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Wednesday: Melange

A mixture of things from around the web:

1.) Charles Pierce writes that Obama’s press conference yesterday featuring Slutgate and contraception left him uneasy.  In Standing Up for Sex, Pierce writes:

Not a simple, mumbling word about the right to decent health-care, let alone the right to choose. Given a golden opportunity to say flatly that he and his administration were foursquare behind these rights, he gave the whole thing a pass. I’m sure he’s got poll numbers that tell him not to say “abortion” in public but, damn, this was disappointing.

This is what I mean when I say that this issue can only be a political winner for the Democrats if they go out and make it one. How hard would it have been for him to say, “Look, it’s probably not a good time in history to be using the war metaphor, but there’s no question that the Republican party is a vehicle in an organized campaigh to roll back women’s rights in the most personal sphere of their lives, and, as long as I’m president, that won’t happen.”?

I’m glad he called Sandra Fluke. I just wish he’d show that he appreciates the incredible political gift she gave him.

Obama thinks his party affiliation speaks for itself and we should read into his statements what his real thoughts and intentions are.  And this worked so well in 2008.  Everyone thought he was a liberal even though he didn’t embrace liberal or even Democratic or New Deal principles.  Everyone thought he was an anti-war candidate even though this was all premised upon what he *might* have done had he actually been present at the IWR vote.  Everyone thought he was a feminist, which flew in the face of hard evidence that we watched and heard with our very own senses.  In the past four years, he has shown himself to be none of the things he was assumed to be so, and, as far as I’m concerned, we should not assume or presume that he is onboard with sex being guilt free for adult women.  More likely, he has no natural empathy for women in this regard so he’s more inclined to do what’s good for him politically and not for women socially.  And right now, he thinks it is good for him politically to reach out to evangelicals and the women’s vote will just flock to him because women are assuming he is not as bad as the Republicans.

I think he is just as bad, if not worse, because his attitude encourages complacency.  It will all be taken care of, don’t you worry.  A year from now, women are going to be kicking themselves for not being more demanding of him.  You’re only going to get a commitment from him under duress and until you hear him choke it out in a high squeaky voice, don’t assume anything.

2.) Speaking of beliefs that may or may not have any basis in fact, have you checked out the Richard Dawkins Belief Scale?  Unlike women’s rights, you don’t have to commit to a god or atheism.  It’s perfectly Ok to land somewhere along the scale.  I’m a 5.78324.  Some people might round that up.  Here it is:

  1. Strong Theist: I do not question the existence of God, I KNOW he exists.
  2. De-facto Theist: I cannot know for certain but I strongly believe in God and I live my life on the assumption that he is there.
  3. Weak Theist: I am very uncertain, but I am inclined to believe in God.
  4. Pure Agnostic: God’s existence and non-existence are exactly equiprobable.
  5. Weak Atheist: I do not know whether God exists but I’m inclined to be skeptical.
  6. De-facto Atheist: I cannot know for certain but I think God is very improbable and I live my life under the assumption that he is not there.
  7. Strong Atheist: I am 100% sure that there is no God.

Assuming that there are not as many 1’s out there as the Beanie Boys would have you think, why should we allow the 1’s to run the country based on judeo-christian biblical principles?

3.) More on belief.  Pat Robertson may have exceeded his stupidity quota.  When asked on the 700 Club about why God kills people with tornados, he had this to say:

There ya’ go, tornado victims.  Let this be a lesson to you.  Don’t buy a farm in the middle of tornado alley.  Don’t be a person who earns a living in tornado alley either.  And woe to you on the west coast in the earthquake zone.  The kinfolk say, move away from there!  Californy is NOT the place you want to be.  Also, if you are anywhere where you could be swept away by a flash flood, get caught up in a hurricane or Nor’easter, burnt to a cinder in a wildfire, trapped in a heat wave, engulfed in a blizzard, frozen in a cold snap, eaten by wild animals or poisoned by insects and plants, or irradiated by a particularly unusual and strong solar flare, well, it’s your own damn fault.  Did God promise you a rose garden?  You should have bought one of the time shares in Glenn Beck’s underground bunker cities and retreated to it with your 6 months supply of dried ravioli and Tang.

