history of science


Gene & Tonic: Disruption in Sequencing, Scientist Politicians, Some Cool Synbio

Join Theral for a quick wrap-up of the week's biotech news:

The biggest news this week has been the flow of stories coming from last week’s AGBT conference held in Florida. This is the annual all out party for the all out darling of our industry, the sequencing space. Like a debutante ball, it’s where anybody who’s anybody comes out and does their curtsy to society.

This year’s debut favorite was no doubt 10X Genomics. It turns out they can almost turn water into wine. Well, almost. What they do is turn short reads into long reads, piggybacking on Illumina’s technology. Have you been following our series on the rise of long read sequencing? It turns out that scientists just decided that they want to actually see the whole genome. Hence the use of long reads.

Illumina has reigned king in sequencing for several years, but their platform is based on short reads. We heard from one of our guests on the program this week that Illumina’s dominance is vulnerable. David Smith at the Mayo Clinic says their platform is about maxed out. Instead he looks for some big stuff from BGI.

Huh? BGI? Isn’t that just Illumina’s platform? Well no. He’s talking about Complete Genomics. Remember them? They were at one time a debut darling then got sold to BGI for a song and a dance. (Every debut is followed by a depression, isn’t it?) But we heard this week that Complete’s still got some juice. David Smith says they’ll be coming out with an assembled human genome for $1,000 come June. That’s an assembled genome.

But this is unofficial. BGI/Complete were not saying anything at AGBT. According to all accounts, the biggest presence at the conference was PacBio. They held this workshop with an incredible lineup of scientific superstars. Temporarily the IQ in the state of Florida rose to the national average.

Craig Venter was there. We heard PacBio flew him in on a private jet with a private security detail.

I mean. Wow. Treatment like the President of the United States.

In fact, I’m going to ask why doesn’t Venter just run for president in 2016? Right, why can’t we have a scientist president? Scientists and technologists are basically in control of the planet anyway. Why not get some on Capitol Hill and recognize them for who they already are.

We found out this week that Harold Varmus is stepping down from the NCI. Why doesn’t he run for a higher office? Why do scientists give up at that level?

Did you see the Science Magazine article this week about the one lone physicist in congress. Bill Foster of Illinois. The news was that he is joining the science committee in the House of Representatives. Wait--there is a scientist committee in congress? So who else is on it then? The lone physicist congressman was quoted in the article:

“There are good conversations to be had on both sides of the aisle. But it’s important that those be fact-based.”

D’ya think?

We asked George Church of Harvard why he doesn’t run for the senate. He looks very senatorial, right? He wrote back and said that if he wanted to hang out with a bunch of Neanderthals, he prefer they be of his own make.

No, he didn’t really say that. We made that up.

But speaking of synthetic biology projects, one of our guests this week is making color changing flowers. You can see it on video. These flowers literally change to another color while you’re watching them. Isn’t it just amazing what mankind can do when we get bored? Next thing you know, we’ll be bringing back smallpox, polio and the measles to the U.S. Because living in the age of vaccines just hasn’t been fun enough.

And that’s Gene & Tonic for Friday March 6th. Stay tuned next week when we’ll continue our conversation on long reads with a researcher from the Ontario Institute for Cancer Research. We’ll also be talking about arrays in this age of sequencing in an exclusive interview with the CEO of Affymetrix, Frank Witney.

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David Schwartz on the Future of Sequencing

David Schwartz was focused on long read sequencing and the structural variations of the genome—the big picture—long before the current trend. His lab at the University of Wisconsin at Madison developed optical mapping and posted the first optical map of the human genome several years ago. And last year, they published the first optical map of a cancer genome.

David is the first guest in our second series to focus on long read sequencing. He was interested in structural variation even before the first human genome was published, an endeavor which he says changed the way we do biology.

How does he see sequencing developing?

“Sequencing will be electronic,” he says. “Ultimately we’ll use synthetic pores. Some sort of non-biomolecule based approach will reign supreme.”

