Curtis's blog

Can the web be used as a tool for scientific discussion? What is preventing scientists from using the web for discussion?

I think it is fair to say that scientists do not effectively use the internet for discussion. I could write a lot about tools that have been available for years and how they have been utilized by other fields for online discussion, but I would prefer to look at the present and future of scientific discussion online. Recently a lot of scientific websites have been launched that are trying to promote scientific discussion. (I'm putting together a list of these sites that I will post soon. Please send me the links to any sites that you use and I will add them.) It is very exciting that so many sites are now available. I’m hoping that this means that there is a lot of interest in these tools and they will be readily adopted by the scientific community. However, I’m concerned that it is going to be a struggle to get them adopted by the majority of the community. Why might this be a struggle? I’m going to try and analyze two examples of these sites and bring up some potential problems to their adoption. The two sites I would like to discuss are this site, JeffsBench.com, and PLoS-ONE. I’m going to bring up more questions than answers. Please add your opinions as well.

Janet D. Stemwedel just posted a couple nice articles about notebooks.

The first article brings up the issue of who owns your notebook. This didn't seem too complicated to me because I was taught that the notebook belongs to the lab/university. However, the article and comments bring up a variety of other possibilities.

The second article is a follow-up that breaks down the functions of a notebook. It's a nice breakdown for anyone who hasn't spent lots of time thinking about how they use their notebook. There's also a very nice quote at the end.

If scientific research aimed primarily to turn the efforts of the scientific community to figuring out how various bits of the world work, free and full communication among the members of that community would be a top priority...and open access to laboratory notebooks would be widely viewed as a good thing.

I commented a few days ago about the new Nature Precedings. There has been quite a bit of commentary in other blogs as well. Most opinions have been quite positive. Also, here's the link to the company that was involved in the design of the site.

For anyone who has not already noticed, Nature just launched a preprint server at Nature Precedings.

Nature Precedings is a place for researchers to share pre-publication research, unpublished manuscripts, presentations, posters, white papers, technical papers, supplementary findings, and other scientific documents.

This site is similar in concept to the very successful physics and mathematics preprint server ArXiv. This is a great development for the biological sciences. Researchers can post pre-publication data/manuscripts and get peer-review from the community. However, one question immediately comes up. If you post a manuscript on Nature Precedings can you later submit it to Nature?

Much of what I write in this blog is about how to modernize the research enterprise. One aspect that I would like to discuss is the concept of the “independent investigator”. I can't deny that the independent investigator has proven to be a very successful way to do research. It is the cornerstone of biomedical research in the United States, and the independent investigator is frequently described as the reason that the United Stated is a worldwide leader in biomedical research. That being said, I believe that our focus on the independent investigator is now hindering our research productivity in two ways: it is creating a tortuous path to being an investigator, and it is hindering collaboration.

One of these days I will put together a list of Web2.0 links for scientists, but in the meantime I would like to let you know about SciTalks. I found this site on the recommendation of some bloggers who also keep up on the science Web2.0, Coturnix and Alex Palazzo.

SciTalks is a website where scientists can upload and post scientific lectures/seminars. To quote the site:

Scitalks is important and needed. In the general trend toward democratizing education, we hope that it can become an important tool for educators, home schoolers and those who are wanting to educate themselves.

I haven't had time to check out much of the content, but it looks like a really great tool. I believe the next step is to get universities to post the videos from their weekly seminar series. That would really help level the playing field across academics.

I came across a very good blog post, here. The author discusses the ethical responsibilities that should go along with research that is funded with taxpayer dollars. I don't think we, as scientists, spend much time thinking about what ethical responsibilities we have to our funders. This is a difficult area to draw a distinct line about what is right and wrong because so much of our enterprise is searching for something unknown, but this article bring up some important questions. When is it unethical to use money from one grant for another project? How much money should be spent to improve efficiency versus finding the cheapest option? How many hours should we be required to work?

The author also responds to comments below the article and brings up more interesting points. Maybe we should spend a little bit more time remembering our responsibility to the taxpayer.

The NY Times just published a good article about the costs of health care. This article brings up a lot of thought questions about how much we are willing to pay for health care. They also discuss some ways to try and quantify these issues.

As a cancer researcher I have been noticing the rising costs of cancer treatments. Very soon we, as a society, will have to decide how much we are willing to spend for end of life care. The latest cancer drugs are getting approved by extending life by as little as a few weeks, but they have price tags in excess of $40,000 per course of treatment. Because we have been willing to pay these prices new drugs will be priced even higher. Cancer is also not the only area where this is happening. Very soon we will have to decide how much we are willing to pay for the last month of life. $100,000? $500,000? $1 million?

I'm not an economist but I don't think that health care functions as a standard free market, therefore it will be difficult to control these prices. As a society we will have to make a decision about how much we can afford to spend on end of life care, then find a way to control the prices without causing financial problems for health care companies. The next 5-10 years should be very interesting for the health care industry.

