Live webcast & Twitter: great combination for scientific conferences

As I mentioned in my previous post, thanks to the internet, I could peek into the meeting of the American Society for Microbiology (ASM), recently held in California, from the comfort of my home at London, UK. This was possible because some of the meeting attendees posted comments on Twitter, in real time, and also because the meeting organizers made a live video broadcast available to everyone through the internet (that is, a webcast).


The webcast, called ASM Live, consisted of nine interviews to researchers on their latest findings. The interviews were very aptly handled by Jeff Fox, Features Editor for Microbe Magazine (a freely available, monthly magazine published by the ASM). Moreover, viewers were allowed to submit questions to the researchers by either using the online chat (provided by UStream) or tweeting to @MicrobeWorld.

Two of the most popular interviews seemed to be The Gulf oil spill: microbes to the rescue? and The first synthetic genome: what does this mean for microbiology, and for everybody else?? [note that there were two question marks in the original title, and this is not necessarily a typo :) ]


All the interviews were really interesting -- and you can still watch them: they are archived at MicrobeWorld (an online community for sharing multimedia resources related to microbiology) and UStream.tv (the live interactive broadcast platform that was used for the ASM webcast).


My sincere congratulations to everybody involved in the making and broadcasting of the interviews, that was a great piece of work!


And now, let's focus on Twitter.


About 1,200 messages containing the #asmgm hashtag were posted to Twitter in relation to the ASM meeting. There were all kinds of messages, and many of them were informative, insightful, or funny. Some of them included links to interesting articles or websites, while others redirected to photos captured during the meeting. I mentioned a couple of popular tweets in a previous blog post, and I'm including here a few more as illustrations.


However, if you search for the #asmgm hashtag on Twitter, you will only get recent messages posted during the last 7-10 days -- which is really disappointing.

Luckily, Alan Wolf had the brilliant idea of creating an archive for #asmgm tweets on Twapper Keeper. The archive is freely available online, so anybody can read and download all the messages.


In addition to archiving, there are other ways of reading 'old' Twitter messages: for instance, I find Topsy quite useful. However, archiving seems a very sensible idea to me -- especially for scientific conferences.

[Note: Twapper Keeper can only reach back as far as Twitter allows, so the archive needs to be started as soon as possible (ideally a few days before the conference, to include any pre-meeting tweets)]

Once the ASM meeting was over, I thought that a word cloud, as a visual representation of 'hot topics' (the most tweeted), could be a nice illustration for a blog post. So, I searched the internet looking for a suitable, user-friendly online tool that would generate -- automagically -- the perfect word cloud for me. But I did not find it.

After a trial-and-error process, I finally made a nice-looking cloud (which was featured image of the week at MicrobeWorld) using Wordle, but the result wasn't exactly what I had in mind:


Why wasn't I fully satisfied with my cloud? Firstly, because I had to do a lot of manual editing of the tweets: removing highly repetitive terms (such as "#asmgm", "RT"), fixing typos, stemming (a little), putting some words together to create meaningful tags (e.g. "San-Diego")... Also, the cloud was colourful and nice-looking, but the words were not individually hyperlinked (as in most tag clouds, see for instance the cloud located at the upper right side of my blog).

[Note: a tweetup is a meeting of two or more people who know each other through Twitter]

There are some online tools to generate tag clouds from Twitter messages. For instance, Tweetcloud seems to get quite close to what I have in mind. It indeed generates a tag cloud for a specific keyword (or user). But it seems to be limited by the Twitter search function (it only uses messages posted in the last 7-10 days). So, I guess I could have used this tool the day after the ASM meeting to create a cloud... but I didn't known about Tweetcloud at the time. Still, the cloud is not customizable at all.


So, I want to finish this post summarizing the characteristics of what I think would be an ideal tool to create word clouds from Twitter messages:

A) General

• Freely available, online tool.


• It could make a cloud for a hashtag, a word, a term composed of several words, or a Twitter user.

B) Searching Twitter

• It wouldn't be limited by the 7-10 days boundary of the present search function of Twitter.


• It would provide options to define specific limits for time (e.g. "only tweets posted between two given dates") and number of tweets ("only the last 100 tweets").


• Options to exclude, or include, certain types of messages (replies, retweets, containing links, linking to images, linking to videos) or users ("exclude these users").

C) Creating the cloud

• Options to use only hashtags (similar to My Tweet Cloud), exclude particular words (common words, numbers), use only particular types of words (e.g. nouns?).


• Stemming.


• It would detect possible typos, showing a list of candidates to be fixed. The user would decide if they should be corrected or not.


• It would suggest possible tags composed of more than one word (e.g. "San" and "Diego" are always found together, do you want the tool to combine them into a single tag "San Diego"?). The user would decide.


• The tags in the cloud should be hyperlinked. That is, clicking on a term such as "San Diego" would redirect to a list of tweets that included such a term.
  

