Friday, October 06, 2006

Interview with Jean-Claude Bradley

Podcast

Interview with Jean-Claude Bradley

Woman 1: Hi are you there?

Jean-Claude Bradley: Hey how are you?

Woman 1: I'm good how are you?

Jean-Claude: all right.

Woman 1: Thanks for meeting with us.

Jean-Claude: Yeah, no problem.

Woman 1: Just so that we have the assignment recapped here. The students have looked at your web sites and have looked at information that has been written about you. And now they are going to talk to you and clarify some of the information that they need to gather for a summary they are going to be putting up on a wiki.

Jean-Claude: Sounds good.

Woman 1: Ok? So we're going to start off with Matt. I'm actually going to sit over on the other part of the room because it is their deal from here on out. Ok?

Jean-Claude: all right.

Woman 1: Thanks a lot for doing this for us.

Jean-Claude: No problem.

Woman 1: all right take care. Here's Matt.

Matt: For I guess the serious question. What was your motivation behind making this project like open source science and what was your thinking behind doing it that way?

Jean-Claude: Well if you work in a lab for a couple of years one thing you realize is almost everything that you do doesn't get published because the experiments are either failed or they're sub optimal in some way and they have to be repeated. And they also have to make a story. So even though you may have done a reaction and we do organic chemistry so it's all reactions that actually worked if it doesn't fit into a bigger story that you can write up you really can't publish it. So what we're doing is we're not avoiding publishing normal articles it's just that we're basically putting our lab book on the wiki directly so that people can benefit immediately on a day to day basis.

Matt: Why do you think that open source science is going to be helpful in the future as compared to today's science broadcasting terms.

Jean-Claude: Well again I don't think it's an either or proposition we're not really replacing what people are doing right now. We are just adding to it. We're just making stuff available publicly that is normally not available. And there is a couple of reasons for wanting to do that. One of them obviously is you want people to understand what you're doing, be able to comment on it and you being able to help other people with their experiments. But another thing that I think is going to become important in the next few years is the integration with automation. So that right now my students are publishing experiments so that over time hopefully we will be getting machines to be publishing and reading experiments. So in terms of the....

Woman 1: Jean-Claude, are you there?

Jean-Claude: Yup.

Woman 1: all right we lost you for a minute. I'm not sure what happened but we are back. Can you back up what you were talking about automation?

Jean-Claude: This is the question of what is going to happen the next few years?

Woman 1: Yeah. Can you start back there? Thanks.

Jean-Claude: Okay. Basically what I was saying that the way that we're doing things right now by putting all of our raw experimental data online right now it is basically people communicating with other people but the way that it's set up because you can publish the smallest experimental result that you can make we can envision a pretty easy way to move over towards having automatic systems, machines basically producing information and reading it. And that's just something that is much much more difficult if you think about using standard journal articles which are really written for a human beings. So that is really one of the big things that I see coming in the next few years. The integration of open source science with a lot of automation.

Woman 2: Hey. Currently about how many scientists are in your group at the moment?

Jean-Claude: I have. How many students are in my group? I have right now one graduate student that is working in the lab, Philippe. I have one undergrad James and another undergrad Lynn. And I have Dave who is working on the infromatics part of this. He doesn't do any of the lab work but he helps us create, if you've had a chance to click around our site you will see that there are various information feeds and he helps out with that. With the infromatics part.

Woman 2: Okay. And where exactly does your funding come from?

Jean-Claude: We don't have much funding right now. It is pretty much on a shoestring, that is one of the things that we want to rectify in the coming year. This is basically done on department accounts. Just very very small sources of funding. In chemistry you don't necessarily need as much money as you do for example if you are doing you know, war or any kind of Bio kind of war. So you can get away with a little bit less but yeah we definitely want to get funding in the coming year.

Woman 3: Ok, my question is how do you expect that because you are publishing everything on open source science how do you expect that to affect your funding and if its going to continue with any kind of funding?

