• Tips gratefully accepted here. Thanks!:

  • Recent Comments

    Sweet Sue on We’re Royals and other…
    Sweet Sue on We’re Royals and other…
    abc on We’re Royals and other…
    katiebird on We’re Royals and other…
    katiebird on We’re Royals and other…
    riverdaughter on We’re Royals and other…
    Monster from the Id on We’re Royals and other…
    cwaltz on Give Democrats a piece of your…
    Mr Mike on We’re Royals and other…
    Monster from the Id on We’re Royals and other…
    paper doll on Give Democrats a piece of your…
    paper doll on Give Democrats a piece of your…
    paper doll on Give Democrats a piece of your…
    r u reddy on Give Democrats a piece of your…
    Mr Mike on Give Democrats a piece of your…
  • Categories


  • Tags

    abortion Add new tag Afghanistan Al Franken Anglachel Atrios bankers Barack Obama big pharma Bill Clinton Chris Christie cocktails Conflucians Say Dailykos Democratic Party Democrats Digby DNC Donna Brazile Economy Elizabeth Warren feminism Florida Fox News General Glenn Beck Glenn Greenwald Goldman Sachs health care Health Care Reform Hillary Clinton Howard Dean Joe Biden John Edwards John McCain Jon Corzine Karl Rove Keith Olbermann Matt Taibbi Media medicare Michelle Obama Michigan misogyny Mitt Romney Morning Edition Morning News Links Nancy Pelosi New Jersey news NO WE WON'T Obama Obamacare occupy wall street OccupyWallStreet Open thread Paul Krugman Politics Presidential Election 2008 PUMA racism Republicans Sarah Palin sexism Single Payer snark Social Security Supreme Court Terry Gross Texas Tim Geithner unemployment Wall Street WikiLeaks women
  • Archives

  • History

    October 2014
    S M T W T F S
    « Sep    
     1234
    567891011
    12131415161718
    19202122232425
    262728293031  
  • RSS Paul Krugman: Conscience of a Liberal

  • The Confluence

    The Confluence

  • RSS Suburban Guerrilla

  • RSS Ian Welsh

    • The Attack In Ottawa will be used to justify losing more rights
      Prime Minister Harper pretty much confirmed it: ‘Our laws and police powers need to be strengthened’ Yup.  Never let a crisis go to waste. I’m very sad that MPs and their staff were scared, and I’m sadder that a soldier lost his life.  But one attack does not justify increasing the police state.  However, if [...]
  • Top Posts

Observing Ebola and some thoughts (not fears)

Note: I am not personally afraid of Ebola. I don’t think even this outbreak will reach the level of pandemic. I worry about the people in the west African nations  who ARE personally affected. I admire the people who have gone there to fight for them.  But, I have to admit to being fascinated by the spread of this disease, the details surrounding it and the affect two cases of Ebola have had on our hospitals and health care system. Also, I think it’s fascinating. I do.

So, what do we know?

UPDATE: Here is the full statement from National Nurses United:

 Statement by RN’s at Texas Health Presbyterian Hospital as provided to National Nurses United

Nurses had to interact with Mr. Duncan with whatever protective equipment was available, at a time when he had copious amounts of diarrhea and vomiting which produces a lot of contagious fluids.

Hospital officials allowed nurses who had interacted with Mr. Duncan to then continue normal patient care duties, taking care of other patients, even though they had not had the proper personal protective equipment while caring for Mr. Duncan.

Patients who may have been exposed were one day kept in strict isolation units. On the next day were ordered to be transferred out of strict isolation into areas where there were other patients, even those with low-grade fevers who could potentially be contagious.

Were protocols breached? The nurses say there were no protocols.

