A career path in academia should not be seen as one of compromise.
A career path in academia should not be seen as one of compromise.
A recent study shows that the French are, to an alarming degree, against vaccinating. Huh? The ultra secular and increasingly atheist, nuclear power dominated, science loving, Voltaire producing French? It doesn’t make any sense. According to this study a whopping 41% of the French are holding out against vaccines. Compare that to just 14% in the U.S. Which nations are best about their vaccinations? Those in Southeast Asia and Africa. They still remember what it’s like to not like pol
Siddharha Mukherjee won the 2011 Pulitzer Prize in non-fiction for his book, The Emporer of All Maladies. The book has received widespread acclaim among lay audience, physicians, and scientists alike. Last year the book was turned into a special PBS series. But, according to a slew of scientists, we should all be skeptical of his next book scheduled to hit book shelves this month, The Gene, An Intimate History.
It’s now been over ten years since John Ioannidis published his now famous paper, Why Most Published Research Findings Are False. What response has John seen from the scientific community? How has the paper changed his career and role in the scientific community? Join us for a look at science itself.
Actually there was no news this week. It turns out the whole industry took the week off to watch the stunning Ken Burns documentary on cancer.
No, that’s not true. We did find some news.
How about this? The Affordable Care Act turned five this past week. Happy Birthday, ObamaCare! So we thought we’d share some important numbers about the ACA:
11.7 million: the number of Americans who have signed up for 2015 coverage.
46%: the increase in enrollment from 2014 to 2015.
0.3%: the increase in new patient/doctor visits. (Remember, one of the criticisms was that there weren’t enough doctors to pull this off.)
5: the number of Supreme Court Justices it takes to screw it up for the newly insured in the current case against the ACA.
4: this is the number of words that the case is all about.
828: This is the number of pages that Congress used to provide a clear context as to what those four words mean.
A decision on the bill’s fate is expected later this year.
Also later this year, on November 21, it's Know Your Genome Day. It was announced this week that on that day anyone can go to Dallas, Texas, have their whole genome sequenced, and receive a clinical interpretation of it. The event is hosted by Genome Magazine--this is a new magazine out for patients and consumers--and by the sequencing company, Illumina. But the event sponsors haven’t made it clear yet just why you should have your whole genome sequenced.
So we came up with ten reasons of our own why you should have your genome sequenced:
1. So you can find out that you married your first cousin.
2. To prove to your business partner that you’re really only 3% Neanderthal.
3. To find out there’s a strong possibility that you might die at some point in the future.
4. So you'll have definitive proof that your parents really are to blame.
5. To get Angelina Jolie to leave you alone.
6. To prove that you really are an alien.
7. So that the sperm you donated in college can come back and haunt you in the form of your own kid.
8. To be the star of that dinner party next month.
9. To make Craig Venter and Francis Collins even more full of themselves.
10. To ensure the good folks in our industry a job.
Do you have your own reasons? Please share them with us in the comment section below or on Twitter.
Finally, some humbling news for today’s biomedical researchers. CBS News reported on a thousand year old remedy for eye infections that works stunningly well. The remedy was found in a 10th Century medical volume called Bald’s Leechbook. It’s one of the earliest known medical textbooks. This is a true story. The remedy calls for garlic and onion, wine, and bile from a cow’s stomach--wait a minute isn’t this what I have for dinner once a week? Researchers mixed the recipe together, let it sit for nine days and tried it against the antibiotic resistant MRSA bacteria. The ancient remedy wiped out the MRSA, killing 99.9% of the bacterial cells.
The “ancient-biotics” team, as they’re calling themselves, plan to continue researching old texts for cures.
Have a great weekend, everyone.
We were off last week, so there’s plenty to talk about.
The big news has been about human germline modification. Do you know about this? MIT’s Tech Review put out an article early in the month that was kind of an expose suggesting that scientists around the world are beginning to modify the human germline. Now, this is not the germs you pick up in a public restroom. No, we’re talking the reproductive cells, our sperm and eggs. We’ve been changing human genes before, it’s called gene therapy, but never the germline because then the changes get passed on to future generations. So it could be a good thing. But it might be really bad. Someone might make a mistake and create a new disease.
And this danger has the scientific community up in arms. Two groups of scientists took to the prestigious journals last week with papers, one in Science Magazine, the other in Nature.
The Nature paper came out and said flatly: Do not modify the human germline. The Science Magazine paper, however was more . . . you might say optimistic. This paper said let’s be careful. If the authors of the Nature paper were setting themselves up as God writing one of the holy Ten Commandments of Life Science with His finger: Thou Shalt Not Modify the Human Germline, then the authors of the Science paper were playing the loving gentle father who takes his son aside one day, and puts his arm around his shoulder, and says, son, or daughter, there’s something I should tell you about the world. Just because you can fly a plane, doesn’t mean you should fly it into the side of a mountain. And son, or daughter, looks dad back in the eye, and says, but dad, no one would do that.
Speaking of cold mountains in Europe. A treasure trove of genomic data was released out of Iceland this week. Huh? Iceland? Well yeah, after going bankrupt, the country may have just found their next big hidden natural resource: genomic data.
This is a treasure for two reasons: first, the homogenous nature of the population. There’s not much genetic mixing going on . . . because who the hell wants to go and live on Iceland?
And two: in hoping to benefit from this new natural resource, the citizens have been very willing to consent.
So we’re seeing some cool stuff in this week's publication of the data. There's been discovery of new disease causing genes. For example, the MYLF gene was found in only eight people, and all eight have early onset atrial fibrillation. There’s also a rare mutation that influences the thyroid.
Unfortunately, they haven’t found the gene yet that explains why someone would want to live on the North Pole.
Daniel MacArthur--he’s a geneticist at Mass General who’s in charge of the genomic data for the whole world--he says the work is very impressive, but completely unfair. He says deCODE, the company that generated the data, has now managed to get more genetic data than he has, and he’s funded by the Broad! It’s just completely unfair.
No he didn’t say that.
People in cold country are not the only ones being sequenced. A report out of Saudi Arabia this week says that marriages are being called off due to genetic incompatibility! One Saudi prince said that before he takes that fourth wife, he wants to be sure this time that she has no 'dominant' genes.
Speaking of arranged marriages, we attended the Techonomy Bio conference this week. It’s an attempt to bring together tech and bio folks and see what happens. One of the pairings was Marc Benioff, you know the tech billionaire and CEO of Salesforce, interviewing Susan Desmond Hellman, the CEO of the Gates Foundation. Benioff told Sue that he loved what she’s done with her bio, and Sue told Benioff she loves what he’s done with his tech. And then they kissed.
No they didn’t. They’re married--to other people. But wouldn’t it be great to have one of these tech moguls marry a biotechie and then have techbio babies. Benioff said that the place where tech and bio will meet is in digital health. So they would be digital health babies. But not everyone is on board with that. One of the most tweeted lines of the day came from an investor, Greg Simon, who said he wasn’t convinced. He said, “wearing your Fitibit into Dunkin Donuts does not a digital health revolution make.”
And that’s our show for March 27th. Have a great weekend everyone.
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.”
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 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?
Comfort, Nathaniel, PhD, Author, Professor, History of Science, Technology and Medicine, Johns Hopkins UniversityBio 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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Guest: Nathan Pearson, Senior Director of Scientific Engagement & Public Outreach, New York Genome CenterBio 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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