Graduate education is in need of some improvements. It takes too long to get a PhD, and there is too little mentoring and training during that time. Many students are just thrown in a lab and required to make a "significant" contribution to be able to finish. I've been meaning to write more about this, and eventually I will. But in the mean time the blogger "Adventures in Ethics and Science" has written a few great words about this topic. I put a great a quote from the article below.

Here's an article discussing the idea of open notebooks for the benefit of researchers. There is also a link to someone who is using a wiki for their notebook.

I agree with this author that open notebooks could be very useful for researchers. Too many mistakes are made again and again because no one published that a certain technique doesn't work. The whole scientific community could improve its efficiency if there was more communication between bench researchers.

The wiki example for an open notebook is a good start but I think it will have many problems for broad adoption. I believe that a user-friendly electronic notebook will be necessary before there is broad adoption of open notebooks.

I recently came a across a scientist who is making a bold statement about how to use the internet as a researcher. He is editing parts of his thesis on his blog. Check it out here.

I'd like to talk a bit about communication among student and post-doctoral researchers. The position of a student or post-doc is very isolated. Long hours are spent slaving away at the bench doing experiments, and the peer group is almost entirely made up of other students and post-docs working in the same lab space, or maybe across the hall. Very few interactions take place with researchers outside of ones own university or institute. I find it strange that in the internet age communication among students and post-docs is controlled by geography.

The isolation of students and post-docs is striking and ironic when compared to the connectivity of the PI for whom they work. For a professor to get tenure and promotions they must demonstrate that they are recognized nationally and internationally. The PI is very connected, it's a part of their job. They travel frequently and communicate with peers from throughout the world.

I haven't submitted a paper to Science or Nature recently, but neither journal is accepting submissions in Word 2007 format. It turns out that Word 2007 isn't compatible with their systems, especially equations and Greek letters. This blog has a nice explanation of the situation, with references.

Should you switch to Word 2007? Probably not yet. If Science and Nature aren't ready for it, then the colleague that you send a draft to won't be either. It looks like a .pdf may still be the most universal format for a while.

Anyone who follows the tech sector has probably already read about this, but Steve Job (Apple) and Bill Gates (Microsoft) shared a stage at the recent All Things Digital conference. The interview was hyped as an historic event. I just watched the videos and thoroughly enjoyed them. They are a little long, about 1.5 hrs, but it is interesting to get the perspective from two of the founders of the computer generation who are still leading the way. There is quite a bit of discussion about history as well as innovation. If you are at all interested in the business behind technology it's worth checking out the videos.

Here's a couple links I wanted to pass along. TED is a group whose mission is "Spreading Ideas". They have annual conferences where they invite brilliant people to share their ideas. Many of the talks are freely available online.

Hal recently posted the link to a great talk from Richard Dawkins. Here's another great one to check out from Richard Baraniuk. He's a professor at Rice University who is a founder of Connexions. Connexions is designing free open-source textbooks. Their mission is fantastic and could really change the way we approach education in the U.S. and the rest of the world.

I've been reading various science-related blogs for a while now, and I haven't noticed much discussion about the future of biomedical research. What will the research enterprise look like in the next 100 years? What new technologies will revolutionize research?

Because of this I have decided to start my own blog to discuss the future of biomedical research, with special emphasis on technology. I'm hoping this will foster discussion and novel ideas about how to improve the research enterprise. With this in mind, I would happily welcome guest bloggers to contribute. If you have ideas or opinions that you would like to share, please contact me.

I would like to start with a discussion about the Internet. Since starting the JeffsBench.com website I have become much more aware of how scientists use the Internet and how scientists communicate with each other. The Internet is an incredibly powerful communication tool. However, scientists have not taken advantage of this power to improve communication with each other. Most scientists still communicate by publishing journal articles, giving presentations, and talking face-to-face. For most tenure professors who are able to travel to meetings and talk with their colleagues these antiquated forms of communication are sufficient. However, most students and post-docs are not able to frequently travel to meetings and are hindered by the lack of communication with colleagues. The Internet has the power to revolutionize the way students and post-docs communicate with each other. This communication is most important because the students and post-docs are the ones getting their hands wet doing the research. They are the ones who have the expertise to help each other and the ability to put it into practice.

Larry Page, Founder of Google, gave one of the keynote addresses at the recent AAAS meeting. He brought up the fact that science and technology have driven the economic growth of the country since the industrial revolution. However, scientists are not in positions of influence or power. Scientists are not leaders of politics or business. He says that scientists have a “serious marketing problem”.
The entirety of his talk can be found here.

This brings up the very important question, “What role should scientists play in the economy and politics?” I do not believe that most scientists consider this question very often, which is part of the problem.