Posts byDax Vivid

How can scientists work with cultural humility?

Coming from a background in science and coming into public health and not ever hearing ‘cultural humility’ in the sciences was very telling for me. Because culture is not something that’s emphasized, it’s not talked about in a relevant way. There have always been very clear barriers present for particular minorities in science. You can

5 Things I wish I knew about Berkeley at least 2 years ago (instead of just 1)

UC Berkeley is a huge melting pot of interesting people, groups, communities, assemblies, departments, services…the list could continue ad nauseum. We’ve seen the impressive interplay of collaborations between these departments put together by Natalia Bilenko, with data scraped from the PubMed database. This article strives to share some of the communities that I have only

Motivated Numeracy

To know inauthenticity is not the same as to be authentic.” —Paul See de Man

20131019_FBD001_0Lately, public media has been expressing increased skepticism towards scientific practices. Consider the recent cover articles in The Economist: How Science Goes Wrong and Trouble in the Lab. In the latter article, Jason Ford artfully depicts scientists in labs that would make EH&S shiver, sweeping poorly conducted experiments and data under the rug. These articles indeed resurface the problems shaped by incentive systems, such as publishing models. They also point out how the disavowal of null results by high impact journals may ultimately promote unethical practices for those who wish to stay in the publication pipeline.

Scientists as people are not the disinterested, communistic, universal, and organized obeyers of the ideals of science proposed by Robert Merton, though they are expected to be when conducting experiments. What The Economist fails to acknowledge is that although scientists are people preserving self-interests (just as any other professional), science itself constantly destroys and reconstructs new hypotheses across fields (in line with Thomas Kuhn’s paradigm shift). Science has self-revision at the core of its process. If an experiment was conducted poorly and the results significant, scientists have the right and expectation to challenge it by conducting their own experiments.

In contrast, the Economist article makes it seem like the mistakes within science are a problem with science itself. Although the problems identified are important to rectify within science, and indeed doing so should be a part of science, it would be a great exaggeration to treat science as though it were broken. What must be acknowledged, in spite of identifiable problems in scientific practices, is “how science goes right” for the most part, and the problems in it should not provoke a skepticism of the entire practice.

If the practices enforced by science correct for cheaters, then should we be concerned by these articles from The Economist? If their goal is to stir public distrust of science, then it is time to reconsider all of the technology (that arose from these “dirty” practices) upon which society depends. Again, these authentic accomplishments are undermined in the guise of inauthentic scientific practices (consider the Paul See de Man quote that introduces this article).

There is an important ideological question raised by this article. Is the underlying message of, or inevitable reaction to, the article one that convinces people that they need to give greater support to science and help facilitate the development of better scientific practices? Or instead, is the message that the public should indulge in politically motivated negative attitudes towards science itself, and divest (metaphorically or literally) in scientific progress. This latter possibility is particularly unsettling given some of the popular politicized positions taken towards issues such as climate change, vaccinations, and the environment.

The scientific method, revisited

What really is the scientific method in research?
bsr_scientific_methodMaybe your high school biology teacher made you recite the scientific method. If you talk to most practicing researchers, they would probably say this method is “more a set of guidelines than an actual rule”; kind of like the pirate’s code. Publications disseminate research using the key terms of the scientific method: background, hypothesis, experimental design or methods, results and conclusion. However, this approach may not reflect the complex reality of conducting research, nor optimize productivity. This article evaluates the scientific method by investigating different ways to approach research, specifically the strong inference model.

Some may argue that without the backbone of the scientific method, the research process is convoluted and complex. But is complexity something to be avoided or embraced? Consider the ecologist, Eric Berlow, as he simplifies complexity in his TED talk. He supports the claim that complexity is not complicated but, rather, simplifies our understanding by encompassing the whole network. Sound like an oxymoron? This abstraction is distilled to a concrete example with a more direct interpretation of an infographic on U.S. strategy in Afghanistan (this infographic looks as overwhelming as food webs over the past ten years). Is the scientific method stripping science of its innate, remarkable complexity, or distilling it into a digestible brew?