I guess Stephanie Decker, who protected her kids from the tornados with her own body and lost her legs as a result, should be thankful that God didn’t demand more of a sacrifice for living in the wrong place.  But I have faith that with the help of doctors, physical therapists and prosthesis engineers, Stephanie *will* walk again.  Hang in there Stephanie.

4.) A couple of days ago, a PR person for Chris Viehbacher tried to do a What Chris Really Meant response to Chris’s insensitive and clueless presentation of the reasons why his company was getting rid of its own scientists and turning to cheap and desperate small company scientists for potential blockbuster drugs.

Now, Viehbacher’s point seems to be that small biotechs and mid sized companies are more nimble and innovative than big behemoth pharma companies so, and here’s the logic of the bonus class in all it’s glory, big pharma scientists just aren’t as good as those in smaller biotechs and therefore deserve to have their jobs eliminated.

This ignores two things that Viehbacher is either denying or completely ignorant of.  The first is that those of us who up until recently worked in big pharma until we were dumped for working in big pharma, did not start our careers in big pharma.  Nooooo, we were in medium pharma.  The first pharma I worked at only had 3 research sites and the one I worked at in Princeton was relatively small having about 400 people total working on about 5 different therapeutic areas.  It was all self contained with chemistry, biology, animal facilities, structural biology, analytical, scale up, everything in one building.  But then came the mergers and more mergers and we added more facilities and companies and satellite research centers in different companies and then we got consultants to come in every couple of years and rejigger everyone, just to keep it light and breezy.  Every time there was a merger, work would come to a screeching halt for two years so the managers could play musical chairs and find a department headship position, usually by doing a real Julius Caesar meets Brutus in the Senate scene.  So, big was never OUR idea.  It was the bright idea of the finance guys, the consultant guys and the Viehbacher guys who got big bonuses from every merger they made.

The second thing that undermines Viehbacher’s argument is that all of those big pharma scientists that he thought were no good are now working for the small companies and acedemic groups that Viehbacher is planning to rape.  Now that they’ve been liberated from the shackles of big pharma wage slavery, they are working more nimbly and innovatively at small biotechs and university labs with vastly reduced salaries and benefits.  And this must warm the cockles of Viehbacher’s heart enormously.

5.) Finally, Titli Nihaan, my new favorite internet chef (until #1 child gets her own show), shows us how to make a Cassoulet and gives us some French lessons as a bonus!  This is the halal version.  I tried it the other night but made some even leaner substitutions.  Delicious. Er, Magnifique!

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Saturday: round up

What else was in the air over Joplin?

Thank you all who were concerned with my big purple toe.  It’s still swollen but I can walk on it now without wincing so I think it will be OK.

This post contains random stories collected from around the web that provoke me.  Forget that.  There’s only one story that got my attention this morning and made me cranky.

I am not an epidemiologist but this story in the NYTimes about the fungal infections popping up in Joplin, MO post tornado leaves something to be desired.

Several people who were injured when a tornado devastated Joplin, Mo., last month have become sickened by an uncommon, deadlyfungal infection and at least three have died, although public health officials said Friday that a link between the infection and the deaths was not certain.

Also on Friday, the death toll from the tornado was raised to 151.

Eight tornado victims have fallen ill from the mysterious infection, and each had “multiple injuries and secondary wound infections,” said Jacqueline Lapine, a spokeswoman for the Missouri Department of Health and Senior Services. Citing confidentiality rules, officials declined to discuss the treatment or condition of the patients.

The fungus that causes the infection, which is believed to be mucormycosis, is most commonly found in soil and wood, according to the Centers for Disease Control and Prevention, which is studying samples from the eight Joplin patients. “It is a very aggressive and severe infection,” said Dr. Benjamin Park, chief of the epidemiology team in the C.D.C.’s Mycotic Diseases Branch. “It is also very rare.”

Mucormycosis enters the body either via a puncture wound or when a victim breathes in its mold spores, officials said. Those who have weakened immune systems have a mortality rate as high as 90 percent. Other people at risk include those with diabetes or cancer and burn victims.