D) Customizing the aspect of the cloud

• Options to change the colour and relative orientation of tags, and the general aspect of the cloud (similar to Wordle).


• Options to create an animated cloud showing changes in time (or location, user, etc). For instance, several clouds could be generated for a hashtag for different days (similar to this example) and could be combined into a single animated cloud. The user would define the period used to create each 'sub-cloud' (e.g. every day, every 6 hours) and the number of clouds needed for a smooth animation.

Please leave your comments, ideas or suggestions on creating Twitter tag clouds, or on the use of live webcast and Twitter for scientific conferences.











Note added on June 23rd:
I just read a great article on this topic: Twitterpated: Using Social Media at Academic Conferences. I found it via Hacking the Academy, a book that was crowdsourced on Twitter in one week. It deals with online education, scholarly communication and much more.


Related links:

- Added July 3rd: How to create a PDF archive of hashtagged tweets by Andrew Spong, STweM. It describes a simple workflow for archiving conference tweets. Found via FriendFeed.

- Added August 15th: SfN the Meh by DrugMonkey. Advice to the Society for Neuroscience (and other scientific societies): how to use social media for your next conference.

- Added August 22nd: Tagxedo - Tag Cloud with Styles. Tagxedo turns any word set (texts, blogs, tweets) into a visually appealing tag cloud. The cloud can fit a predetermined shape or silhouette. Link found via Andrew Spong's FriendFeed.

- Added September 4, 2010: Summarizr is a service that creates "a brief summary of a Twapper Keeper tweet archive. It works for #hashtag archives, keyword archives and @person archives. Just enter a hashtag, keyword, Twitter account name or archive URL in the form". See Twitter usage at the ASM meeting, based on TwapperKeeper archive of hashtag #asmgm.

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Highlights from a scientific conference, observed via Twitter - #asmgm

Lots of conferences and meetings on science-related topics are held every year, all over the world. Many of them cover wide topics with potential to excite the curiosity of a great number of scientists and --more importantly-- common people. Sometimes, a few highlights of a conference are reported by the mass media, and that's good...

...but wouldn't it be even better if anybody could catch a glimpse of a particular conference, in real time? What about getting comments made by some of the attendees about a talk that is happening right now? And, what if the speaker could answer, in real time, a question asked by anybody from anywhere in the world?

Well, this is already happening, thanks to the internet!

In this blog post and an upcoming one, I'll describe some examples on how social media and other internet tools were used during a recent meeting of the American Society for Microbiology.

If you keep reading, you might learn a couple of interesting things about microbes. I also hope that these blog posts may give us all some food for thought about possible, better uses of the internet (and, in particular, social media) for the communication of science.

I'll be waiting for your comments, so don't be shy, I'm learning here!


The American Society for Microbiology (ASM) is the largest life science membership organization in the world, with over 43,000 members (and more than one third of them, like myself, are located outside the United States). General meetings, held once a year, are huge events with over 10,000 attendees, and cover new research related to the biology of microbes.

The latest general meeting took place in San Diego (May 23-27), and I tried to follow the event as closely as possible through the internet. Good for me: many attendees shared their thoughts, in real time, using social media. Also, and I think this is praiseworthy, the ASM actively used a battery of social media channels, and broadcasted on the internet several live interviews with selected scientists. And all this internet activity was freely available to anyone.

During those days, I followed the messages that the ASM and the attendees posted on Twitter, the popular microblogging service. To do this, I didn't need to know who was attending the meeting -- I just searched for Twitter messages (a.k.a. tweets) containing the following tag (or hashtag) that was chosen beforehand by the organizers: #asmgm (abbreviation for "ASM general meeting"). In the simplest way, this can be done using the "search" function of Twitter, as you can see if you click here (but note that tweets older than a few days are not retrieved).

So, when somebody wanted to post a tweet related to the ASM meeting, they just added the #asmgm hashtag, as in this example:


The tweet was written by science writer Carl Zimmer, and was one of the most retweeted messages during the meeting. It referred to a talk entitled "The biochemistry of beer" being given at that precise moment by Charlie Bamforth, a professor from the University of California, Davis.

Other Twitter messages posted by meeting attendees were also retweeted many times. I wonder how far the #asmgm tweets reached, having in mind that some of the twitterers at the ASM meeting had many hundreds of Twitter followers (e.g. Carl Zimmer has over 18,000)... Is there a practical way to calculate the total audience that a single tweet has had during a certain period? I don't know -- but I'm pretty sure that the room where Charlie Bamforth gave his "beer talk" wasn't big enough to hold all the people who read his "mustache quote" on Twitter.


Another memorable quote from the ASM meeting was:


The quote was pronounced by Edward DeLong, professor at the Massachusetts Institute of Technology, during his talk "Evolution and ecology in microbial ecosystems: unity in diversity." On a later tweet, Zimmer wrote: "Clarification of previous tweet/koan: genomes are not fixed. They are ever-changing, swapping genes, shuffling segments, mutating,etc."


