Archive for September, 2012

Problems with Publish or Perish

September 19, 2012 Leave a comment

Research is a combination of collaboration and competition. We collaborate in order to discover new things, to understand the processes of nature at a higher level. We compete not only because we wish to be pioneers and be the first with our foot in the door, but also because limited funding leaves 90% of all labs in the dust without a government grant. Laboratories are judged primarily on the ability of its members to publish good science. While this makes sense, it also gets us into trouble.

In cancer science, many “discoveries” don’t hold up. Researchers at Amgen took 53 groundbreaking publications and attempted to reproduce the results. They even performed some of the same experiments in the laboratories where they were originally done in an attempt to decrease any possible variability. Only 6 of the 53 papers actually had reproducible results.

The publish or perish mentality is obviously failing. Most claims that are published never get repeated, and research progresses based on the assumption that previously done work is true. While trust is a good thing, the thought alone that nobody will repeat your experiments can lead scientists to skew results and publish false inferences that they may have believed to witness.

I believe the problem stems from our funding system. My PI is an excellent story teller, and one thing he tells me is that grant funding applications had a far higher acceptance rate 20 years ago than now. This makes sense given the fiscal situation of our government. To correlate, a sharp rise in retractions has lead some to push for an ethics reform. The rise in scientific misconduct can be traced back to increasing competition for funds.

Most people would lie (or skew data), given the opportunity, especially if it brings them one step closer to that million dollar grant. There is urgency in science; if you don’t publish a result as soon as you find it, then a competing lab next door will snatch it away. Rarely double checked results and limited funds brings out the worst in science. Competition may breed the best research, but when pushed to the limit, it can also bring out the worst. An increase in science funding may aid in reducing the number retracted publications. In the end this would save us all time, and hopefully a truly landmark discovery can be made to help save lives. Come on lobbyists, push for science funding!


What the Hell, Humans?

September 16, 2012 Leave a comment

COME ON, PEOPLE! Honestly. Muslim riots, Anti-Japanese protests, hate-everything-not-me attitude. We are, astronomically speaking, living in the same zip code, same town, same house, same room even. And yet we can’t just get along. We’re no better than Ruby, my betta fish that requires a weekly bowl cleaning, a daily feeding, and can’t be put in a tank with another fish simply because it won’t play nice.

Now, take a close look at the picture on the left, courtesy of BBC news. Those are children at the center of the Anti-Japanese protests in China. How is it at all possible that children can have such strong opinions about something they likely can’t even mentally process?

Indoctrination. The impressionable young minds of today are the radicals of tomorrow. Parents can’t resist the temptation of inflicting their opinions on their children. Understand that I have no problem with opinions; you have them, I have them, we all have them. However, I do have a problem with the imposition of those opinions. If you’re a vegan, I’m not going to force feed you bacon and likewise I wouldn’t want you replacing that delicious slab of meat and grease with a soy, broccoli, corn slime. Subtle, I know.

The things we teach our children should be based on facts. There is a plethora of information literally at our fingertips, and yet we choose to hinder the progress of future generations through pounding creationism and racism in their brains. I’m not saying that good parenting means letting your children develop their own opinions. Oh wait, yes I am. Let them develop their own damn opinions! Guide them, and give them options, but let them make their own decisions about the existence or absence of deities. Don’t raise them as jerks, and they probably won’t become jerks. Tell them that the 7 billion of us are a stuck on this little floating rock and fighting about it won’t make it easier.

I wonder if the dinosaurs ever had this problem. Stop telling your kids to hate everything.

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Libya and Beyond: Don’t Worry, it’s Only Anarchy

September 14, 2012 Leave a comment

I posted last December some reasons as to why countries might be better off with “bad” dictators. Exhibit A: Libya. Exhibit B: Syria. Clearly something has gone wrong.

While ousting their dictators to free themselves of the tyranny, it seems pretty clear that these rebels are unaware of what they are getting themselves into. The absence of leadership makes room for something worse to take its place. Similar to how Clostridium difficile infects the gut after doses of post-surgery antibiotics rid the body of good commensal bacteria, these countries become easily overrun by other religious zealots.

BBC: Syria Conflict: Jihadists’ Role Growing

Zawahiri urges Muslims to help rebels in Syria oust dictator

Right now, several western embassies are coming under heavy fire due to the anti-islamic video produced by Sam Bacile. While several middle eastern political heads claim not to blame the American government for the creation of such a video, it seems that they do not hold the same opinions as their religious members. The situation is incredibly complex, with politics, religion, media, and military all colliding. However, there appears to be a root to all of this dissent, and it is religion.

Religion has been an impressive tool for keeping its members in check. What better way to impose rules on a group of individuals than to tell them that a god is watching? Regardless of my negative views on religion and its dissemination through indoctrination, it has clearly sent this situation from bad to worse and soon to impossible.

And irony hits them directly in the face. For a long time, religious groups have been portrayed by their fanatics and general misbehavior. These riots do an excellent job of legitimizing those depictions. Although it seems that I am speaking of the Islamic riots, I mean the same for the Christian right-wing. There is no place for religious ideals in politics; there’s no room for unfounded beliefs in social welfare, or anything for that matter.

We need to deal with this situation (and every situation) logically. But with religion having a strong grip on the masses, each day that passes just brings us one step closer to anarchy and irresolution.

“For men change their rulers willingly, hoping to better themselves and this hope induces them to take up arms against him who rules; wherein they are deceived, because they afterwards find by experience they have gone from bad to worse.” – Machiavelli in The Prince

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Gripes with Antibiotic Resistance Research

September 13, 2012 2 comments

Thanks ASM, I enjoyed attending my first Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC). Getting out of the lab was enjoyable, but upon hearing all the talks about antibiotic resistance I became more anxious with getting back to the lab. But you know what grinds my gears? Why all the concern with betalactamases?!

Outside of virology and fungal disease, I would estimate that 80% of all the posters and presentations were either NDM-1, OXA, BLA, or ESBL related. We have developed numerous classes of antibiotics outside of penicilins and carbapenems, and yet we focus so much of our attention on this single class.

I don’t refute that betalactam antibiotics were once an incredible tool for treating nosocomial infections. But our obsession with these antibiotics seems to be hindering forward progress. Therapy is already so limited when treating Klebsiella, Acinetobacter, or Pseudomonas, and as soon as colistin resistance becomes more prevalent, we’re done for. Didn’t we learn not to put all of our eggs in one basket? ESBL’s (Extended Spectrum Betalactamases) are a prime example of how we jam packed our basket with eggs.

I propose that we focus on other classes of antibiotics; macrolides, tetracyclines, quinolones, aminoglycosides, etc. Resistance to these antibiotics may be enzyme mediated, and although various inhibitors have been found for betalactamases, few, if none, have been found for those that mediate resistance to the other classes of antibiotics. We can improve therapy options for patients if we expand our areas of research.

Come on microbiologists. Get out of your ESBL studying niche, lives are at stake.