Tuesday: The state of science

Staph Aureas colonies growing on what looks like a blood agar plate

Guys, the state of science in this country is truly messed up.  Pharmageddon continues with the big research companies still laying off in high numbers, especially here in the US, and getting out of certain research areas. (Jeez, 2009 was a very bad year for US scientists.  58,000+ of us let go in an industry where hiring freezes have been the norm for over a decade.) Some of those research areas might be important to you even if you don’t know it right now.

For example, did you ever wonder how your great grandparents coped without antibiotics?  We’re only a couple of generations away from the dark ages when unchecked infections lead to gangrene and amputation, sepsis and death.  But have you ever wondered how little it would take to get that whole ball rolling?  Well, here’s one modern account that should chill you to the bone.

Meet Lucy Eades, youtuber extraordinaire.  Lucy has been documenting her family’s evolution in intimate detail for several years now.  Lucy and I have wildly dissimilar lives.  She’s young, blond, pretty and busy with three children under the age of five.  She’s into homebirths, cloth diapers and attachment parenting.  I like dropping in on her channel because it’s like watching a documentary on some exotic culture I will never visit.

Last November, just after Thanksgiving, her daughter Jacelyn scratched herself below the waistband of her underwear.    No biggie, right?  Wrong:

The day after on Saturday she asked why it was so itchy as she was trying to find comfort while rubbing & scratching at it. I talked to her about how wounds can itch as it heals & it’s best not to touch because any open wound could become infected & that would result in an ouchie…more so in kid friendly terms.

Sunday she pointed the area saying it hurt & upon inspection I noticed a pimple. Not sure if it was a pimple or not, ant bite, or what, but a small pimple look alike bump that hurt. Nothing more.

Monday morning after she woke we immediately looked it over & noticed a small black dot in the middle of it. Aside from that nothing else had changed. We were thinking maybe a spider bite? Never know when you stay in a hotel. Called the Dr and we brought her in later that day during one of their open “sick” appointment time frames. Dr said it could be staph, we’ll keep an eye on it. Since we had just battled staph (what 2 weeks ago? if that?) that it was a likely that even if it wasn’t staph it could turn to staph. She prescribed us some oral & topical antibiotics and gave us instructions for hibiclens, etc. for if we needed to use them eventually we wouldn’t have to bring her back in & expose her to more winter illnesses being passed around. She was fine at this point. Nothing hurt, we went about our day.

Tuesday-Wednesday is when my memory starts to fail me. At some point she becomes uncomfortable & it’s confirmed staph. We were told staph is on every surface every person & we naturally have it on our skin because of this.Some are effected while others are not. Some people with open wounds are more susceptible to staph than others for no known reason. Jacelyn is one I guess. We go fill the script at the pharmacy on Wednesday and resort back to warm soaks in the tub & attempting to squeeze out the infection with no success. Dr office swapped patient information & called in wrong prescriptions. We received anti-fungal meds.

Thursday we call the Dr office back still trying to get the right meds & to inform them that the infection appeared to be spreading. She had a fever, her hip/leg hurt, & it was no longer draining the way it should resulting in a massive hard rock like lump. Her skin was even starting to look raw in that area. They said she needed the antibiotics for a while & it would help. That evening I told Joel I wasn’t comfortable with the situation & I was taking her to the children’s hospital.

It was officially Friday by the time we arrived here (still here). She was running a 102 fever at arrival. They set up the IV’s & talked about procedure in depth with me. They had to sedate her using three different types of medicine. We talked about all our options, pros, cons, side effects, etc. The whole works. I apologized for being annoying but told him I wanted to be as informed in this process as I could be.

In walks 2 nurses, the Dr, a medic & 2 other employees. This goes from being scary to serious feeling. It was like one those ER episodes where 50 rush in the room all doing something different. One dose of sedation was enough to put a grown 200+ lb guy under.

