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A paper recently published by Science online documents the spread of Ebola from Guinea to Sierra Leone.  The spread of the virus can be followed by genetic sequencing of virus, as mutations accumulate as the virus is passed from host to host.  The scientists document over 300 mutations among 99 viral genomes sequenced.

The data is consistent with a single transmission from an unknown animal to a human (believed to be a two year old child in Guinea) with human to human transmission thereafter.

The genome of Ebola is rather simple, consisting of genes for only six proteins.  Mutations have occurred in all six genes, although there is a concentration of mutations in the viral NP gene.  The current study does not address the functional significance of the mutations, although a number of the mutations would result in altered proteins.

Sadly, five of the researchers who contributed to the Science study have died in the Ebola outbreak.

A rapid mutation rate would be expected in an RNA virus like Ebola.  In general, most mutations are not adaptive, but a worry is that natural selection during exponential spread of the virus might lead to a virus that is even more contagious, particularly since humans (up until now, anyway) have not been the natural host of Ebola.

One might also hope that spread into the human species would attenuate the virus, since a good virus does not rapidly kill its host. However, as long as the spread is exponential (doubling time of epidemic is about 30 days, but probably accelerating), there is no selection pressure to become less lethal, while its victims are still plentiful.

A separate Ebola epidemic now seems to have started in the Democratic Republic of the Congo, with 13 cases now confirmed.  Senegal has also now recorded its first case, a student who crossed into the country of Guinea, despite the border being officially closed.  Senegal is a major hub for business and aid agencies in West Africa.  There is also a suspected case of Ebola now inBrussels, a Doctors without Borders volunteer who recently returned from West Africa.

The World Health Organization now has an action plan to contain the virus, which they think will take 6 to 9 months.  However, with the epidemic doubling every month, it is clear that tens of thousands will likely die before this is over, making this epidemic more lethal than all of the previous infections combined.

Hopefully, vaccines and drugs, now in accelerated development will prevent this virus from following HIV out of Africa and becoming endemic worldwide.


My nightmares are becoming realities.

I am a biologist (semi-retired) with training in virology.  My Ph.D. thesis concerned a retrovirus (Moloney murine leukemia virus) with a lot of similarities to HIV, although I did my thesis defense a decade before HIV was recognized.

The path of my research diverged to other things, but I have always kept an interest in viruses. Viruses, it seems to me, are the biggest threat to mankind, because they use our own cellular machinery against us.  We have antibiotics to protect us against most bacterial infections, but anti-viral medicines that actually work are few, and viral evolution is very rapid.  Viruses that have RNA genomes (HIV, Flu, Ebola) evolve even more rapidly because RNA polymerases or reverse transcriptases, in general, are more error prone than DNA polymerases.

Besides science and teaching, I have done some science writing, including publishing a book on nanotechnology.  I have also written a novel (The Latter Day Adventures of Luis and Clark), so far unpublished.  The premise of the novel is that a vaccine against HIV goes awry.  The idea was to use an aerosol delivered flu virus to deliver an HIV protein, to which people would make antibodies.  An unfortunate recombination event occurred resulting in an active respiratory HIV virus with the rapid action of a flu virus.  Most of the people in the world died.  The survivors were 99%+ male. Survival was unfortunate for most of the females.

The Ebola virus outbreak, while probably over-hyped in its threat the West, is a serious threat not only to Africa, but basically anywhere that medical care is sub-standard.  Like previous outbreaks, this one probably started with animal to human transmission, but human to human infection seems to be much more effective than previously, possibly because of higher population density. And similar to my fictional  work, 75% of the infected are female. This is not a quirk of the virus, but a result of cultural practices, wherein females are usually the caregivers.  In this case, Africa is not unlike the rest of the world.

Why things just got worse below the elaborate orange squiggle.

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The Abe government in Japan has passed a ridiculously repressive government secrecy law that goes beyond anything the NSA could even dream about.  According to the state can now declare virtually any given fact a state secret, and anybody divulging that secret, even if he or she didn't know it was a secret, can get ten years in jail.  Even asking questions about a state secret is a new crime, that of "instigating leaks", and could result in a prison term.  And of course, anything to do with nuclear power is a secret, so you can forget about getting any new information about leaks from Fukushima.  More after the fold.

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Though science fiction as a genre has its origins in the many tales of the incomparable Jules Verne, or earlier in Poe’s Hans Pfall, the first science fiction story ever was undoubtedly The New Atlantis  by Francis Bacon, published first in Latin in 1624.  At that time, the very idea of science as a coherent enterprise was more or less a fiction.  The first lucid description of the scientific method was the Novum Organon Scientiarum, also by Bacon, published a few years earlier.