 Apparently the nurses who treated Thomas Duncan didn’t where those “Moonsuits” while exposed to him. Monday evening I saw this video of Gupta suits up in Ebola protective gear according to the CDC protocols.  As you will see it’s lucky he was covered in chocolate sauce and not Ebola vomit: http://www.cnn.com/video/data/2.0/video/health/2014/10/14/sgmd-gupta-ebola-suit-demo.cnn.html.I’m glad I saw this before I heard the statement from National Nurses United (discussed below) — it made it MUCH easier to follow the details:

Nurses’ union slams Texas hospital for lack of Ebola protocol, by Catherine E. Shoichet, CNN

Here’s a look at some of the allegations the nurses made, according to the union:

Claim: Duncan wasn’t immediately isolated

On the day that Duncan was admitted to the hospital with possible Ebola symptoms, he was “left for several hours, not in isolation, in an area where other patients were present,” union co-president Deborah Burger said.

Up to seven other patients were present in that area, the nurses said, according to the union.

A nursing supervisor faced resistance from hospital authorities when the supervisor demanded that Duncan be moved to an isolation unit, the nurses said, according to the union.

Claim: The nurses’ protective gear left their necks exposed

After expressing concerns that their necks were exposed even as they wore protective gear, the nurses were told to wrap their necks with medical tape, the union says.

“They were told to use medical tape and had to use four to five pieces of medical tape wound around their neck. The nurses have expressed a lot of concern about how difficult it is to remove the tape from their neck,” Burger said.

Claim: At one point, hazardous waste piled up

“There was no one to pick up hazardous waste as it piled to the ceiling,” Burger said. “They did not have access to proper supplies.”

Claim: Nurses got no “hands-on” training

“There was no mandate for nurses to attend training,” Burger said, though they did receive an e-mail about a hospital seminar on Ebola.

“This was treated like hundreds of other seminars that were routinely offered to staff,” she said.

Another post covering this topic, No hospital ‘protocols’ for Ebola treatment: US nurses’ group by MICHAEL LANGAN (AFP) has a little more information:

Deborah Burger, the NNU’s co-president, said Duncan’s lab samples were sent in the hospital tube system “without being specifically sealed and hand delivered,” Burger added.

“The entire tube system was potentially contaminated,” she said.

“There was a lot of confusion about (gear) protocol, and frequent changing of instructions.”

The nursing staff said that they were directed to wear standard or generic hospital gowns that are flimsy and could be permeated or ripped.

They also complained that they were advised to use surgical masks, not the plastic welder-type shield mask considered a best option.

And while they wore protective gloves, parts of their heads and necks remaine exposed, she explained

DeMoro pointed the finger not just to the Texas hospital where Pham worked, but at the US health care overall.

It “is a chaotic system,” she said.

If I can find the complete transcript, I’ll add it here because it was an extensive and damning list.

It makes complete sense to me that a hospital, any hospital, wouldn’t be prepared for an actual Ebola patient. The chances have been pretty good for several months that some hospital would get an Ebola patient but predicting which one would have been impossible in advance. However, I am pretty shocked to learn that there’s no “infectious disease kit” that could be sent to a hospital faced with an outbreak something like Ebola. How hard would it be for the Centers for Disease Control (CDC) to stock sufficient emergency supplies that could be sent overnight to any hospital — including a couple of experts.

The nurses statement says that Duncan was left in an area with several other patients for hours before he was isolated. That was bad enough but, things went downhill from there. Couldn’t the Centers for Disease Control (CDC) send an expert to Dallas during those hours? I’m not a medical person but, it seems like the CDC should have a contact list of people – maybe from the US hospitals that have already treated Ebola patients who could help local hospitals control outbreaks of diseases.

So what else do we know?

Nurses wrapped tape around their necks to protect them. (I can’t even control tape on a Christmas present! What would I do if I had to work with Ebola drenched tape after a shift in Duncan’s room?)

Duncan’s lab samples were sent through the tube system without being protected! (I didn’t even know they sent lab samples through tubes, much less Ebola samples!! That’s just gross)

These are some thoughts from a non-medical reader. Again, I’m not afraid. And I don’t think the above issues mean we’ll get an epidemic here.

Ebola Updates: Still no reason to panic

Another big headline at the NYTimes: A Second Healthcare worker in Dallas has tested positive for ebola.

Is anyone shocked?  Please raise your hand where I can see you.

Didn’t think so.