Mucormycosis is a rare fungal infection that makes death by any other method look like a cakewalk.  Normally, hospitals see only one or two cases a year.  The cluster in Joplin is very disturbing.  When I read the Times article, I got the impression that these infections were the modern day equivalent of the bubonic plague.  No one knows the source of the infection.  It’s a horrible way to die.  Very unsettling.  It’s yet another mystery disease that popped up in the couple of weeks.  Earlier, we heard about the antibiotic resistant ecoli infections in Europe.  Diseases and random acts of microbes, out of control.  OMG, we’re all going to die!  Why so many scary biological stories lately without the cause, effect and perspective?

The Times reporter suggests that the cluster of fungal infections was caused by the incomplete disinfection of wounds at emergency triage centers that we erected immediately after the storm passed through Joplin.  You may recall that one of Joplin’s hospitals was destroyed during the tornado so makeshift medical treatment facilities had to be erected quickly.

Ok, let’s back up for a minute.  When I read this story, I suddenly remembered a pseudo-science cable channel medical voyeur special about a man without a face (cue the Billy Idol).  From what I can remember, Mark Tatum starting experiencing severe headaches, which his doctors determined was caused by a massive mucormycosis fungal infection in his sinuses and behind his eyes.  The infection is 90% fatal.  The only way to save his life was to treat him with anti-fungal medications and to cut out the infection.  That meant removing his eyes, nose and upper jaw.  Imagine having that conversation with your doctor.  Once you decide, there’s no going back.

Anyway, back to Joplin.  What I find so unsatisfying about this story of the mucormycosal infection cluster in Joplin is that there are so many moving parts that could have made it more informative and interesting.  Isn’t this what the paywall is supposed to promote?  For example, I read recently that meteorologists are studying this year’s severity of the tornados and locations with interest because they are working on a theory about dry soils and moist soils and the generation of tornadic activity.  Oddly enough, there is a new article about this theory in earthzine that was posted today, and speculation, not yet proven, that the shift in location and severity of this year’s tornados could be the result of global climate change.  From the article, Seasonal Predictability of Tornadic Activity Using Antecedent Soil Moisture Conditions:

If Intergovernmental Panel on Climate Change (IPCC) [1] projections are accurate, the frequency and severity of extreme water cycle events (e.g. droughts, floods) will increase as a consequence of climate change. The IPCC notes that hydrological extremes such as flooding and drought occurrence have increased markedly in the last three decades, with more intense and longer episodes. Large variability in the atmospheric component of the water cycle is directly linked to terrestrial soil moisture distributions. The consensus on soil moisture-atmospheric feedbacks is that surface heat fluxes and moisture gradients can influence convective development (e.g., [2],[3], [4], [5], [6], [7], [8], [9], [10], [11], [12]).

These studies and others have discussed the following connections between soil moisture and convective storm development: (1) Partitioning of surface energy into latent and sensible heating, which in turn affects the atmospheric boundary layer and regional convergence through moisture and energy exchanges; (2) Higher evaporative fraction; (3) High concentrations of entropy (or moist static energy) in the lower atmosphere; and (4) Development of mesoscale (e.g., sea breeze-like) circulations.

However, there is a lack of literature on the extension of soil moisture-atmospheric feedbacks to extreme hazards like tornadoes. At the same time, there is convergence of hydroclimate processes scales and weather-climate model resolutions, such that explicit feedbacks and connectivity between soil moisture and the atmosphere should be resolved [13]. Further, seasonal predictability of tornados has clear societal implications for safety, insurance companies, the construction industry, and even retailers like Home Depot or Lowes.

I’ve underlined the last line because it doesn’t seem outside the realm of possibility to me that the dry soil/moist soil theory might also be applied to the outbreak of mucormycosis in Joplin.  Is there a connection?  Let’s start with the fungus and disease that it causes.  Mucormycosis is spread by spores, presumably airborne.  The deadliest of these fungal infections is the rhinocerebral variety involving the nasal cavity, behind the eyes and in the maxilla, or upper jaw.  The infection is most commonly found in people with compromised immune systems and in diabetics but the wiki on mucormycosis says that “traumatic innoculation” is also a possible route to infection.  But even though the Times srticle doesn’t go into detail, the number of cases in Joplin suggests that the epidemiology of the disease there is unusual and doesn’t follow the normal rules.  Maybe the people affected are not immunocompromised.

