Adult Onset Atheist

Thursday, October 9, 2014

Ebola

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.







Thursday, July 31, 2014

Antarctic Ocean Ice

It looks like we are headed towards an historic record maximum ocean ice extent in Antarctica. It will likely beat the previous record of 19.47 million square kilometers (7.51 million square miles) set in September of 2013. The 2013 record beat the 2012 record of 19.44 million square kilometers. All of these records are somewhere in the neighborhood of a million square kilometers above the accepted average.



“The paradox of expanding Antarctic sea ice has troubled scientists for many years. Although climate models predict southern sea ice should shrink, it has stubbornly refused to do so.” -- Julia Rosen from the LA Times

Our planet’s annual tilt races towards its autumnal minimum, and the length of day in the southern hemisphere increases more and more each day. It is still cold –very cold- in Antarctica, but it is averaging little less very cold each day. It will soon be springtime in Antarctica, but right now it is still winter. Winters in Antarctica are VERY cold. Even if greenhouse warming increased Antarctic temperatures by several degrees Celsius the Antarctic winters would still be freezing cold; literally. The lowest temperature ever recorded was -89.2C at the Antarctic Vostok station in 1983.

The extent of ocean ice at the poles is not limited by whether-or-not the temperature drops below the freezing-point temperature; it will likely do that every year regardless of the amount of greenhouse warming the planet experiences (by all estimates). An increased temperature will decrease the length of the year where temperatures are below freezing, and decrease the overall rate at which energy is removed from the freezing portion of the sea.  In other words –all else being equal- one expects an increase in temperature to decrease the amount of ocean ice.

We are seeing average temperatures increasing in the Antarctic. They have increased by as much as 2C since 1970 at some stations. Ocean ice in Antarctica has also increased during that period.  An alternative hypothesis for the relationship between temperature and ocean ice in the Antarctic region is needed.

Some data re-analysis has called into question the amount of sea ice increase, but it has not called into question the fact that the amount of ocean ice has been increasing. Geographically there is nothing around Antarctica to physically impede the growth of ocean ice. The ocean ice can continue to form without ever running out of open ocean to form in. This is not the case in the Arctic. Small changes in the large expanding margin of the Antarctic ocean ice extent can result in large changes in the official amount of ocean ice.

I have written several posts concerning the extent of Arctic ocean ice; using this metric as a measure for the extent of warming in our current state of global climate change. I do think it is a good measure, but I often neglect to point out that the melting of Arctic ocean ice will have little effect on human civilization. In fact all of the Arctic ocean ice could melt and –if it were not for the other effects of the factors causing the melt- we might not notice much difference.

The main threat to humanity from melting ice is from rising sea levels. Ocean ice does not contribute to this threat. Ocean ice is already floating in water, and melting it all would result in no major change in sea level. In order to increase sea level the ice on land must melt, and most of that land ice on the planet is in Antarctica. So much land-ice is in Antarctica that it accounts for almost 70% of the total fresh water on the planet. The fact that ice is frozen fresh water, as opposed to frozen seawater, is important.

Ocean salt water has an average concentration of about 35 grams per liter of salt; as low as 30 near the deltas of large rivers. Freshwater is pretty-much anything with less than a third of a gram of salt per liter. There is a lot of water on the planet, but only a tiny amount (2.5%) of it is fresh. The average depth of the oceans is four and a quarter kilometers; so putting all the freshwater into the oceans at once would only raise them by a little over 100 meters. Melting all of Antarctica would only raise the level of the ocean by about 70 meters. This is enough to cause big problems for the majority of the world’s population, but not me; I live over a thousand meters above current sea level.

Salt water requires much lower temperatures to freeze. There is a direct relationship; increase the saltiness of water, and it has to be that much colder for the water to freeze. Partially freezing salt water in a container will result in a separation; the ice will be mostly fresh, and the remaining unfrozen water will be saltier than the water sample was before freezing.

I use the term “ocean ice” (though I use ocean ice interchangeably with sea ice in other posts) to mean ice that is floating in the ocean. This could be ice that broke off from the land or ice that froze out at sea. The later is the species of ice that is properly termed “sea ice”.

The species of ice called sea-ice begins forming as hair-like crystals of freshwater freezing out of the salty ocean water. When these coalesce into blocks of ice they typically trap little droplets of salty liquid brine. These trapped brine droplets make new sea ice taste salty. As the sea ice ages the droplets of brine will slowly melt down through the ice, giving the sea ice characteristic microscopic vertical striations. The saltiness of water in which sea ice forms therefore affect both its rate of formation, and, until most of the brine ages out of it, its stability once formed.

This means that if you were able to decrease the salty of a water body… say by melting a sizeable portion of 70% of the world’s fresh water into it… it would actually freeze as fast as undiluted salt water exposed to lower temperatures.

Ocean salinity measurements around Antarctica show a steady decrease in overall salinity of as much as 0.03 grams per liter every decade. These lower salinity data are the result of the mixing of huge amounts of freshwater from some source with vast amount of saltier ocean water. There has to be a huge source of fresh water to make sense of these data. A further decrease in salinity is expected as one physically approaches the source, and the water has had less time to dilute by mixing into the ocean water. The temperature difference in freezing points for seawater at river deltas whose salinity is around 30 grams per liter (5 grams per liter less than the open ocean) is about 1.78 degrees Celsius. This is close to the increase in temperature observed in Antarctica since 1970.

Once ice has formed in seawater it is fairly stable until the temperature rises considerably. Ice that is floating in seawater that is cold enough to start the sea-ice formation process will not melt. A patch of ocean is considered “covered” by sea ice if it is really at least 15% covered. The forces of diffusion facilitated by wind and weather would move ice away from areas of rapid formation/ high concentration to more open ocean. In this way smaller areas of substantially lower salinity could create many square kilometers of sea ice.

Land ice does not just melt into the sea. The gigantic glaciers –huge rivers of ice- flow into the sea in solid form. When the glaciers meet the ocean seawater cuts under them, and float off massive chunks as icebergs. These icebergs in turn break into smaller blocks, which in turn float off in a multitude of directions. This floating former land-ice contributes to the high Antarctic ocean ice coverage values.

A better direct measurement of the effect of greenhouse warming in the Antarctic would be a measurement of land-ice. How much is left? How thick is it? Unfortunately these direct data are extremely hard to acquire. Sea ice coverage is a much easier measurement to obtain.

Antarctic ocean ice coverage values appear on first blush to not provide direct evidence for global warming. However, if this hypothesis is correct, they do appear to provide direct evidence for a significant impact of global climate change, and these may be more valuable data. There is no real need to use satellite imagery metrics as a huge thermometer as we have data from actual thermometers showing warming trends; although I do like the gigantic data sets because they are impressive, and changes in them melodramatic.

Because the changes observed in the Antarctic may be evidence of actually bad things happening to the planet as a result of global warming they may even be worthy of more attention that the Arctic data.