Update: So, now we find that the second nurse who was infected was on a plane from Cleveland to Dallas the day before she reported symptoms.  Ahhh, now here is where Americans should start to get concerned.  Americans get around.  That is, it’s  relatively easy to jump on a plane for a weekend getaway, though why anyone would want to go to Cleveland is beyond me.  Sorry about that, Cleveland.  And Pittsburgh is only a few hours from Cleveland by car.  Nevertheless, there is still no reason to panic, though the CDC seems to think the passengers on that flight need to be tracked down. The nurse landed in Dallas-Ft. Worth on Monday night at 8:16pm and reported symptoms on Tuesday. That is a very tight timeframe so passengers probably have more of a reason to be concerned but not panicked. But the bigger problem is that it will be harder to keep ebola in Texas if infection rates blossom.

Reminder: Back in May, I went to a user group meeting in Cambridge, MA where I met several researchers who had just come back from a visit to the CDC.  They reported that the budget cuts had demoralized the CDC and researchers there sometimes didn’t know who they reported to or who was in their group.  That’s not a slight on the CDC.  It has been a world renowned institution but if you starve it for funds, it is going to have problems.  If you do it over a period of 14 years, it’s going to have BIG problems.

I’m copying a few comments I made in a previous thread on the latest ebola news.

On the CNN report about the Nurses Union that is speaking out for the Dallas health care workers, Katiebird may be posting on this later once she has tracked down some information.  These are just my uninformed, idle speculations to the news that Texas Health Presby Hospital may have put its employees and others at risk:

I read that CNN article late last night and I was shocked but not surprised, if that makes any sense. Shocked because the hospital was caught so unprepared and was really botching it. But unsurprised because it made a lot of sense in how the infection was spread to this nurse. No health care worker in their right mind wouldn’t take the utmost precautions given the media frenzy over ebola.

I could only conclude that the hospital itself was at fault for being caught off guard and, probably, considering cost over treatment protocol. After all, who was going to pay to isolate Thomas Duncan? Rick Perry turned down medicaid expansion and the Texas legislature has severely cut back on state board of health offices. Laissez faire apparently means anything goes when it comes to profiting off of health care and Duncan was a money sink.

The 90 minutes gap where Duncan was with other patients before he was isolated may have referred to the emergency room. Here’s my best guess: The ambulance dumps Duncan off at the ER with a barf bag. He has to sit there with other sick patients while calls are being made to the hospital administrative staff to decide how to admit him. He’s a foreign visitor, not even an immigrant, with no health insurance, dumped on Texas Health Presby Hospital. He doesn’t qualify for Obamacare, there’s no medicaid for him either because, hellloooo, Americans, especially those living in the south, don’t want to pay for the health care needs of foreigners. Are there funds set aside in Texas to manage a highly infectious disease like ebola? Are you kidding?? Decisions, decisions. The hospital might have thought of transferring him elsewhere but I’m betting the other facilities said they were no better able to care for him. It’s your problem.
Damn, Duncan could wipe out the profit for the entire year, what with the isolation and ruining ventilation and dialysis equipment, not to mention how to get rid of hazardous waste.

So, he sat in the ER for 90 minutes, vomiting and sweating all over the chairs and gurneys, before the hospital decides it doesn’t have a choice anymore and has to take him. Who knew how many people came in contact with him while he was shedding billions of viruses? Poor Nina Pham probably did what she was instructed to do with very little CDC oversight.

On the ebola forum symposium held yesterday at the Johns Hopkins School of Public Health that was held yesterday:

Peter Jahrling showed all of the possible drug treatments in the pipeline. It’s a joke. No, seriously. ZMapp looks like the best bet but the company can only make about 20 doses in its next batch. It’s not their fault. They’re just overwhelmed by the scale and logistics.

A couple of vaccines are being tested in the field. And they have to have a control group so 1/3 of the participants are getting Hepititis C vaccine. It can’t be helped but the participants must know that some of these people are going to die. There’s no way around it. That’s the way science is done. And these vaccines are not in anyway ready for FDA approval.

