philosophy of science


Was That Anti-Scientism Article in Nature Just a Fancy Rant or Some Real Breakthrough Stuff?

I’m afraid it was a missed opportunity.

Let's applaud the Johns Hopkins science historian, Nathaniel Comfort, for testing out the tires--and carburetor--of his new tenureship and publishing a piece on scientism.  And in one of science’s top journals at that.   Obviously Comfort touched a nerve, generating a wave of reaction on Twitter, including a rebuke from the top celebrity Enlightenment fundamentalist evangelist, Steven Pinker. 

All Sport Is Unfair, According to Geneticist. Is That True?

Yesterday a court ruled that the South African running sensation Caster Semenya must take medication to lower her level of testosterone to compete in certain women only running events such as the 400 and 800 meters.

Some are calling the ruling discrimination against a certain athlete or against transgener or intersex athletes.  Some say the ruling is necessary to keep the sport fair.  It’s a worthy debate.  

What I find particularly useful about the debate is what it tells us about how our colleagues in the science community are thinking.

It’s a Gold Rush in Single Cell Genomics, Says Joachim Schultze, U of Bonn

The title says it all here. Herr Professor Schultze directs a major facility that he calls a single cell genomics platform. They have most of the single cell technologies available and partner with labs from all over the world on research.

Advances in single cell technologies are changing basic research and also delivering results for translational work in everything from immunology to obesity.

“Biology will never be the same again,” says Joachim.

Dr. Schultze is also heavily involved in epigenomics. He says that despite the ups and downs in this field, it still holds some exciting promise.

Talking to a leading genomicist in Germany, we ask for an outsider's view on our American approach to genomics.

Who Do You Want to Hear From During the Holidays?

It's a tradition at Mendelspod to bring you unique shows that go off the beaten track at the end of each year. In the past, we've brought you interviews with a science historian, a science comedian, sci-fi writers, and futurists.

We're just planning our lineup for holiday season 2014, and we want your suggestions. On the list so far are a philosopher, a popular sci-fi writer, and the former Deputy Director of the NCI.

Make your suggestions here.

Thank you, Theral & Ayanna

What a Physicist Can Tell Us about Cancer

Guest:

Paul Davies, Principal Investigator, Center for the Convergence of Physical Science and Cancer Biology, ASU Bio and Contact Info

Listen (4:05) The phone call

Listen (3:39) Too focused on a cure

Listen (8:21) What is your theory about cancer?

Listen (4:55) Evolutionary roots of cancer can suggest new therapies

Listen (3:31) Is your message taking root?

Listen (5:21) We must have new ideas

Paul Davies has had a full career as a theoretical physicist. He’s the author of some popular books, most notably, God and the New Physics. In 2007 Paul received a call from someone he’d never heard of before, Anna Barker, then the Deputy Director of the NCI. She wanted to recruit him to the War on Cancer.

“Anna said that she felt that physicists had been very successful in their own sphere. They figured out how the atom works and how the universe works. What about figuring out how cancer works. My reply was that I didn’t know anything about cancer. And she said, 'that’s fine.’”

In today’s interview Paul explains the theory he has developed by following cancer back to its evolutionary roots.

“Cancer is a reversion, or throwback, or rewinding of the evolutionary clock at high speed,” he says.

And therefore, looking at the conditions of life and of the earth at the time cancer developed, Paul argues, can offer new ways of developing treatment. Paul says that we’ve been too focused on “the C word” or a cure. He thinks that rather, we should look at ways to be able to delay cancer.

Is his message taking root? Join us as we probe an entire new way of looking at cancer.

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."

The Story of Aubrey de Grey and How the Study of Aging Became Mainstream

Guest: Aubrey de Grey, CoFounder, CSO, SENS Research Foundation

Bio and Contact Info

Chapters: (Advance the marker)

0:35 First Rejuvenation Biotechnology Conference

4:50 Shackled by “short-termism”

6:00 Aging was not a topic for biologists

11:32 A serious nuisance

17:13 Smoking out the opposition

22:05 Is the body really a machine?

24:52 The community takes a longer view

30:15 What is your challenge today?

Gerontology, or the study of aging, was a “backwater” science when Aubrey de Grey began his career. Today there are well financed companies with the word "longevity" in the name (i.e., Craig Venter’s latest project).

Today we bring you the story of Aubrey de Grey—scientist, author, provocateur--and how he became one of the world’s leading gerontologists. Currently CSO of the SENS Research Foundation, Aubrey tells how he went from working in artificial intelligence to the leader of a new movement in biology. Thrilled that the research community has “come to him,” Aubrey finishes the interview by explaining some of the challenges he faces today.

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."

Why Internet Traffic Directors Should Sit Down with Biologists: George Poste Talks Complex Systems

Guest:

George Poste, Chief Scientist, Complex Adaptive Systems; Regents’ Professor and Del E. Webb Chair in Health Innovation, ASU
Bio and Contact Info

Listen (5:51) A paradigm shift to systems thinking

Listen (4:28) Note to those setting curriculums

Listen (4:37) How do we bring the clinical and research worlds closer together?

