Monday, September 8, 2014

Ebola 4

So - more people are getting scared about it.  Including the BBC; which  to my amazement has this as their top headline right now: Ebola crisis: Liberia 'faces huge surge' says WHO.  Not the #1 Most Read article on the Washington Post right now; New Royal Baby!!

The BBC goes on to say "Ebola is spreading exponentially in Liberia, with thousands of new cases expected in the next three weeks, the World Health Organization (WHO) says."

I'm still not quite buying the "exponentially"; but yes, this sounds more serious.  As SquashPractice pointed out in a comment on the previous post here, Wikipedia Ebola page now does have the graph I've been looking for (new deaths and new cases / day); and it does have an "up curve", which, yes, is more scary - there are two unrelated phenomena which could account for that, without meaning Ebola is actually becoming more aggressive.  Which is not to say it's not; you understand.

The two factors; A) The reporting of new cases has possibly/likely increased dramatically in the past weeks. B) The disease is expanding- think of an ever increasing circle as it moves into the population. There will be many more infections on the circumference of the larger circle.   That's to be expected; and to me is not any more threatening than previously.

It was always expected the cases would expand, and accelerate; no mutations required.

So; bad, but not OMG we're all going to die.  The "thousands of new cases", however, do mean the risk to spread to distant cities will go up rapidly in the near future.  Keep paying attention.

So, now the bad Ebola news.  What they're not telling us.

One factor, reported in Wikipedia and nowhere else at all, so far as I can tell; the small, unrelated outbreak in the DR Congo?  Is less small; and not unrelated.

"On 20 August, several people, including four health care workers, were reported to have died of Ebola-like symptoms in the remote northern Équateur province, a province that lies about 750 miles north of the capital Kinshasa.[102] By 21 August, 13 people were reported to have died with similar symptoms."   So - at least 20 dead in DR Congo, including 4 health workers, not the 13 the WHO reports.

And: "Blood samples were sent for testing and on 24 August it was reported that the samples were positive for Ebola; one tested positive for the Sudan ebolavirus, which is a different species of ebolavirus than the one responsible for the West African outbreak; the other tested positive for a mixture of the Sudanese and Zaire species, the species that is responsible for the present outbreak in West Africa.[104][105]"

Italics mine.  Ok, that's scary, from the evolutionary standpoint.  2 virus strains are mixing (I don't use the word "species" here, I don't think it's correct.)  That means- lots more chances to evolve, now.

And one more; this is my own guess, unsupported by any official statements; I think the WHO knows, and is not telling- that the Ebola virus has already mutated to become more transmissible.

Take a look at the photos in the BBC article.  The health workers are wearing isolation outfits designed to prevent breathing in contaminants.  Which, they tell us officially, does not happen.

And also from that article: "Transmission of the virus in Liberia was "already intense", and taxis being used to transport infected patients appeared to be "a hot source of potential virus transmission", the WHO said."

Taxis?  Also - not a big source of "direct contact with body fluids".  But; if the virus can now survive in dried sweat or sneeze droplets?  That would do it; and I do think - it has already happened.

Keep paying attention.

Sunday, September 7, 2014

Ebola 3

Roz just made this comment on the previous post:

          hey Greenpa - is this chart a little like what you were looking for? It's a bit scary, it is.

         BBC- Ebola-How bad can it get?


  Good catch, Roz; I was just getting ready to make a post here about that exact article.

The graph is not what I want to see; but this is the presentation that made "that other guy" go all wacky and start saying "OMG, Ebola has gone asymptotic!"

This looks so scary because they are adding all deaths in the epidemic together to make the next point on the graph.  That's not an entirely illegitimate way to look at the numbers; but from the epidemiology standpoint, it is not as informative as a graph tracking "number of new cases this week" or "number of new deaths this week" would be.  

Those graphs give an appearance that is much less accessible to the general public - they're very jagged, and the "trend" is harder to see; and most of the jaggedness is purely accidental; caused by differences in reporting, not differences in actual infection/mortality.

