genomic medicine


Antireductionism and Biology: An Interview with John Dupre, Philosopher of Biology

Guest:

John Dupre, Professor, University of Exeter

Bio and Contact Info

Listen (2:19) Why should scientists think about philosophy?

Listen (8:47) Antireductionism

Listen (6:04) Have molecular biologists suffered from reductionism?

Listen (9:20) Underestimating the problems of biology

Listen (2:01) Are biologists getting the message?

Listen (5:29) Do you think much about the GMO controversy?

When a researcher is doing basic science, what is meant by that? Indeed, what is science? Ernest Rutherford, a British chemist and physicist at the turn of the 20th century remarked, “all science is either physics or stamp collecting." Is this true? Can all science be reduced to physics or does a discipline such as biology need to be studied in its own way? We can ask more specific questions pertaining to life science. What is a genome? And is the tree of life really a tree? And furthermore, are these questions really that interesting?

Here to answer these questions and kick off a new series, "Philosophy of Science," is John Dupre, a philosopher of biology and professor at the University of Exeter in Southern England. John is an antireductionist. In today's interview he argues that molecular biologists have been limited by a system of science inherited from physicists and other scientists that has been overly reductionist. For example, he says that biologists have relied too much on certain models of the cell without remembering that these are abstract models.

"The real nature of the parts is really shaped by the sort of system that it's participating in," he says.

It's true that we've recently seen biologists become more concerned with "systems" and move away from the overly gene-centric view of biology. The power of new tools and cheap computing are now opening up new possibilities to look at the vast network of connections that transpire in biology. However, John questions whether the new systems biologists aren't just more reductionists working at large.

Should scientists be studying philosophy? John answers, " . . . some scientists need to think more about what they're doing than they're often given time to do."

We finish with a question about the public controversy over GMOs.

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 Scientists Should Study Philosophy

Since the first human genome was sequenced, there has been disappointment in and with the life science community over the fact that we haven’t figured out more of the big biology problems.  Cancer, for instance.  Oh, there’s been rapid technological progress.  Illumina announced this year that the human genome that cost $3 billion to sequence originally can now be done for the cost of a root canal, or $1,000.  

So why the disappointment?  Why were scientific expectations so high?  

FDA Crackdown on 23andMe Delays a Revolution in Medicine, Says Medical Geneticist, Gholson Lyon

Guest:

Gholson Lyon, Assist. Professor, Coldspring Harbor

Bio and Contact Info

Listen (3:39) Why are you a fan of 23andMe?

Listen (4:58) What about the quality?

Listen (1:13) PGP limited in participation compared to 23andMe

Listen (11:45) Are you against regulation of CoDx or Rx?

Listen (4:29) Delaying the revolution

Listen (2:25) How do you envision the revolution?

About a week ago we featured a regulatory expert on the program explaining why the FDA's letter telling 23andMe to stop selling their PGS test is a good thing. Today we feature an outspoken fan of the DTC company, Gholson Lyon, medical geneticist at Cold Spring Harbor Laboratory.

Gholson is himself a happy customer of 23andMe, and says he's found the service invaluable. In 2011, Gholson led a team in the identification of a new rare genetic disease, Ogden Syndrome, which caused the death of a four month old Utah boy. At the time, Gholson did genetic tests on the boy's family, but was unable to return their results because the tests were not done in a CLIA laboratory. This led Gholson to become an advocate for doing genetic tests for research in a CLIA facility so that results might be returned to patients. Since the 23andMe service is done in a CLIA approved lab, Gholson found the company an excellent place to do genome wide testing.

But is CLIA regulation--which guarantees analytic validity--good enough for the kind of disease risk reports put out by 23andMe to their more than 500,000 customers? Gholson says yes. And regulating the tests further will cut out an important part of a new revolution in medicine.

Gholson acknowledges the diagnostics industry is attempting to bring up the quality of genetic tests, but says that industry companies are producing one-off tests done without the broader context of the genome. This is why he likes the 23andMe service.

"If you don't sequence or genotype the rest of there person's genome, then you have no knowledge about their ancestry and what population they come from. And so you really cannot predict the expression of a particular mutation in that person," he says in the interview.

Gholson also points out that by being a DTC company, 23andMe has been able to recruit many many more participants and data sets than a non-profit, such as the Personal Genome Project, of which he's also a member.

Just how far does Gholson go in his stance against regulation? And how does he envision this revolution in medicine?

Podcast brought to you by: See your company name here. - Promote your organization by aligning it with today's latest trends.

An Industrial Revolution of Digital Healthcare: Interview with Sultan Meghji

Guest:

Sultan Meghji, Founder, Reformation Medicine

Bio and Contact Info

Listen (4:20) The end of technology as a specialty

Listen (4:12) Sequencing devices still a bottleneck for clinical genomics

Listen (4:39) How to become a bioinformatician in six months

Listen (4:39) Basic scientists vs. technicians

Listen (8:19) Going through the Industrial Revolution of digital health

Listen (5:05) Do you think about bioethics?