Listen (8:53) Simulating complex adaptive systems

Listen (2:46) Science only one of the challenges

Listen (5:13) Why the disparity in reimbursement rates for Rx and Dx?

Listen (7:51) Something special happening at ASU

If you’ve ever heard a talk by today’s guest, George Poste, you’ve no doubt come away scratching your head, overwhelmed by the complexity of human biology. As if the science challenges don’t give one enough of a headache, George continues his carpet bombing approach with all that is wrong with our healthcare ecosystem as well.

Back in the '90s at SmithKline Beecham, George realized that the field was way overly reductionist and that we must do more to look at human biology as a system. He made his way to ASU where he then launched the Complex Adaptive Systems Initiative to bring together biologists, engineers, data scientists, and others.

What is a complex adaptive system and how can simulating it help us decipher human biology?

"A complex adaptive system,” George answers, “is one in which the collective behavior of the component parts cannot be predicted by an analysis of one or more of the these component parts.”

Whether you’re looking at global climate or intracellular wiring, George says it’s all about information transfer in a "network architecture."

The architecture of George’s way of speaking is also complex. With frequent use of the “dash”, George mimics in his own sentence structure the systems he’s describing. His syntax tends to bloom like a natural organism.

An example:

“The question now, then, is how can--by understanding the molecular pathways and coupling of those pathways—because we all tend to think in linear terms (you see the diagrams of a molecular pathway tend to be a series of straight arrows, but in fact what it is is a series of pathways that are interlinked)—because the one other feature of complex adaptive systems is that they have enormous redundancy built into them, so that if one bit goes down --you know it’s the classical model of the internet—if you take out a series of nodes, there are whole ways of distributing traffic around that . . . if you extrapolate that to cancer therapy, yes, you may knock out a particular node with your targeted therapy, but what you need to know now is what are the most likely network couplings of that particular pathway for the compensatory redundancy pathways which will kick in that will confer resistance on a cancer cell.”

Did you get all that? The internet is an interesting comparison. So if we bring together some of those engineers who work on routing internet traffic with some biologists they should be able to have a good time, right?

"Absolutely," George says.

As we conclude the interview, he acknowledges that there is something special going on at ASU, a new paradigm and openness to inter-disciplinary work that is unique. How is it fostered and funded? And what can we expect from this approach?

Fasten your seat belts and hold on for the ride. Suspend your need for short, easy sentences, and rewards await. Presenting systems thinker, George Poste.

Podcast brought to you by: National Biomarker Development Alliance - Collaboratively creating standards for end-to-end systems-based biomarker development—to advance precision medicine

Training the Next Generation of Bioinformaticians: Russ Altman, Stanford

Guest:

Russ Altman, Dept Chair, Bioengineering, Stanford University

Bio and Contact Info

Listen (5:32) A bioinformatician bottleneck?

Listen (4:19) Does the engineer or coder have enough basic biology?

Listen (5:04) Have we been overly reductionist?

Listen (5:16) Beautiful but useless algorithms

Listen (4:13) New breakthroughs in natural language processing

Listen (3:39) A new regulatory science

For our last episode in the series, The Bioinformatician Bottleneck, we turned to someone who has not only done lots of bioinformatics projects (he's been lead investigator for the PharmGKB Knowledgebase) but also one who is training the next generation of bioinformaticians. Russ Altman is Director of the Biomedical Informatics program at Stanford. He's also an entertaining speaker who's comfortable with an enormous range of topics.

It's been some time since we had Russ to the program, so we had some catching up to do. What are his thoughts on the recent philosophy of science topics we've been discussing? Are the new biologists becoming mere technicians? What is meant by open data? Etc. He warns of being too black and white when it comes to reductionism or antireductionism. And agrees that the new biologist needs quite a bit of informatics training. But he's not worried that all bioinformaticians have to be better biologists, saying that there's a whole range of jobs out there.

What's Russ excited about in 2014? The increased ability to do natural language processing, he says.

"We have 25 million published abstracts that are freely available. So that's a lot of text. Increasingly we're having access to the full text and figures. I think we're near the point where we'll have an amazing capability to do very high fidelity interpretation of what's being said in these articles," he says in today's interview.

Russ finishes up by talking about a new West Coast FDA center in which he's involved. The center is focused on a program for a new emerging regulatory science, which he defines as the science needed to make good regulatory decisions.

"This area of regulatory science," he says, "has great opportunity to accelerate drug development and drug discovery."

I saw Russ at Stanford's Big Data conference after our interview and asked him at what age he decided against Hollywood and for going into a life of academia and science.

"Who says I did?" he retorted without hesitation.

Podcast brought to you by: Roswell Park Cancer Insititute, dedicated to understanding, preventing and curing cancer for over 115 years.

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."



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