So, here’s my hypothesis: the dry soil/moist soil theory says that tornados form along the boundary between dry soil conditions and moist ones.  We know that parts of the midwest and southwest have been suffering from droughts this year.  If spores are airborne, would dry soil/moist soil boundary areas have a greater number airborne spores?  Think weaponized anthrax.

Ok, so along comes this massive tornado packing walloping winds and in a place like Joplin, there aren’t many places to hide.  The nature of the fatal infections suggests that it gets into the body through the respiratory tract.  The nose and sinus cavities seem to be the primary location of the “fungal ball”.  Is it possible that the route of infection was through the nasal cavity from exposure to tornadic winds or their aftermath?

How might we test this hypothesis?  Here are some of the questions I might have asked if I were the Times reporter:

Were any of the victims immunocompromised?  Did any of them have diabetes?  Is the infection the rhinocerebral variety, suggesting that the spores were inhaled, or are the infections somewhere else?  The mortality rate due to mucormycosis in Joplin suggests inhalation rather than skin infection.  Presumably, you can remove parts of skin without killing the patient.  It’s not so easy to remove sinuses and, potentially, parts of the brain.  Where did the survivors ride out the storm?  Does their location and level of exposure to disturbed air currents correlate to the level of infection?  Were they in an enclosed area during the storm or was the wind in their faces?  If wind wasn’t forced up their noses, that might suggest that the spores remained airborne after the tornado passed through the area. If we look at the region where tornados occurred this year, are there additional cases of mucormycosis?  If we plot these cases on a map, is there a pattern?  Does it correlate with the dates of tornados?  For example, is there an increased number of cases of mucormycosis in Alabama?  How about further east?  Does the rate of mucormycosis increase directionally?  If the infection is caused by airborne spores that are inhaled, does it seem correct to place the blame for the infections on emergency workers who tended to skin wounds and not nasal cavities?  If we discover that the number of mucormycosis infections increase after tornados in general, what course of emergency treatment would be appropriate?  Saline rinses?  An immediate course of anti-fungal medication?

I only ask.  Call me a ‘satiable Elephant’s Child and spank me but the NYTimes article could have presented us with a grim but fascinating medical mystery that might be linked to climate change.  Instead, we get the equivalent of an inexplicable horror story.  Maybe a different information provider, like  Chris Smith and the other NakedScientists, could do a better job of exploring this story.  Chris??

The reason this story bugs me is that the reporter seems so incurious.  The story and investigation goes nowhere.  It’s just a big question mark.  There are so many unanswered questions, some of them due to confidentiality rules, that I might not have put it on the front page.  It makes me irritated that there are so many stories like this that reporters fail to explore.  Journalists are notoriously bad at explaining science and frequently let their biases show.  The reporting on the reactors in Japan after the earthquakes and tsunamis was particularly egregious.  Yes, radiation readings a million times greater than normal are indeed disturbing- until you consider how many zeros follow the decimal point in a normal reading.  That doesn’t mean the situation wasn’t serious or that every nuclear regulatory agency in the world shouldn’t be studying Fukushima very carefully.  It’s just that the level of panic generated by the media was disproportional to the risk to the target audience of that breathless reporting.

I guess I’m just disappointed at what passes for expertise in any field these days.  How many journalists, or members of any profession for that matter, get their jobs through patronage instead of merit?  What is the energy penalty that we pay for this kind of selection process?  Is sensationalism more important than investigation and does that affect how journalists are hired? Do we as a society value loyalty and conformity to our master’s point of view more than independence, diligence and curiosity?  And what does this tell us about the future prospects of Americans without a network, or what Jane Austen would call “connexions”?  How would Edison do in this environment, with a homeschool education and lacking a degree from a prestigious university?  Is there a connection between the lackluster reportage and our stratified society or am I just rambling?  I’m rambling, aren’t I?

Ok, I’m done now.