Doing it for the right Reason

Geneticist and champion of open access to scientific research, Michael Eisen, recently announced his intention to run for the US Senate in 2018.

In an interview given to Nature, he stressed that his decision is not merely driven by concerns about research funding under the new US administration, but by the latter’s “basic rejection of the fundamental principles upon which science is based.”

Also he pointed out that scientists may be “paying the price for having been politically disengaged for such a long time.”

Despite his relative lack of political experience, he understands that bringing reason to the political debate will require more than simply voicing aspirations. Moreover, as emphasized via @SenatorPhD, his political platform is “about bringing facts and logic back to the policy table”.

With his decision, Eisen seems to be answering a call to stand up and take action in a time of global crisis. He acknowledges the risks and obstacles that lie ahead.  Risks and obstacles in the way of defending science and human decency. To me, that is a noble endeavor, in the US and everywhere.

Code of gratitude

Giving due credit to scientific software development.

A substantial amount of work involved in data-intensive problem-solving is based on resources that virtually cost nothing to the end-user. Nada, gratis. You find it, you download it, you use it, and in some cases, you can modify it to tailor it to your own needs.  You might even benefit from the experience of a large community of developers and users. Almost everything you need to learn or advance in your work.

Nowhere is this more apparent than in scientific research, across disciplines and application domains. The positive effects of free software and other types of open resources on scientific advancement are priceless. No single indicator of “impact” and “return on investment” could do justice to the benefits generated by such tools, languages and platforms.

Although users and other stakeholders often cite sources when reporting their work, this is not even consistently done. There are so many people (and work hours) invested in the noble idea of making and sharing code. So many anonymous contributors, unknown leaders and unselfish enablers who make such a moral choice every day. And yet, there is so much work that goes unrecognized.

The marvelous thing is that the communities that bring us all these ideas and solutions are made up of a particular kind of people. Mostly, they are people who care about societal challenges and do things just for the fun of it. They nurture projects that are fueled by unremitting passion, enjoyment and curiosity. This is not a world particularly suited to the celebrity wannabe and the bullshitter.

There is the rub: There is always the temptation to take the labors and contributions from these communities for granted. Almost a sense of entitlement among direct and indirect beneficiaries. The expectation that all those great tools and resources are self-made and self-perpetuating. The presumption that somewhere, somebody will make them for you, one way or the other.

In times of increasing excitement about “all things data”, it is crucial that stakeholders continue finding concrete ways to support, motivate or give due credit to those who create and share software. Multiple reward instruments, monetary and non-monetary, will be important. Impact assessment will also be necessary. This is more than a matter of fairness for a particular group of people. This is also about sustaining scientific and societal progress.

For now, I take a step back to tell the men and women behind the screen: It is a privilege to have access to the products of your talents and hard work. To the good people who give us the languages, databases and tools that make science happen: I am grateful to you.

The learning of joy

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The joys of learning.

Learning about things in and out of this world.

Learning to look into a problem, its underlying systems and its potential solutions.

Taking things apart, distilling how they function and imagining their inner workings.

The joys of discovering.

Seeking truth, finding the facts and not believing what one prefers to be true.

Taking a break from boredom, the passing of unidirectional times, the illusion of universal meanings.

Looking into your own eyes and admitting ignorance to bypass ignorance.

The thrills of hacking.

Doing it for the fun of it, the pleasure of finding things out, the need to trespass on what is known.

Putting things back together, seeing new possibilities and trying out new ways to connect them again.

Preserving curiosity as a childhood secret, the tenacious search for what has been lost or left behind.

The aching to lose something not to lose it all.

These are the joys of life too, the good life.

An insurrection of senses against the non-sense.

A riot against conformity.

The days of the enlightened rebel, the noble prankster, the outsider, the undesirable.

These are the joys of creation.

Against all biases: Do we really need more diversity in research and innovation?