What follows is a nightmare of bad reactions to sedation, two surgeries to remove dead tissue and drain the wound, and a hospital quarantine.  Jacelyn has MRSA, Methicillin Resistant Staphylococcus Aureus.  MRSA has developed resistance to standard antibiotics and some strains of MRSA are resistance to Vancomycin, which has been considered the last line of defense.  Ironically, MRSA is dangerous because of the overuse and improper use of antibiotics.  Nevertheless, you would think that the drug companies would be all over this area of research, designing new antibiotics or different approaches to combatting bacterial infections.

You would be wrong.  This is one of the therapeutic areas that big pharma can’t wait to dump, along with reproductive health and central nervous system (CNS) drugs.  That’s because they’re difficult, expensive to develop, have narrow safety profiles, or, in the case of women’s reproductive health, prone to class action lawsuits.  Women have been their own worst enemies when it comes to reproductive health.  Some feminists have a tendency to see every therapeutic agent as a weapon of the patriarchy to control their bodies.  As if.  And side effects are unavoidable, although we’re getting better.  But the cost of defending what was intended to cure has become so expensive that pulling out of these areas is more cost effective than sinking more money into research.

It takes a long time and a lot of clinical trials to get a new antibiotic approved.  Not so much with oncology where the life or death nature of the disease leads to speedier approval of new drugs. And in the case of cancer treatments, there are far fewer lawsuits when the drug doesn’t work out quite as well as hoped.  Patients’ families are grateful for any extension of life.  So, that’s where pharmaceutical companies are putting their money. It’s a callous and mercenary business decision.  It wasn’t always like this but this is what results after mergers, quarterly earning mania, a quirky, capricious, anachronistic FDA and the high cost of defending lawsuits have worked their own special magic for a couple of decades.  No more research on antibiotics.  Don’t expect that big pharma will care about your staph infections or birth control after you’ve sued their asses off.

Yes, they’re greedy bastards at the top but that’s a different topic.  They weren’t always this bad.

So, sports fans, we’re getting perilously close to the days when a simple break in the skin could kill you.  Lovely.

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Katiebird sent me a link to this article about scientific publishing and plagiarism by two University of Kansas bioinformatics researchers.

In the technical world of bioinformatics, the two University of Kansas computer scientists were riding high in 2009.

Mahesh Visvanathan and Gerald Lushington published three articles with an international audience. They were invited to make a poster presentation at a conference in Sweden.

Although a lack of airfare kept them from going, their real problem wasn’t a tight travel budget — it was plagiarism.

Portions of all three of their articles had been lifted from other scientists’ work. The entire summarizing statement in their presentation had come from someone else’s journal article.

In an endeavor such as science that relies on original work and trustworthy information, plagiarism and fraud seem out of place. But misconduct is being detected with increasing frequency. And while it may be that the scientific community is just getting better at sussing out fraudsters, some scientists fear the problem is growing.

Competition among researchers has taken on a harder edge, they say. More scientists are competing for limited grant money, faculty appointments and publication in top journals. This intense rivalry makes it tempting for some to cut corners and fudge results.

The number of scientists caught committing fraud remains small, but each case can cause real harm, from wasting time and resources of other scientists who follow false leads to putting lives in jeopardy with bogus health findings.

There is a difference between the kind of plagiarism that the Research Works Act is supposedly trying to address where researchers frequently lift methods, diagrams and pictures from other papers routinely.  That’s a kind of excusable plagiarism because new work frequently is dependent on older work.  In that respect, the RWA could have a chilling effect on scientific publishing if it were rigorously enforced.  It’s quite another thing when your conclusions and whole paragraphs of explanatory text are lifted straight out of someone else’s publication.

But the pressure to publish is intense and, unfortunately, there are a lot of unscrupulous people out there who rationalize about what they’re doing.  While I can’t comment on how rife the academic world is with examples of plagiarism from other people’s publications, I suspect that the practice is alive and well in the corporate setting where the Wall Street financier’s value system has trickled down to the laboratories.  Well, you can hardly blame the more senior people for doing it or rationalizing about it later.  Their pedigree and PhD creates a field of excellent and  superior brainwaves around them that the more junior people can’t help but pick up and be influenced by even when the senior person has done little to nothing on the project.  Sort of like Lady Catherine DeBourgh in Pride and Prejudice who credits herself with a sensitive prodigy’s talent in music and would have been a great musician had she only learned to play.  Or the rationalizer’s work/family circumstances are more important than the person’s who actually did the work.  Or the rationalizer needs a green card.  Or <fill in the blank>.

