There are many in the Nielsen lab with strong opinions about social, economic, and environmental policies. We don’t always agree, but we have many civil discussions.

While the presidential race is getting most of the attention, here in California, we have several other things to vote on as well:
11 propositions (there are very strong, and conflicting, opinions for a few of these)
US Congress members
– State senate and assembly members
– Local ballot measures

You can check out to learn more about propositions in your area.
You can find your polling place by simply googling “polling place” and entering your address.

If you are able to vote, and haven’t yet done so, please make some time today to contribute your opinion to the political process.

I voted by mail last week.

Summer Internship for Native Americans in Genomics

Many thanks to Mike DeGiorgio for bringing this announcement to our attention:

Check it out here: From the website:

Genomics may be a tool of interest to Native American communities. However, Native Americans are underrepresented in occupations and careers incorporating genomics and the sciences in general. According to estimates from the Census Bureau, Native Americans hold at least 5x fewer occupations involving science and engineering relative to their total population in the United States. Furthermore, there is a lack of Native Americans in advisory roles to the scientific community, which prevents proper relay of cultural values and concerns that developed as a result of difficult histories of Native American encounters with science. This lack of leadership also leaves few individuals who can explain the uses and limitations of scientific research to Native American communities that are considering participating in a scientific project. To address this problem, faculty and students at the University of Illinois Urbana-Champaign campus are working with leaders in scientific and Native American communities to create the Summer Internship for Native Americans in Genomics (SING) Workshop.

Tips for good presentations

Some of the guys in the lab already know my aversion (almost like a phobia) to presentations with slides full of text, or slides cluttered with lots of distracting things. We all give presentations from time to time, in lab meetings, in conferences, when teaching, etc. The problem is that we lack the necessary skills to give good presentations. So here’s the link of a short video by Susan Weinschenk about some very useful tips on how to give a better presentation.

5 Things Every Presenter Needs To Know About People

The lab in photos: Happy unbirthday

Feast of cakes

Sometimes, though not very often, events with “minor occasion frequencies” take place in the lab. Stars align, murphy’s law stops applying, the weekly lab meeting is postponed, we forget that our air conditioning unit is broken… and a feast of cakes magically appears in our headquarters for no special celebration whatsoever. What better excuse to have a happy unbirthday and get some treats in the form of an extra sweet carrot cake, a delicious strawberry cheese tart, a giant cup-cake, some pastries, and a yummy apple pie.


One hour later after the rumor of the cakes existence spread like fire, the verdict is unanimous: the strawberry cheese tart is the most naturally selected! In contrast, the less fitted carrot cake seems to be too sweet to be consumed.


The lab in photos: Behind the CGB Retreat


CGBR Beast

Don’t let the outside appearance fool you. This isn’t President Obama’s customized bus with bulletproof black windows, puncture-proof tires, five-inch thick doors, and its own oxygen supplies. Instead, this more modest bus is the preferred mode of transport for the geneticists, bioinformaticians, and biologists attending the annual Computational and Genomic Biology Retreat at the Marconi Conference Center.

Inside the bus
Crossing the bridge

An hour and a half trip starts from UC Berkeley Campus and crosses the bay by the San Rafael bridge. In the meantime, we have time to talk about whatever happened the day before and other things of minor scientific relevance compared to what we are going to hear and discuss in the talks at the retreat.

One of the Halls at the Marconi Conference Center

There are always points of controversy and topics of debate but we all agree in one thing that admits no critics: the extremely comfortable chairs in the conference hall. At first I wish we could have some of them in the lab, but then I think it twice and I detect its obvious dangers. With chairs like these, we would be so tempted to relax and forget our academic mission.

During a break

We also thank the organizers for the well organized agenda and the necessary breaks that we all need. I am one of those guys that hate those marathonic conferences without those essential breaks that allow you to do networking, exchange ideas, discuss interesting questions, and of course, keep well hydrated and be able to enjoy some snacks.

The all mighty drinks

The lab in photos: La Dolce Vita

A deserved break

Matteo Fumagalli takes a more than deserved break with the comfort of a fluffy pillow, a warm blanket, a revitalizing cup of coffee, and a handful of organic maple leaf creme cookies. All these luxuries have their raison d’être. Our most valuable and precious resource, after our coffee machine, is in our members: our human capital. Proof of their commitment to the lab and dedication to science, these guys take research very seriously. Or at least that’s what they try to accomplish. No wonder why it is not uncommon to see them in the lab working almost 24/7. Really. Come in any Sunday evening and chances are that you will find someone in the lab running some simulations while discovering that their scripts still contain a couple of bugs. However, their brains are not tireless computers, and their adaptation to long periods of research is not without limitations. If overexploited, their fatigued brains could suffer a collapse with the consequent risk of running out of good ideas and interesting hypotheses. For that reason we proudly take care of our limited human-intellectual capital. It is fundamental to keep them motivated, in good shape, and also to spoil them from time to time, letting them feel a few minutes of La Dolce Vita so they can be ready to start working on their next papers.


The lab in photos: A typical lab meeting

Lab Meeting 1
View of a typical lab meeting

Everything is getting ready for the weekly lab meeting in one of the conference rooms at the Valley Life Sciences Building (VLSB). Most of the lab members attend the meetings with old fashion pen-and-paper in order to take notes of the latest research details, as well as for making drawings of somewhat not that really different from abstract and modern art. However, you can also see a small minority of the members with more modern electronic devices that makes transcription tasks more efficient.