Last I really looked at the numbers, the data for "new cases" looked something like "43, 17, 30, 59, 28, 37, 19, 67"  etc.   The question is "is the disease accelerating",  not "totals".  Still have not seen the data presented that way.  There are standard ways to draw a line for "best fit" that evens out the jags.  If you have a straight, but up-slanted line; that means the epidemic is still speeding up, and that's not great.  It's when that  line goes asymptotic- that it's time to be very, very scared.  Not happening yet, I think.  The WHO was reporting "new" cases in mid August; but they're not, now.  Not sure why.

That BBC article - is notable for 3 things; basically all good, actually.

 1)   It's the first "scary" article in the major press I've seen - telling the truth about the epidemic.  Yes, it's potentially dangerous, to the entire world.

  2) The author did a good job of talking to researchers, and translating for the public.  That's been very uncommon on the BBC in the past few years, and getting worse; but this one is excellent.

  3)  Some of the researchers raised good points I had not thought of in particular, which could easily lead to epidemic outcomes that are less than apocalyptic.  That would be nice.  In particular, the scenario where the virus mutates to "more transmissible"; which could then lead to evolving to "less lethal" more quickly than if it stays as it is.  Reaching a point where it never goes away, but subsides to normal "bad disease" status, where it is all around the world; it still makes people very sick during outbreaks, but maybe only 5% of infected people die.  

That's actually a fairly high probability in the evolution of pathogens scenarios.  I was focusing on the vastly increased chances for it to become easier to catch; now that there are uncountably more virions available for evolution to act on.  That's very scary.  But yes; the next evolutionary tactic is usually to: stop killing your host.

I recommend folks read that article.  Twice; once today, and again in a couple days.  Lots of information to absorb there, and it's far more honest than other stuff still being circulated.

There are several other hopeful developments too; like the preliminary finding that there may be many people in the region who are already immune to Ebola; for reasons they're guessing at.  Fewer susceptible people would be a huge help.  And; those fighting the disease think they may be able to use blood from those who managed to survive the infection to treat active patients.  That would sure help.

All in all; keep paying attention.  But total imminent world collapse is looking a little less likely - from Ebola, anyway.

Thursday, August 28, 2014

Ebola 2.

The Ebola news is not great.  I'm a little more worried than previously; enough that I have added the WHO reports URL to my news menu bar, and check it daily.  This is where most of the press get their update information; and if you look at this one from yesterday, you'll see that - the press is not passing on the news: Ebola now in Congo; different strain.

Also; the Washington Post is reporting research from Harvard that the mutation rate in the main outbreak is "very high".

And the BBC reports that the WHO expects 20,000 cases before they can bring the outbreak "under control".  We're a little under 3,000 cases right now.  That's a big expansion.

All that adds up to significantly increased risks that the virus may become more transmissible; and also that the virus may escape much further away from current sites.  Maybe into a big city.

The fact that the press is not putting all this together, and passing it all on quickly - indicates official actions to suppress news, and decrease panic potential - so you can't believe what they're telling you.

So; as before; pay attention.

Wednesday, August 13, 2014


I've been hit hard by the loss of Robin Williams.  Many of us have.

Here is something I first saw years ago, that I want to share with you.  This is an "unlisted" YouTube video; you only get the link if you're looking at Koko's site.  If it runs slow or fuzzy- try again, it's actually good quality video.  And you'll see Robin.  An exceptional human.

A little more, on Koko's site..

Me too.

Friday, August 8, 2014

It's just all a bit much. And, Ebola.

Hi Guys.

According to Blogger- you're all still here, tuned in.  I'm honored.

The reasons I've been quiet are still the same; massive overloads In Real Life - and a lack of anything genuinely useful to say about current world insanities.

Today, though; I do have something useful to tell you; out of my particular Biology/Evolution/Etc. background.

We're experiencing the largest outbreak seen of the Ebola virus.  Should you worry?  Or not?

You need to pay attention, is what you need to do.  (Not to me.  To what's going on.)

So far I have seen a great many of the disasters, problems, conundrums that are known to occur during "plague" outbreaks; already happening.  We have history to look at; I recommend it.  People can be harmed in epidemics by many things other than the bug itself.