The New Atlantis relates the story of a group of Europeans on a sailing ship who had lost their way in the Pacific somewhere west of Peru.  Sick and without provisions, they chance upon the island of Bensalem, which happily is a kind of Christian Utopia blessed with material abundance.   After their recovery, they are given the run of the island.  The pre-eminent institution on the Bensalem is Salomon’s House, which is the medieval equivalent of the National Science Foundation and the National Institutes of Health rolled into one, “dedicated to the study of the works and creatures of God.”   This unique institution has allowed the island to prosper by the introduction of new technology.   Biotech had been particularly fruitful—the islanders ”have means to make divers plants rise by mixtures of earths without seeds, and likewise to make divers new plants, differing from the vulgar, and to make one tree or plant turn into another.”  They apparently had no problems with animal rights advocate—they had “beasts and birds... for dissections and trials, that thereby may take light what may be wrought upon the body of man.”  Optics were a research priority—there were  “demonstrations of all lights and radiations and of all colors; and out of things uncolored and transparent we can represent unto you all several colors, not in rainbows, as it is in gems and prisms, but of themselves single (the first lasers!). We represent also all multiplications of light, which we carry to great distance, and make so sharp as to discern small points and lines.”

Bacon’s plot is minimal and his stilted prose should be exhibit number one as to why Bacon could never have been, as has been claimed, the true author of Shakespeare’s works.   Bacon sought not to entertain but to make a large point; that science should be the centerpiece of society.  Salomon’s House eventually became the model for the Royal Society of London, founded in 1660, the oldest learned society in existence.  Robert Hooke was the first Curator of Experiments.  The Royal Society is a big player in writer Neil Stephenson's excellent trilogy, The Baroque Cycle.

The New Atlantis is also the name of an Ursula K. Le Guin novella, an echo across the ages.  She describes a dystopia stifled by an all-powerful state, very much the negative image of Bacon’s optimistic vision.  But her story is well worth reading, for an opposite perspective.

This diary was originally published in Scientia, a blog from the American Association for the Advancement of Science members webpage.  That page requires membership in the AAAS to view.  I get the copyright back after six months so I thought I would share some of them with dKos, where I know there are a lot of science geeks.
The first Daily Kos diary in this series was:

Back to the Future: Haldane’s Daedalus Revisited


“It is the whole business of a university teacher to induce people to think,” noted geneticist J.B.S. Haldane, so in 1923 he gave a talk to the Heretics of Cambridge which has kept people thinking ever since.  His talk was later published as a longer essay, titled Daedalus, or Science and the Future. Daedalus was the Minotaur keeper and Greek tinkerer who invented strap-on wings and taught himself and his son Icarus how to fly.  Haldane glosses over the tragic outcome of that experiment and accentuates the gifts that science and technology have to give.  He offered some predictions:

•    He regarded it as “axiomatic” that coal and oil fields will eventually be exhausted and that we will have to tap those intermittent but inexhaustible sources of power, the wind and the sunlight.”  He saw an England lined with windmills.

•    Surplus power will be used for cleavage of water to hydrogen and oxygen, the former to be liquefied and stored underground, because it is “weight for weight, the most efficient method for storing energy.”  

•    Sugar and starch, converted from cellulose, will become “as cheap as sawdust.”  New nitrogen fixing organisms will double wheat yields and lead to abundant cheap food, collapsing agricultural economies.

•    The first ectogenetic child” will be born in 1951, leading to a society where reproduction is separated from sexual love.  By “ectogenetic,” he meant born from a uterus kept in organ culture, a la Brave New World.  In fact, Haldane’s discussions with his friend Aldous Huxley inspired the novel.  

Haldane turns out to be a decent but imperfect prophet.  Peak oil is already in sight, wind and solar energy have seen dramatic development in recent years, and the hydrogen fuel cell exists but is not yet a commercial entity.  Cellulose is looked at now as more of a feedstock for ethanol production than actual food.  The first “test tube baby” was born in 1978 but came to term within a normally-situated uterus.  Birth control has done much more than ectogenesis to separate sex from reproduction.

Haldane was criticized for his Panglossian view of science and its fruits, particularly by philosopher Bertrand Russell; his answering essay Icarus was decidedly gloomier in outlook.  But Haldane was not a total optimist, either.  “In the next war,” he wrote, “no one will be behind the front line. It will be brought home to all whom it may concern that war is a very dirty business.”  Certainly they agree in Hiroshima.

