Category Archives: Editorial

Editorial: Return from blog hiatus

For the past six months this blog has sadly been completely silent. The good news is that I plan to get back to blogging now. My reason for the blog hiatus has been exceptionally busy times in the group.

The Novo Nordisk Foundation Center for Protein Research has undergone its first five-year review. As I was the first group leader to start at the center, I have also just been through the first five-year evaluation of my group, which was concluded with a site visit three days ago by Janet Thornton, Alfonso Valencia, and Dmitrij Frishman. Finally, because I was employed as a professor on a five-year contract, I am in parallel being evaluated for contract renewal.

In parallel with these three big evaluations, my first two Ph.D. students Damian Szklarczyk and Heiko Horn have handed in and successfully defended their theses. Congratulations to both of them!

Enough bad excuses. Time to get back to blogging :-)

Editorial: Goodbye Google Reader – a reminder why open standards matter

This morning I woke up to the announcement that Google will be powering down Google Reader, which has long been my RSS reader of choice. RSS feeds crucial to me because it is where I follow numerous science-related blogs, read automated PubMed searches, and receive tables of content from selected journals.

When I recently bought an iPad Mini, however, I discovered to my surprise that there was no Google Reader app for iPad. This made me strongly suspect that Google had no plans to continue Google Reader. It also made me discover Feedly, which turned out to be so good that I preferred reading my RSS feeds on the iPad as opposed to on my computer. I have now installed Feedly for Chrome as well as the Android applet on my phone, so I consider myself fully migrated already. I think this is a lesson that shows the importance of open standards – whereas RSS feeds are crucial to me, replacing the viewer is no big deal.

Editorial: Open KPGP – when open means closed

As a computational biologist, I can only be excited about the Personal Genome Project (PGP). What is especially exciting about this particular project is that they release all data under the Creative Commons Zero public domain dediction, which gives everyone complete freedom to use the data as they wish.

The bad news is that there is still only sequence data available for 16 individuals. I was thus thrilled to see the announcement late last year that the Open Korean Personal Genome Project (KPGP) had released data on another 32 individuals. I was a bit mystified why the data were not available for download from the main PGP web site, though.

When I went to the KPGP web site, which has the very promising URL, I was greeted with this message:

However, the moment I tried to download any data, I was faced with the following long legal agreement, which I had to agree to to get any further:

1) Data Type
Every derived genetic information should be approved by relevant facility board.
1. Genetic information data- Individual’s sequenced DNA and analyzed data.
2. Clinical information data- Clinical information does not include family tree, Phenotype and family medical history.
2) The Commission Process
1. Bioethics committee of Genome Research Foundation will make a decision through policy reviews and case consultation.
2. The Standards Commission
This commission should be controlled by Korea National Institute for Bioethics Policy. Research, associate with potential social risks, eugenical problem and discrimination on the basis of genetic information when it comes to any aspects of physical looking, should be forbidden.
3. The Commission Process
Research project and IRB document, approved in each countries, will be required. If there is no provision for IRB approval, User must agree with additional consent documents that embodies the purpose of the data.
4. Evaluation (It will take at least one week)
3) Policy Agrement
Informed consent shall be documented by the use of a written consent form approved by the IRB, and signed by the subject or the subject’s legally authourized representative. And if necessary, the committee may request, require or otherwise obtain detailed investigation.
Data Release
Any additional costs to the subject that may result from participation in the research.
4) Data Source Agrement
The Genome Research Foundation should review and approve specifying the conditions under which data may be accepted, and ensuring adequate provisions to protect the privacy of subjects and maintain the confidentiality of data. To cite the data source in any publications or research based upon these data, and to provide a copy of any publications, the following citation should be included in any research reports, papers, or publications based on these data: Produced and distributed data should have references in Acknowledgement, Methods, Abstract.
5) Genetic Data Access Use Agreement
1. To use the data set solely for statistical reporting and analysis.
2. Not to share these data with, or provide copies of these data to, any other person or organization. Genetic data user will not use for commercial interests or potential commercialization of the results bring troubling ethical aspects the suggest greater potential abuses than clinical benefits.
3. To make no attempt to link this data set with individually identifiable records from any source, or in any other way attempt to identify the persons in this or other datasets.
4. Personal data will neither be disclosed to any exterior third parties nor be used for any other purposes.
5. That if the identity of any person or establishment in this data set is inadvertently discovered, then (a) no use will be made of this knowledge, (b) the Director of Genome Research Foundation will be advised of this incident immediately (c) the information that would identify any individual or establishment will be safeguarded or destroyed, as requested by Genome Research Foundation, and (d) no one else will be informed of the discovered identity.
6. To return or destroy the data set, and any derivative data files, upon request from Genome Research Foundation.
7. This agrement is contingent upon the approved Genome Research Foundation, and is subject to all the requirements of that agreement.