Here is a list of "Already here" bad things, that do not help:

Politicians lying about the extent of the epidemic.
Politicians telling you :"There's no risk to us!"  then- 'There's almost no risk to us!"  And I've already seen "We'll probably get a case or 2 inside the US, but we can handle it."
Press printing any blathering nonsense they can find.
Finger-pointing between nations and agencies.
New committees.
An experimental "cure" - with a tiny supply; and fights about who gets it.
Con men selling fake cures to desperate people.  (saw an ad on Facebook already)
Wall Street types jockeying to capture the profits.
Military roadblocks going up - and cities sealed off - too late.
Desperate people sneaking through roadblocks, and bribing their way.
Soothsayers announcing "This is IT!  Run!"

All of those are happening now; and will likely get worse.

Here's my "no bull" advice.

Don't panic.  It doesn't help.  Is this virus dangerous - to you and your family?  Yes, it is; but we don't know how it's going to turn out.  Disease organisms follow the "rules of Epidemiology" - when you can average 1,000 different viruses and bacteria together.  Individually - they do not have to follow anyone's rules.  It could mutate to be more infectious; or less.  Or both, on different expansion fronts.

This scenario is possible: You live in Denver?  Far from everything.  But; the incubation period for Ebola is stated as "between 2 and 21 days."  That's really dangerous.  An infected person, at day 15 of his infection; gets on a plane.  Yes, he might be shedding virus by then.  Gets off the plane in Cairo, Egypt, 2 hours later, having transmitted it to 2 other people; the steward, and the lady in the next seat.

He stays in Cairo, vanishes into the countryside and is never recognized as dying of Ebola.  The steward flies next to Paris, becomes symptomatic and infectious 17 days later, infecting an entire flight crew...  and on; until an infected but not yet symptomatic person gets off the plane in Denver... goes to a rock concert/ all night rave-revival party - throws up...

"It's not likely!"  No, it's not; but the bigger the epidemic gets, the more chances; and there's really no way to prevent that kind of scenario - short of shutting international air traffic; off.

If that happens?  You'll know it's getting serious; and that it's too late to be effective, and the next step is martial law.  In Denver?  Yes.

This kind of thing has happened repeatedly, historically, in plague events, going back to Rome, at least.  But they didn't have air traffic; or the Mexico City slums - etc.

This virus is not capable of suddenly mutating into a disease that can blow in the air from somewhere miles away.  An epidemic in Africa is not a threat to you - today.  One case in NYC - is not much threat even to NYC.  If, however, we wake up one day and there are 2,000 new cases in NYC today- that's a threat.  Neither hospitals nor police will be able to control things.

Think about what you can do, if you have to.  I would say start thinking now.

And the statistic I would watch is the daily CHANGE in death rate and infection rate.  That was a  lot of the reason I decided to write this; I've already seen one "seer" shrieking "It's gone asymptotic!!"  My respect for that source dropped through the floor; not that it was all that high.  Just as pure statistics; that's crap.  Yes, there's a jog up in deaths and new cases - in the past 2 days.  It could very easily be a pure fluke; better reporting yesterday, for example.  The probability of "fluke" is much higher than "asymptotic!"

If the rate of change keeps climbing up for a week- yes, I'd start to worry.  If the rate of increase keeps going up for 2 weeks, with no break; I would have to predict that a great many people will die before it's over; but we still cannot know when, or where, it could suddenly shift into a trivial virus.

Like everything else in our future now; we do not know what will happen next.

Keep an eye on the Wikipedia "ebola" page.  Seriously.  I know, that used to be a joke line; but it's not anymore.  It is the only source of information on the technical knowledge of the virus that just says this; right up front: "Transmission: It is not entirely clear how Ebola is spread."  That's from a CDC document; not one I could find, but its cited here.  The WHO at the moment is putting out the official line that "ebola is very hard to catch, and requires direct 'bodily fluids' contact".  The Russian weapons experts are saying "maybe not."

 The great majority of sources will have some "agenda" they want you to swallow.  Wikipedia now has dozens of actual experts monitoring the information changes - and if you put something up that anyone can criticize as "not true" - down it comes. 

Don't panic.  Pay attention.

And find a copy of Sinclair Lewis's "Arrowsmith" - a novel about exactly this situation; from the viewpoint of the medical researcher.  They gave him the Pulitzer Prize for that novel; and he refused it. His insights into human behavior during a plague - are... well, Pulitzer material.

The entire text is online; here; Arrowsmith text   Public domain, pretty sure.