Finally, another tweet by Carl Zimmer summarised a general idea that is common knowledge among microbiologists (or so I like to think) but might sound like news to many other people:


I'm not sure where the quote came from, as there were many talks going on at the same time (the meeting program has 350 pages, and that's without abstracts!). But it's clear that most types of bacteria on Earth are harmless to us. I would even say that most microbes don't even know that we humans exist... It's only because of our hard-to-eradicate anthropocentrism that we feel that microbes exist only to make us sick (and to provide us with beer, of course!).


But this blog post is getting very long, so I'm interrupting it here. The story about the ASM meeting and social media continues in my next post.

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A Twitter view of the general meeting of the American Society for Microbiology - #asmgm

The above image is a word cloud generated from about 1200 tweets (that is, messages posted on the microblogging service Twitter). All these tweets are related to the general meeting of the American Society for Microbiology (ASM), which was recently held in San Diego, California (May 23-27).

Please wait for my next blog post, where I'm going to tell you about a few things that could be learnt about microbes by following the ASM meeting on the internet -- no matter your physical location on Earth (and beyond?). Also, I'm going to explain how I made the word cloud -- I'm pretty sure there must be a better and easier way to do this, so I would certainly appreciate your feedback on my next post.

Note: unfortunately, the tags in the cloud are not hyperlinked. The image was generated using Wordle.

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Media for Science Forum: poor organization, disappointing use of social media

A science journalism congress was held last week in Madrid, Spain, under the name Media for Science Forum (MFSF). This was a European congress dealing "with strategic issues about science communication and science journalism and its social dimension." One of its specific objectives was declared to be: "Explore new trends in Science Communication due to the web 2.0".

Well, this sounded really exciting to me (and registration was free!), so I planned to attend the congress. Unfortunately, the organization rejected my application due to the huge amount of requests received.

So, I couldn't attend the meeting in Madrid --but I followed the events from my home at London, using the internet.

This post describes my personal experience of MFSF, including a few thoughts about the use of social media. You are more than welcome to add your comments at the end of the post.


March 18th

I first learnt about the upcoming Media for Science Forum (MFSF) through an announcement made on the SINC webpage (in Spanish). SINC (www.plataformasinc.es) is a news agency focused on scientific research done at Spanish institutions and research done by Spaniards at foreign institutions.

After visiting the MSFS official webpage, I filled and sent the online registration form the very same day. Registration was free but seats were limited: the organization would contact me in due time to accept or reject my application.

After registration, I was expecting to receive an email, automatically generated by the system, acknowledging my registration and providing some additional information --this seems a common procedure for online forms--, but this message did not arrive.

Anyway, I sent a tweet to inform my Twitter followers about the event, suggesting a possible hashtag. I also announced the conference on the Science Writers Facebook page.


April 4th

Over two weeks passed, but I didn't receive any email from the organization, and no new information was posted on the MFSF website. So I sent them an email including all my personal information and a link to my CV. I also explained them that I needed to know about the success or failure of my application in a short time, as I eventually had to make some arrangements for my trip London-Madrid.


April 6th

The MFSF organization forwarded me an email, which was supposed to be sent to me on March 18th (but I had not received). The message thanked me for the registration and informed that I'd be contacted again by the organization about the possible success of my application. When? "Soon." No more details were included.


April 7th

I received an email with the following request: "We have had problems in our system, and I have to ask you to reconfirm the dates that you are planning to attend the Forum".

The problem is that the email did not come from the congress organization but from a known Spanish travel agency. I checked the MFSF website (again) looking for some explanation or connection to this travel agency: I couldn't find anything. Anyway, I replied with the requested information: I planned to attend both days (12th and 13th May).


April 12th

MFSF started to use Twitter and Facebook!

I thought: "Great, they'll keep us informed about what's going on."

Oh, how wrong I was...


April 14th

New email from the travel agency, including a message from the MFSF organizers: they started a blog!

"Excellent, another channel to keep in touch with us! Now we'll get some news!" -- or so I thought.

I wasn't sure if that message meant that my application had been successful, so I requested some information about it. They replied immediately: "Nobody is receiving any confirmation. The organizers are still receiving applications, and they haven't made any decisions yet. We will inform you in due time" (my Spanish-to-English translation).


April 28th

During the previous days I had exchanged a few messages with other members of a LinkedIn group (Periodismo científico y divulgativo, which is Spanish for "Science journalism"), and learnt that nobody seemed to have received any confirmation regarding their MFSF application.

So I posted a message on the MFSF Facebook page, requesting information (to see my message there, you need to click on "Media for Science and others", as the default page only shows messages written by the organizers).

They never replied to my message on Facebook.


April 29th

Six weeks after my registration, and 13 days before the event, the MFSF organizers sent me an email: "Unfortunately your request to participate on the congress has been denied due to the huge amount of requests received."

You can imagine this didn't make me very happy.

