philosophy of science


Philosophy of Science, Part IV with Nathan Pearson: A Scientist Responds

Guest: Nathan Pearson, Senior Director of Scientific Engagement & Public Outreach, New York Genome Center

Bio and Contact Info

Chapters: (Advance the marker)

0:44 Asking the "why" questions

5:55 The biological editor

11:53 Has the language of biology limited us scientifically?

16:02 Latin vs. plain language

20:17 Presenting genomics to the lay audience

23:30 Has the reductionist approach been codified into the language of biology?

29:58 Do scientists listen to philosophers?

For the next segment of our Philosophy of Science series, we talk not with a philosopher, but with a scientist. Nathan Pearson has been a genome scientist at Knome and Ingenuity Systems, and just this month began with the cool title, Senior Director of Scientific Engagement & Public Outreach at the New York Genome Center. On today's program Nathan responds to some of the ideas that have surfaced in this series. How is the study of biology limited by language? Is a certain amount of reductionism codified right into the language of biology?

Nathan studied linguistics in college, so his knowledge of language is deeper than that of many scientists. But he's also part of the working industry of science. Starting with a discussion about the many ways language and biology intersect, Nathan explains how the history of language affected the study of biology.

Becoming aware of his own language in the interview, Nathan says that since Latin was first used as the language of science, we have always "prized the long flowery way of saying something as somehow being better than the one syllable--or beat [he corrects himself]--way of saying it."

He's against the flowery approach, and says there's a movement in science, law, and business toward using plainer language. And what is the argument against this transition?

"That it's less precise," he says, "which is fluff."

He recites several older Saxon words which are every bit as precise--and more impactful, he argues--as the latinate words. Gut vs. intestine and gullet vs. esophagus, for example.

That's all fine and interesting, but the big question is whether Nathan thinks language is responsible for an overly reductionist approach to biology?

The culprit is more math than language, he says. We end with a discussion about whether scientists even listen to philosophers.

While chatting about philosophy of science at a recent conference with Nathan, industry veteran Lee Hood walked by, and we threw some ideas at him. Always focused and in a rush to somewhere with a retinue following him, Lee nonetheless stopped in his tracks and demonstrated some enthusiasm for the topic.

"Scratch a scientist and you get a philosopher," quipped Nathan.

So we put Nathan in front of the camera and scratched him.

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

Rethinking Biomarker Development with Anna Barker

Guest:

Anna Barker, Co-Director, Complex Adaptive Systems Center, ASU

Bio and Contact Info

Listen (7:54) Have we been overly reductionist in the study of disease?

Listen (6:32) Applying new knowledge about complex adaptive systems to biomarker development

Listen (7:09) The National Biomarker Development Alliance

Listen (3:05) What do you think of the 'Snyderome' model?

Listen (5:44) Confident that FDA will regulate LDTs

Southern Arizona is emerging as a hotspot in the world of diagnostics. And one of the leading lights there is Anna Barker, who has been bringing folks together to think about biomarkers for a long time. As the former deputy director of the NCI, she assembled many different groups including the Nanotechnology Alliance for Cancer and The Cancer Genome Atlas (TCGC). She's now at Arizona State University where she co-directs the Complex Adaptive Systems Center and seeks to establish a new paradigm in the way we look at the biology of disease.

Beginning with some philosophy of biology, Anna takes us into her latest thinking on complex systems.

"We have to start thinking of a disease like cancer as a system," she says. "As you perturb one part of it, you perturb all of it. . . . We have to think more 3D."

Anna is someone who likes to go back to the basics, not only in the study of biology, but also in the business side of diagnostics.

In the interview she announces a new National Biomarker Development Alliance (NBDA) that is bringing a higher level of standardization to every phase of biomarker development. She argues that there are several decision points in the process, whether it's to validate an assay, or take it into commercial development. Right now, she says, the diagnostics community does not agree on the current standards for these decision points, or modules, and this is a problem. The aim of the Alliance is to bring the community together to agree on higher standards. The NBDA has just launched their website and is publishing their standards in an effort to better educate those developing diagnostics.

"We believe this approach will really enable us to develop biomarkers more predictably all the way through regulatory approval."

And what are Anna's thoughts on regulation? She says outright that the FDA is going to regulate LDTs.

Ms. Barker's vast experience and deep commitment to better science and better industry standards shine a light for anyone involved in translating biomarkers to the clinic.

