Is it becoming dangerous to NOT blog?

Guest Blogger Jean-Claude Bradley

Jean-Claude Bradley is an Associate Professor of Chemistry and E-Learning Coordinator for the College of Arts and Sciences at Drexel University. Jean-Claude writes for several blogs including  Useful Chemistry and Drexel CoAS E-Learning. He is  Open Science advocate and coordinate the Open Notebook Science Challenge established to collect and share non-aqueous solubility measurements. You can find him online at Drexel University, Blogger and NextBio.

It wasn’t so long ago that the big discussion about scientists blogging was whether or not it would hurt your career. Granted, some the examples used involved personal content that would have been problematic on any platform. Still, many scientists chose to blog anonymously, even for the most uncontroversial scientific musings.

Recently I have noticed a change in the tone. The question doesn’t seem to be “Is blogging bad?” anymore but rather “Is blogging a waste of time?”. Often this involves the rather ironic situation of naysayers using a blog to express their opinion that blogging is a waste of time. There are many examples of this but a particularly controversial discussion took place on Nature Network recently.

And then yesterday I came across a particularly good example of why blogging is not a waste of effort. I was checking my Sitemeter referring links and found a few from Nature Chemistry. Unfortunately the article is toll access but I was able to get my hands on a copy. It was Michelle Francl’s article about the history of the periodic table and all the creative ways that people have used to demonstrate order in the elements.

Michelle used my blog post about Andrew Lang’s 3D representation of the periodic table in Second Life as a reference for this type of table. This is a very short (4 sentence) post but it has the key elements of a good reference – answers to who? what? and where?. That is enough information to visit the exhibit and contact the creator for a copy.

Now Andy and I are witing this up as part of a larger article on chemistry in Second Life (see draft here). If that article had been completed and published, it is likely that Michelle would have used that as a primary reference. But it can take a really long time for the journal publication process to reach completion. If I had not blogged this I am sure Michelle could have adapted her article and found another similar reference.

The point is that mainstream scholarship (Nature Chemistry is certainly an example of that) is able and willing to use Web2.0 references when these are the most appropriate.

There are very few examples of mindblowingly original ideas. People working in related areas tend to come up with similar ideas. In a world where any of your competitors can blog their ideas as soon as they think of them, hoarding ideas might be the more dangerous choice.

It doesn’t matter what you think about the professional status of blogs. It doesn’t matter most scientists don’t blog. The only thing that matters is that at least one of your competitors is willing to blog their research and that the traditional journals in your field are willing to accept blog posts (and other Web2.0 publication formats) as valid references.

Happy Birthday Rita

 

 

Today Rita Levi-Montalcini becomes the first Nobel Laureate to reach 100 years of age.  Her scientific career is a source of inspiration for many people, scientist and non-scientists alike. 

Dr. Rita Levi-Montalcini is a fighter.  As a young woman she fought against the Victorian gender stereotypes dictating that women were only suited for domestic roles and should not be permitted to participate in higher education. After graduating from medical school in Turin, she fought against the anti-Semitic laws that barred her from working in a university or a public institution. Working in a makeshift laboratory in her home she did experiments and actively published until Hitler invaded Italy. 

Though the end of the war brought stability and a research position at a US university, Levi-Montalcini still had battles in ahead of her.  When her experiments demonstrated the existence of nerve growth factor (NGF), the scientific community was highly skeptical and did not accept her conclusions for over a decade. She was persistent and worked for many years to convince the scientific establishment of the existence and action of NGF. This work earned her the 1986 Nobel Prize in Medicine and transformed our understanding of biology. 

Even after receiving the Nobel Prize, Levi-Montalcini did not rest.  In 1992, she founded the Fondazione Rita Levi-Montalcini Onlus, to support education for African women.  Since 2001, she has been a senator in the Italian senate where she fights for the improvement of Italian science.   

As Rita Levi-Montalcini turns 100 she continues to inspire – she works every day in the lab and in the offices of her educational foundation, she attends every parlimentary vote in Italian senate, and just last week she declared “At 100, I have a mind that is superior, thanks to experience, than when I was 20.” 

My heartfelt wishes for a very happy birthday to an inspirational woman and an inspirational scientist.

 

Sketch reprinted with the kind permission of the artist Miguel Herranz.  To see the sketch in its original context, click on the image above or this link. 

Is the Human Ego good for Science?

Guest Blogger Jean-Claude Bradley

Jean-Claude Bradley is an Associate Professor of Chemistry and E-Learning Coordinator for the College of Arts and Sciences at Drexel University. Jean-Claude writes for several blogs including Useful Chemistry and Drexel CoAS E-Learning. He is Open Science advocate and coordinates the Open Notebook Science Challenge established to collect and share non-aqueous solubility measurements. You can find him online at Drexel University, Blogger and NextBio.