Such complexity can arise through logic trees, and imagine designing experiments using one! In 1964, John Platt presented the concept of strong inference, stating that the development of logic trees and alternative hypotheses are essential to rapid advancement of scientific inquiry. Platt exposes the weakness of the classical scientific method’s single-hypothesis. Actively pursuing an answer to one specific hypothesis may cause confirmation bias at each level of the scientific method, including background research on the question, modes of approaching the question experimentally, data collection and interpretation. Blind and double-blind experiments attempt to control for this, but if the methodology is biased, does the data quantified still lack bias? Platt suggests with anecdotal evidence that greater scientific progress is made through inductive reasoning (metaphorically, casting a fishing net into an ocean of unknowns) and conducting thoughtful experiments to eliminate alternative hypotheses and produce subsequent logical ones, instead of simply going to one fishing spot at a time through the deductive reasoning, as outlined by the classical scientific method.

Three Ways to Consider Psychoanalysis in Understanding of Science


Chris Holdgraf’s article “On being ‘right’ in science” addresses the importance of sacrificing the full truth (i.e. scientific jargon and acronyms) for understanding. This article will elaborate on the concept of how one “understands.” That is to say, we will understand understanding before trying to be understood. Research in psychoanalysis is contributing to how scientists communicate with the public on controversial topics like climate change, such as described here.

Instead of showing graphs and figures to convince the public of the existence of a problem, Slovenian philosopher Slavoj Žižek walks through consumers’ growing piles of garbage while he discusses the hidden reality of climate change in his documentary Examined Life. “Nature is not a balanced totality of which we humans disturb. Nature is a big series of unimaginable catastrophes. We profit from them. What is our main source of energy today? Oil.” Take a moment to reflect on how oil is formed. Instead of rejecting the existence of waste, we will have to accept that it is a part of how we live and collectively work with ways to minimize its impact on the environment. There are a few considerations to make with these regards in the context of psychoanalysis.

Christopher Shaver, graduate student from the computer science department and co-instructor of the Berkeley DeCal Altered States of the Brain, shares the top three reasons why psychoanalysis is an important consideration to make in scientific discourse:

A Modern Recipe for Scientific Revolutions: Inspired by Thomas Kuhn, Condensed by BSR

Thomas Kuhn, world-renowned philosopher and historian of science, published The Structure of Scientific Revolutions while teaching at U.C. Berkeley in 1962. Kuhn took on the challenge of describing the historical and sociological setting of academic scientists, in the manner one would describe, “What is water?” to deep-sea fishes.

Over five decades later, avant-garde researchers still venture down the library rows to borrow this particular book (as shown by its many annotations!). Over five decades later, avant-garde researchers still venture down the library rows to borrow this particular book (as shown by its many annotations!).
Image is the author’s own.

At the time of publication, it was not the easiest medicine to digest for extreme orthodox practitioners of science. Surprisingly, his lessons are extremely relevant in present-day discussions of scientific discourse. (One example is academic publishing, which will be discussed by an evolving manifesto at the 4S conference this October.)

What is a mentor?

mentorshipMentoring is like parenting. Not to say you are being a parent, but rather, that the “training” you receive beforehand may be, “You’ll figure it out as you go along.” We have all seen movies or read books with classic mentorship roles—the coach of the football team, the cheerleader, and even the high-school counselor/gatekeeper that says, “You will never make it into that college with your grades.” These are all examples of mentors in the course taught by John Matsui, MCB15). This was the first course in which mentors were neatly categorized from their previously ambiguous roles. What is a mentor? Does being a good mentor require mentees with particular characteristics? Here are interesting perspectives I have heard from other mentors I greatly admire.

Men’s Room, Women’s Room: An Overlooked Binary Division?

an-old-fashion-mens-and-womens-bathroom-signThis article scratches the surface of a complex issue. It asymptotically approaches topics surrounding (1) the binary division of “men” and “women”, (2) its historical significance, and (3) the work being done to promote “unisex” mentality, including unisex restrooms. It is important to take these efforts into careful consideration when considering the topic of women in science and gender equality (for more information, Nature publishing did this special issue on Women in Science: Women’s Work).