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There are reasons for achieving greater diversity in science. Diversity in the widest sense, including gender, ethnic and social background diversity. This is not simply a matter of justice, which by itself should represent a sufficient argument for defending diversity. Actually, it goes beyond such an “ideal” into the accomplishment of “practical” purposes. Prerequisites that are crucial for advancing knowledge and generating socio-economic advantages.

Scientific progress depends on openness. The openness that allows deeper examination of evidence against, or in favor, of a hypothesis. The openness needed to verify and reproduce results. A condition that is essential to understanding a problem and finding possible solutions without having to revert to notions of faith or ideological loyalties. Openness is strengthened by a diversity of ideas, and at the same time openness encourages new perspectives that are worth investigating.

Scientists, as well as all types of innovators, benefit from context awareness. This refers to understanding the background underlying a specific problem. This is also related to empathy: our capacity to be sensitive to the needs and experiences of others.  Based on such awareness, scientists and innovators can come up with new applications that are both novel and relevant to humanity. These abilities are less likely to be developed in highly homogeneous or uniform organizations.

Scientific research and innovation are cooperative enterprises. Discovering and exploiting new knowledge typically involves interactions among people of diverse socio-economic backgrounds and cultures. Challenges of local and global significance, such as those concerning human health and the environment, demand the combination of resources and expertise that cannot always be linked to a single institution or geographical region. Moreover, intellectual and economic outputs may target varied stakeholders worldwide. Therefore, improving diversity is a necessary step towards properly framing complex questions and identifying what is needed to reach a solution.

Do we understand this problem? Is this the right technique? Should we move in this direction? These are questions that researchers address on a daily basis. To answer them, scientists pursue their own perspectives and methods, while simultaneously considering competing approaches and explanations. Thus, finding “truth” entails a persistent effort to reject partial views influenced by individual assumptions, historical circumstances or particular organizational settings.

To better understand the world and bring greater benefits to people, researchers must fight preconceptions that are imposed by the narrowness of their own knowledge and experiences. The restraints forged from our ignorance. However, to effectively struggle against such biases, we need more diverse research environments and leaderships, not less.

The PhD defense: “disaster” avoidance strategies

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The date for your PhD thesis defense is approaching. In many ways you have already started your preparation: the thesis writing and submission, going through the administrative procedures, verifying conclusions, refreshing your knowledge and rehearsing for the big day.

It is likely that you have already been there through the eyes of another student. First: A stuffy room, the presentation that is seemingly a mere formality, those yawns from the audience, the nervous smiles from your supervisor.

And then, here comes the part you really have been waiting for. The moment when the thesis committee is no longer a list of names: it is question time.

Questions: The ceremonial ones, the easy ones, the “good” ones, the difficult ones. What about those harsh questions? The dry mouth, the perspiration, someone playing drums with a pen and desk, the laser pointer moving like crazy all over the screen. Also you have wondered: What’s with the little tapping on the microphone? Is she about to have a stroke? Give that man a glass of water please!

Until now you have hoped for the best.

But are you adequately prepared for the worst?

Trying to anticipate all possible types of situations during your PhD defense is a wishful, almost hopeless, task. But envisioning “worst” possible scenarios and considering the actions typically leading to such undesirable situations are both feasible and necessary. These are relatively common and preventable mistakes that students can make, time and again, in different doses and combinations. A selection of them and accompanying advice follows.

1. Huh? I don’t know. Here is the question, and you may not know the best possible answer, or you think that it is outside the scope of your research. Nothing wrong with it. Unfortunately, your gestures, words or even tone can tell the committee a more troubling story: you are not sufficiently concerned with the point made by the examiner.  A simple “maybe, I don’t know” or “this is outside the topic of my research” are more than unsatisfactory replies. Although honesty should be at the center of your responses, such simplistic answers are also different ways to say: I do not care enough.  A rephrasing of the question may make things clearer to you, and at least it will buy you some time to think about what to say next.