I have just finished reading the fascinating book “The Emperor of Scent” by Chandler Burr. It starts off describing the world of perfume with a focus on Luca Turin, a man with the unusual talent of being able to review perfumes with great eloquence, conjuring up beautiful metaphors of experiencing their scent.

The book then takes an unexpected turn into the description of Turin’s theory about the mechanism of olfaction. There is some truly interesting science there, such as Turin’s discovery of a binding site for NADPH and another for zinc on a protein thought to mediate smell. This supports his hypothesis that the protein functions as an electron tunneling spectroscope detecting differences in vibrational modes. Further evidence is provided by comparing the different smells of deuterated molecules like acetophenone and the similarity of the stench of boranes with thiols, which share similar IR spectral bands. This idea is at odds with the conventional view that molecular shape is responsible for the activity of odorants. (For a summary of Turin’s theory I would suggest watching his recent TED talk “The Science of Scent” and his Wikipedia entry).

This is all very interesting stuff and would have made for a good read but what makes this a truly fascinating story is that Burr spends the rest of the book detailing the way the scientific community responded to his findings. As Turin waits a year to finally get rejected by Nature, the reviews, rebuttals and other communications with the editor are examined to expose the intense emotional components that can arise from the peer review process. The author even follows Turin to conferences and reports in detail how various members of the audience react and comment during his talk and at informal meetings over lunch.

People who are not in science may find this disturbing. All too often science operates like the judicial system, where winning can take on more importance than finding the truth.

The fundamental problem is conflict of interest. If you have patents or run a company it may not be in your financial best interest to look under every rock, except as required by law. If you have built your career on a certain theory it may not be in your professional best interest to open every can of worms. Burr actually wrote a chapter explaining why the book appeared to be so one sided: it was hard to get detailed comments from Turin’s detractors because, although they disagreed with his theory, they had not read his paper and did not have time to do so.

But Turin was really not that different in his conflict of interest related to ego. There are descriptions of him reading articles in a state of dread and delaying experiments for fear that he might be proved wrong. Still, I like to root for the underdog, so the book did have me hoping that he would be vindicated.

If most scientists are motivated by ego, is it possible to do egoless science – and what would that look like? For starters I think that keeping a true Open Notebook (All Content shared Immediately) does a lot to keep your ego in check. If you report on what you find, when you find it, you don’t have time to succumb to the temptation to cherry pick results and embellish the story of what happened.

Another trend that I think will emerge in the next few years and will change the way science gets done is machine-driven science. It will probably prove too much trouble to take into account a researcher’s ego and career objectives when coding for AI to plan and analyze experiments to solve problems. Just like Turin, a lot of researchers (including myself, especially early in my career) procrastinate doing certain experiments for fear of not liking the outcome. The key again here is making the experimental logs of those machines public in real time.

When I refer to egoless science, I am speaking at the level of experimentation. I am driven by ego, like everyone else. But I have found it more useful to place its focus at the meta level. Instead of taking pride in appearing to run a perfect operation – and of getting high yields for our reactions – I am most pleased when the members of my group do their best to record exactly what happened, as they do science.

And being a strong proponent of Open Science, my ego is linked to those activities. Even though it is somewhat ironic, I do enjoy competing at being as openly collaborative as I can.

FriendFeed and Twitter

Guest Blogger Hope Leman

Hope Leman is a library technical specialist, co-founder of Next Generation Science, a staff writer at AltSearchEngines and the Web administrator of ScanGrants. You can find her on NextBio, FriendFeed and Twitter.

It is 5:10 a.m. I am working on a netbook in a hotel room in San Francisco. I am attending the Web 2.0 Expo and covering it for the blog AltSearchEngines. While I am attending that event, I have been invited to a dinner sponsored by Microsoft Live Search. Yesterday I attended sessions about Web site monitoring and about how to build online social communities.

All of these activities tie into the world of Science 2.0 and Open Science. For example, the presenter on the online social communities asked what we would leave disappointed about if it were not addressed. I immediately shouted out, “FriendFeed!” because the Science 2.0 and Life Scientists rooms of FriendFeed are fascinating venues for those of us interested in how science is being conducted in the age of Web 2.0.

Indeed, it is very difficult to keep track of the many topics that interest people on the periphery of both science and search. I work in a medical library and also spend a great deal of time looking for grants in the health sciences for a site I help on, ScanGrants. I feel driven to do that because of the obvious brilliance abounding in communities like FriendFeed. It is incredibly rewarding to find substantial grants offered by sometimes obscure foundations and post them on ScanGrants, post that info in FriendFeed and in Twitter and hope that the pool of applicants will thereby be enlarged, thereby helping to ensure that the grantor will be able to pick and choose among highly qualified applicants and that a greater number of scientists will learn of the grant that might not otherwise have heard of it.