Other treatments are even less ready. Interferon actually makes the infection worse. There’s an interesting research topic. What is it about the cell signaling that makes interferon treatment worse? Then there are a couple of “drugs”. Honestly, I think biologists are analyzing the high throughput data. They think any hit is a drug. The compounds presented may have some efficacy (probably in the millimolar range from the looks of them) but they’re not very bioavailable and the toxicity could be a major problem.
So, in short, we’re pretty much screwed if we can’t get West Africa back under control and the infection spreads.

Not that we have much to worry about here in the US. We don’t. But it’s not very reassuring to me that we are sooooo far behind in the drug discovery area on infectious diseases. Again, shocked but not surprised.

The symposium can be found here. Most of it is School of Public Health academics trying to one up each other on modeling the progress of the disease. It got to be too insidery and less informative after awhile. Jahrling’s presentation was more straightforward, to the point and alarming. If the general public truly understood what Jahrling’s presentation was saying, they’d never vote for another budget slashing Republican. Ebola is only one of a number of devastating infectious diseases that we are not prepared to deal with because we cut funding, blocked nominations, and let private industry, dominated by shareholders and billionaires, dictate the research and manage the pipeline portfolios. It’s baaaaad.

About quick and dirty drug design using publicly available ebola virus crystal structures and the funky vocabulary that goes with it, this is a little primer on what I was initially thinking and about some of the obstacles:

FASTA is a format for amino acid sequences. Every protein has a sequence of amino acids and they are all unique. Families of proteins are related to one another. You can perform an evolutionary trace on a single protein if the sequence of that protein over time has been determined. The FASTA sequence is stored in publicly available databases. The NIH allows access to these sequences for researchers and provides tools to search them. One of these search tools is called BLAST. It can do sequence alignments. So, if you have a fragment of a sequence or a new sequence, you can search the database to find the entire sequence or similar sequences. I used to use a related tool called BLASTp. That allows the user to find protein sequences that have been crystallized and are stored at the RCSB.

So, let’s say you have a protein that you know has mutated away from its original source. In this case, we are talking about the ebola viral proteins. The crystal protein I referred to last night was from a strain found in Zaire, in a place called named after a nurse called Mayinga. But the newest outbreak of ebola is located in West Africa and it is a different strain, therefore, different mutations in the amino acid sequence.

If you designed a drug based on the Zaire Mayinga strain, it may not be effective against the West Africa strain because the amino acid sequences may be different. But we can make a homology model of the new viral protein structure if we know where the new mutations are. It’s the next best thing to a experimentally determined crystal structure.

The questions to ask are: do all of the viral proteins mutate at the same rate? We would know by looking at the latest FASTA sequences and mapping them onto the structure. Can we identify a binding site? The protein I looked at yesterday processed RNA. I can make an educated guess as to where this occurs. But when it oligomerizes, that is, forms a new structure by self assembly, it has a couple of different binding sites. That is, the binding sites of each subunit to the subunits adjacent to it can also be targeted for drug design. I worked briefly on a different oligomer previously and it was possible to create a drug like entity called a paptamer by extracting a chunk of the secondary structure of the subunit and modifying it very slightly. This prevented the subunits from self assembly, or so the theory goes.

But in the ebola protein I looked at yesterday, the protein-protein interactions between subunits appeared to be dominated by beta sheets, which relate to one another along parallel and antiparallel strands. So, extracting a piece of this binding surface would be difficult if not impossible. Another, more complex and time consuming drug design process would need to be done. If it were just a matter of a helix, it might have been a different story. So, this viral protein target might not be amenable to quick and dirty drug design work and it might have to be abandoned for another ebola protein.

In any case, the FASTA sequence is very informative. It has likely been deposited at the NIH. They usually do that for Flu viruses and you can track mutations as they zip around the world. But I’m not sure we have the very latest info for ebola.

Ok, that was long.  I’m going to eat lunch.

 

 

Ebola Post: Request for papers

Given that the number of cases of ebola in Africa is rising exponentially, and given that ZMapp is not going to be available in sufficient quantities any time soon, is it possible to find/screen for a small drug entity or protein aptamer that would interfere with the oligomerization of ebola matrix proteins or inhibit the action of other ebola virus proteins?