With his illustrative history in genetics, we can’t help but ask David a couple of our favorite questions here at Mendelspod--such as, how much wet lab vs. dry lab for the new biologist?

A Dangerous Book? Science Historian Nathaniel Comfort Discusses “A Troublesome Inheritance”

Guest:

Comfort, Nathaniel, PhD, Author, Professor, History of Science, Technology and Medicine, Johns Hopkins University

Bio and Contact Info

Listen (4:20) Debate about race and genetics is really about social justice

Listen (2:32) The radical middle

Listen (4:45) How to define race when genetic variation is continuum

Listen (6:03) As a society are we trusting science more as the ultimate source of knowledge?

Listen (6:04) Does Wade's book help free scientists and clinicians?

Listen (2:04) On blogging

Is race biological, or is it a cultural construct?

This question lies at the heart of a debate sparked by this year’s publication of “A Troublesome Inheritance: Genes, Race, and Human History.” Writing that race is biological, former New York Times science journalist, Nicholas Wade, ignited a furor in the life science community, with many scientists denouncing the book and the misrepresentation of their research. Science writer, David Dobbs, called it a “dangerous book.”

Joining us today to work through some of the tough questions in this debate is Nathaniel Comfort, a science historian at Johns Hopkins University. Comfort describes his position in the debate as the “radical middle”, accepting some of Wade’s arguments but insisting that science is always in a context, that it’s always political.

“The debate over race and genetics is really about social justice,” Comfort says in today’s show.

Comfort argues that Wade is not honest about the book’s agenda and uses science as a proxy argument for his own preconceptions. Comfort warns that genetic explanations, such as the one Wade makes for race, usually tend to reinforce the status quo.

So what about using race as phenotype for treating various diseases? For example, some racial groups are more likely to get certain diseases than other groups. Working at a major medical research facility, Comfort has the opportunity to talk to clinicians on a regular basis about whether, in today’s world of personalized medicine, race is still relevant as a phenotypic marker.

For more, visit Comfort’s blog on the topic.

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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.

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Spreading "Particle Fever"

On July 4 of 2012, we all watched with suspense for the outcome of one of the biggest and most expensive experiments in the history of science: the discovery of the Higgs Boson at the Large Hadron Collider at CERN in Switzerland. What many of us were not aware of at the time was that an entire generation of physicists were hanging in there to see whether their careers had been in vain.

The Real Deal: Sam Colella, Versant Ventures

Guest: Sam Colella, Co-Founder, Versant Ventures

Bio and Contact Info

Chapters: (Advance the marker)

1:05 Where did it all begin for you?

4:23 What's in your magic sauce?

9:50 How did you get involved with Fluidigm?

13:30 "Build to buy" model

17:23 Is there a way to match the VC model to the long biotech cycle times?

19:59 "We're the real deal"

Today we're excited to welcome a special guest to the program for a rare and exclusive interview. Sam Colella is being honored this year at the BayBio Pantheon Awards ceremony in December for a lifetime achievement award. We sat down with him in his office at 3000 Sand Hill Rd.

Encouraged into venture capital by Tom Perkins (indeed, Colella replaced Perkins at Spectra Physics as CEO when Perkins headed to work for Hewlitt and Packard), Colella has become a legendary figure in our industry for picking winners. Talking first about his early years in the industry, Sam goes on to discuss his magic sauce for picking companies that go on to achieve success. He's a co-founder of Versant Ventures where he and his partners have come up with an innovative "build to buy" model of funding.

Sam sits on several boards of directors including Fluidigm, Veracyte, and Genomic Health. He tells how he came to invest in Fluidigm, a company who has seen their stock shoot up this past quarter. Speaking with a poker face and steely blue eyes, Colella says he still falls in love with deals and is motivated by the huge medical needs that are still unmet.

"This isn't a fad," he says. "We're not a social media. We're the real deal."