Claude Steele and many other sociologists elaborate on the concept of stereotype threat, which leaks into discourse surrounding the topic of women in science. While this field of research is only recently accumulating more quantitative evidence, the idea of women in science reporting greater inclination to feelings of imposter syndrome and the like is easily related to the discourse of Robert K. Merton on the sociology of science in general over half a century ago:

…when statements are doubted, when they appear so palpably implausible or absurd or biased that one need no longer examine the evidence for or against the statement but only the grounds for it being asserted at all.*  Such alien statements are “explained by” or “imputed to” special interests, unwitting motives, distorted perspectives, social position, and so on. In folk thought, this involves reciprocal attacks on the integrity of opponents; in more systematic thought, it leads to reciprocal ideological analyses. On both levels, it feeds upon and nourishes collective insecurities…

: Freud has observed to seek out origins rather than to test the validity of statements with seem palpably absurd to us…On the social level, a radical difference of outlook of various social groups leads not only to ad hominem attacks but also to “functionalized explanations.”

–Robert Merton “Paradigm for the Sociology of Knowledge” 1945

Ideally, we do not let our perception of gender interfere, consciously or unconsciously, with our interpretation of the quality of another individual’s work (i.e., ad hominem attacks). Problems include (1) overcoming our initial reaction to categorize individuals in broadly defined stereotypes associated with historical (out-dated) gender roles and (2) appealing to any fallacies supporting the maintenance of out-dated gender roles.

Ask me to describe myself, and I will describe my aesthetics: biology, foreign languages, philosophy, post-modernism, and critical theory. Ask a stranger to describe me, and “female” is a socially acceptable general category.From this category, one may already make many assumptions of who I am and the quality of my work; however, the social category of “woman” is not one with which I would immediately self-identify, though I reside in this category when I check boxes on documents, select a gender pronoun, or use the restroom. Restrooms in the work place are usually segregated into binary divisions of men and women, and there’s a historical (subjectively out-dated) reason for it.

Open access: Top 5 ways to engage, why you should, and precautionary measures to consider


Today’s post was written by Kristina Kangas and Chris Shaver.

There’s a lot of hype about open access (OA). Anna Goldstein did a great overview of Open Access Explained, and 55% of respondents to the poll say, “Viva la revolución! I only publish in open access journals.” If you are not yet a part of this vibrant, emerging world of scientific dissemination, here are five ways and reasons to engage in open access as well as precautionary measures worth considering, to ensure that you are not infringing on copyright laws.

Follow the link to read the five why’s and how’s of open access!

Beyond the PDF and the division of labor

imageRecently, a search through the winding canals of Amsterdam would reveal more than the usual Dutch cheeses and Stroopwafels. You would discover tools for scientists to enhance communication, expedite publication, and engage annotation. Tis the city where Beyond the PDF2 Conference (#btpdf2), funded by Elsevier and hosted by FORCE 11 (the Future of Research Communications and e-Scholarship), took place March 19th and 20th.

Librarians, techies, professors, researchers, publishers, and students gathered in an older Dutch building Pakhuis de Zwijger to share novel ideas on how scientific communication should change with the advances of technology. A live twitter feed projected on the right wall, artists drawing cartoon visual notes on the left, and the traditional podium and PowerPoint in the front only to fool onlookers into believing this was a traditional conference. Not so! With the full program on Lanyrd showing speakers and their Twitter usernames, everyone watching (either in person or on the live stream) knew otherwise.

While many interesting topics where addressed, there were a few that stood out…

More on the future of scientific discourse

Hearst EdificeTechnology is inevitably changing how scientists interact with journals and, ultimately, with each other. Consider workshops such as BeyondthepPDF2 and platforms hosting primary literature discussion such as Journal Lab. If this is the future, how can graduate students find security in future incentives with subjectively “classical” contributions? By re-evaluating the assessment criteria and the process of dissemination for scientific findings in a technological age, we can work identify the gaps in scientific discourse that need to be filled.