Jean-Claude: Publishing open source is actually very, is not becoming expected from the, a lot of the funding agencies like NIH is expecting that if you receive money from them that you will put in open access within six months. Now that is not requiring it to be open source. There is a difference in open source you are making available everything. Every little piece of information you get out of your lab. In open access it's just you're making available normal papers its just that there available for free to the public. So I think that open source follows directly open access. I think that the funding agencies are going to be very receptive because they want what they are funding to be shared. It is tax payers dollars after all.

Woman 4: Ok, well I guess I'm next. I was just wondering if your project is successful how are you going to continue with animal testing and if you are even going to do that where you are now?

Jean-Claude: Well we're not going to be doing, we have an organic chemistry lab so we're not going to be doing any animal testing. We may do a little bit of in vitro testing but most of it going to be done with collaborators. Right now we're making a library of anti-malarial compounds and there are some people once we have the molecules made that are going to test it on red blood cells to see if it has any chance of inhibiting malaria. Those are all things that are going to be done by other people and they will have access to all of our experimental results so it should make collaboration a lot easier than it normally is.

Woman 5: Ok, my question is considering that open source science is a relatively new concept, how optimistic or confident are you in its success. Not just in regards of finding new ways of fighting malaria and other tropical diseases but also its success in gaining support and relevance in the scientific community as a whole.

Jean-Claude: Well it depends what you define as success. I don't think that all scientists have to adopt open source science for it to be successful. In fact it really requires very few people to have an affect I think because a lot of scientists are working on very similar issues, okay? So if you have on group that's working on AIDS research and they make all of there raw experimental data available immediately. That's going to be available before other groups publish using traditional methods. So the fact that that one group is participating in open source science affects a lot of other groups and they have to think about how they are going to be distributing their information because this is a form of publication so somebody can't come six months later and say that they were the first to do it. This will be in the record and they'll have to take that into account. So that's what's really neat about this is that you can have a pretty large impact with relatively few people doing it.

Woman 6: I have a question about blogs. I was wondering which ones you can trust and how do you know that they are reliable and then how do you know that people trust your blog and your information.

Jean-Claude: So a question about trust. I think you gain trust by redundancy. If there are many sources telling you the same thing then it's more likely to be true. You should never really trust any single source. Even a source that has been reliable in the past. People can make mistakes we've had that happen in our own group we'd been trying to do this reaction and we were using, ok so a question about trust. The basic thing about trust has to do with redundancy. If you have multiple sources telling you the same thing the odds of it being true are far greater. So even sources that are usually reliable are not always going to be because people make mistakes so you have to make sure you get as many possible different view points as you can. So you know, you don't follow necessarily just one blog, you have a dozen blogs that you listen to what everybody has to say about certain things and you can see if there are any out lyers if people think differently. And the other point is that a good blog will be linking to its sources. So if you write something as an opinion obviously there is no source for that but anything that you state as a fact has to be linked to something that will back it up. So that's really how you can tell. There isn't any single source that you can count on.

Woman 1: Why should people trust your blogs.

Jean-Claude: They shouldn't. They should follow everything that I say and see what my sources are and they should make up their own minds about if what I'm saying is making sense. You definitely shouldn't trust it just because I said it.

Woman 7: all right we're going to be going backwards a little bit because before you were talking about having little or no funding for the project so what kind of people can you expect outside of your groups who contribute to this project if there is going to be no money in it for factual research?

Jean-Claude: Well people that are doing different things will have their own funding that has really nothing to do with what we are doing necessarily. We're applying for funds to make chemicals. That's what we do in the lab. But if people are doing testing for example on malaria, they have their own funding and they have you know the info structure that's needed to do that part. So the situation about the funding is really not any different than any other kind of collaboration.

Man 3: all right my question is through open source science have you received any support from any organizations or met up against any resistance from anyone that is against open source science.

