Tag Archives: Science

All things scientific

Dark Science: on freeing the negative results

Hi all. Sorry for the long silence. My dissertation is defended – I passed. I’m qualified as a PhD!

So this whole presentation and dissertation thing reminded me of some work I did a few years ago. I got it published after a struggle, but one reviewer specifically recommended against publication because it was a ‘negative result’. I showed that a peptide implicated in Alzheimer’s disease does not affect synaptic vesicles. It seemed like al ikely hypothesis at the time.

I think a “Journal of Negative Results” would be a good idea. There’s been some rumbling about this on the net. Wired magazine did a great piece on it called “Freeing the Dark Data”.

Well, in any case, there is one, now, it turns out. The Journal of Negative Results in BioMedicine publishes studies that show that show things that are useful in the sense that they say “don’t bother trying this hypothesis. We already tested it.”

That’s a simplification, of course, but from a researcher’s standpoint, things in that spirit have tended to go unpublished. Articles like this make it sound like scientists are hiding data that doesn’t suit their fancy. Really, if they have some hypothesis (“I’ll bet drug A will work a lot better if we include drug B”) and then they test it and find out it’s totally false, it feels like failure. And it’s hard to publish. Journals don’t want low-impact articles like “Drug B does not change the activity of Drug A.” They want titles like “Drug B enhances effects of Drug A by 1000%”

Plus, it seems like scientists should know what they are doing. Why were we wrong when we predicted that Drug B would enhance Drug A? Were we being foolish? Nobody wants to look foolish.

So maybe with this kind of journal, this will start to change. This is good for science in the long run. If somebody, later, reads that the fact that Drug A and B don’t affect each other, it might have huge implications that are not obvious now. Why repeat the experiment? If the data is out there, that’s to everyone’s benefit. It even seems like Google (“don’t be evil”) is getting on board.

Cheers,
Peter

Extremely cynical: the Politics of Fear

I have tried to avoid making the topic of the Big Upshot political. I’ve skirted the line with that recent post about Ukraine and Russia. I admit that. For the most part, I just don’t think that I can do a lot of good in the political sphere. I could write inflammatory, poorly-researched posts about surface issues, but there are lots of those already. I could write well-researched, well thought-out, powerful analyses, but I suspect nobody would read them. So, instead, I try to focus on the humor of science and the humor of living around science.

 

But this was just too much. ScienceNow at Science Magzine (Arguably the most prestigious publication on the map) posted a piece called “The Politics of Fear.” Not too long ago, The Jester talked about our culture of Fear and Consumption.His opinion is that the fear-memes of that kind prey on our natural responses to scary, threatening things. Evidently, it is more than just speculation. The article over at ScienceNow sums up an article by Okley et. al. called “Political Attitudes Vary with Physiological Traits.” The article correlates genetics, fear responses and political decisions.

The implication is that some people have a more pronounced fear response – they are easier to scare and upset. And this correlates with the person for whom they vote. People who are threatened easily (“Are you threatening me?!”) probably are easier to influence with lies and scary pronouncements in paid TV commercials. Evidently, this is so much the case that they will vote against their own selfish interest.

I’m afraid that I have a hard time not reading this with a very cynical eye. The implication is that it is hopeless to try to have a good political debate (in my naivete, I thought I would see one this election). This scientific result implies that inflammatory, poorly-researched diatribes will win consistently over well-researched, well thought-out, powerful analyses. They will excite different kinds of brains, and I’ll let you guess which are more strongly represented in the general population.

Sorry for the cynicism today. I miss my girl.

-Peter

Ukraine and more biofuels – politics and energy research and development

My mind is on the Ukraine a lot these days. My dear betrothed lives there. For those of you living in a cave, Russia and NATO were having a little tiff over Georgia. Last month, a US official, Richard Holbrooke, predicted that Ukraine would be next. I think the situations are pretty different, and the Guardian agrees. From some reports I heard through the underground grapevine (who can you trust these days?) Georgia tried to expel some ethnic Russians. That’s why Russia stepped in. Or Russia cooked up the story as an excuse after they moved in. Who knows? But Georgia has allies and European ambitions… so we got escalations.

Will Ukraine try to expel its ethnic Russians? Doubtful. It’s a much bigger country with a lot more Russians. Could Russia claim this was happening as an excuse to annex Crimea (where they have navy bases)? Maybe. If Russia tries to annex Crimea for whatever reason, I don’t know what I’ll do.

I’m a scientist, not a soldier. And what side do you fight for? Besides, I don’t speak Russian well at all.

