My Labonews

Free has its price

Charles Betz — Wed, 04 Nov 2009 17:03:15 +0000

I'm writing this not only because of the recent events on Austrian and other universities that Joel is very enthusiastically engaged in. I had this on my mind for quite some time. So let me just make it clear at this point that this is my personal opinion and not a personal attack against anybody who does not agree with me.
Being a student is frustrating. I should know it, I'm a academic student since 2003 and will probably be for couple more years. Don't get me wrong, I love it, but I can see why so many other students are so much more annoyed by "the system", "reforms", lack of money and motivation on the academic side. The current discussion in Austria among other places is whether is is legal / ethical for the universities to demand a fee from the students. While I agree wholeheartedly with the statement that knowledge should be accessible to anyone, I do not agree with the UN Charta stipulated free access to universities, at least not as is. Of course I also agree that there should be world peace and equally distributed riches. But I also know that's not how our world works, and a bunch of revolutionary students won't change that fact. Purely calculated, most governments could financially bear the load of financing free access universities (not including housing and living costs of the students though). But this would in my mind result in an abolition of academic quality in general.
Another thing I know from being a student is that we sometimes tend to be lazy and like stuff that comes for free. We need lots of motivation, and for me, finishing the university with the best possible grades in the least amount of time is quite motivating when facing the fact that I do not want any longer to be dependent financially of my parents or a student loan that I have to pay back. Bear in mind that I do not accuse any of the students demonstrating now of anything. I'm just saying that in life, most things worth having don't come for free, and people should learn to appreciate that. By now you're probably shouting that me thinking I'm an arrogant snob with too much money (which I can guarantee you I'm not). Of course everybody with the potential should have access to the university. This could be achieved with student loans guaranteed by your respective government. The amount should be adapted to your & your parents financial situation, the university you like to study at and last but not least your grades (I know this is difficult to calculate in on a personal basis). People having finished their studies should then get a personalized plan depending again on their financial situation on how to pay back the loan. Maybe this is exactly what the protesters want and I got them all wrong. Still I don't like their way of showing it, because first of all I think that any protest involving adolescents and missing courses will attract way too many people that just care about this latter matter and think it's cool to go on a strike (man, I do sound like I'm 80). Second, I personally would be really pissed to have my courses boycotted by people whose opinions I do not share.
Sure you can not just allow anything happening to you. And I'm also in favor of young people taking an interest in their own future. My university is comparatively well funded in comparison to other foreign institutions, but I still think that a university is more apt to decide its budget (e.g. by raising fees) than a government (who almost exclusively cuts down budgets to fund for more short term expenditures). Sure it sucks that every couple of years you have to pay more fees. But I much rather have this and a constant quality of education, than governmental cut downs that change with every legislation. To put it plainly: I think the universities should be (at least partially) funded but the people who take advantage of these institutions (i.e. students), who will later on (hopefully) have a better paid job, rather than the general public (by raising taxes for everybody to pay for the education of the few). Then again, what do I know.

Mice applications

Charles Betz — Wed, 29 Jul 2009 10:10:23 +0000

I know that quite a number of my readers not actually coming from science are not overly enthusiastic about animal experiments. I probably had a couple of discussions before about this subject and it very often leads to a dead end since most people still see horrible images of chimps with diodes in their brains or cute bunny rabbits that are being tested for cosmetics. This does not really help in the discussions and it's without any doubt that any responsible scientist is against unnecessary animal testing. It's also without any doubt that any time soon we could stop doing animal testing, there simply wouldn't be any medications and new treatments anymore.
Right now I'm correcting parts of our animal license renewal application that we send in to the authorities. Switzerland has one of the most stringent animal protection regulations and this is why fulfilling all the criteria for these licenses is not trivial (and shouldn't be). One very important and legally difficult to grasp word that entered the new Swiss animal protection law is the protection of an animal's dignity, where possible. I still think its a shame that the farmer's lobby managed to get exempted from some of these points, but also the legislators themselves have trouble defining the dignity of an animal, since many people have different interpretations of this value (e.g. farmers vs scientists vs vegetarians). If I understood correctly though, one of the consequences of this law means that breeding certain breeds of animals will become illegal in Switzerland, and I warmly welcome this. I always considered it ridiculous that for example deleting a gene in a mouse necessitates a license ensuring that you thought of all (the obvious) consequences, while dog breeders are freely allowed to breed dogs that have trouble breathing or walking because of their deformed ("cute") anatomy. Not even mentioning what a lot of people do to their animals behind closed doors. And I'm not only talking about obvious abuse but also about overfeeding and the like.
BTW one interesting interpretation of such laws protecting the dignity of animals goes so far (if applied literally) that living in the wild may actually be illegal in some circumstances, because we willingly accept that a lot of the animals will be killed because of natural predators, lack of food etc... You know, survival of the fittest at its best.
Anyways, I welcome such stringent laws as long as they allow medical research to progress and I think it is very important that they are controlled by highly trained personal that understand how science works. As far as I can tell ,this is working quite well here in Switzerland. I have actually no idea what the legal situation is in Luxembourg, I should look it up at some point though.