UPDATE: 8/14 - I managed to find the WHO current statistics page.  They report new totals for deaths and new cases, every 2-3 days.  There are lots of ups and downs in the numbers- imagine the difficulties of "counting", and reporting, in the middle of it all.  It's clearly horrific for those caught in it. Overall, it does appear that new cases and numbers of new deaths are increasing; but it's a long way from "asymptotic."  Somebody out there - could use these data to produce a good graph.  I'd rather see a graph of new cases and new deaths than total cases and total deaths, and I haven't seen one.  I'd do it; but- several people would kill me if I stole that time.  :-)

Sunday, May 18, 2014

Not dead yet!

Hi, guys.  I haven't forgotten you.  Just busy; and boy is it hard to find non-depressing stuff to write about these days.  Which, since we are bombarded with new depressing stuff daily, I'd rather not add to.

I am still active in various ways, when I see something I can tackle; and I thought you'd be interested in seeing this one.  Which is; actually, about someone special who is NOT not dead yet.

You may remember that I had the top comment on the NYT when Norman Borlaug passed away- another huge scientist just passed, and the NYT gave him top coverage; for hours, he was the top feature on the paper, front page, center, "above the fold", or above the scroll, these days.  But unlike Borlaug, who thousands knew of; almost no one knew of Dr. Snow.  But he was so important; and a shining light for anyone hoping to be a good human being.

Here's my comment.  Read his obit; it's worth it.  And how very odd this post should come right after one about bones.  Ever watch "Bones" on TV?  Or any of the dozen like it- or read any of the novels on forensic anthropologists?  With maybe 2 others, he created the entire field.  And, he was a good man; a good human.  I have vague fantasies that someone might read my comment- and be moved to act on it.  Not impossible, right?

Hang in there.  Keep your sleeves rolled up.

Sunday, March 2, 2014

Burning my old friend's bones.

A year ago, at the end of that exceptionally hot, dry, summer, I lost a very old friend.

This friend was someone I'd watched, walked beside, touched, admired, and cheered for, for decades.

She was a very large, strong, and beautiful red elm.  I say "she", which is not biologically accurate, because she often shed large amounts of seed.  At least twice, I put down tarps beneath her, collected her seed, and planted it.

I'd watched her nearly die, and then fully recover, 20 years ago; so I'd been hoping she'd make it this time.  That year had been hot and dry, too.  This one was apparently too much.

Red elm is one of my favorite trees; I like their attitude and behavior.  They can grow very fast when they're where they belong, tend to make big strong logs that can be used in more ways than oak.  The wood is beautiful; almost as dark as freshly cut black walnut, with lovely grain; the wood is as strong as oak, tougher than oak, very rot resistant, often splits as easily as any wood can; burns hot, makes the best long lasting coals for holding fire overnight - and - it will dry out completely just standing in the woods for a year.  Oak will never- ever- dry out on the stump; not if dead for 2 decades.  Oak requires great foresight, and careful storing to dry for use as fuel.  And a lot of sweat, wrassling all that soaking wet, heavy as pig iron, oak biomass- at least twice.

Elms are more forgiving (our elms, anyway) - if you weren't able to get this winter's wood cut and stacked under a roof two years ago- you can just cut an elm that's been dead for a year- and burn it efficiently today.  (Well, the top.  The butt log will be wet enough it will need drying.)  Red elm is the same as "slippery" elm; humans have used the inner bark for food and medicine for millennia (which is one reason the tree is less common these days), but in addition to food from bark, the red elms in Canada produced such heavy seed crops that Ernest Seton reported the passenger pigeon flocks migrated specifically to gorge on slippery elm seed.

Probably part of why I like red elms is they are ignored, misunderstood, and undervalued.  Underdogs in the canopy.  If you look them up on the internet, you'll find the pharm pages usually calling them by a Latin name the botanists declare obsolete; and both sources say "the wood is of no commercial value" - therefore, it's fine when they die after all their bark is stripped.  No value?  The mind boggles.  Never mind all the creatures dependent on them in the ecosystem, in the early 1980's, many of my neighbors made a lot of money- selling their big red elms- to Italian wood buyers.  True, local loggers didn't want them.  But the Italians paid the same money as for black walnut.  They shipped the logs to Italy.  Where they were veneered, and the veneer used to make very expensive furniture.