Graduates are confronted with using new approaches to scientific discourse while maintaining previous Gutenberg-inspired methods (e.g. paying publishers to sell it, paying more for color photos when ink is no longer an issue, etc.) . Chris Holdraf writes an insightful overview to how training in graduate school is shaping the world beyond the walls of academia in his article Beyond Academia: a new approach to PhDs. Future jobs for scientists include the possibility of filling in these gaps, and science hubs and blogs are becoming epicenters for real-time data sharing and discussion, like platforms being established by PLOS, for instance.

Future of scientific discourse and education

tree of knowledge1How well do you think people outside of your department could understand your primary literature? Outside of academia? What do you think about constantly reading through rigid, link-less, old-fashioned PDF files?

We can only know if the meaning of our work has been understood by others if we receive feedback, i.e. the interpretation of others of our work. If we want our work to withstand the test of time, and still carry the meaning we intend it to further down the road, it is time we harness the power of technology and benefit from public feedback at all stages of the scientific process. To accomplish this, we will have to reconsider the topic of accessibility. I, along with my co-authors, Benjamin Smarr, Chris Shaver, and David Jay, have developed this interactive article to both comment on these issues, as well as serve as an example of how to better convey scientific information.

You are cordially invited to interact with these questions and ideas here. (And if you would really prefer a PDF version, I would grudgingly oblige.)

In addition to the uses for technology and applications in education mentioned in this article, also hear UC Berkeley’s computer science professors Armando Fox and David Patterson talk about their approach for revolutionizing online education with MOOCs (Massively Open Online Courses), Berkeley Resource Center for Online Education, and edX in collaboration with MIT, check out

“What to post? When to post? For whom?” Optimizing the dispersal of science on social networks

Pilobulus SporesI met George Ludwig at a wine tasting in Noe Valley last week. He is the founder of, “a content marketing automation suite that drives new customer acquisition via #Twitter.” This site facilitates the process of a company or an individual obtaining followers that share interest in a particular topic. (Target marketing at its finest.)  The question I posed to him is this: can individual scientists gain credibility as a reliable source of information using this tool the way companies gain trust from their followers when marketing their product? I believe that this is an important way to connect with the general public.

So–what, when, and for whom to post?

Social networks are undisputedly tools for dispensing information, be it objective or not. Well, I’m relatively new to Twitter. Call me old fashioned. Maybe Twitter is already a thing of the past, and I am just starting to get on the bandwagon at the last stop. Maybe the way we have been using social networks is an antiquated approach. I propose that researchers who haven’t “updated their status” should consider harnessing social networks to effectively communicate their science and better public engagement of the research as well as the people behind the scenes, the researchers.

Artists speak: Advice for scientists when communicating science

The descending roar of a bus as it accelerates away from a stop. A spider clings to its web on a streetlamp nearby. Students divulge the complexities of life in comestible stories. Silence doesn’t really exist, but if you listen closely, you can trick your mind to perceive it underneath the tiers of sounds of various decibels enveloping the air that surrounds you.

Simple components make up our banal existence, but to a scientist, or an artist, or a storyteller, these overlooked details edify life. The Creative Communications of Science Panel, hosted by Initiative for Maximizing Student Development, consisted of four innovative harbingers of modern scientific explorations: Todd Gilens is an artist that studied landscape architecture at Harvard’s Graduate School of designs; Shane A. Myrbeck is an acoustician, sound artist and composer; Lauren Sommer is a science reporter for KQED radio staff; and Gail Wight is an assistant professor in the Art and Art History department at Stanford University. Together, these panelists shared how they each uniquely integrate science into art and recommended how scientists can use art, in its uncountable forms, to communicate science.