Anyway, I still expected to know more about the MFSF talks and discussions through the internet, by making use of social media.


May 12th: first day of the congress

Early in the morning, I learnt from Twitter (actually, I think it was through this Topsy search) that the MFSF talks were going to be broadcasted through live web streaming.

Oh, wait, it appeared that only the opening talk was to be transmitted.

Note that I didn't get that information thanks to MFSF "Web 2.0" tools: their blog, Twitter and Facebook pages were all mute about this issue at the time (and even later).

The opening talk --the only one that was to be live streamed-- was untitled and in charge of the General Director of FECYT (Spanish Foundation for Science and Technology). This didn't sound very exciting to me. So, I forgot about MFSF for the rest of the day. My plan was to check the internet for related discussions on the following days.


May 13th: second and last day of the congress

At midday, I was surprised to know (through Twitter, but not MFSF Twitter) that the forum broadcast was still live!

Although with some interruptions in the service, they had been transmitting the whole thing!? Apparently, this was just an unplanned, happy idea. Well, I guess nobody had thought about this possibility before...???

Anyway, so I was able to watch the afternoon talks. These included brief descriptions of European scientific news services (such as AlphaGalileo), and the final conclusions (which were not such a thing but a list of general recommendations). Nice, but not incredibly useful.


Today, May 20th
Today I've been searching the internet, including Twitter, for reactions to MFSF (see links below). It seems that the congress was quite popular on Twitter: the hashtag #mfsf (not the one I suggested) became the second trending topic on Twitter in Spain. That's pretty good for a science journalism congress!

...Although it must be said that many tweets were messages of the lifecasting type ("On my way to Madrid...", "Having a beer in...", and the like), which in my opinion only contribute to the noise -- when they are tagged with a congress hashtag.

From what I can read on the internet, it seems that most people found the forum interesting -- too bad my application was rejected. On the negative side, MFSF was poorly planned, and failed to provide essential information to potential attendees and the general public.

In particular, their use of social media (blog, Facebook, Twitter) for updates and conversation was really disappointing -- and remember that one of their specific objectives was to "explore new trends in science communication due to the web 2.0". After the first hello message, MFSF published only 10 messages on Twitter and 13 updates on Facebook (numbers correct at the time of writing this) -- and all these messages were just announcements of new blog posts. No updates about registration issues, no announcements concerning the live web broadcasting, no comments on specific talks, no conversation at all. That is useless to me.


Reactions to MFSF:
- No hay que ser innovador... tan sólo parecerlo [in Spanish] by Javi Peláez. La aldea irreductible, May 12th, 2010.
- Media for Science Forum (1), (2) and (3) [in Catalan] by Miquel Duran. Edunomia, May 12-13-14, 2010.
- Media for Science Forum and (II) [in Catalan] by Pep Anton Vieta. Pepquímic, May 12-15, 2010.
- Media for Science Forum 2010 – ein Rückblick [in German] by Hans-Dieter Zimmermann. FHS eSociety Blog, May 18th, 2010.
- El estado del periodismo científico, en el Media For Science Forum de Madrid [in Spanish but with English introduction] by Pere Estupinyà. Knight Science Journalism Tracker, May 19th, 2010.

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My selection of YouTube videos related to the microbial world

During the last couple of years I've been collecting some YouTube videos related to microbiology. My microbiology playlist includes now over 70 videos of very different styles, including not only academic lectures and documentaries, but also animated movies and funny songs.

You can watch many of these videos using the embedded viewer (see below).

Or, you can watch all of them on my YouTube channel. You will find there other playlists, including:
- Microscopy
- Molecular and Cell Biology
- Other sciences

Please let me know if you find any of the playlists useful or, at least, entertaining.

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Uncovering beauty in proteins to fight the pneumococcal fratricides

This post is about pneumonia and pneumococci, fratricide at the cellular level, and a pretty protein. And there's a video too!


First things first. Pneumonia is a common disease characterized by inflammation of the lungs that can be deadly: 4 million people in the world die from it every year. Half of them are children under 5 years of age -- in fact, no other illness causes more deaths of children under age 5 worldwide. However, this is a preventable and treatable disease in most cases.


Many organisms can cause pneumonia, but the usual culprits are the bacteria Streptococcus pneumoniae (or pneumococcus, see above image) and, less frequently, Haemophilus influenzae type b (a.k.a. Hib). Safe and effective vaccines and antibiotics have been developed for these infections. Unfortunately, they are not commonly available in most developing countries, where pneumonia allies with poor nutrition, other illnesses (e.g. AIDS) and lack of resources to contribute to the cycle of poverty. To know more about the impact of pneumonia on world health and what can be done about it, I recommend listening to this podcast and visiting the World Pneumonia Day website.