And the freshly cut wood is fragrant.  For me, it's a scent associated with childhood- in an unusual way.  When I was 8 years old, or so, my family spent 3 weeks in Japan.  The shops that specialized in wood carvings all had the same strong, pleasing, fragrance as you walked in the door.  I was too young to ask which wood it was, but many of the boxes and figures of dark wood carried it.  I'm pretty sure, now, it was Cryptomeria wood, Japanese cedar.  The smell of red elm is identical, as far as I can tell, and when I split it, or handle it, it brings many bits of those years and that trip back.

When I first got here, in SE Minnesota, our farm woods had 3 (at least) species of elm; American elm (Ulmus americana) predominated, then red elm (U. rubra), then rock elm (U. thomasii), which I confused with American for years.  We had huge American elms; but 90% of them died in my first 10 years here, from Dutch Elm Disease (DED).  American elm trees are lovely to look at- but of very little use to humans otherwise.  The wood rots immediately; making it dangerous to fell a big tree dead more than a few months- they call them "widow-makers", because huge portions of the top can crack off in felling- and fall the opposite way.  On you.  The wood is pretty, distinctive, but very little used because it tends to crack as it dries, and warps like crazy. And when the wood burns- it stinks; the farmers in most of the midwest called it "piss-elm".  Dry American elm does make a hot fire, though, if stinky; apparently unlike English elm.  Most versions of the firewood rhyme from England say "Elmwood burns like churchyard mould; even the very flames are cold."  Ew.

Red and rock elm are just a little resistant to the DED fungus.  Part of the picture is that American elm is a tetraploid species- it has 4 copies of the chromosomes, which often makes a plant more vigorous.  And it was faster growing, and often bigger than red or rock- but they are diploids; and sometimes slower growing means tougher.  Sometimes, the diploids can get DED - and get over it.  My old friend did; in that previous hot dry year; I watched, afraid I was going to lose her.  The stress of the drought brought on a serious attack of DED- I watched the leaves in the crown wither and die.  And rejoiced, in the literal meaning of that word, when she recovered over the next few years.  I admire survivors.  That was when I started gathering and planting her seeds.

No, I never named her.  Though I knew her intimately.  She stood just beside the tractor road I made into our woods, which we immediately also used for walking and skiing.  There were very few times when I traveled that road, in any mode, when I did not pause and look up at her crown, to see how she was doing.  I watched hard in the spring of 2013.  But she was gone.

She was big.  By anyone's standards.  I felled her yesterday, and the stump where I cut is about 30 inches in diameter.  Very large, for this area; our Minnesota hardwoods are lovely- but smaller than those East and South.  The wood from the crown, fully dry after one year, will heat two households for several weeks.  Her crown was unusual.  Very broad; branching, rising, and spreading with curves that I can only describe as Art Nouveau.   And each branch sensible, individual, and functional.

The big trunk is blocking the road now- and will likely block it for a couple weeks, until we can get in through the deep snow and haul the log out with the tractor.  I have fantasies of getting one or two of the logs cut for boards.  We can use them.  And I'll try to get some of the top turned into a bowl or two; red elm is a favorite of wood turners, too.

How does it feel, to burn my old friend's bones?

Warm.  Decades of warm.

Long years of memory; long years of companionship.  She was my companion.

I don't know if she knew; the gulf between our species is very large; but I knew.  And it wouldn't surprise me at all, as either human or scientist, if she knew.  Most tree species are tens of millions of years older than our paltry 2 and half or so.  They are very sophisticated creatures- and survivors.  Their life-pulse is so slow, few humans can sense it; they live in an utterly different way, and time.  Right beside us.

She is my companion still.  With every chunk of her I put into the stove, I remember our lives.  I think she's glad.  Now she's warming two houses, full of my family.  Her stump is 4 feet tall, and will last for at least 20 years.  Big enough to sit children up on; big enough to host hundreds of smaller creatures yet, in that time.

She's taking care of my babies.  I'll take care of hers.  Some 20 or so of her seedlings are growing; I'll see to it they get a chance.

There is no goodbye here.  I looked at her crown so many thousands of times, I'll always see it when I look at her children.  Clear as clear.