2. The dog ate my data. Gone are the days when you could blame the dog for eating your homework or announce the death of your grandmother for the third time.  During your PhD, blunders or omissions may rightly be explained by different factors: Lack of funding, “unforeseen” mishaps, supervision problems and family issues. But regardless of whether or not they represented major obstacles to your work, never use them as an easy way out of your individual responsibility or to shift it on to others. It is alright to explain the conditions that influenced a particular outcome, an obstacle that you had to overcome or a difficult turn that you had to make. However, even if you are still recovering from these complications or you feel that you were treated unfairly: focus on the problem and your approach to dealing with it. Even better, tell the audience how you adapted to new circumstances, and outline the lessons you learned.

3. Nah, it is not so bad. An effective way to piss off committee members is to downplay the significance or seriousness of their concerns. If something in your work looks to them “surprising” or “weaker”, then for a moment consider that there must be some truth to their criticism. If you disagree with the reviewer’s position, then respond to it as you are expected to do: through argument based on the most solid evidence available. All of this without forgetting that in research there is always some room for improvement.

4. Duh, obviously.  Even if you think that a reviewer asked you a trivial or obvious question, never express this view (either in words or mannerisms) to the committee. It’s the reviewer’s job to assess your knowledge irrespective of whether you or anyone else believe that you know the answer. If you have the impression that the committee is testing you, well that’s right, get over it.  This is also related to another not less common situation: the candidate displaying hints of exasperation or amusement when asked questions that, at least in the candidate’s opinion, have already been addressed during the defense. These reactions not only may be seen as impolite to the reviewers, but also they offer a negative glimpse at your intellectual maturity.

5. I showed it in the thesis. It is not unusual for students to answer a question by simply indicating that a particular point was already explained in the thesis. Never assume that the reviewers will remember everything from your thesis. Even if they have amazing memory powers, the reviewers are there to ask anything considered relevant for evaluating the quality of your research. In some cases, they just want you to refer to a specific thesis section to obtain further clarification. So, focus on the question and answer it, even if the answer is impeccably clear in the thesis.

During and after your PhD defense you may feel that you did not offer the best answer to one or several questions. That could be especially frustrating if you are confident that you had the necessary knowledge to make it better. This is perhaps unavoidable and will represent a recurrent theme in your research career. Moreover, error and failure are inescapable realities in science. However, what you should not contemplate is ignoring basic recommendations that are known to be conducive to a professional, and hopefully less painful, discussion.

Keep up the hard work on route to your PhD defense. Celebration will be coming next.

Mentoring young researchers

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Confidence nurturing

Around the time I entered the second half of my undergraduate studies, I joined a research group as a trainee or sort of apprentice. Despite my eagerness to become more involved in research- and teaching-related activities, I was entirely ignorant of the day-to-day dynamics of a research environment. Soon I learned that the links between advisers and advisees, or between mentors and mentees, were more complex than those between conventional teachers and students.

It rapidly became clear to me that our advisers led the group, first and foremost, through their moral authority. I learned that advisers can positively impact their teams without relying on an authority given to them solely by hierarchy. They interact with younger researchers with courtesy and consideration, even when facing stressing or demanding situations. Such advisers do not trash talk about their advisees, or expose their vulnerabilities to others in an attempt to downplay the adviser’s responsibilities.

Even when they express their most critical assessments, inspiring advisers possess the ability to make you feel free and secure. Responsible advisers do not have the need to control through fear. Truly good advisers thrive in large part because they promote accountable freedom, and because they earn the trust and loyalty of their teams.

Long after graduation I came to more deeply appreciate another guiding principle: Effective learning requires an unavoidable interplay between progress and failure.

When a learning opportunity arose my advisers did not give me reasons to doubt the potential value of the new experience. They did not ask me to overthink whether I was worth it or not. They told me to go for it and get it done to the best of my abilities and resources available.  When the challenge became bigger than one could have anticipated, they did not regret it or tried to find excuses in preparation for a possible failure. If failure occurred, we were allowed and guided to try again, harder, better. Repeating mistakes learned from previous failure was the only mistake to be afraid of.