My only direct contact with pneumococcus research was... hum... many years ago. As an undergraduate student, I spent two months at the Centro de Investigaciones Biológicas (CIB, Center for Biological Research) in Madrid, Spain, where I learnt how to cultivate pneumococci and some techniques for the study of lytic enzymes. These remarkable enzymes play a key role in bacterial physiology by cleaving, in a regulated fashion, specific linkages in peptidoglycan (that is, the highly cross-linked polymer that forms the bacterial cell wall). This apparently destructive activity is essential for cell wall turnover, and allows cell growth and division. Interestingly, the genomes of some bacteriophages (or bacterial viruses) also encode lytic enzymes, which the viruses use to break the cell wall and escape from its dying host after viral replication. These enzymes could be useful as antibacterial agents.


A few days ago I was happy to learn that a group of Spanish researchers --some of them from the CIB-- had solved the 3D structure of one of the pneumococcal lytic enzymes, called LytC. What I find remarkable is how the 3D structure elegantly explains the peculiar role that this protein plays during a process known as pneumococcal fratricide.

Some bacteria produce substances that kill surrounding microbes, and use the resulting dead bodies as a source of nutrients. Sometimes, killer and victim belong to the same species, or even they are siblings. In these cases, researchers speak of cannibalism or fratricide; although if you view microbial populations as coordinated, multicellular entities, then you may prefer to use the term programmed cell death.

Among pneumococci, some cells in a population become competent in response to certain signals; which means that they are able to take up DNA from their surroundings, and incorporate this genetic information into their own chromosome. This way, competent cells can acquire new inheritable abilities -- such as production of a new capsule type, or resistance to an antibiotic -- that can be very important for their survival (this was the underlying mechanism in the famous Avery-MacLeod-McCarty experiment that helped identify DNA as the hereditary material in cells).

But competent pneumococci do something else: they encourage non-competent siblings and other closely-related bacteria to commit suicide. They do this by releasing a particular lytic enzyme, called CbpD, that diffuses through the milieu and --somehow-- activates LytC and other lytic enzymes that are already present in the non-competent siblings. Cell wall weakening finally results in a big bang; that is, the explosion of the non-competent pneumococci. The materials released serve not only as nutrients and sources of genetic information (DNA), but also as virulence factors that help competent cells to survive in their human host.


The 3D structure of LytC now provides the clues to explain the enzyme's peculiar behaviour during pneumococcal fratricide. Have a look at the model of LytC on the left: ain't it a beauty? A substrate-binding module (in blue and green in the image) recognizes and binds the cell wall peptidoglycan, whereas a catalytic module (in red) is responsible for breaking a specific linkage in the substrate. Because of the unusual hook shape of the protein, the substrate-binding module and the catalytic module partially block each other. As a result, LytC cannot bind the highly cross-linked peptidoglycan that is predominant under normal circumstances. Only when CbpD or other lytic enzymes cut specific linkages in the cell wall, LytC is able to bind the 'loosened' peptidoglycan and comes into action -- with deleterious consequences for the non-competent pneumococci.


To make the story even more attractive (at least to me), the researchers bothered to produce a video that illustrates -- in a fascinating way -- the pneumococcal fratricide and the mechanism for LytC activation. Please watch it, the background music is nice too. The video includes some captions in Spanish, but I uploaded the video to YouTube and added English subtitles for a wider audience. I hope more researchers will get into the trouble of making visually attractive videos or presentations of their work (and make them freely available), it really makes a difference...




I also add here a nice composite image from the press release, just because I think it's so beautiful:




Reference for the 3D structure of LytC:
Pérez-Dorado, I., González, A., Morales, M., Sanles, R., Striker, W., Vollmer, W., Mobashery, S., García, J., Martínez-Ripoll, M., García, P., & Hermoso, J. (2010). Insights into pneumococcal fratricide from the crystal structures of the modular killing factor LytC Nature Structural & Molecular Biology DOI: 10.1038/nsmb.1817


Recommended links:
- World Pneumonia Day (November 12th).
- Keith Klugman - Pneumonia: the hidden giant. In this podcast, Carl Zimmer interviews Keith Klugman, Chair of Global Health at Emory University, USA.
- Klugman's crusade by Valerie Gregg. Public Health Magazine, Emory University, spring 2006.
- Neumococos fratricidas [in Spanish], noticia publicada en la web del CSIC (20 de abril, 2010).
- Los neumococos fratricidas [in Spanish]. RTVE.es (20-04-2010).


Other relevant scientific articles:
- Bacterial programmed cell death and multicellular behavior in bacteria [free article] by Hanna Engelberg-Kulka et al. PLoS Genet. (2006) 2(10): e135.
- Cannibalism and fratricide: mechanisms and raisons d'être by Jean-Pierre Claverys & Leiv S. Håvarstein. Nat. Rev. Microbiol. (2007) 5: 219-29.
- Bacteriophage lysins as effective antibacterials [free article] by Vincent A. Fischetti. Curr. Opin. Microbiol. (2008) 11: 393–400.
- Pneumococcus: the sugar-coated bacteria [free PDF] by Rubens López. Intl. Microbiol. (2006) 9: 179-190.