For those who cannot or do not want to read (poorly formatted and phrased) legalese, this is the polar opposite of open. It explicitly forbids redistribution, commercial use, and deidentification of individuals. It even goes as far as requiring that if I use the data in a publication, I must cite KPGP in the abstract. It is in other words closed.

To add insult to injury, I subsequently filled in a form to request access and waited for weeks for someone to grant me an account, only to discover that I cannot download the data even when logged in with said account. Instead the web site requests me to go through the same approval procedure again.

Editorial: What is the difference between Twitter and Second Life?

I admit that this may seem a strange question. One is a microblogging platform that allows you read and write messages of at most 140 characters. The other is a 3D virtual world. They are, however, both communication tools, and I think there is a completely different reason why Twitter is so much more useful to me than Second Life is.

If I go to the Twitter web site and log in, I see this:

It is Twitter. It immediately shows me the main content: tweets. It also allows me to create content, that is to tweet.

By contrast, if I go to the Second Life web site and log in, I see this:

It is not Second Life. It is a complex web interface that gives me access to account administration tools and shows me lists of blog posts by Linden lab, comments from Second Life users, items for sale on Xstreet SL, and video tutorials. In the lower left corner it shows me the only really useful information, namely which of my friends are online. That is, the friends that I would have been able to chat with, had I been in Second Life and not on the web site, which does not allow you to read or write messages.

Imagine if the web interface of Second Life would instead show me this:

It would be Second Life. It would immediately show me the main content: the virtual world. It would also allow me to interact with the content, that is to move around, to chat with people, and even to create content. Do you think Second Life would have more users if it would run inside your web browser? I think so. Linden Lab is and has been focusing on improving the initial user experience in Second Life to improve the retention rate (i.e. the fraction of new users that continue to come back). I am not saying that this is not important, but I think that most of the potential users are lost long before they even get into the virtual world.

This is by no means a problem that is specific to Second Life. Today, asking users to install a piece of software on their computer will cause the majority of people to shy away before they have tried your product. Even just asking users to create an account will cause many to turn around and walk away. When it comes to social networks, the decisive factor is users. If your friends are not there, why should you? Imagine a virtual world that would run in your web browser and which you could sign into using OpenID, Twitter Connect, or Facebook Connect. Would your friends be there? Would you?

Editorial: Social network plumbing

I guess it is no secret to anyone that Facebook as agreed to acquire FriendFeed. Several people seem puzzled why I left FriendFeed only 3 hours after learning this news. I can understand that this may look like a knee-jerk reaction, but there is logic behind the madness.

The truths is that my existing setup of Web 2.0 services was not working nearly as well as I would like. The sheer amount of content being shared on FriendFeed meant that it was easy to overlook a blog post from one of my favorite bloggers, for which reason I still subscribed to their blogs as RSS feeds. This caused me to waste time because the same posts appear in two place, and I could not filter out the blogs on FriendFeed because most comments would be posted there and not on the blogs. Receiving everyone’s tweets on FriendFeed tended to create a background noise that would drown all other conversation; however, I could also not filter out the Twitter streams on FriendFeed and follow people directly on Twitter instead because many cross-post all their FriendFeed “likes” and/or comments to Twitter!

Given the new situation, it was clear to me that the time had come to fix my broken social network setup and redo the plumbing in such a way that FriendFeed would no longer be responsible for gathering most of the content. Looking at FriendFeed, I discovered that most of the content of interest originated from just three sources: RSS feeds of blogs, Google Reader shared items, and Twitter. By following people directly on Google Reader and Twitter, both of which I was already using on a daily basis, I was thus able to relegate FriendFeed to a much less important role. I still feed my content from other sources into FriendFeed and I occasionally check for comments on my posts; however, it is no longer where I read content posted by others. Coincidentally, the new role of FriendFeed is almost identical to the role that Facebook has played all along.

To make a long story short, I’m not leaving the friendly community at FriendFeed in anger. I still read the content produced and shared by the same people as before. I have just fixed the plumbing.

Editorial: Virtual conferences in Second Life

This blog has been very quiet for a long time. There are several reasons for this, most of which are positive: I have not had many boring or negative results to write blog posts about, I have been busy writing manuscripts about the positive results instead, and I have moved to Copenhagen where I am busy starting my own research group at the Novo Nordisk Foundation Center for Protein Research. There is also one more reason for the absence of blog posts from me: I have spent a lot of time experimenting with Second Life, and that is the topic of this blog post.

I first got interested in Second Life when I heard that Nature Publishing Group was setting up a virtual conference center called Elucian Islands. In the beginning I felt very alone on Elucian Islands. There was a good reason for that – I was alone most of the time. My view on Second Life was thus that it was pretty (see images below) but rather useless.