Podcast brought to you by: Myraqa Clinical Research: The CRO for Point of Care and PMA Diagnostics.

And by: DxInsights: Presenting a Diagnostics Summit at the Miraval Institute May 4-6.

Myths of Big Data with Sabina Leonelli, Philosopher of Information

Guest:

Sabina Leonelli, Philosopher, University of Exeter

Bio and Contact Info

Listen (6:44) Not a fan of the term Big Data

Listen (4:20) Something lost in bringing data together from various scientific cultures

Listen (3:36) Are data scientists really scientists?

Listen (4:11) Controversies around Open Data

Listen (3:03) Data systems come with their own biases

Listen (6:22) Message to bioinformaticians: Come up with the story of your data

Listen (1:15) Data driven vs hypothesis driven science

Listen (2:46) Thoughts on the Quantified Self movement

For the next installment in our Philosophy of Science series, we look at issues around data. Sabina Leonelli is a philosopher of information who collaborates with bioinformaticians. In today's interview, she expresses her concerns about the terms Big Data and Open Data.

"I have to admit, I'm not a big fan of this expression, 'Big Data,'" she says at the outset of the show.

Using data in science is, of course, a very old practice. So what's new about "big" data? Sabina is mostly concerned about the challenges of bringing data together from various sources. The biggest challenge here, she says, is with classification.

"Biology is fragmented in a lot of different epistemic cultures . . and each research tradition has different preferred ways of doing things," she points out. "What I'm interested in is the relationship between the language used and the actual practices. And there appears to be a very strong relationship between the way that people perform their research and the way in which they think about it. So terminology becomes a very specific signal for the various research traditions."

Sabina goes on to point out that the nuances of specific research traditions can be lost as data is integrated with other traditions. For instance, most large bioinformatics databases are done in English, whereas some of the individual research data may have been originally done in another language.

This becomes especially important with the new movement toward Open Data, where biases are built into the databases.

"The problem resides with the expectation that what is 'Open Data' is all the data there is," she says.

In fact, the data in Open Data tends to come from databases which are highly standardized and often from the most powerful labs.

How can bioinformaticians deal with these challenges? Sabina says researchers should be more diligent about creating "a story" around their data. This will help make the biases more transparent. She also says that a lot of conceptual effort must go into creating databases from the outset so that the data might be used for yet unknown questions in the future.

We finish the interview with her thoughts on the Quantified Self movement.

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

Noam Chomsky on Language and the Study of Biology

Guest:

Noam Chomsky, Professor of Linguistics, MIT

Bio and Contact Info

Listen (6:34) Reductionism? Not so fast

Listen (3:10) How does a scientist come up with better questions?

Listen (2:54) Do we need new metaphors in biology?

Listen (5:29) Are data scientists getting enough basic science?

Listen (5:13) Does science have a PR problem?

Listen (2:07) How does a culture go about solving ethical issues?

Our guest today is the intellectual giant, Noam Chomsky. He is widely known as the "father of linguistics," and joins us for our Philosophy of Science series.

If linguistics is the scientific study of language, the purpose of today's interview is to talk about the language of scientific study.

We begin with the question of reductionism and whether the study of biology is being limited by a method of inquiry developed with physics and chemistry. (See earlier interview with John Dupre.) Chomsky urges caution.

"If you look at the history of the hard sciences, it has not been consistently reductionist by any means," he says.

Using examples from the history of chemistry, Chomsky points out that though there were attempts to use principles of physics to study chemistry, it often didn't pan out. By the time you get to the twentieth century, there was a real break between chemistry and physics. With the work of Linus Pauling came about the unification of physics and chemistry. But "this is not reductionism," he insists. Chomsky says it may turn out the same for biology. That biology must be studied in its own way "with an eye to unification" and this unification may or may not be reductionist.

What about our overly gene-centric notion of biology which is now being replaced by systems biology?

"What should be done in science is to pursue all directions and see which ones work out," he suggests.

Chomsky is surrounded at MIT with data scientists. Does he think that "code writers" who are increasingly taking over biology with their ability to mine huge data sets are trained enough in basic biology?

An outspoken activist, Chomsky doesn't shy away from a discussion of the politics of science. Is science suffering from a PR problem in the US? And if so, what can be done about it?

We conclude with a discussion of the murky area of bioethics in which Chomsky says "there are no algorithms to tell you how to proceed."

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

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