This diary war originally published in Scientia, a blog from the American Academy for the Advancement of Science members webpage.  That page requires membership in the AAAS to view.  I get the copyright back after six months so I thought I would share some of them with dKos, where I know there are a lot of science geeks.  

That the United States of America is an oligarchy, I think, is beyond question.  The government responds only to money, and money is in the hands of those who have money.  I don't have much, and most of you don't either.

That is not to say that all oligarchs are bad.  There are some fairly decent people who are insanely wealthy.  Warren Buffett, Bill Gates, and George Soros come to mind. If we lived in a benevolent dictatorship run by Warren Buffett, I imagine, we would all be better off than we are today.  But it would still be a dictatorship.

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Another offshore fiasco:

A Venezuelan natural gas exploration rig sank in the Caribbean Sea early Thursday, but all 95 workers were evacuated safely and there was no leakage, the government said.

Proving that offshore drilling is not an easy prospect, for anybody, not just the BP's of the world.

OPEC member Venezuela has struggled to attract investment to develop its vast natural gas reserves, with offshore projects developing slowly and without any production so far.


About offshore drilling:

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The title, I will admit, is deliberately provocative.  I have been involved in enough Israeli/Palestinian threads to realize they generate a lot of heat without ever getting anywhere.  My point in presenting this diary is to point out how long this debate has been going on.  Not just since 1948, when the state of Israel was born, but far, far longer.  And yet nothing ever gets settled.  (I expect to called anti-Semitic or anti-Israeli, in the comments.  I vehemently deny the former; I admit to a little of the latter.  I am not anti-Israeli, per se, but I believe that the state of Israel has been overly brutal in asserting its territorial claims.)  

What follows are excerpts from an article published in Atlantic Monthly in 1920 by Anstruther Mackay, who was a military governor of part of Palestine during World War I.

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Dear friends, let me beg of you to hear me patiently.  Let me beg you, most of all, to believe that I am not saying what I shall say for the fun of the thing.  I would rather some one else said these things and said them better than I can; but I have waited for that some one to speak until I can wait no longer for the time is growing short.  You must let me do it as best I can, and make allowances for my bluntness, not for my sake but for your own; for there is no longer any time to beat around the bush...

What follows is a rant, a civilized rant from an earlier era, from Seymour Deming, published in Atlantic Monthly in 1914, as the First World War had begun.  It seems curiously appropriate to today.  The items in parenthesis were added by me.

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Mon Mar 08, 2010 at 07:02 PM PST

Ignorance: A Rant

by MadScientist

This is a rant that's been building for awhile.  I am in an aggravated state today as the result of grading lab reports from college students who can't put together a simple declarative sentence.  But I can't blame them.  In a way, they are victims of an educational system that is in trouble, part of our infrastructure is rotting away as surely as our roads and bridges.

But the ultimate origin of this particular diary is the appearance of Sarah Palin at the Tea Party Convention in Nashville.  I caught just a portion of her speech before I ran screaming from the room (follow on):


Obama is

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Nashville, my former home town, is about to hold what is being billed as the first ever "National Tea Party Convention" with Sarah Palin and Michelle Bachman as the headliners.  Should the progressive movement be shaking in its boots?  

Tea Party Nation, the for-profit company putting on the convention next month at Gaylord Opryland Hotel, is charging delegates $549 a pop for the privilege of attending. Politicoreports organizers are asking a whopping $50,000 for corporate sponsorships. According to one insider who's talked to Pith, Tea Party Nation hopes to clear $300,000--and he says that's after paying Palin's hefty $120,000 speaking fee. She doesn't come cheap.

So is there any doubt as to why Palin quit her low paying job as governor of Alaska?  She may never run for President, but is she ever raking it in now, what with a best selling book and speaking fees in the six figures.  Is this a great country or what?



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Thu Dec 31, 2009 at 08:10 AM PST

Perky Pat Saves the World

by MadScientist

Perky Pat may yet solve global warming and the U.S. balance of trade deficit.  For you that don't know her, Perky Pat was invented by my favorite sci-fi author, Philip K. Dick in his book The Three Stigmata of Palmer Eldritch.  Perky Pat served as entertainment for hapless colonists on other planets:

Life on the colonised planets is so arduous and soul crushing, however, that new colonists must be rounded up with the use of a draft system. The only entertainment the colonists have comes from the consumption of Can-D – a psychotropic substance that induces collective hallucinations. The consciousnesses of the users become disembodied and "translate" into Barbie-like "Perky Pat" dolls, allowing them to lead an imaginary, idealised version of the lives they left behind on Earth.


Do you purchase virtual goods?

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