If you have the power to steal a colleague’s work, the reasons for doing so aren’t hard to conjure up.  It’s your word against theirs.  With the patent lawyers sitting on publications and project data for so long, it’s easy to slap your name on a paper or patent when the actual inventor is out of the way.  All the skullduggery and credit stealing happens before the paper ever hits the journal or patent office.  Who’s going to know?  I’ve even heard that in some companies and departments credit is awarded to favorite underlings like a reward for loyalty.   Those favorites can swoop down on a project in its final stages and hog all of the years of credit to themselves at the last minute.  You’d think this would be an ethical problem requiring accountability and punishment. Not so.  It’s just the way things are done.  Not all companies operate this way but the current layoff environment makes it more common and brazen.  Yep, research is a sick business.

Well, it will all sort itself out in the end and the researchers who are left can always go into sales if they are ever exposed.

Science is baaaaaad  for you, children, Very bad.  You’ll spend years working and studying on project for which you will get no credit and end up flipping burgers at McDonald’s. Run away! Run Away!

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Susie Madrak cites a post today about how 3 female regulators’ warnings about the impending financial crisis were ignored.

Bies was a central bank board member from 2001 to 2007. Several times in the transcripts she said she was worried about the housing bubble.

Bies warned fellow board members that exotic mortgages — for instance, negative amortization loans in which balances become bigger and not smaller over time — were too dangerous for consumers.

She warned about the Wall Street-created securities backed by risky mortgages.

“I just wonder about the consumer’s ability to absorb shocks,” she said at Fed meeting in May 2006.

“The growing ingenuity in the mortgage sector is making me more nervous as we go forward in this cycle, rather than comforted that we have learned a lesson. Some of the models the banks are using clearly were built in times of falling interest rates and rising housing prices. It is not clear what may happen when either of those trends turns around.”

Later in 2006 she told Fed board members: “A lot of the private mortgages that have been securitized during the past few years really do have much more at risk than investors have been focusing on.”

Bies is an economist and was a former Tennessee banker. But the two most powerful men at the Fed and the Fed staff dismissed her concerns.

That May meeting was Ben Bernanke’s second as chairman of the Fed. He said the cooling off of the housing market was a “healthy thing.” And that “so far, we are seeing, at worst, an orderly decline in the housing market.”

In June 2006, Tim Geithner, then president of the Federal Reserve Bank of New York, said that “we see a pretty healthy adjustment process under way. … The world economy still looks pretty robust to us.”

A Fed staff report said: “We have not seen — and don’t expect — a broad deterioration in mortgage credit quality.”

Tim Geithner, Tim Geithner… Where have I heard that name before?  No, no don’t tell me.  Let me work this out…

Tol’ja

White House vs Women: Joe Biden Does it Wrong

Obama and Women: Two views

Um, I’m glad that the rest of the blogosphere is starting to pay attention to the way womens’ expertise is ignored in the public sphere and especially by the Democratic White House and party in general.  We here at The Confluence have been covering this very thing for a couple of years now, including one post that cited the story about the female musicians who get orchestra seats after they’ve auditioned behind a screen.   Wow, that’s an old reference.  You’d have to look long and hard to find it, unless someone already found it for you in other posts, like:

The Gender Gap and Female Bodied People

Yeah, why *did* we do that?

WTF?? Another example of how Sexism costs us all

Bairly Downgrading the FDIC

There are many more on the topic.  Try keywords “Sexism Costs” or “Costs of Sexism”.  Well, it’s not like it’s plagiarism or anything.

Unless someone is going to say they invented the Plum Line Metric too.  (that would be here, and here as well) Then I will have to raise a snit.

Welcome Susie!  We will send out our complimentary new members package complete with white sheet (‘cos an accusation of racism is just around the corner) and you starter pack of hormone replacement therapy.   No, no, don’t thank us.  Most members don’t.