Now, just think of the relatively new tools and technologies that have enabled just one person to be able to do a little bit to alert quite a few researchers to large amounts of scientific funding. I use various browsers. I use Google and other search engines to find grants. I list them on ScanGrants and render the categories subscribeable by email and RSS via FeedBurner. I publicize what I have done in Twitter and FriendFeed. Those are almost all free and open source and ScanGrants is free and not a hugely expensive proprietary database like Community of Science. And the oldest of these technologies are the browser and the search engine and the Web sites listing the grants I refer ScanGrants users to. This is indeed a revolution in how scientific communication takes place.

I would spend days in the science-related rooms if I could. There is so much for librarians and anyone interested in such topics as Open Access and Open Science to learn there. I have just popped over there and noted that around 16 hours ago an item was posted about new features of the PLoS journals (and the Public Library of Science publishing venture is a an absorbing saga in and of itself):
We read,

“These improvements have significant implications for both authors and readers and will make it considerably easier for users to navigate around articles; to find related articles; and to discover the impact that a paper might be having in the wider academic community.”

What remarkable developments these are. Librarians and publishers have to figure out how function in a world in which scientists are doing the editing, the publishing and the searching. And that is just one development noted in one item one morning on FriendFeed. Anyone who cares about science, medical libraries and scientific publishing should visit those rooms. What is more, I have found my questions answered by the scientists there with the utmost courtesy, patience and skill.

We are living in a period of economic hardship. But there is huge reason for optimism. Amazing things can be done for free these days. Social networking and the various kinds of 2.0 (Web 2.0, Science 2.0, Research 2.0) are accelerating scientific progress to a degree unimaginable even thirty years ago. This is a great time to be alive.

Announcing the Recipients of the NextBio Travel Grant!

We are very pleased to announce the recipients of the NextBio travel grant!

We received numerous outstanding essays and it was quite difficult to select just three winners. After much deliberation the following students were selected:

 

Bryan Dickinson

Laura Mariani

Khader Shameer

 

Bryan is a chemistry graduate student at the University of California Berkeley who studies neural stem cells and is interested in NADPH-oxidase (NOX) proteins. Bryan’s essay describes how he used NextBio to find relevant information in the publicly available experimental data.

After a few clicks I was able to find array data on multiple types of stem cells under both growth and differentiation conditions and the expression changes in my NOX proteins. When I read the original research articles that the data supported, I was surprised to see that NOX proteins were not even mentioned.”

 

Bryan goes on to say:

…NextBio has allowed me to quickly and easily find information about my project that not only saved me the time and effort to screen lysates for the various isoforms of the proteins I am looking for, but also saved my lab money since we did not need to purchase as many antibodies. I have since confirmed by western blotting the presence of the proteins that the data NextBio mined for me during that original search suggested should be present in my neural stem cells. I am now in the process of confirming the expression level changes also suggested by the array data during both stress and differentiation conditions.”

 

We were thrilled to hear that NextBio made Bryan’s research more efficient!

 

Laura is a first year PhD student in neuroscience at Emory University who used NextBio to help her in studying Parkinson’s Disease (PD). In her essay, Laura discusses how NextBio helped her sort through a massive amount of public data.

When I entered my gene of interest – coding for the relevant protein – into NextBio, pages of information appeared about its expression in a range of tissues and its role in different human diseases. After sorting the search results by disease, I immediately discovered two recent studies on gene expression in PD that involved this gene. When I viewed the articles cited, I was unable to find any reference to the gene in the text, but saw that the Affymetrix GeneChip data associated with each study had been published to NCBI’s Gene Expression Omnibus (GEO) database. I hadn’t heard of this database before, but even if I had, I could not have found the most relevant papers so quickly on my own (a GEO search for this gene returns an astonishing 2,000 results!).”

Khader is a computational biology PhD student at the National Centre for Biological Sciences in India who works on sequence and structure analysis of proteins. Khader’s essay details how NextBio literature search helps him with his research.

As part of my work, many times my hit lists will throw me a set of new proteins for which I have to identify interesting functional aspects. I always require extensive manual literature curation to obtain detailed aspects by going through multiple papers and cross-reference with related literature. Using NEXTBIO, literature curation is a unique learning experience; it provides an annotated version of PubMed abstracts with interesting tool tips for organisms, genes, proteins, small molecule, disease type etc. This is a very useful utility that will provide a perfect understanding of the abstract by providing the apt information as context dependent dynamic tool tips.”

 

The full texts of the winning essays are available here. They are great essays and I hope you take a few minutes to click through and read them.

All of the essays submitted to the travel grant were well-written and I wish we could have given out grants to every applicant. On behalf of the entire NextBio team, please allow me to offer our sincere thanks to all those who applied and to everyone who helped us to spread the word about the grant.