I think the answer is yes.  The RCSB, the publicly available repository of protein structures, has over 40 ebola virus proteins, some deposited this year.  I have to assume that someone(s) is screening ACD or other compound databases with docking programs to find potential hits.  It would be great if those of us who used to do this type of work would also be able to contribute.

However, while the structures are available, and much work can be done just using the structures, the papers that are associated with them frequently are not.  The journals involved can charge up to $33/copy for each paper.  This cost is prohibitive for most independent researchers.  Come to think of it, so are the applications I used to use to dock libraries of compounds into structures.  But even with the limited public software, we could still get a lot done if we were able to read the papers for free.  Like I said, reading the structure papers is not absolutely necessary but it can be helpful.

So, if there is anyone out there who has influence with PubMed, could you look into it?   Also, is anyone aware of a crowdsourcing effort to design drugs based on these structures?  Just give a shout out if you know of one.

One more thing: It would be very helpful to know the latest mutation data in FASTA format in case homology models need to be created on currently available crystal structures.  I see that the octamer was crystallized in 2002 and is from strain Zaire Mayinga.  If I’m not mistaken, the current epidemic is from a different strain. (though this protein may be more resistant to mutations?  Dunno.  Need to read the papers.)

Freaky Weird Prescience (Ebola Post)

Well, it’s not looking good on the ebola front.  We still don’t know why the nurse in Dallas has ebola despite all of her precautions but I’m still not panicking.  My relatives in Houston are probably safe, though what did they say during the Black Death?  Run fast, go far, stay long?  Ok, that’s not really funny and is only encouraging a kind of hysteria that isn’t helpful.  Two ebola patients in Texas does not an epidemic make.  Then again, it’s Texas.

Nevertheless, there is a some speculation that the virus has become more virulent.  Peter Jahrling of the National Institute of Allergy and Infectious Diseases says this may be due to the increased viral load in infected individuals:

You’re seeing all these patients getting infected, so people think there must be aerosol spread. Certainly, it’s very clear that people who are in close contact with patients are getting a very high incidence of disease and not all of that can be explained by preparation of bodies for burial and all the standard stuff. But if you are to assume that the differences in virus load detected in the blood are reflected by differences in virus load spread by body secretions, then maybe it’s a simple quantitative difference. There’s just more virus.

Jahrling says that HIV was actually a hotter disease, primarily because carriers weren’t obvious and were able to spread the disease easily.  It also helped that HIV attacks cells in the immune system, which prevents a vigorous response.  But it’s a little hard to make this argument when comparing it to ebola.  HIV is a long, slow death and we now have drug cocktails to treat it.  Ebola is quick, excruciating, bloody and the lethality is alarming, especially because the treatment options are so few.

Which brings me to the next bit of bad news.  Frances Collins of the NIH says we might have had a vaccine for ebola except our politicians, with anti-governmental fervor, cut funding to those very institutions that might have helped to develop one.  I’d heard from researchers I met in Cambridge who had recently been to the CDC that morale was pretty low and disorganization was high.  Then, I lived through the summer of sequester when university research groups lost a sizable chunk of their funding as grants became more and more unattainable.  Layoffs quickly ensued.

One of the reasons I have been reluctant to pursue a job in research is because the money isn’t there anymore and I’m really sick of layoffs.  And let me make it clear that while scientists like to get paid fairly for the work they do, they don’t work for the money, for the most part.  They just like the work.  It can be frustrating and maddening and discoveries take a long time.  But it is also intensely rewarding in a way that money isn’t.  That’s not to say that we don’t have our own caloric requirements and shelter needs.  Also, no one likes to be exploited.  But bankers and Jack Welch types don’t understand the nature of science or the vast majority of people who do it for what is turning out to be a vanishing living.  But I digress.

The problem is that the patent cliff spooked pharma shareholders and they abandoned American research in search of get-rich-quick schemes and foreign research that isn’t ready for prime time.  At the same time, rabidly anti-government Republicans, abetted by complacent Democrats, have been slashing research budgets.

