals will bleed. The skin itself will begin to boil in blood-filled blisters. Grape-sized blisters will erupt from the skin, and burst to release virus laden bloody fluid.

All of these copious fluids are infectious. They are not easily handled. Sticky virus-laden goo gets in everything. Untrained individuals can get it in their hair, and noses, and in their car, and bring it home, and all without noticing. It is unsurprising that EVD spreads; even without the formation of the respiratory droplets which worked so well for Spanish Influenza.

The voraciousness with which viruses like Influenza and Ebola eat through their target cells actually makes it more likely that effective vaccines can be made against them. Good vaccine candidates have already been created for Ebola. Ramping up production of at least one of those candidates will only take months rather than years. It will likely be the fielding of a vaccine in the first half of 2015 that will end this epidemic.

The fielding of the vaccine will stop the epidemic in its tracks. Over a hundred thousand corpses will likely be left in its wake, but it will be impossible for any future EVD epidemics of the Zaire strain to reach the numbers we see even today.

So, should you be scared of Ebola? Yes. Ebola causes a terrible-horrible-scary disease which will kill tens of thousands of people in the coming weeks. That sort of thing is scary. It scares me.

Will Ebola destroy civilization as we know it? No. Not even close.

Thursday, August 14, 2014

Canaan's Ark

We have had enough soaking storms lately to turn the neglected parts of my lawn green. The storms have not been gentle either. One of the last one whipped up electrical pyrotechnic displays, and generated weather service severe storm warnings. In celebration of this “Utah is not like California in a good way” situation I rented the movie “Noah” from RedBox.

Yesterday brought flooding to everywhere in the country making nowhere like California. A couple mountains in Southern California managed to scrape a deluge from the humidity passing overhead, but in general it is very dry in California this year, very dry.

“The National Weather Service had not, as of Monday morning, issued any official flash flooding watches or warnings. But as sure as an "R" designates the seemingly eternal political affiliation of a super-majority in the Utah Legislature, Utah’s slot canyons, usually dry washes and burn scars are at risk for inundating storms.” – Bob Moms for the Salt Lake Tribune “Utah forecast: The monsoon strikes back” 11 August 2014

Recently I have been told that Noah’s biblical flood is best explained as some sort of local phenomenon, and that “40 day’s simply means “quite a long time” in biblical speech. It sounded like some sort of reductionist-apologetic dancing; if it could be right in some small way the bible could still be true, but they were trading away relevance.  Some confusion is understandable if god really did come to earth a couple pages of Genesis later and “confound all the world’s languages” as the bible suggests. I would think it difficult to have any cogent history until a couple generations after The Tower of Babel; let alone a tediously specific train of begats.

However, it does little good for god to promise not to destroy the earth again if he never really did so in the first place. And if god was promising not to have any big local flooding like the localized version of Noah’s flood then… well there are some folks who will be returning to their cars in low lying long-term parking lots at Baltimore Washington International airport that may have some questions for god.

Darren Aronofsky has added a narrative clarity to the story of Noah that was impossible before the invention of CGI. He captures the general nastiness of old-testament life by filming almost everything on treeless landscapes (until god magics up some trees from Methuselah’s trufula seed to generate wood for Noah’s ark) and color is hard to come by. Darren even creates some baby killing Abrahamic tension to make some indistinct old testament morality tension, and he makes all of the wives of Noah’s sons primary relations to multiply the magnitude of incest needed to repopulate the earth. It is like Darren said unto his script writers “Bringeth forth some evil old-testament plot elements to createth dramatic tension”, “And the evil old-testament plot elements did cometh forth”.

“ And Abraham stretched forth his hand, and took the knife to slay his son. And the angel of the LORD called unto him out of heaven, and said, Abraham, Abraham: and he said, Here am I. And he said, Lay not thine hand upon the lad, neither do thou any thing unto him: for now I know that thou fearest God, seeing thou hast not withheld thy son, thine only son from me.” – Genesis 22:10-12 KJB

However, Darren muddled up one of the most evil old-testament plot elements in the entire old-testament. An evil story that actually occurs to Noah and his family. Darren ignored –mostly- the curse of Canaan.

“Noah, a man of the soil, proceeded to plant a vineyard. When he drank some of its wine, he became drunk and lay uncovered inside his tent. Ham, the father of Canaan, saw his father naked and told his two brothers outside. But Shem and Japheth took a garment and laid it across their shoulders; then they walked in backward and covered their father’s naked body. Their faces were turned the other way so that they would not see their father naked. When Noah awoke from his wine and found out what his youngest son had done to him, he said,

“Cursed be Canaan!
The lowest of slaves
will he be to his brothers.”

He also said,

“Praise be to the LORD, the God of Shem!
May Canaan be the slave of Shem.
May God extend Japheth’s[b] territory;
may Japheth live in the tents of Shem,
and may Canaan be the slave of Japheth.””
-- Genesis 9:20-27 NIV

The curse of Canaan is a bit severe. For many generations it has been used to justify the existence of dark skinned people, and using them as slaves. I was a teenager in the 1970s, and as a young child this story was used to explain the creation of black people to me; a liberal minded lay pastor told that the curse was a bit capricious, and that it might be ok to raise voice against the use of water cannons being used every evening on the nightly news to knock the descendants of Ham back to their rightful place in society.

Instead of a curse Darren pens regret into Noah’s alienation from his son Ham. Ham holds a grudge for his father’s refusal to save a woman he was fond of from a bear-trap facilitated drowning. There is no talk of slavery… Ham just heads off into the draining horizon .

I also like the way Darren re-wrote god’s specific instructions to Noah. In the bible “god says”, and in the movie Noah hallucinates.

I think Hollywood screenwriters should re-write the whole bible; at least the old testament.

Or, perhaps we could just agree on a cannon of film noir movies to show our children. Nothing after the invention of color, except maybe the wizard of Oz.