Listen (4:49) Yes to regulation, and yes to access for everyone

Data scientists like Sultan Meghji are a highly valued species in today's world. Beginning his career at the National Center for Supercomputing Applications (NCSA) where he worked on original internet technologies, Sultan has used his expertise in several industries, including finance, air transportation, and now biotechnology.

We've had Sultan on for a couple shows already, and his broad experience and far reaching vision made him an obvious choice for our series, The Bioinformatician Bottleneck.

"We could graduate ten times what we're graduating every year for a decade, and I still wouldn't be convinced that we have enough [bioinformaticians]," he says in today's interview.

What to do about it? Sultan has suggestions, one of which is to have a "Khan Academy style program for How to Become a Bioinformatician in 6 Months." What about the years it takes to train great basic scientists in an age when biologists are already being called "mere technicians?" Sultan says technicians can handle much of the work of commercializing research.

Sultan goes on to suggest there are other important bottlenecks, including the sequencing tools space. Does he stop to think about bioethics? And is he for or against FDA regulation of personal genomic information? Today's show is far reaching and centered around Sultan's goal of bringing genomics to the masses.

"It's almost like the Industrial Revolution of digital healthcare," he says. "We're going to call it something else, but . . .at some point my blood, or some part of me, is going to go into a diagnostic black box, and out is going to come some recommendation that a doctor didn't actually look at. And I'm going to take it to the bank."

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

5 Myths of Genomic Medicine

No topic has been more popular at Mendelspod than that of genomic medicine.  This is partly an editorial decision.  But it also comes to us from every direction.  And it is very exciting to hear stories of new knowledge about human biology being translated into precision healthcare.  We have featured the major players in the NGS tools industry and some of the newcomers working on “next next gen”.  We’ve featured data analytics companies and some of the new genomic interpretation and reporting groups who are setting up shop.  We have interviewed professors talking about their latest discover

The Fun Problems: Hank Greely Talks Bioethics

Guest: Hank Greely, Professor of Law, Stanford

Bio and Contact Info

Chapters: (Advance the marker)

0:39 What led you to bioethics?

3:51 Problems that can't have clean answers

7:27 How do you know when you're successful?

11:17 Informed consent, privacy

20:18 What is your definition for ethics?

25:35 Intentional selection/eugenics

30:02 Carefully drawn regulation will help the industry

The advance of biotechnology presents society with some thorny issues. And it's just these problems which Hank Greely, a law professor at Stanford, seeks out. In today's interview, Greely asserts that, as if it wasn't already tough enough pursuing the scientific problems, there are others which are hard in different ways.

"Some of these problems can't have clean answers where principles that we really care about generally are in conflict," he says. "The best you can do is look for less bad compromises."

What are Greely's ideas on incidental or secondary findings? On informed consent and privacy? On eugenics? What is his definition for ethics in general? What for many in the industry is a briar patch, Greely nimbly dances through with aplomb.

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."

Toward a New Paradigm in Regulating Diagnostics: Liz Mansfield, FDA

Guest:

Liz Mansfield, Director of Personalized Medicine, OIVD, FDA

Bio and Contact Info

Listen (5:04) New report on personalized medicine

Listen (1:54) How is the FDA handling CoDx associated with breakthrough therapies?

Listen (1:52) Is the FDA open to seeing the use of POC tests as CoDx?

Listen (5:11) How much authority do you actually have?

Listen (3:10) Regulating whole genome tests

Listen (2:00) Are we headed to a world of CoRx?

Listen (5:35) Moving toward a new paradigm of diagnostics regulation

We're happy to have Liz Mansfield from the FDA to the program as part of our series on CoDx. Liz is Director of Personalized Medicine in the Office of In Vitro Diagnostics.

The symbiotic relationship between business and regulation has been part of our American history from the days of the railroads to the present age of genomic medicine. New technology is constantly presenting difficult questions to the public, opportunities for business, and challenges for regulators. For example, there are a slew of new point-of-care tests coming on the market. How open is the FDA to seeing these tests used as CoDx? And how is the regulatory body preparing to evaluate a test on 3 billion base pairs, a whole human genome. Some wonder if the FDA will lose its relevance in the genomic age when there are vast amounts of data floating around and a whole genome test is easily available.

In today's interview, Mansfield chips away at these questions with confidence and a certain amount of humility in the face of the coming technologies. Unable to say whether any company has yet sought approval on a whole genome test, she does say that the team at FDA is preparing for such time.

"We've seen this coming," she says. "Huge amounts of data can be drawn out of a single sample. And we've had to come up with a new paradigm for regulation where we're not to look at each individual measurement so closely. We're going to have to ask for representative measurements and trust those more than we have in the past."

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

Editor's Note: Our apologies for the static in the interview. Liz was on an internet phone at her office and there is slight interference. Also, since this show was published, the FDA cleared a Dx Assay on Illumina's MiSeq platform (Nov 20, 2013).

Pioneer in the Virtual World Announces Three New Life Science Conferences

My first LinkedIn invite was sent by a young businessman named Greg Cruikshank.  He was listed as the founder of Labroots.

Not knowing a thing at the time about social media, I wanted to understand more about this site that expected me to type in my resume and share it with the whole world.  And who was Greg Cruikshank and Labroots?



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