Image sources:
- Streptococcus pneumoniae in spinal fluid. FA stain (digitally colorized). Content Providers(s): CDC/Dr. M.S. Mitchell. Source: Wikimedia Commons.
- World Pneumonia Day logo.
- Nature Structural & Molecular Biology cover, May 2010, Volume 17 No 5.
- LytC model, LytC and pneumococci: both images from press release, CSIC.es

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Elio Schaechter comments on state microbes at NPR (podcasts)

It seems that Wisconsinites are not getting their own state microbe after all. What a shame!







Transcripts of these radio podcasts are available at the NPR website:
- A state microbe for cheese-crazed Wisconsin? April 16th, 2010.
- No state microbe for Wisconsin. April 28th, 2010.


From Wikipedia:

National Public Radio (NPR) is a privately and publicly funded non-profit membership media organization that serves as a national syndicator to 797 public radio stations in the United States.

NOTE added on May 7th, 2010:
For a thorough list of candidate state microbes, see State Microbes at Small Things Considered, May 6th, 2010.

NOTE added on October 11th, 2010:
More suggestions (including several streptomycetes) by Joan W. Bennett & Douglas Eveleigh (Rutgers, The State University of New Jersey): State Microbes, Microbe magazine, October 2010.

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"Hope he's only a Sunday creationist" by G. Trudeau

This comic strip by Garry Trudeau was published in 2006, so you may already know it. Here, a doctor offers two antibiotic choices to a patient suffering from tuberculosis (TB). The choice appears to depend on the patient's religious beliefs. I hope the patient chose wisely -- for his own benefit and for that of all the people that could be otherwise infected by his spreading of TB microbes.



Interestingly, cartoonist Garry Trudeau is the great-grandson of Dr. Edward Trudeau, who founded the Adirondack Cottage Sanitarium for the treatment of pulmonary TB, at Saranac Lake, New York State, in 1884. It was found at the time that tuberculous patients greatly benefited from a "rest cure" that included lots of mountain fresh air, and good nutrition. The sanatorium was later renamed and reorganized as a biomedical research center. Known today as the Trudeau Institute, it is devoted to researching our immune system to find better ways of preventing and treating human diseases, including TB, influenza, tropical diseases and cancer.



Credits for images:
- Cartoon:
Author: Garry Trudeau (Doonesbury.com). Source: GoComics.
- Stamp:
United States Postal Service. Stamp designed by Howard E. Paine and created by Mark Summers, based on a photograph of Dr. Trudeau provided by the American Lung Association. Source: The Stamp Collecting Round-up. See also a press release at EurekAlert.


Hat tip:
Comunicar ciencia con humor [in Spanish] by José Pardina, Asociación Española de Comunicación Científica (AECC) [Spanish Association for Science Communication].

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Social media for microbiology education and research

Vincent Racaniello is a well-known Professor of Microbiology at Columbia University Medical Center, New York. As a complement to his research and his classes on virology, he successfully uses different social media tools (blogging, podcasting, microblogging) to spread the love for viruses -- I mean, to teach the public about viruses (the kind that make you sick... or not).

The following video is a recording of a great talk he gave at the Spring 2010 meeting of the Society for General Microbiology in Edinburgh, UK. In this presentation he explains -- in simple terms -- how he uses blogging, podcasting, and other social media tools for the popularization of virology.

I'm wondering if the talk could convince a few of the microbiologists in the audience to jump on the social media bandwagon...? Anyone?


The video is licensed under a Creative Commons Attribution license, and can be watched also at BioCrowd or at Virology Blog.


Image credits: "Jump on the social media bandwagon" by Matt Hamm. Source: Flickr. Image used under an Attribution-Noncommercial Creative Commons license.

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Beauty contests for promoting science?

I was browsing the printed edition of a local newspaper (for a London borough), and a brief story caught my eye: Top genes expert is UK Miss India.

To be honest, I had to read the headline twice to grasp its meaning. "Top genes expert" is not a very common expression (actually, I searched Google and found no results, which is remarkable these days!). And "UK Miss India" was also a little confusing to me... but it may be just me.

The story was about a local resident who happened to win a beauty contest. Nothing special here -- lots of pretty people live in my neighbourhood :) . What caught my attention was that the beauty queen works as "a stem cell researcher at Imperial College Healthcare Trust." At the official Imperial College website I found that she is a professional model and actress, and "she intends to spend her reign promoting science and medicine, while undertaking community projects."

First I should say that I admire anybody who does research and, at the same time, is engaged in a different activity in a professional way (not just as a hobby). I wasn't capable to do that in my research days.

Anyway, I used to think that beauty contests and science popularization were two unconnected issues. But now I'm not so sure. Science can be promoted in many different ways...

Perhaps a modified version of today beauty contests could be used for the promotion and popularization of science.

What do you think? Do you know of any examples of this, or anything similar?



