November 2008 – Page 2 – David Bradley

Social Media for Scientists

NB This post is more than a decade old.

Towards the end of October 2008, I received a flurry of emails asking me to check out new social networking sites for scientists, I’ve already reviewed the nanoscience community, of course. I suspect that, the academic year having moved into full swing, there were a few scientists hoping to tap into the power of social media tools and the whole web-two-point-ohhhh thing.

This from Brian Krueger:

“I came across your blog during my weekly google search for “science social network.” I thought you might be interested in my website, LabSpaces.net. It’s a social network for the sciences that I’ve had on-line for the last two years and I recently got my University to send out a press release about it. I think you should stop by and check it out. Let me know what you think, I’m always looking for suggestions on how to improve the site.”

LabSpaces has all of the features of a social-networking site with the addition of a daily science newsfeed, lab profiles, a science forum, blogs, and a science protocol database. Apparently, the site provides space for researchers to create their own user profile, add their publication history, upload technical research protocols, blog about science, and share research articles with the community. The site will soon host a free video conferencing service to facilitate long distance collaborations and journal clubs.

New Zealander Peter Matthews who works in Japan emailed:

“I am a full-time researcher from NZ, working in Japan, at a museum with many international research visitors. This multilingual environment made me very aware of: (1) the difficulties that non-English based researchers face when using English, and (2) the difficulties that English mono-linguals face when trying to access or publish research in other important research languages, such as Spanish, Chinese, Japanese, French, and so on. Hence my website: The Research Cooperative – http://cooperative.ning.com. Please have a look, join if you want, and please tell any friends and colleagues about this site if you think they might find it useful.”

Pascal Boels, Managing Director of SurgyTec.com emailed with a medical tale:

“Our website is for and by medical professionals. It’s a video-sharing site for surgeons and medical professionals to show off their newly minted skills. It makes it easy for medical professionals to upload videos or slideshows and share those with the community. You can search for videos by specialty, organ/region, tissue, etiology, operation type, or technique. Many surgeons perform original and high-quality techniques in their operating room and equally many surgeons would like to learn from these new and inspiring techniques. Up till now it was very difficult, time consuming and expensive to take a look in each others operating room and share practical knowledge, tips and tricks. Surgytec.com provides the solution for this problem. We are currently serving over 4000 surgeons from more than 124 countries, sharing over 400 procedures

Priyan Weerappuli had long been interested in scientific research but felt that applied research was guarded by private institutions while basic research was held within the confines of colleges and universities by overpriced journals and an oversimplification that occurred whenever research results were translated for more general audiences. His forum/platform will attempt to open this research to a general audience – http://www.theopensourcescienceproject.com

Some correspondents are claiming they’re approaching web 3.0 nirvana:

“ResearchGATE is proud to announce a major update: We greatly improved our search functionality and called it ReFind. The name symbolizes the importance of an efficient and result-driven search functionality within research in general and within our network in particular. ReFind is one of the first search engines based on semantic, “intelligent” correlations. It enables you to find groups, papers, fellow researchers and everything else within and outside of ResearchGATE without having to read through dozens of irrelevant results. Just type a few sentences into ReFind or simply copy and paste your abstract. Our semantic algorithm will then search the leading databases for similar work, providing you with truly relevant results.” [Sounds like my Zemanta/ResearchBlogging.org idea, DB]

One observer pointed out, however, that ResearchGate’s semantic search is maybe not the greatest thing to happen to search in a decade (especially, when we have the likes of True Knowledge Ubiquity, and Zemanta. Indeed, some users have said it is not much of an improvement on conventional search.

Then there was:

“ScienceStage.com – Science in the 21st century – A wide forum for science – on an interdisciplinary, international and individual level. ScienceStage.com, the only universal online portal for science, advanced teaching and academic research, bridges a major gap in scientific research and learning. ScienceStage.com is a virtual conference room, lecture hall, laboratory, library and meeting venue all in one.”

But, perhaps the best is saved for last. An Oxford graduate student, who has completed his PhD, Richard Price, has launched Academia.edu, which he says does two things:

“It displays academics around the world in a ‘tree’ format, according to which institution/department they are affiliated with. And, it enables researchers to keep track of the latest developments in their
field – the latest people, papers, and talks.”

Price wants to see every academic in the world on his tree and already has Richard Dawkins, Stephen Hawking, Paul Krugman, and Noam Chomsky as members. But, that’s the hype what about its potential? It resembles BioMedExperts because both use a “social” publishing tree, but is that enough to engage scientists?