At a relatively early time in my research experience, I was asked to give a presentation for the group. Initially I thought that I did not deserve such an invitation. I felt that I was wrongly appropriating a place that only graduate and more experienced researchers were entitled to. Fortunately, those thoughts gradually became irrelevant. My mentors did not use this presentation as a mere test of my work performance or skills, they did not ask me to do it just to satisfy some internal procedure, and they never questioned the significance of the occasion. They had simply given me an opportunity to advance my learning experience, to strengthen my connections with my work and that of others.

That first presentation provided me with a profounder message though. An explicit reminder of something that had been encoded around me all the time: I belonged and was welcomed to a community. Furthermore, all those student presentations and discussions allowed us to understand that mutual respect and support were the glue that kept such community advancing together, despite material obstacles or other difficulties.

This was confidence building as a patient nurturing of intellectual growth. Mentoring seen as the unselfish gardening and sculpturing of young minds. Those were our advisers. Incessantly, almost imperceptibly, exercising an unpretentious brand of leadership based on ethical conduct and professional integrity. A generous exemplification of respect for the efforts and capabilities of others, in triumph and in adversity.

For that and more, I will always be grateful to the mentors of my early years in academia: Gianfranco, Guillermo and Fernando.

This post is also available at Medium.

Bullshit fighting


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According to American philosopher Harry Frankfurt, a key difference between liars and bullshitters is that the former tend to accept that they are not telling the truth, while the latter simply do not care whether something is true or not.

Bullshitters strive to maximize personal gain through a continuing distortion of reality. If something is true and can be manipulated to achieve their selfish objectives, then good. If something is not true, who cares? All the same. These attributes make bullshitting worse than lying.

Furthermore, according to Frankfurt, it is the bullshitter’s capacity to get away with bullshitting so easily that makes them particularly dangerous. Individuals in prominent positions of authority may be punished for lying, especially if lying has serious damaging consequences. Professional and casual bullshitters at all levels of influence typically operate with freedom. Regardless of their roles in society, their exposure is not necessarily accompanied by negative legal or intellectual consequences, at least for the bullshitter.

Instances of bullshitting are found on a daily basis across public and more private domains. It is not only the politician or marketing campaigner who can put a big smile in front of a bigger pile of bullshit. They also include the masters of fear mongering, the attention seekers and the deniers of scientific facts.

Science, the natural ground for combatting non-sense, also hosts and even promotes a good deal of bullshitting. This is done when scientists and entrepreneurs put “great stories” above strong empirical evidence, marketing above demonstrable expertise, and soundbites above critical discourse. Scientists also become bullshitters, or at least facilitate bullshitting, by over-hyping their findings in an attempt to make the news or demonstrate to politicians the “impact” of their research. This in turn can be abused by other bullshitters in their quest to favor particular political or economic agendas.

Researchers may also be guilty of bullshitting by omission. This is the case when they do not openly challenge bullshitting positions, either in the public or academic settings. Scientists frequently wrongly assume that the public always has knowledge of well-established scientific facts. Moreover, scientists sometimes over-estimate the moderating role of the media or their capacity to differentiate facts from falsehood, and solid from weaker evidence.

Bullshitting happens. But very often it is a byproduct of indifference. Indifference frequently masking a fear of appearing confrontational to peers and funders. Depending on where you are or with whom you work, frontal bullshit fighting may not be good for career advancement.

In a world with an imperfect scientific peer review system and increasing market-oriented pressures, there are few options but to continue fighting bullshit. Scientists and informed citizens cannot just simply ignore it. They can also help to identify and expose it for what it is. Bullshit!

Bullshit fighting must be accompanied by a more active involvement in day-to-day discussions of science and technology, in and beyond classrooms and laboratories. Above of all, this means not accepting that bullshit should become the norm in our lives, rather than the exception. As H. Frankfurt put it, bullshit is an insulting substitute for the truth. Thus, we need to reject it wherever we find it. It is both the right and intelligent thing to do if we care about reality.

This article is also available at Medium.