Jean-Claude: Yeah there certainly is a lot of resistance. In fact you can see some of that by some of the comments on my blog or with other people that are saying similar things that I am saying. You can see where some of the resistance is. But you know people who are resistant to this kind of procedure are not going to be doing it. So it's kind of irrelevant, we are really interested in interacting with people who understand why we are doing open source science and want to participate in it. Was there a second part to your question?

Man 3: Have you reviewed any support?

Jean-Claude: Yeah, there are people who have been coming in and commenting on some of our experiments.

Woman 1: You were talking about chemist without boarders when we lost your audio so can you talk about a synaptic leap and chemists without boarders?

Jean-Claude: Well a synaptic leap is an organization that is a non profit that is trying to coordinate open source science mainly linking biology, a lot of these people are biology links because that has some useful consequences to treat diseases and things like that. So these are just different groups that have their own software and their own experience and some people are doing science and other people are trying to coordinate and by working together I think that your going to get a lot of proper's out of it.

Woman 8: Going along with resistance and support do you personally find anything negative about using open source science on blogs, wikis etc.

Jean-Claude: Well I don't know that its so much negative I mean there are always challenges for example using a wiki. It's a little bit hard to tell if people are citing you especially if they're not using a wiki. The situation is a lot better with blogs but those are all things that we can deal with as long as we stick to the fundamental philosophy of making everything available as soon as possible. But so far there really hasn't been anything that has led me to question what it is that we're doing.

Woman 9: I have a question about challenges. What would you say was your biggest challenge with making this open source.

Jean-Claude: What was the biggest challenge?

Woman 9: Yeah.

Jean-Claude: I guess maybe convincing my students that is was a good thing to do. And that just took time. It took a while to figure out an appropriate format to work with. And to convince them to put their data in on the same day that they do it. If you keep a lab book sometimes you can wait a while before you put stuff in but if you're making this available ultimately you do have to input your data fairly frequently. We'd like it to be there the same day so people can comment. So that's probably been a challenge that I think has been overcome.

Woman 10: We also have a question about the patenting process and because you're using open source science has that caused more challenges in making your information more credible and making sure that you get the credit and your students get the credit for what happens and what goes on?

Jean-Claude: From the patent point of view, as soon as you disclose what you are doing you are not eligible to international patents. You still have a year in the United States to get just a US patent but that's not something that we have any intention of doing with UsefulChem. So the patent issue is a non-issue. As far as the credibility - again - if you are a chemist and you are looking to make a molecule and you find a procedure and it's explained through appropriate sources and it has the appropriate evidence to prove that you've done what you say you've done I think that any chemist would use it, because it's fairly easy to tell if something is competent or not just by reading it, at least in organic chemistry. I can't speak for all the disciplines but in organic chemistry it's pretty easy to tell if something is real or not.

Woman 1: And one last question.

Man 2: We were just kind of wondering - we've already mentioned critics of your open-source science policy. But what about critics of your chemistry work with malaria and about how you post that on open-source sites, like your blog? Have you had any criticism about that, like science writers or anything?

Jean-Claude: Well, science writers have been very kind. If you take a look at our blog, David Bradley, who is not related to me, has written some very nice things about UsefulChem and what it can do for malaria and that kind of diseases. This I can understand as malaria is not a very lucrative disease for drug companies because the people who are sick don't have a lot of money. So you are not going to get much of complaint from anyone who has any economic stake in malaria. If we are looking at other things they might be a little more resistance just from the science end, but so far it has been pretty positive. We'll see what happens down the road!

Man 2: Thank you!

Woman 1: All right, you are getting me back again. I'm going to try to facilitate a discussion. All right?

Jean-Claude Bradley: OK.

Woman 1: Let's actually a good segue way because the project that's been run over the course of this semester is.. they are going to be researching other factors that involve the treatment of malaria, AIDS or arsenic in drinking water. So, how do you feel from a science perspective, what are the scientific challenges to addressing any one of those diseases right now? What are the scientific challenges in the global community?

Jean-Claude Bradley: You mean in terms of the chemistry?