It will be interesting to see whether any of these sites gain the traction their creators hope for and how things will pan out as the credit crunch bites harder. “There are a bunch of them out there,” Krueger told me, “It’s kind of scary how many came out after Nature and I went on-line in 2006. There’s definitely a lot of competition out there, it seems like a new one appears every month. I wonder how the economy and loss of tech funding is going to affect the larger start-ups.”
Then, there are those perhaps more well-known social media sites and networks for scientists, some of which are mentioned in Sciencebase and its sibling sites (tomorrow), in no particular order:

Nature Network – uber network from the publishing giant (discontinued December 2013)
BioMedExperts – Scientific social networking
BioWizard – Blogged up Pubmed search
Mendeley – Digital paper repository and sharing
Labmeeting (blog) – Ditto
YourLabData – socialised LIMS
SciLink – Sci-Linkedin
Myexperiment.com – mostly workflows.
Laboratree.org similar to Researchgate. Not particularly social beyond groups and sharing documents with collaborators, but email is better, and arguably more secure.
scitizen.com – collaborative science news publishing
SocialMD – Med-Linkedin
Ozmosis – Ditto
DNA Network – network of DNA/genetics bloggers
ResearchCrossroads – Socialised grant databases
MyNetResearch – Socialised LIMS at a price
SciVee – YouTube for scientists (see also Watch with Sciencebase page
Scientist Solutions – science chat
Twitter science group and Scientwists list

There are so many, I can barely keep up, but if you have any you think I should add to the list, let me know via the comments box below. Or, more importantly, if you have used any of these systems please leave your thoughts.

Meanwhile, my apologies if you were expecting a lesson in how to use the likes of Twotter, FiendFreed, Ding, Pyuke, or Facebok’s feeble science apps, to help you get on in science socially, but I thought it was about time I did some linking out to the web 3.0 brigade in the world of science, so here they are.

Election Special

barack-obama Congratulations to Barack Obama and well done America, you should feel proud to voted for your 44th President in Barack Obama. But, now that’s done and dusted on with the real news:

In Issue 100 of the relaunched ChemWeb Alchemist, we report on energy is top of the agenda with a record-breaking solar cell material from Australia. New insights into the ripening of bananas reveals they get the blues while crystallography has been thrown a curveball as scientists discover the active sites in many models of protein receptors are not what they seemed to be. The chemistry of alternative medicine sits toxically under the glare of the Alchemist’s lamp and revelations about yet another small molecule with a crucial role to play in cellular control. Finally, a double ACS award for research on the structure and reactivity of molecular oxygen binding to copper and iron complexes, which could have future energy applications.

In SpectroscopyNOW this week, rather than designing and building new instrumentation from bespoke components, researchers in Canada have turned to the laser-based optical read-write technology of DVD and CD players to create a biomedical diagnostics system that requires no hardware modifications. Hua-Zhong “Hogan” Yu and his colleagues Yunchao Li, Lily M. L. Ou in the Department of Chemistry, at Simon Fraser University, in Burnaby, British Columbia, Canada, are all for recycling. They have now developed a digital signal readout protocol for screening disc-based bioassays that uses a standard optical drive (CD/DVD) from an ordinary desktop computer.

blue-bananas Also, this week “Yes, we have blue bananas!” – Forget the so-called morning banana diet, blue is the new yellow and researchers in Europe and the US have no intention of slipping up when it comes to explaining why ripened bananas glow blue under ultraviolet light.

A gold star for SERS – Scientists at the National Institute of Standards and Technology (NIST) in Gaithersburg, Maryland, are using surface-enhanced Raman spectroscopy (SERS) to test the properties of star-shaped gold nanoparticles. They have found that these particles have optical qualities that outshine the competition and could make them useful in chemical and biological sensing and imaging.

Athletic support – Researchers have used NMR to show that endurance-trained athletes have a higher resting muscle metabolism than couch potatoes. The work suggests that the dissociation of oxidation and adenosine triphosphate (ATP) production could be another route by which exercise improves insulin sensitivity and burns excess energy and may have implications for understanding the development of type 2 diabetes.

Crystals foxed – Obtaining a high-resolution crystal structure of a protein, a receptor or an enzyme, for instance, has been at the forefront of the drug design field for many years. Finding small molecules that will dock with the active site of the protein and either stimulate it or inhibit it is the basis on which many pharmaceutical products were built and are thought to work. But, what if that fundamental concept were wrong? This is the sobering and at the same time very important conclusion made by researchers at Leiden University in The Netherlands and the Scripps Institute, La Jolla, California

Science of Spam

spam ethics Who hasn’t received a spam email with some kind of clause laying claim to compliance with the CAN-SPAM Act of 2003? They usually say something about the message being anything but spam. But, it quickly becomes obvious, if you actually waste the time to read the content, that it is a generic marketing message for some kind of herbal remedy for enhancing one or other, or two, parts of your body, making you money, or offering an ugly gold-plated watch at a knock-down price.