Somewhat related links:
- Science Babes and Science Hunks. I, Science (a science magazine for Imperial College), 15th January 2010. A list of sexy scientists in cinema.
- Sexy Science- "a look into the hottest science currently going on today and the hot scientists behind that work." Or so they say...
- Science Babe - "the science of everyday life". The first video, "The physics of high heels", is interesting. I'm curious about how this effort for science popularization will develop...
- We're scientists AND we're sexy! - a Facebook group.
- Sexy Science - stock photographic images. It seems that you may become a sexy scientist by wearing a white labcoat and big glasses, AND looking like an expressionless robot...
- Geeks are Sexy - "tech, science, news and social issues for geeks".


Beauty and sexiness are relative concepts. You may find this scientist pretty or attractive in some way...

Image credits: the science of fizz, by goopymart. This image is included here under an Attribution-Noncommercial-Share Alike Creative Commons license.

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Tuberculosis and AIDS: two diseases, one response

Today is World TB Day, an excellent time to watch the following video (available at the World Health Organization YouTube channel):



You can read about the current state of the disease -- which kills almost two million people every year -- here: A world free of TB (Word Health Organization).

You can also watch a few more videos on the topic at Stop TB Partnership. I especially recommend two videos:
- Actions For Life - A flash film about the Global Plan to Stop TB
- The Human Face of TB, an informational flash film

I'll finish the post with some words written by Margaret Chan, WHO Director-General:

"If the right action is not taken right now, the continuing spread of MDR-TB [multidrug-resistant tuberculosis] could transform a disease that is curable with affordable medicines into a costly and deadly epidemic. If the right action is not taken right now, the continuing rise of XDR-TB [extensively drug-resistant tuberculosis] could take the world back to the era that predates the development of antibiotics, with nothing in hand to guarantee treatment success."

"The microbial world has given us a clear either-or situation. Either we tackle the problem now with rational and proven approaches, or we pay later with an epidemic of an airborne disease that renders our modern-day medicines and straightforward treatment regimens obsolete. This would truly be a tragedy, on a huge and costly scale, that should not happen."

Related links:
- World TB Day. Twisted Bacteria, March 24th, 2008.
- An 'open source' approach to drug discovery. Twisted Bacteria, July 1st, 2008.
- Robert Koch y la tuberculosis. En Días Como Hoy, RTVE.es , 24 de marzo, 2010. [In Spanish] Se trata de un fragmento de un programa de radio (dos minutos y medio) en el que Nieves Concostrina nos recuerda, de forma amena, el momento en que el gran Robert Koch presentó al mundo la bacteria causante de esta enfermedad ("su bacilo").

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Year of Biodiversity: only for cute animals and plants?

The United Nations declared 2010 to be the International Year of Biodiversity. This sounds great, let's celebrate and protect the variety of life on Earth! We must learn more about current (and past) biodiversity and the impact that human activities have on the distribution and abundance of organisms. Also, we should explore any effective ways to protect biodiversity, if only because it benefits us.

However, it strikes me as short-sighted that most biodiversity advocates seem to care only about "the cute organisms" (cute by most human standards, I guess); that is, a few particular animals and plants. But... for Pete's sake, life on Earth goes well beyond a few vertebrates, trees and corals! Surprisingly, the true diversity of life is not obvious at all in the writings of most biologists, conservationists or environmental scientists when discussing biodiversity and its protection.

I know, I know -- when a clear message is to be delivered to the general public, you cannot be comprehensive. If you can mention only a couple of examples for endangered species, you better go for the much-like-us mammal, or the colourful bird, or the pretty tree or flower. Most of us can easily sympathize with a chimpanzee (that is, really, almost one of us) or with many animals: they have faces, with two eyes and a mouth, and it's hard not to see part of our own reflection there. We often show emotional responses also to trees, flowers or grasses (even mushrooms). So, when explaining the importance of biodiversity to a general audience, sticking to the cute guys might be the wise choice.

But how is this topic treated inside the scientific community? Well, in general, I don't see much difference. When biodiversity is discussed -- in general terms -- in scientific articles, editorials or websites, the focus is again on certain plants and animals that can be seen by the unaided human eye (that is, macro-organisms). By contrast, microbes are hardly ever referenced, if at all.

Why are microbes not even mentioned most of the times? Why are some particular organisms (let's call them "the cuties" for short) the focus of research and protectionist efforts? I can think of a few possible answers:

1 - The cuties, among all the living beings, might suffer the highest risk of extinction.
2 - Although there are other organisms at higher risk, the cuties are perhaps more important (in some way) either for the preservation of particular ecosystems or for human well-being.
3 - Our current knowledge of life diversity might be very limited, and is focused on particular organisms because of historical and technical reasons.