Woman 2: Yes, in terms of the chemistry and the science. Is it just that nobody is doing the research because there is no money in it, or are there other projects that are more important to the US government to fund?

Jean-Claude Bradley: If I understand your question correctly, the scientific problems, especially the chemistry ones is something that we discuss on the blog and try to get as much feedback from scientists as possible so that we can address them. Right now, we are making molecules based on the fact that there is an expectation that there could be new anti-malarial agents that could be useful. We are making this specific molecules because we receive them from another organization, called Find-a-drug that computed that these molecules have a good chance of being active, so that's scientifically why we are working on that. If somebody were to say they have already made all these compounds and tested them that would not be a problem whatsoever; we would simply just move on to the next problem. So we are working on where we think some chemistry needs to happen. The automatic can't tell you. That's why it's important for you guys to interview biologists and preferably people out in the field who are trying to deliver these medicines because nobody has the complete picture. I can tell you from the chemistry end but what we are doing here is a little bit larger than making anti-malarials. It really doesn't matter that much that we are making anti-malarials; the point is that we are demonstrating that it's possible to do open-source science using free tools for the most part and we are developing an infrastructure that hopefully can be replicated very easily for other people and other projects. So I'm not that concerned about the chemistry at this point because we can change that pretty quickly if we learn new information. It's really a scaleable system that we want to develop.

Woman 4: How has DDT been used? Can you talk a little bit about what DDT is for this non-chemist population and how it has been used and about the pros and cons of its use in treating malaria?

Jean-Claude Bradley: I'm not an expert on DDT, by any means. But I think it's the compound that is credited for saving the most human lives ever because the problems with malaria have been so extensive in human history and DDT basically acts by inhibiting the mosquitoes that carry it, so is has nothing really to do with malaria itself. It has to do with the mosquito carrier. Now, we talked about this before, about DDT, and depending on where you come from, there may be some non-scientists that are writing articles saying that it's good or it's bad, but it's going to be important if some of these things are going to be looking at DDT to look at the source of information they have used to support their claims because you will find people that have very different opinions. I'll tell you my opinion, which is based on - I haven't done any research on it, it's just that in chemical circles something that we sort of know, but definitively would try to find out to get some objective measurements. Because there are people that believe now that by banning DDT that's actually killing a lot of people that wouldn't otherwise die. So I think you will have to look for solid resources to figure that one out.

Man 2: My question is if we were to summarize your work in about two paragraphs, what would you think are the main points that you want to get across about OSS?

Jean-Claude Bradley: I'm not going to give you your paragraphs.


[laughter]

Woman 1: Can't you do that?

Jean-Claude Bradley: I said I'm not going to write your paragraphs.

Woman 2: Aah, he's not going to write them.

Man 2: How about the main points, maybe, please?

Jean-Claude Bradley: I think a really important point is that we now have tools to do open source science that are free and hosted that are easy to use and that's really the turning point right now of why I think that it's going to be adopted in the larger area.

Woman 1: What is your background? What did you do before you did this?

Jean-Claude: I got my PhD in synthetic organic chemistry at University of Ottawa and then I did two postdocs. I did one at Duke working on DNA chips and one in Paris working on gene therapy and I've been at Drexel for about ten years now working in nanotechnology and this is actually a fairly recent project this useful-chem. It just actually started last summer.

Woman 2: How do you see your work as it works through our classes and then ends up in Kabbalah, Sierra Leone? How do you see that tied to what your students do in the lab?

Jean-Claude: What I would like to see is everybody feeling really comfortable asking questions and just talking about what it is that we're doing because we are the chemists and we can definitely address the chemical questions but we don't have time to be reading about all the aspects of malaria and they're all important to actually getting it implemented and helping people. So some of what can be done now, maybe there is a chemical solution that doesn't have to do with making a new anti-malaria compound. Maybe there is something that people are not doing because they don't know chemistry and that we could help, but we can only help if we understand that that there is a problem and that can only happen if everybody talks about the details of their problems. So that's what I really look forward to with all the students there looking a different angle of this problem that will recognize that we can do something that other people didn't recognize because they don't know enough chemistry.