Sponsor: Today’s show is brought to you by the 10th Annual BayBio Pantheon Ceremony, presenting the 2013 DiNA Awards on December 5 in San Francisco. The Pantheon Awards Ceremony is a celebration of the contributions and achievements of the Bay Area, a moment to pause and reflect on the industry’s legacy over three decades.

Nola Masterson: "Guru of Biotech"

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."

Guest: Nola Masterson, Founder, Science Futures

Bio and Contact Info

Chapters: (Advance the marker)

0:59 A career with many "firsts"

5:00 Some very creative financing models in the early days

9:11 Going for the "big one" and the founding of Sequenom

17:08 What excites you about the industry today?

20:10 Bioethics and the Dalai Lama

23:47 The open science conflict

26:16 Bullish about the IT industry bringing biotech into the 21st Century

28:25 A childhood dream come true

Today's show will give you some of everything. Our guest is Nola Masterson. She was the first biotech analyst on Wall Street, she's a founder of Sequenom, and she blazed trails in venture capital. Ever on the front lines, she reminisces about earlier times, but also weighs in on issues of today. What perspective has her career given her on bioethics? What does she think of the strong movement toward "open science." Never at a loss, Nola Masterson has been called "the guru of biotech."

Documenting the History of Biotech and its Relevance: Mark Jones, Life Sciences Foundation

Podcast brought to you by: Chempetitive Group - Who for more than a decade has helped science-based companies build and execute innovative marketing campaigns. "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

Guests:

Mark Jones, Director of Research, Life Sciences Foundation Bio and Contact Info

Listen (7:14) Why is recording biotech history important?

Listen (11:48) Biotech history, such as that of recombinant DNA, can shed light on current ethical debates

Listen (6:04) A history of tech transfers

Listen (4:12) Can history provide insight to current gene patent case?

Biotech has been around for a while now. Some of the original pioneers of the field are getting along in years or have passed. To record and preserve the history of biotech, the Life Sciences Foundation has been established. Their website is becoming a rich, one stop source, to trace back the big achievements of the last 40-50 years with lots of videos and articles on the pioneers and major players in our field. In addition to the website, the foundation puts out a regular magazine and sponsors events such as the talk and reception at UCSF recently entitled the Centaur and the Whale and the emergence of biotech, an event devoted to remembering two early biotech companies, Chiron and Cetus.

Mark Jones is the director of research at the Life Sciences Foundation and has recently been going around the country taking down oral histories. In today's show he talks about what the history of the industry can tell us about issues of today.

Eugenics Not Just a Thing of the Past: Nathaniel Comfort and "The Science of Human Perfection"

Podcast brought to you by: Assay Depot - the world's largest cloud-based Research Exchange for pharmaceutical research services.

Guest:

Nathaniel Comfort, Science Historian, Author Bio and Contact Info

Listen (3:49) A different viewpoint on genetics

Listen (7:45) Garrod and Galton, two different early visions for genetics

Listen (6:12) An uneasy relationship between medicine and eugenics

Listen (5:27) State control vs individual control

Listen (5:56) Is yours a provocative message?

Listen (1:35) Did early geneticists foresee genetics becoming such big business?

Listen (4:09) Genetics and the 2012 election

Listen (3:34) Genetics not the only tool

Most of us think of the eugenics movement as a blemish on American history. How could they think like that, we ask. But in his latest book, The Science of Human Perfection: How Genes Became the Heart of American Medicine, science historian Nathaniel Comfort talks about the ongoing current of eugenics throughout the last hundred years and more. "Genetics became medical, and medicine became genetic through eugenics," Comfort says recounting the themes of his book. Anyone who makes their livelihood in genetics will find Comfort's meticulous and well researched argument compelling. Comfort says that there are some using the word eugenics again in a positive light, and he says it's his job as historian to record it. Always the skeptic--see his blog at genotopia.scienceblog.com --Comfort urges us at the end of the book to remember that genetics is a powerful tool, but there are other tools as well in the kit.

Nathaniel also weighs in on the presidential election and Prop 37 in California requiring labeling of GMOs.



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