Papers

Charles Betz — Sun, 26 Jul 2009 20:16:47 +0000

Judging from the low number of posts on this blog, you'll probably guess that scientists can be quite busy, especially if they're working in a competitive field. One of the reasons you'll even end up having very little time/motivation to write left after work, is that you're expected to read a lot of scientific publications. Most non scientists don't exactly know what our work flow looks like, so I'll try to sum it up here. A paper is basically a condensed and digested version of your project, and usually takes up a couple of years until you end up with a first draft. You try to convey the idea you had at the beginning of your work and progressively move through your data, which for clarity's sake you don't necessarily present in a chronological order. Most papers have some 5-7 figures, which contain your data, illustrations and models (no not the models you'll find in Playboy...), each with several subfigures. The abstract is a short summary of your major findings, then comes the introduction which should remind the reader of what is already published in your field. The results show and interpret the data from your figures, and the discussion looks where your findings fit into what is already known, and why you may have found controversies and ambiguities. Usually you also have a couple of supplementary figures which provide background data that did not fit into the main publication. Depending on your lab and the project, you'll be more or less involved in the writing process. As a PhD student for example, you're expected to write at least on paper with your data, which will make you first author of the paper (thus the paper will be referenced as e.g. Betz et al, 2009 (yeah dream on)), and the last author is usually your professor. For big publications, you often find multiple authors, which are then referred to as second/third etc author, although sometimes people also become joint first author if they contributed the same amount of work.
Next step is the submission. Your data doesn't count if it's not published in a peer reviewed journal (the peer part is critical, since some pseudoscientific journals (such as Homeopathy) use reviewers that they know are generally in favor of such ideas). This means that you submit your work to the editor of a journal, who decides to approve for revision or to decline. He then choses major professors from the same area and asks them if they will review your publication (they don't get paid for this btw). They have to sign agreements not to steal any of your data of course, but they can also chose to decline reviewing, e.g. if there's a conflict of interest. If they review it, they will critically analyze your work, point out the weaknesses, although they don't know who the other reviewers are. They send it back to the editor with their opinions, e.g. that they give it a go if the author manages to correct this and that. If overall the reviewers had a positive opinion, you'll have the chance of revising the things they pointed out and resubmit it again. These revisions depending on their severity might take again a couple of months. If you did good, you'll usually receive a positive answer from the reviewers and the editor (who has the final word) quite soon after the resubmission, although this is not always the case. Choosing the scientific journal you want to publish in (there are thousands) is critical. Generally people measure a journal's importance in an "impact factor" which sort of has become a much discussed criterium. The impact factor is a complex calculation, but you can basically compare it to the Google pagerank. Some of it is real, some of it is fake. Medical journals like the New England Journal of Medicine have a huge Impact factor, since the people in the field constantly reference themselves, however the most valued journals for scientists are Nature, Science and Cell, where Science and Nature publish generally short publications that are very condense and that are considered (at least by the editors) as being a major scientific discovery. Cell has usually very long publications with a huge amount of data. Publishing in these journals is however a privilege that only few scientists will face in their career. Some however seem to be able to produce one after the other, and it is generally much easier to be accepted in these journals if you're considered a big cheese in this area (a fact that some people misuse to publish data that should never have made it to such a journal).