This is not the same America that we had in the post World War II days.  This is an infrastructure that is rapidly being gutted.  If you have any doubt of how bad things are, consider that Mapp Pharmaceuticals is virtually the only company on the planet with a possible treatment for ebola (we won’t know how the GSK vaccine is doing for awhile yet) and it is a small company in San Diego facing a logistical nightmare.  How does it grow the monoclonal antibodies and purify them on a scale to meet the urgent need of thousands of patients around the world?  Where is the CDC/NIH/Private Industry SWAT team that can get this off the ground?  We are asking this company to do the impossible on a massive scale in such a way that would attract every class action lawyer in the country if there wasn’t a health care emergency.

But it’s even worse than that.  As Collins says, ebola is only the tip of the iceberg.  The vast majority of us will not die of ebola.  We’re going to suffer from other maladies that no one is studying right now.   The funding is low on antibiotics, certain central nervous system disorders, heart disease, etc.  Companies just stopped working on these diseases because the research was expensive and shareholders didn’t think the profits were high enough.

All of this is happening when there is a revolution in biology.  The most ironic aspect of this problem is that thousands of trained researchers have been sidelined right at the same time that there is more than enough work to keep every one of them extremely busy for the rest of their lives.  There’s a profound disconnect between the people who are experienced enough to do the work and the funding mechanisms, either private or public, that will allow it to get done.

I see a lot of fuming on the ebola twitter feed about how scientists should just step up and get it done.  We’re all going to be saved by scientists.  How this is going to happen without funding is anybody’s guess.  It takes money to buy the equipment and reagents and research the papers and feed these scientists who everyone seems to think are going to be self-sacrificing for the betterment of mankind and to save their asses from some exotic African disease.  But as soon as the crisis is over, will we go back to chain sawing through the NIH budget?

From what I can see, neither private industry or our political leaders are taking the threat seriously.  So, I stand by my earlier prediction.  It’s going to take a plague to focus the nation’s attention on our crumbling research infrastructure.  It might as well be ebola.

 

No one could have predicted… (Ebola post)

How did it get in??

I’m sure you’ve seen the headlines this morning.  Another ebola patient turned up in Texas.  This time, it’s a health care worker who was at the hospital when Mr. Duncan came back in the ambulance.  This person was wearing protection, or so the hospital says.  Given the way that the ambulance ignored the family when they were screaming about Duncan vomiting all over the sidewalk, who knows what precautions the hospital actually took once he got there.  Ok, let’s assume that they were as rigorous as they said they were.  The fact that someone got infected anyway suggests that either the virus became a lot more infectious or that the health care worker was extraordinarily unlucky and something managed to seep through the latex anyway.

I’m going with another option.  I’m going to guess that the hospital got wise only after Duncan came in by ambulance and that the gloves, mask, full body armor and shield got implemented only after the hapless health care worker (Hapless from now on) was exposed.  The hospital may not have had time to explain the precautions everyone needed to take until after someone had touched the vomit with their gloves and then scratched their faces.

Well, it was bound to happen to someone else in Texas.  I’m still not panicked.

Last night, I caught up with Nova on PBS, which produced an episode on Ebola that ran last week.  You can view Surviving Ebola on Nova here.  This program delves more deeply into the monoclonal antibody treatment, ZMapp.  As I suspected, producing the proteins in ZMapp is a bit of a logistical challenge.  It has not been scaled up and growing the tobacco is only half the battle.  According to this segment, it takes just as long to purify the protein as to grow it.  Actually, that doesn’t sound right either.  It used to take me and my partner about 3 days to lyse the cells, spin the pellets, make the buffers, run the columns and check the fractions with electrophoresis.  I’m not sure how it differs with antibodies though.  Like I have mentioned before, antibodies tend to aggregate, or so I’m told, and purifying any protein is still a bit of an art form.  So, maybe they have additional steps to go through before it can be used in humans.

In any case, Hapless is probably not going to get ZMapp.  Let’s hope they caught this infection in time for other treatments to work.

