The cost does not count

Researchers, like, say, teachers or bricklayers, can be bad, average, good or excellent. One criterium to tell among the tens of thousands of scientists on our planet is analyzing their scientific production. And one way to do so is the -already famous- H-index. Wikipedia defines H-index as follows: "A scientist has index h if h of his/her N_p papers have at least h citations each, and the other (N_p − h) papers have no more than h citations each".

In other words, a scientist with a h-index of 8 (that's me) has eight papers with eight or more citations. It seems fair, as it takes into account both production (number or papers) and their impact (times they have been cited by other reports). In fact it is far from being fair. First, the index strongly depends on the age. The older you are the longer is the period during which your papers can be cited. If I die today, my h-index will continue to grow as my articles are being cited post-mortem. Articles need time to be cited and young researchers have young articles too. There are many more criticisms to h-index (see http://en.wikipedia.org/wiki/H-index). But I would like to highlight one reason that, to my knowledge, has not been stressed up to date among the cons of using h-index as an evaluation parameter: funding.

The index does not take into account how much the published research costed. An article may be the result of a 100,000 euros project, but a similar quality research paper may have only costed, for example, 10,000 euros. This means that with the first sum it would be possible to publish 10 papers instead of only one. In my view, taking into account the ratio between bulk production/citation (used to calculate the H-index) and funding (F) makes a more realistic proxy for productivity (P).  Therefore, I propose an alternative parameter to h-index, P-index, which as you can imagine, is calculated as simply as this:

P-index=H-index/F

What do you think?

Synthetic Biology:  iGEM after the storm

The international Genetically Engineered Machine (iGEM) competition has been marked this year by the catastrophic passage of hurricane Sandy. Flight cancellations and delays prevented some teams to reach iGEM’s headquarters in Boston area on time, but the competition proceeded successfully as scheduled. Besides the storm, the 2012 edition might well be remembered as a turning point in many aspects: In January this year the iGEM Foundation was set as an independent non-profit organization located in Cambridge, MA, and the iGEM expanded beyond the Collegiate division in two parallel competitions for entrepreneurs and high school students; five regional Jamborees (Americas East and West, Latin America, Europe and Asia) served as a first round of selection for 190 teams worldwide, only one third of which advanced to the World Championship Jamboree that took place last November 2-5^th; and, finally, a new judging process based on multiple entries organized in a computer-managed rubric has been set in place in order to help choosing among the many excellent Synthetic Biology projects presented this year. In the last day of the competition, four European teams reached the final and one of them, Groningen, with a holistic and heterodox (standard-free) strategy for the identification of promoters to identify volatiles from spoiled meat by microarray analysis, was awarded the Grand Prize. Year after year, team projects, logistics and judging are getting more and more complex and this life-like increasing complexity will be –if the weather allows it- the major challenge future iGEM editions will have to cope with.

Botton up cooking

In Synthetic Biology, there are two different yet complementary approaches. Bottom up requires cooking from scratch with membranes informational molecules and transport protein and built de novo a synthetic cell. Protocell research is part of this approach. Top down, by contrast, uses either naturally reduced or artificially simplified cells as a chassis in which orthogonal and modular genetic systems can be implemented. 

In Catalonia, there is a vast range of sponge cakes called "cócs" or "coques". They consist of flour, olive oil, eggs and baking powder, and other common ingredients are almonds, cinnamon and lemon peel. I like them all but I particularly appreciate light ones. I have a trick to make this. From a pre-existing chassis recipe, I have incorporated from italian pannetonni the trick that allows them to be incredibly fluffy without deflation: once it is cook, I immediately put it belly (bottom) up.

Cóc à la pannetonne. 

1 yogurt (125 ml)

50 ml olive oil

175 ml milk

200 ml of sugar

400 ml of flour

3 eggs

1 sachet of baking powder

Optional: cinnamon in powder and lemon peel (1/2, finely ground)

Mix everything, bake at 160ºC for 45 min and keep belly up until cool.

Those moments

We researchers know very well the feeling: after a weekend, you enter the lab and want to see what has happened to your plates. Are there colonies on them? Are they blue or white?  Often, the pleasant excitement is followed by a deception, but when things have worked as expected...That is indeed a nice feeling. Another moment I like very much is when you enter the lab and find your students having done something like what I show in the picture below. Engineering students from Valencia Biocampus team helped their wetlab friends, who needed more magnetic stirrers. The solution? A PC fan with a magnet on top and suitable resistances for it to turn at a desired speed. It works as well as the commercial ones. Low cost, high motivation.