Man 1: When you started the useful-chem program, what spurred you in the first place to start research in malaria and research this as actively as you have?

Jean-Claude: Well if you look at our blog, the useful-chem blog itself, you'll see that in the very first couple of posts how the project started. It didn't start off with malaria at all. It started off with a question of what would be one of the most pressing, urgent needs that is currently out there that can be addressed using chemistry and you'll see that some of the answers that came up, a couple of them had to do with malaria, another had to do with AIDS, another was the arsenic issue that came up subsequently to that I think and malaria just kept popping up because it happens to be that kind of a problem, where there's still so many people that are effected with it that still is a very large problem around the world. So it really had to do with a desire to do something that could be really useful in the short term not do research that may useful in ten or twenty years but to do something that has a realistic chance of making a difference in the reasonable short term.

Woman 3: So do you have any words of wisdom as students make their way through this semester of researching the ancillary topics for the diseases or are there other things that you think they should keep in mind as they're doing that research?

Jean-Claude: Well you know, I would say that make sure that you cite all of the places from which you are getting information so that anybody can basically see whether or not it can be trusted or what the probability is that it's correct and to really free to talk to us. I know that Khallid and James are very anxious to interact with you guys, to talk with you and give you feedback on your things and don't hesitate to contact us.

Woman 4: Do you have any questions for us?

Jean-Claude: Has it been difficult what you guys have been doing so far or is this a pretty easy project?

Woman 4: We have one person who is saying it's time consuming. What else?

Woman 5: It's different than any English class we've ever had. Like I've never researched this hard or talked or actually ever interviewed with anyone for research for a paper.

Woman 4: So it's interesting.

Woman 6: It's kind of hard because it is a lot of science and you have to like, I don't know, dig through the science to find the English that we need to create the paper, but other than that, it's not so bad.

Man 2: I mean all the stuff we're saying is pretty true. The only real thing that I think is different, I mean, this is a completely different teaching style than in high school, because a lot of us our freshmen. We've gone from doing all this literature research read a book, write a paper on the book, review the book lather, rinse, repeat the whole semester. [laughter] And then jumping into this where we actually - she's teaching us how to apply this stuff in real life instead of just saying ok this English is only good for literature, she's saying that English no matter what you write is still applicable even if it comes to science, just helping people into charity. That's the word I knew it begin with a C. Just all kinds of stuff. English stretches beyond our limits as students. It stretches into a realm where all of us coexist as race and we're just trying to define that language.

Jean-Claude: So you guys are more used to single source kind of research? Is that what I'm hearing?


[sounds of agreements]

Woman 7: I think we all prefer this better even though it takes a little more time.

Woman 4: The technology, it too, has been a challenge. Some of our students are very proficient and some of our students are still trying to figure out the on button, but we're getting it. What do you predict as far as technology ten years in the college? At the college level? Do you think that blogs, wikis are going to be the standard?

Jean-Claude: You mean in terms of doing classes? Yeah, I don't know. I don't know what's going to come along.

Woman 4: We watched a clip last week about the use of technology and they predict that the technology we use today, which is wikis and blogs, that will be outdated by the time that they are juniors in college. Do you think that's true?

Jean-Claude: I think that you can't predict the future.

Man 3: Good answer.

Jean-Claude: You have to use the best tools that you have available.

Woman 4: They're loving you now. Their assignment for today was to prove parts of a predictions clip. All right, anybody else have any questions? This is your big chance to ask him. You can always email him if you think of something when you're doing your notes. We're going to be putting this up onto their class blog which is Nerdicity and I'll send you a link over.

Jean-Claude: Okay.

Woman 4: Thank you so very much for doing this with us.

Jean-Claude: Hey, it's been fun.

Woman 4: All right take care.



Transcription by CastingWords

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