 

I had a faint notion in the back of my mind of going to Ukraine some day to see if I could start a biofuels R&D business. It’s a fertile country with a huge energy deficit and an underused intelligentsia. It seems like a prime location. But the political situation, clearly, leaves much to be desired.

A company spin out just started up here at the U. of Washington with what seems to be the basic business model that I think could succeed in that kind of environment. Rapid development of new algae strains for fuel production on land or sea. It sounds perfect. The don’t do recombinant genetics, it looks like just forward screening, but I think I would add some splicing if budgets allowed. But I would definitely consider rapid screening using micro-scale systems. How fast can a new algae strain go into production?

I would bet that the main practical problems will be political. A dollar can go a lot farther in Ukraine, but not if it gets taxed at the 40% tariff rate. And if government dissolves, then where is a company that depends on a laissez-faire tax system and a free energy market? Because those would be pretty important to this company.

You know… that could be an issue here.

-Peter

More biofuels musings

I wrote up a little piece a bit ago on the complexities of the food-or-fuelchoice implied in the manufacture of biofuels.

 

Richard Jones at Softmachines.org wrote about biofuels a while back (Driving on sunshine). He has returned to the matter more recently. “It seems that some of the drawbacks were more easy to anticipate than others. What’s sobering about the whole episode, though, is that it does show how complicated things can get when science, politics and economics get closely coupled in situations needing urgent action in the face of major uncertainties.”

I love biofuels in principle. The idea that we could use the agricultural technology of the whole of human history to power the most modern inventions seems appropriate. But the economics are complicated. There is always switchgrass which promises to make use of otherwise useless land. And there’s algae on which I did my high school science project. There you can use huge regions of the ocean to produce energy. That won’t have unintended consequences.

In any case, I think there could be a future in biofuels. If it raises the value of agriculture, then we can see more agriculture. I think that could be a good thing for people at the bottom of the economic ladder. Traditionally, agriculture was how cultures developed themselves. That seems like a worthy subject for development. I’m not sure right now, though. Corn ethanol, for instance, barely breaks even on the energy balance.

What that means (in simplified terms) is that you burn a gallon of gasoline to grow, process, and transport a gallon of corn ethanol. Ethanol is “green” except if you burned a gallon of petrol to get it. In that case it is utterly useless in energy terms. It makes a job or two, but you might as well pay people to not grow corn. Some of you might remember the discussion of the lucrative possibilities in getting paid to not grow corn in Catch 22. More recently: “Acreage Reduction Programs (ARP) paid farmers to set aside an amount of land on which they would not grow corn.”

Anyhoo, I have a dissertation to write and a second job to pay the bills. I wish I could believe that greenwashed fuels were the solution to the energy crisis.

-Peter

Some people are more Flexible than others

I’m still in Germany and I’m having a great time. Writing the dissertation is a slow, but steady process. I think I’m done processing the data for which I worked so hard last month. It lines up nicely.

I read an interesting article in Newsweek on Monday that I wanted to share with you all. The notion was that scientists (Frank et. al. 2007 ) found evidence that there is a genetic link to a person’s ability to learn from mistakes. I honestly don’t know how controversial that is. It seems pretty common-sense to me. Some people will be more able than others to discern when they have made a mistake, and upon realizing this, some people will be more able than others to change their own behavior.

If anything, the controversial issue (and the thing that is the subtle beauty of the proposition) is that this in not trained. It seems intuitive to think that if someone doesn’t learn from their mistakes, they could be trained to do so. This result, if true, suggests that the degree of trainability is, itself, variable.

I imagine this has implications for parents everywhere. Take a child who is less capable of intuiting that a repeated mistake will have repeatable consequences. That child should be reared differently than one who immediately modifies behaviors in after making a mistake. A child who responds immediately might be allowed to make some mistakes so that he will learn limits on his own before mistakes are life-threatening. On the other hand, such mistakes will be less useful experiences for the child with this newly identified genetic condition.

But what about the subtle implications? This also suggests that the degree of “habit plasticity” is variable among the population. It suggests that there are outliers on both sides: people who need external structure and limits to survive, and people who will immediately adapt their behavior to the social structure around them. Furthermore, I would venture to guess that this won’t correlate with intelligence or other personality traits (e.g. introversion/extroversion). In fact, it is more like a meta-trait.

Take the Myers-Briggs Type Indicator. It has 4 dimensions along which a person will score somewhere on a continuum. People who score any given way on the test will tend to have certain preferred modes of living. What this new result suggests is that, for some people, this preference is more fixed than others.

If nothing else, it’s a caveat on any predictions based on most psychological tests.

-Peter