Serial spinoff from This American Life is Gripping

Back in the 19th century, famous authors Charles Dickens and Thomas Hardy would serialize their novels for the papers.  Readers could check in with Bleak House or Jude the Obscure on a weekly basis.  Even though soap operas have serialized fictional lives for decades, it has only been recently that series like Fargo, Homeland and True Detective have presented complete plots in a serialized format instead of an episodic one.  This new kind of series season consists of one plot line, one story.  There is a beginning and an end.  The series could end after a single season, like a book without a sequel.

That kind of story telling has come to podcasting with the new This American Life spinoff, Serial.  Serial presents one single story, in this case told over twelve episodes.  TAL alum Sarah Koenig breaks down the elements of the story and constructs a gripping narrative that will leave you on the edge of your seat wondering what is going to happen next.

Her first serial is a whodunit based on a real life crime and mystery.  Who killed Hae Min Lee, a pretty and smart high school student from Baltimore?  We know at the outset that her well-liked, equally smart boyfriend, Adnan Syed, was convicted of the crime based on the testimony of his friend Jay, who confessed to helping dispose of the body.  But there was no physical evidence linking Adnan to the crime and, in the end, what gets Adnan locked away for life is that he can’t account for about thirty minutes of his life on the cold January day in 1999 when Hae disappeared.  Was he at the library like he said, and some of his friends back up?  Or was he riding around in Hae’s car, looking for an opportunity to strangle her?

What is really fascinating about this series is Koenig herself flips back and forth on Adnan’s culpability as she peels back the layers of the onion of this story.  The series is twelve episodes long and Koenig is still in the midst of recording.  We will know what conclusion she comes to just about the time that she comes to one, though she says she has about as much information as the prosecutors and the detectives have on the case.  She’s just missing one or two bits to put the whole thing together- or have her theory blown apart.

She has already discarded the prosecutors’ theory for what motivated Adnan to do it, if he did.  I was likewise convinced that the motive was an improbable stretch but the fact that the jury didn’t think so is more interesting to me.  What we find out in this serial is that there’s more going on here than just a murder.  There are a lot of assumptions that every character caught up in the investigation and trial is making.  It seems like a specific motive and suspect was zeroed in on like a tractor beam from the very beginning and cultural influences may have lead to confirmation bias. That confirmation bias may explain why some people were dismissed as suspects or witnesses earlier and why some people were believed too soon.

In any case, I have no idea how this serial is going to end but I’m fascinated by the great storytelling.  If you have a house to clean, subscribe to the podcast for the first three episodes of binge listening.  Start from the beginning so you don’t miss a thing.

Five sponges.  Highly recommended.

Beautiful theories destroyed by ugly facts- part 129845

Chopper and his gang, A Bank’s, er, Bug’s Life.

David Leonhardt wrote about why the economy seems to suck for the vast majority of us in his post The Great Wage Slowdown of the 21st Century.  Once again, he drags out that idea that will not die that if we just graduated more people from college with the right technical skills, our wages would rise.  Zombie conventional wisdom like this is what turns perfectly nice days into weeks of frustration, anger and despair for hundreds of thousands of unemployed, underemployed and “terrified of the next layoff” STEM workers.

Look, Dave, may I call you Dave?  This simply isn’t true.  I have been there and I have seen PhD after PhD after PhD in the hard sciences laid off for no other reason than because they cost too much money to employ according to some seed corn eating grasshopper with an MBA and a big bonus in his future.  The laid off are people who were uber educated.  They went to Yale and Stanford and had multiple patents to their names.  Yes, they even knew how to use Microsoft Office.  I don’t know how many times I have had to tell people lately that I know Microsoft Office like it is my native tongue.  This notion that we are all technological dinosaurs and need even more education after decades in the lab, and reading and writing papers that would make the average American’s eyes bleed, is just beyond maddening.