Of course, the can-the-spam legislation was meant to squash spam forever, although by not making spam officially illegal across the globe, it did nothing of the sort. It was baloney, in a can. In fact, Petur Jonsson, the Professor of Economics and Chair of the Department of Finance, Economics, Entrepreneurship, and Marketing at Fayetteville State University, in North Carolina argues that while CAN-SPAM may have stemmed the tide of traditional marketing spam, it did nothing to protect net users from the subsequent tsunami of malicious spam. The surge of phishing spam, scam spam, and messages bearing malware has washed over many of us time and again left many users beached and hung out to dry, digitally speaking, in its wake.

In 2002, when the Act was first proposed there were some 30 billion e-mail messages being sent across the globe every day, almost half of which were “unsolicited and unwanted” spam. The legacy accounts of many email users, my first ISP email account and work account included, had no filtering or spam protection and were drowned in hundreds of spam messages every day. Some pundits argued at the time that spam would become such a huge problem that it would herald the demise of email. This was at a time when people still worried that if someone’s email signature, their .sig file, was too big it was wasting bandwidth. Oh, the irony…

“The Act banned a variety of deceptive practices,” Jonsson says, but unfortunately, “it also pre-empted the passage of stricter state laws that would have outlawed spam altogether.” Some of the states, led by California, were at the time preparing anti-spam laws that would essentially have outlawed all unsolicited bulk email. But, the CAN-SPAM Act nipped these state efforts in the bud.

Some commentators have described spam as “information pollution”; it is simply the waste product of an industry marketing its product. And, while this is a reasonable analogy when discussing benign spam, it no longer applies to much of the bulk email flooding the net today.

In the last few years, spammers have exploited technological loopholes for malicious ends. Thousands if not millions of computers have been recruited without their owners knowledge into zombie networks or botnets that propagate malicious spam. Open proxies are harvested and their systems used to reroute email rendering it essentially untraceable, while open relays allowing email header spoofing to confuse spam filtering systems on a massive scale as well as allowing slice after slice of spam to be sent at zero cost to the spammer.

The bottom line is that spam pays even if just one in ten thousand recipients is scammed, the spammers are then in profit when sending out millions of spam messages each day. Jonsson points out that the risk of being caught while phishing is smaller than the risk of getting caught peddling illegally imported bogus Viagra. This means phishing makes more sense. Spam is not just about annoyance it is about cybercrime on an enormous scale. The sooner the authorities recognize and respond to that fact the better for all of us.

Petur O. Jonsson (2009). The economics of spam and the context and aftermath of the CAN-SPAM Act of 2003 International Journal of Liability and Scientific Enquiry, 2 (1), 40-52

Melamine in baby formula, an open secret

melamine-eggs Thousands of babies had apparently taken ill having drunk formula milk to which the organic compound melamine had been added. The melamine was being added by unscrupulous operatives somewhere in the milk supply chain, to artificially boost the nitrogen content of the product, and so spoof higher protein levels than are actually present.

Subsequently, lists of contaminated products appeared in the media and on the web and as the melamine scandal widened, the Chinese government issued an apology and promised to crack down on the problem.

However, with news this week that batches of eggs imported into Hong Kong from China have tested positive for melamine, which is suspected of causing kidney problems, it now appears that the compound is being added routinely to animal feed in China. According to the BBC, this news has been released into the Chinese state media by a government realising it has far less control over food standards that it ought to have.

The melamine scandal is not new. It is essentially an open secret in China that the compound is added to all kinds of foods, particularly animal feed and pet food to artificially inflate the protein readings at the so-called quality control stage. Melamine was at the heart of the petfood scandal in 2007, but that was simply the first time that the West learned of the problem. It seems obvious that melamine could have been in the food chain much longer than that.

But, whether the open secret of melamine in the food supply is actually as serious a problem as the media would have us believe is down to toxic dose. AP quotes Peter Dingle, a toxicologist from Murdoch University, Perth, Australia, who says that aside from the tainted baby formula that killed at least four Chinese infants and left 54,000 children hospitalized in September, it is unlikely humans will get sick from melamine. The amount of the chemical in a few servings of bacon, for instance, would simply be too low, he said. But he is not recommending that the practice continue unchecked. China should have cracked down sooner on feed companies he and others have said.

However, if the melamine open secret is as big as it appears from the outside, it is unlikely to be stopped any time soon, particularly because of the heirarchical government system in China. “It could take five or even 10 years” before some companies stop adding the chemical to food products, Jason Yan of the US Grains Council is quoted by AP.