Transgenic Communication

EFSA, the European Food Safety Agency, has received many criticisms these last months. After a bitter controversy between a group of researchers and EFSA experts (http://www.nature.com/embor/journal/v13/n2/full/embor2011254a.html), Science publishes today an interesting opinion  article on systematic communication failures at EFSA, and highlights the negative perception that might arise from the fact that many researchers are “too close” to biotech companies: http://news.sciencemag.org/scienceinsider/2012/09/report-efsa-is-sufficiently-inde.html

Regarding the uncomfortable ties of the EFSA experts and the industry, Monica Macovei, a member of the European proposes a "cooling-down period" of 3 to 5 years for experts switching from industry to EFSA or back”. And she adds "If the best expert has worked for the industry, no problem. But be transparent about it. That is the least they can do." This seems reasonable: public opinion must trust EFSA. But if we take literally many of the arguments given in Science’s article today, it seems that the best expert in terms of public perception is the one not having any link with the technology he/she is evaluating. Communication in science (yes, all this is about science) is indeed imperative, but not at any cost.

On chickens and chicks

One of the things I like the most about Synthetic Biology is that this is a brand new scientific framework. No one can say ‘I have been an expert on that for three decades’. In fact, a senior researcher is likely to have a shorter research experience than a 30-years old synthetic biologist. And this is good, because it crashes down barriers such as the ‘experience length’ factor.

One of the things I like the least about the scientific career is the condescending attitude towards young researchers, particularly in the Old World. Getting older is just a matter of time, not a merit. And very often incredibly bright very young researchers are not given the merit they deserve for their contribution, which of course lacks the depth of experience but often shows a sparkly and amazingly creative character. It’s like a chicken making fun of a falcon chick, so small, so thin. Yes. But it will grow up and become the fastest creature on air, whereas the chicken…Well, we all now about chicken’s flight ability.

Now, look at the picture below. These are the twelve students participating in the Valencia Biocampus 2012 iGEM project. They are working 7/7 days, designing the experiments by themselves, analyzing data with almost no help and designing and building with their hand the devices they need for the project (I will show several amazing examples of those in this blog).

A handful of falcon chicks? Maybe. But falcons, indeed.

Microbial consortia can yield full of flavor!

Home-made bread with home-made sourdough. Wonderful flavor. I will post a bread recipe (yes, a protocol) for researchers shortly.

iGEM news

I coordinate the Valencia Biocampus team participating in the iGEM Synthetic Biology competition. Our 2012 project is Talking Life (http://2012.igem.org/Team:Valencia_Biocampus)

Do you speak to your bacteria? We do. We have designed, constructed and characterized an inter-specific translator based on light pulses that allows to literally dialogue with microorganisms. We have built seven biobricks with fluorescent proteins under the control of environmentally-sensitive promoters. The process is as follows: human voice messages are electronically- and then light-encoded in excitation wavelengths, and microbial proteins’ emission wavelengths are electronically- and voice-encoded back. We have used this system to find out the fermentative status of budding yeast and to dialogue with E. coli allowing it to answer questions such as “are you hungry?” The three pillars of our project (human practices, modeling and wetlab) yielded continuous feedback with each other, illustrating an integrated interdisciplinary approach. For example, in human practices, we qualitatively discussed the possibility of cheater mutant (“liers”), which was quantitatively supported by our results in both our modeling simulations and in the wetlab.

And for our Human Practices work, we even shot a short movie!

Synthetic organisms: threads not that new

Genya Dana and colleagues (Nature 483, 29; 2012) describe a scenario of synthetic biology perils they claim should be urgently –and expensively– addressed in order to avoid a “synthetic biology disaster”. Their statements on the specific difficulty of regulating, managing and monitoring synthetic organisms have been partially refuted by Tait and Castle (Nature 484, 37; 2012). In my view, assessment of the risks of synthetic organisms must always be based on the study of their harmful potential compared with that of both transgenic and naturally occurring organisms. From this perspective, synthetic organisms are indeed risky, but no more than transgenic or even wild species.

The ability of living beings, particularly –but not restricted to– microorganisms, to disrupt normal ecosystem functioning, transfer DNA to other species, increase competition for resources or disrupt crucial ecological functions has been well documented by all branches of biology for decades. Synthetic organisms, as proposed by Dana and colleagues, might well produce toxic compounds, survive for a long time in the environment and evolve to fill new ecological niches. But are these environmental risks “more dangerous” because a synthetic organism is involved? Just to use two examples cited by Dana et al., synthetic microbes are assumed more sophisticated because they can lack a particular metabolic pathway or spread an antibiotic resistance gene. But in nature, pathogenicity islands, recalcitrant compounds degradation and many other gene networks are horizontally (inter-specifically) gained and lost on a daily basis. Regarding antibiotic resistance traits, they are almost ubiquitous –unfortunately– in hospitals, where undesired artificial selection accounts for their spreading.

We should stop treating synthetic organisms as inherently “different”: they might be artificial but, as living entities, share the same evolutionary features –and threads– of both transgenic and natural organisms. The risks lie in their use, not in their nature.