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Thoughts but not prayers on Dallas

To whoever did it in Dallas,

Diamond Reynolds was unnaturally calm when she made a video of a police officer pointing a gun in her car after shooting Philando Castile while her 4 year old daughter was sitting in the backseat.

Then the phone kept recording when they forced her out of her car and onto the ground while her daughter screamed from the backseat and Philando Castile expired in the front seat soaked in blood.

Then Diamond kept the phone running while she was put in the backseat of a police car handcuffed while her daughter tried to console her and Diamond unleashed her anguish over the death of Philando Castile.

You would have to be inhuman to not feel how horrible and devastating it is to be black and driving a car with a broken tail light. Diamond showed us what it is really like.

And now, Diamond’s bravery and calm and final grief is going to be quickly forgotten because you had to take matters into your own hands.

Those of you who survived your terrorist activities will receive better due process than Philando Castile or Alton Sterling ever did. But who is going to remember that?

Who’s going to tolerate another march for black lives who are being slaughtered for minor traffic violations when they can see how you mowed down 11 police officers, 5 of whom are now dead?

It’s Dallas, where assassinations are not unheard of. It’s in Texas. And everyone and their brother has a gun. This nation is armed to the teeth and we have an orange colored loose cannon running for president. But it’s not him I’m worried about. It’s his crazy ass followers. It’s going to start to look like the Wild West. That’s not the country I want to live in.

Retribution is bound to follow and Diamond Reynolds will be replaced on the front page by pictures of you and the heartbroken family members of the people you killed.

What a stupid waste.

 

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Why Ebola spread in Dallas: Americanism

Lorenzetti’s Allegory of Good Government, 1339

We’re number one.  That’s what we always tell each other.

We have the best health care in the world.

Our public safety institutions are number one in the world.

We  are the richest country in the world.

We are supremely over confident.

How many people know that when Dr. Kent Brantley and Nancy Writebol returned from Liberia with ebola that their care was paid for by Samaritan’s Purse?  I’ll bet a lot of us just assumed that the US government picked up the tab for the flight, biocontainment units, ZMapp doses and hospital stays.  Not so.  So, who is paying for the transport and treatment of Nina Pham and Amber Vinson?

Probably a few more of us have questioned whether money was behind the shoddy care that Mr. Duncan got in Texas.  I have.  I’m betting that his lack of insurance and status as a foreign national had a lot to do with why he wasn’t immediately isolated when he first came to the hospital and why he was left in the ER for hours, some nurses say days, before he was transferred to a critical care unit.

As for the best health care in the world, the nurses were very unprepared for ebola.  The biggest chunk of the blame goes to the hospital.  It’s a hospital for the middle class and those who can afford the best health care in the world.  That’s where people go to have their babies and bypass operations.  Maybe they didn’t associate their kind of hospital with an epidemic in a third world country.  Bad things happen to THOSE people over there in Africa.  Not their kind of people in Dallas.  At best, that’s a benign form of American narcissism.  We’re so used to having clean water and streets and good food.  So, why should the hospital get all Girl Scouty and be prepared for a situation that will never happen to it?  Training for such an eventuality takes time from nurses doing their duties and time is money.  It’s the American way.

The CDC seems to have vastly overestimated the outcomes of our educational institutions, especially our K-12 schools, where everyone should have a pretty good understanding as to where Liberia is.  But then again, Liberia was a state created by former American slaves in the 19th century and Texas is a state notorious for trying to rewrite the past when white Americans might have done bad stuff to anyone.  But still, don’t these ER intake people, nurses and doctors watch the news??  At least one nursing supervisor seems to have been on the ball and insisted on moving Mr. Duncan to an isolation unit instead of letting him shed viruses all over the ER but she was shot down by her administration.  Still, you’d think that a hospital so concerned with its reputation and profits would have been more proactive in limiting the damage that his presence was causing.  Not so, apparently.

And what was the hospital thinking when they gave antibiotics to Duncan when they hadn’t bothered to find out whether he  had a bacterial infection that required them?  Does Texas Health Presby Hospital routinely overprescribe antibiotics?  Is this a hospital or a student health center?

What were Republicans and Democrats thinking when they cut the budget for the CDC by 12% and the NIH by 20%?  Friedan said yesterday that $30 million was restored earlier this year in an “anomaly”.  How the hell are you supposed to prepare for emergencies if you never know what your budget is going to be from one year to the next?  We complain about administrators making decisions for our health care instead of physicians but our bigger problem is that we have politicians making decisions for our disease fighting institutions.  Should the CDC and NIH know in advance what diseases are going to become epidemic on some kind of 5 year plan and ask for the right budget money in advance?  Or are their functions compromised by their unreadiness brought on by this reckless political posturing?

And everyone, politicians, journalists and people who should know better, is under some mistaken belief that the private sector is going to step up and perform the tasks in research and disease prevention that the CDC and NIH were created to do.  But they’re too busy trying to reap profits for the shareholders to engage in such money sucking activities like research. Meanwhile, we underfund the NIH and CDC.  Is that so Republicans can point to what a sh*%%y job government does?  Are they paying no attention to how our scientific infrastructure is being dismantled in this country and concentrated on a few narrow therapeutic areas?  They are leaving a gap that no one is able to fill.

This may be the richest country in the world but the riches are hoarded by some pretty selfish individuals and we don’t seem to be able to get our act together to force them to give up their loot for the greater good.

A little ray of hope came through yesterday when I saw that some television content providers are breaking away from the package deals offered by cable companies to allow viewers ala carte channel selection.  That’s great because eventually I will no longer have to subsidize right wing propaganda from Fox News or be forced to pay for Fox to mislead unsuspecting American viewers.  I’m betting that a lot of like minded individuals across the country will drop Fox from their lineup the second they are able to do it.

But the damage may already be done.  The Senate may fall into Republican hands this November and in the next two years, the predators who have been stalking us since FDR got us out of the Great Depression will finally be able to finish us off.   The willfully ignorant elderly and angry white males will finally stick a fork in us, and allow the extremists to carelessly destroy Social Security, roll back women’s rights and plunge us back into recession with unrestrained austerity.  The only thing that will stand between the power extremists and us will be Barack Obama.  That right there is a very depressing scenario.  But maybe he will have the courage to stand aside when we finally pick up our torches and pitchforks.

We have been living a myth of our greatness.  We’ve been in denial about how government works.  We have told ourselves lies about how we can “starve the beast” that once made our country a formidable force of good around the world.

I’m only glad that the ebola crisis here will be under control before the next session of Congress begins and before the gung-ho, American exceptionalists who take over show us just how unexceptional we are to the hunters who prey on the young, old, and weak.

Section from Lorenzetti’s Effects of Bad Government, 1339

 

More speculation and budget numbers at Angry Bear Blog.

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.