“Extra! Extra! Read all about it!”: Science writing for press releases

Just like a bad first date, a good first sentence is best kept short. Dr. Evelyn Strauss, science writer and editor, shared her writing secrets as a guest speaker for Professor Mimi Koehl’s graduate seminar, “Communicating Science to the Public.” With experience in writing for magazines and journals such as Science, Scientific American, and Current Biology (just to name a few), Dr. Strauss expertly divulged the challenges of science writing and techniques that we, as scientists, can harness while taming our own science-writing beasts. May your readers make it to the second date, id est the second paragraph.

Dr. Strauss revealed what personal characteristics paved her path as a science writer: for instance, she enjoys learning about topics beyond her field of expertise. Her uncanny ability to write about science in layman’s terms makes it to understand. Although she conducted freelance work without formal writing training, Dr. Strauss was led by curiosity to investigate what writing “secrets” were being disclosed in the science writing courses at UC Santa Cruz. With her experiences in the classroom and in the real world, Dr. Strauss skillfully addressed the field of science writing while visiting Berkeley.

As an exercise, the participants wrote a “press-release” paragraph to bring to the seminar. We were faced with the impending doom of hearing our first sentence read out loud, twice. Mine was particularly long, so doubling the time necessary to read it reinforced the importance of a short and simple first sentence for engaging readers.

Click through for more tips from Dr. Strauss.

The rules of (science) writing

The quotation, “If you can’t explain something to a first year student, then you haven’t really understood it,” is commonly attributed to Richard Feynman. It highlights the fundamental challenge of being a good scientist: communicating your discoveries to others. This is a challenge that the scientific establishment only sometimes meets. After delving into the books provided by our university library addressing scientific writing, I have contrived this précis of commonly expressed concerns from critics (at least those that were so bothered by the mayhem of science writing that they felt it necessary to write a book about it).

Jean-Luc Lebrun develops a clever acronym to keep in mind when considering the FOCCCI of your writing: Fluid, Organized, Clear, Concise, Convincing, and Interesting. He emphasizes that truly proficient writers will MINIMIZE the time needed to read and MAXIMIZE the motivation of the readers. I find this advice holds true for all forms of science writing, be it a grant or an article.

To Whom It May Concern: How reviewing letters of recommendation shaped my opinion on who to ask

In Berkeley, it’s not just summertime. It’s also application season, and across campus beads of sweat are forming on the brows of Cal students. Who, they wonder, will they be asking for letters of recommendation?

One of the most common dilemmas arises in large lecture courses. As a former Berkeley undergraduate myself, I can sympathize for students in courses with almost 300 students who face the ineluctable fate of requesting letters from their professors or graduate student instructors. The first question many undergraduates have asked me regards this very dilemma: do I ask the graduate student instructor who knows me as 1 out of 30 students, or the professor who barely recognizes me?

Anne Hoey and John Benton discuss artificial intelligence in the military

Over fifty years ago, scientists began to discuss the possibility of designing a pseudo brain that worked at the capacity of a human brain, and the field of artificial intelligence (AI) was born. Although they brutally underestimated the complexities associated with such a task, they were right about the array of conceivable uses—especially by the United States military. Two scientists who partook in the golden era of AI research  in the 1980s, Anne Hoey and John Benton, formerly of the Center for Artificial Intelligence (CAI) in the United States Army Topographic Engineering Center (TEC), have agreed to share top secret information with Berkeley Science Review.

Improving the lives of those with Crohn’s Disease

When Jo Andrea Napoli sent out e-mails and Facebook messages in efforts to raise money for research in Crohn’s disease, the first reaction people gave was off the charts. Some people have friends or family suffering from Crohn’s Disease, but most people are not familiar with this incurable autoimmune disease.

Ashok Kumar, a post-doctoral researcher at Children’s Hospital Oakland Research Institute (CHORI), works in a lab currently applying for funding to investigate the underlying mechanisms of Crohn’s disease. “It’s like a lock and key mechanism. There is no effective treatment specific for this disease,” says Dr. Kumar. Non-steroidal anti-inflammatory drugs, like aspirin, are “non-target treatments,” meaning that they are not specific to the inflammation in the intestines and can affect the whole body, producing undesirable side effects. “Our goal is to identify a good target and find a drug to activate or inhibit that target.”