It is very important to have a good assortment of pastries (donuts, muffins, scones, etc) and it is strongly recommended to have a good mug full of coffee so you don’t fall asleep in the middle of a presentation with the latest results about human evolution, population genetics and statistical genomics. Until now, the kitchen in the room remains ignored but don’t discard the possibility that in some near future it can be used for some lab meeting with breakfast or brunch included.

Another view of a lab meeting
Another view of a lab meeting


Teachers at UC Berkeley Condemn Police Violence

My inbox has been flooded with discussion from faculty, staff and students in the Integrative Biology programs regarding the protests/violence/response here on the UC Berkeley campus. Unlike the knee-jerk protests by students at my former University (Penn State), the protests here are the result of planning and careful consideration of the issues (especially the egregious tuition increases). Coverage of the Occupy Cal protests will be updated and archived here.

This weekend a petition was formed to express the frustration, anger, and desired changes shared by many people across the UC system. To highlight a couple passages from it:

We are appalled by the Chancellor’s account, in his November 10 “Message to the Campus Community,” that the police were “forced to use their batons.” We strenuously object to the charge that protesters—by linking arms and refusing to disperse—engaged in a form of “violence” directed at law enforcement. The protests did not justify the overwhelming use of force and severe bodily assault by heavily armed officers and deputies. Widely-circulated documentation from videos, photographs, and TV news outlets make plainly evident the squad tactics and individual actions of members of the UCPD and Alameda County Sheriff’s Department. This sends a message to the world that UC Berkeley faculty, staff, and student protesters are regarded on their own campus with suspicion and hostility rather than treated as participants in civil society.

We call on the Berkeley administration to immediately put an end to these grotesquely out-scale police responses to peaceful protest. We insist that the administration abandon the premise that the rigid, armed enforcement of a campus regulation, in circumstances lacking any immediate threat to safety, justifies the precipitous use of force.

Please go here to read the full petition (and sign if you like).

Violence and hope at UC Berkeley

The last few days at UC Berkeley has been an educational and emotional journey for many of us.  On Wednesday we witnessed a sadly violent police response to a peaceful and orderly student protest against the skewed economic policies that have dominated our society for the past several decades.  If you are in doubt about whether the police response was justified, take a look at these pictures.  Notice the cop first looking around to see if he can identify any cameras – then attacking when he decides that there are no cameras following him.  Unbelievable.  Students and postdocs from our group have gone to the protests and have witnessed some of this themselves.  You can read more about their experiences here.

Friday we heard the response from our chancellor, Birgeneau:  “It is unfortunate that some protesters chose to obstruct the police by linking arms and forming a human chain to prevent the police from gaining access to the tents. This is not non-violent civil disobedience.”

Apparently our chancellor believes holding hands is a criminal offense that should be punished with a good beating.

Now these events are all incredibly sad.  But there are also some shining lights of hope in this story.  First, I am amazed at the discipline and dedication shown by the students.  Faced with a violent response by the police, not a single one of them decided to respond with violence in return.  It is truly remarkable.  They set an example for us all and give me a lot of hope for the future.

Secondly, the response I have heard from faculty, staff, and students so far has been overwhelming in its dedication to try make this right.  Our community is really coming together over this.  It is heartening to see such a strong unanimous response.

Birgeneau may end up regretting blaming the students for the violence, instead of using these events as an opportunity to bring the UC Berkeley community together.  I wonder if he will be surprised next week to witness more reprehensible holding of hands at the UC Berkeley campus – this time with faculty and staff joining hands with the students.  Birgeneau lost our confidence with his response this past week. The next weeks will tell us if there still is a role at UC berkeley for a chancellor who endorses police violence against his own students.



nielsen lab, occupy, and berkeley protests


Some of us from the Nielsen lab have been following the Occupy movement closely. Why?

I guess many of us, if not all, think spending more on education and science is one of the best public investments a country can make for its future. And the resources for such investment can be procured from social sectors who already own and waste large portions of the US and world economy.

The current situation, among many things, leads to a terrible human waste – millions of smart kids who could be great scientists never ever have the opportunity to go to university (and in many countries, not even to school). Meanwhile, we haven’t solved even some simple problems in biology, from evolution to cancer to ageing. Nobody can deny that working out these problems could have huge improvements to human wellbeing, and that we need more science and technology for the benefit of all. In short, redistribution of wealth, a central demand of the Occupy movement, would also contribute to scientific progress.


We’ve thus been taking part in multiple ‘Occupy’ activities, starting the first meeting of Occupy Oakland in mid-October, marches in SF, and the Nov 2 Oakland general strike. This was a great moment – young and old, blue and white collar workers walked and rejoiced together the whole day. Our sign said ‘rEvolutionary Biologists say: Capitalism Reduces Fitness!’

Well, it’s the objective truth. A flyer distributed in the demonstration was pointing out that an African-American boy born in West Oakland has 15 shorter life expectancy than someone born up in the hills. If that’s not reduction in fitness, what is?

Finally, on Wednesday Nov 9, we were at Sproul Plaza to support the Cal students protesting better conditions for education. It was a totally non-violent (even arguably naive) demonstration. It was unbelievable that police could attack this. Amazingly, the students kept calm and did not respond the same way (the police were greatly outnumbered by the students).

I have real doubts about the competence and sincerity of the administrators allowing this police attack.