I guess that most scientists and many learned people would agree with me that answer number 3 seems about right (but if you think otherwise, please leave a comment). Actually, it seems that we know very little on the matter. Scientists are starting to agree -- I think -- on a broad definition of biodiversity. But the field faces (at least) two huge challenges. First, there are many organisms living on (and inside) this planet that we haven't met yet, and our estimates of how many species are awaiting discovery are little more than educated guesses. Second, although biodiversity can be measured at various levels, it's often understood as referring to the number and relative abundance of different species. And deciding if two organisms belong to a single species, or to two different ones, can be really hard. Moreover, the difficulty in agreeing on species definition depends greatly on the type of organism it applies to: whereas this issue causes some serious troubles when studying cuties, it appears almost insurmountable when trying to define microbial species. Why is this so? Well, I'm not getting into this here, but let's say that the species concept was originally created and crafted for the cuties, and microorganisms just don't fit into such clothes.

However, even lacking a suitable species definition (to the embarrassment of microbiologists), we can confidently say that the microbes are much more diverse than the cuties. This diversity is shown at different levels: genetics, biochemistry, ecology... You can find microbes almost everywhere, and often in amazingly high numbers. No matter if you count individuals or you measure biomass: microbes are the (silent?) majority. Some microorganisms are essential not just for the preservation of particular ecosystems but for the continuity of life on Earth as we know it (and when I write "life" I mean "life", not just "cuties"). Under any non-human-centred point of view, life is microbial -- with a few exceptions, yes.

So, just to recapitulate... Some animals and plants appear to be on the brink of extinction because of human actions, and it doesn't seem a good idea to let them go. However, we don't know how many types of organisms are out there, or how many of them are endangered by our activities, and we don't understand the long-term effects of the extinction of any particular life form. Yes, more research is definitely needed.

But we do know that life is incredibly diverse and mostly invisible to the human eye, and that the cuties are not even the tip of the iceberg. So, any serious research or scientific communication on the diversity of life should include (in my opinion) some mention to microbes, the main actors on this movie -- at least we should acknowledge our ignorance! Microbes play key roles in nature: shouldn't we worry about the preservation of microbial diversity?

Don't get me wrong: I don't want any cuties to become extinct. But I think that scientists can do a much better job when discussing biodiversity.



Further reading:

If you find the topic of this post interesting, you must read the following excellent articles written by Sean Nee, University of Edinburgh, UK (articles can be downloaded from the author's website):

- The great chain of being. Nature (2005) 435: 429.

"Our persistence in placing ourselves at the top of the Great Chain of Being suggests we have some deep psychological need to see ourselves as the culmination of creation."

- Extinction, slime and bottoms. PLoS Biology (2005) 2(8): e272.

"There is an old Chinese curse: ‘May you live in interesting times.’ According to those who know about such things, we live in a momentous time, the time of the Sixth Mass Extinction! But most of us do not feel at all cursed. Because, in fact, the Sixth is quite different to the previous Big Five—no-one would notice this one if we were not repeatedly reminded of it by ecologists."

- More than meets the eye: Earth's real biodiversity is invisible. Nature (2004) 429: 804-805.

"We are still at the very beginning of a golden age of biodiversity discovery, driven largely by the advances in molecular biology and a new open-mindedness about where life might be found. But for this golden age to be as widely appreciated as it should, our view of the natural world must change — as radically as did our view of the cosmos when we began looking at it with technologies that allowed us to see more than can be seen with the naked eye."

- Beyond the tangled bank (pdf). This manuscript seems a slightly longer version of More than meets the eye: Earth's real biodiversity is invisible. Interestingly, it includes many references that were not incorporated into the published article.


I also recommend a thought-provoking article by Maureen A. O’Malley & John Dupré, University of Exeter, UK:

- Size doesn’t matter: towards a more inclusive philosophy of biology. Biology and Philosophy (2007) 22, 155-191.


NOTE added on April 17, 2010:
A Letter has just been published by Andrew Beattie and Paul Ehrlich in Science, highlighting what The Missing Link in Biodiversity Conservation is:

"the many millions of species within the numerous phyla of microbes and invertebrates, which represent perhaps 95% of total species and genetic biodiversity."

The authors propose to deliver a new message to the public:

"a new message, one we would like to label "production biodiversity": By protecting microbes and invertebrates, we also protect the primary industries upon which we all depend."

I agree!


Related links:
- (Added April 20, 2010) A commentary on the same subject has been published by Mercè Piqueras in her blog, La lectora corrent (in Catalan): La biodiversitat invisible.

- (Added June 23, 2010) See Dear New Scientist by Ed Rybicki, who reminds us that "the greatest part of the biodiversity on this (and probably any other) planet is viruses."

- (Added August 19, 2010) Preserving endangered species – of gut microbes, by Grant Jacobs. Or the need to preserve the human gut microbes found in ancient rural populations.

- (Added September 11, 2011) Bacteria & archaea don't get no respect from interesting but flawed #PLoSBio paper on # of species on the planet, by Jonathan Eisen.

- (Added September 11, 2011) Don’t forget to count microbes, by David Hooper & Bonnie Bassler.

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