If you don’t believe what I’m saying, Dave, check out what Pfizer did to Wyeth five years ago.  Pfizer bought Wyeth and then proceeded to lay off all 19,000 employees including all but a handful of research staff.  That’s all of my former colleagues but about two people who Pfizer retained.  Gone.  All their years of education, years of experience and technical expertise, all their livelihoods, and in some cases houses and college funds, eliminated.  There’s a reason why Nutley, NJ, the home of Roche, is becoming a ghost town.  There’s a reason why I fled NJ and moved to Pittsburgh.  I got out just in time.  Housing prices are crashing through the basement as all of the stunned STEM workers scramble to grab whatever work they can find before the next layoff or the soft money runs out or there’s another sequester.  Or they get the hell out.  I got the hell out.  I’m not crazy.

You know what else is crazy making, Dave?  That someone with your talent and access can’t look s&*% up on The Google to back up what you are writing. (Type “pharmaceutical layoffs 2010″ for some really scary numbers)  It’s like all those mysterious congresspersons who parrot all this nonsense about STEM jobs not being filled- because they read people like you.  You have a responsibility to report the truth.  If you don’t, there really will be a shortage, just like there is with some programming jobs.  Back in the naughties, American programmers got laid off in droves and companies outsourced much of their development to Asia.  Now, I see a lot of positions on job boards for people with computer science degrees and those jobs go begging.  Well, what do you expect when the wages and jobs weren’t around for a decade and the programmers gave up and told their children to avoid programming like the plague?  Why should anyone dedicate themselves to difficult degrees if there’s no payoff or way to make a living in the end?

So, stop doing it, Dave.  Better yet, get out of the office and take NJT down to Princeton and pass all of the sites on your way that are now shuttered in the name of shareholder value.  Not to sound all Marxist or anything but the problem is not that we have too few educated people, it’s that the shareholders own the means of production and they aren’t investing their capital in research anymore, at least not here.

Nothing is going to make wages rise until the shareholders see that it is in their best interests.  And right now, they’re partying like it’s 2008.

************************************

There’s a great post on Naked Capitalism by Roy Poses, MD, titled Can Our Commericalized Health Care System Contain Ebola?  The answer is of course it can but it has to be more proactive and that’s difficult these days when health care and drug development decisions are not being made by people with the expertise to make them but by “generic managers”.

Poses has another post on his own blog about how the “generic manager” is extracting value from various industries that is a must read.  In short, there is a growing awareness that the grasshoppers have almost finished the seed corn and there must be policy imposed on them to stop the process.  Time is short.  Our policymakers can still save the day.  Given the way the 2014 Senate races are going, it looks like this will fail.

Oh well.  Prepare for a new Dark Ages.

************************************

Moving on to Princeton, Krugman has a blog about disinvestment at the public infrastructure level.  When I think of infrastructure, I am reminded that this is what I asked Hillary Clinton about at YearlyKos 2007.  She had a lengthy answer based on some well thought out policy, the highlight of which was a plan to expand our sorry excuse for broadband.  What a missed opportunity that was. But I digress.

Wait, aren’t we trying to privatize absolutely everything anyway?  Is it any surprise that investment in public infrastructure is going down?

Paul should realize by now that the 2008 election was all about saving the banks.  They set it up that way.  There wasn’t a plan for what came next.  Ta-da!

************************************

One more thing: Thomas Duncan, the Liberian ebola patient in Dallas, is getting an antiviral experimental treatment called brincidofovir.  Who names these things??  Anyway, he’s in critical condition but his liver function seems to be improving.  That’s great.  Unfortunately, brincidofovir messes up your kidneys so he’s now on dialysis.

Here’s a little bit of drug design/medicinal chemistry geekery.  The structure of brincidofovir is shown below:

 

When I was doing high throughput screening data analysis, I might have chucked this structure into the delete bin because of that long tail.  It’s big, it’s bulky, it’s greasy as bacon drippings.  No one is going to get a decent drug out of that.

And that’s kinda true.  Brincidofovir is a prodrug.  That big, long greasy tail improves its bioavailability (you have got to be kidding).  Once it gets into the body, that tail piece gets cleaved off to leave cidofovir, a viral DNA polymerase inhibitor:

I thought I’d mention that for No. 1 child who is taking a related class in the subject and now understands that when chemists say “cleavage”, they’re not always talking about your boobs.

 

 

Follow

Get every new post delivered to your Inbox.

Join 468 other followers