So anyways, even though these publications are peer reviewed, that does not mean they are correct. Truth in biology is not an absolute value such as in Mathematics (or religion for that matter), and this is often confusing to the general public and especially the media. It only means that your data seem to be reproducible by other people and your conclusions for these observations plausible (at least to the reviewers and the editor). Humans make mistakes, and sometimes they are grave and the paper has to be retracted, which can easily destroy any hopes for a scientific career. Most of the times however, they are more subtle, and could either be partially wrong or just over interpreted. The general media however usually do not make their ludicrous claims (x cause cancer, y is the cure) from erroneous publications, but very often from interpreting mere press releases by universities or by drawing the wrong conclusions from one single publication while ignoring the rest. Scientists however need to read a lot of often controversial publications in order to come a step closer to the reality, and if necessary try repeat those experiments for themselves. One of the best arms in this fight are meta analyses, especially in the medical field. The problem while investigating a large datasets of people for a given fact (e.g. treatment of a new drug) is that purely by chance (statistics) you can end up with a correlation that even while being statistically significant is not real. Metastudies are studies analyzing a large number of studies of high (and similar) quality, looking at the same thing but in different labs, countries, people... This procedure has saved already lots of lives, discovering potentially harmful effects of drugs and procedures. Metastudies are also the best weapon in the fight against superstition, pseudoscience and the like. Even though journals like homeopathy regularly find strong effects of their voodoo cures, no benefits from practices like homeopathy, acupuncture, praying etc over placebo (this being the crucial part) could be demonstrated in meta analysis (which automatically exclude most of the "positive" papers for their lack of controls. Another important practice are so-called double-blind studies, in which neither the doctor nor the patient know whether they get a placebo or the real thing.
Sometimes in science, people also refer to the publication bias. This means that traditionally, scientists only publish positive findings. It makes sense in a way, however by publishing what didn't work you may save lots of people lots of time and money.
Another controversy in the field is the economics behind publishing. Basically it works like this: You as a scientist pay a lot of money to a journal to publish your data (usually a couple of thousand ?). The editor as mentioned above will send the paper to reviewers who review the data for free (though usually it's their post-docs and PhDs who do the job). Then after it is published, you have to pay again a large sum of money to read the publication. Traditionally every lab had a couple of journals relevant for their area subscribed, while they could find more journals in their university library. Nowadays, basically everything gets published online, and people have access to them via their networks and vpns. This makes life much easier and helps saving the rainforest and all, but the universities still have to pay huge amounts of money for accessing data somebody payed to publish without any financial benefit. If your library doesn't have a subscription to a given publication, you easily end up spending 50$ for viewing the article. There are several attempts to create so called open access journals, which still cost you money to publish but at least are then freely available. I guess this is also here the future will go, but this is still a long stretch.
Wow now I ended up explaining you how science works, while I initially intended to write you about which songs I listen to while reading papers, since not everything will just do. For example I find classical music and jazz much to complex and distractive, but lots of times, good old rock will do just fine. My musical paper reading tips of the day: Scorpions (I think it's a best of album). I was listening to it yesterday while reading in the lab with my new overly awesome AKG mammoth-sized earphones. Well maybe next time I will tune it a bit more quiet, since I realized after some time that there was a fire alarm telling me for 10 minutes to get the hell out. Stupid earphones and stupid Scorpions. Oh btw, right now I'm listening to Seu Jorge's fantastic David Bowie interpretations from the Life Aquatic soundtrack. Though now I wish my stupid phones back to help ignore a screaming boy that nobody takes care of.

Biozentrum PhD Retreat 2009 in Engelberg

Charles Betz — Sat, 20 Jun 2009 11:57:34 +0000

Pics are here.

Paper of the Day

Charles Betz — Thu, 28 May 2009 10:16:54 +0000

Optimizing the sensory characteristics and acceptance of canned cat food: use of a human taste panel. Link

The Jeantet Prize for Medicine 2009 - Michael Hall

Charles Betz — Fri, 08 May 2009 05:59:53 +0000

My boss Mike Hall received this year a very important scientific prize (actually you get more money than for the Nobel prize, but that's not the important part) from the Louis-Jeantet foundation, and they decided to film our lab for a whole day. This is what came out... Don't worry, I hid well.

Phylogeny of tasty animals

Charles Betz — Wed, 06 May 2009 06:04:42 +0000

Man I really love this chart. Should be expanded though!
Tastes Like Chicken?, Joe Staton, Museum of Comparative Zoology, Harvard University.

Risk vs hype

Charles Betz — Tue, 05 May 2009 09:16:37 +0000