I obviously took a look at the SciFoo presentations (seen in the background of the image above) and the other scientific displays at Elucian Islands and elsewhere in Second Life. However, these mostly reinforced my negative view of Second Life being fairly useless, since almost everything I saw was already being served better by dedicated resources. For example, slide shows are much more conveniently viewed and shared in SlideShare than in Second Life, and 3D protein structures can be examined and analyzed better in programs such as PyMOL.

Over at FriendFeed, Jean-Claude Bradley fought a brave fight trying to convince me that Second Life is in fact useful for science. His key point was that Second Life is all about interacting with people, so I should try to go to some scientific events in Second Life. Sadly, there are still not many such events, and although they have changed my view on Second Life, they have also shown that there are many problems that remain to be solved.

The first virtual seminar I went to was “Cancer, Cell Cycle, and Check Points” organized by Digi S Lab. This was a perfect match since I work on cell-cycle regulation myself. The seminar consisted of two excellent presentations given by Letizia Cito from Sbarro Health Research Organization and Fayamdria Foley from the American Cancer Society.

Meeting on Cancer and Cell Cycle 1

Meeting on Cancer and Cell Cycle 2

Whereas the presentations were great, the seminar also illustrated several of the problems that need to be overcome before virtual conferences in Second Life are ready for prime time. When the first talk started, I could not see any of the slides. Restarting my Second Life client did not solve the problem, nor did a reboot of my computer. After giving up solving the problem, the entire region in which the seminar took place suddenly crashed causing speakers and participants to all be logged out. When it came back online after some minutes and everyone had found their way back, I could suddenly see the slides. Even then, however, they took so long to appear on my screen that the presenter had typically explained half of what was on a slide by the time I could see the slide. I see this as a major problem that must be solved before Second Life conferences can work properly – it must be possible to change slides without a noticeable delay.

The second event I went to was the “ESRC Complexity Research Seminar in Second Life” that took place at Elucian Islands. This seminar was very different from the one described above in that it was not a purely virtual seminar; instead it was a video feed from a real-world seminar that was being transmitted into Second Life. Think of it as a virtual overflow room – the image below shows the people who had gathered shortly before the event started.

ESRC Complexity Research Seminar

Sadly, this event was marred by technical problems. The sound stream was of such poor quality that the Second Life participants could barely understand a word of what the speakers were saying, and the video stream was of too low quality to be able to read their slides. I do not want to dwell on this but just note that good quality microphones and cameras are a prerequisite for streaming events into Second Life.

The third event I went to was the “Virtual Conference on Climate Change and CO2 Storage“, which again took place at Elucian Islands. This was again a mixed event taking place both in the real world and in Second Life. The presentations were excellent and important lessons had been learned from the previous events. The microphones worked perfectly this time, and the video feed had been abandoned in favor of showing a copy of the actual slides in Second Life, which greatly improved the readability.

In addition to these events, Elucian Islands now also runs regular events such as the weekly Nature Podcast event where a fairly large group of people gather to listen to the latest podcast shortly after it has been released (image from Joanna Scott’s blog).

Nature Podcast at Elucian Islands

Regular events are crucial in SL because they bring people together in the same place at the same time. The need for people to be online at the same time is in my view one of the major drawbacks of Second Life compared to other tools that researchers can use for social networking. In my view Second Life should thus not be seen as competing with tools like FriendFeed or Twitter, which you can read when you feel like it, but rather as virtual reality alternative to video conferences. I think that Nature Publishing Group is on the right track with this, and I hope that the few remaining technical hurdles will be overcome in the near future.

Full disclosure: I have been working with the staff from Nature Publishing Group trying to solve technical challenges on Elucian Islands.

Editorial: Live blogging – not so easy

I am now back from two weeks in Italy where I experimented with live blogging. You have probably noticed that some presentations from the meeting at CoSBi in Trento were covered on Buried Treasure within a matter of minutes of them ending. Also, quite a number of pictures were posted in the associated Picasa web album while the presentations were still ongoing. Here is a brief explanation of how I planned to pull this off and how it worked in practice.

My original plan was to use WordPress through the web browser on my smartphone together with a foldable bluetooth keyboard. This was how I first imagined that my live-blogging platform would look:

Live blogging - WordPress, HTC S710, and bluetooth keyboard

It seemed a good idea at the time, but there were a couple of “minor” problems:

I thus started looking around for alternative clients for WordPress and eventually found ShoZu, which allows you to upload pictures from your phone to a variety of services including WordPress blogs and Picasa web albums. However, it is not a true blogging tool and only enables you to write a short description for each picture. I thus accepted to the real blog posts would be written on my laptop, whereas the following platform would be used for live blogging in the form of images with short descriptions:

Live blogging - ShoZu and HTC S710

This seemed like an even better idea at the time, but again I ran into a few technical problems:

  • Due to strange combinations of firewalls, HTTP proxies, and complex login web pages, I never managed to get my smartphone reliably connected to the internet.
  • The camera in the smartphone was unable to take even half decent picture under the poor light conditions.

In reality, I thus ended up using my old Apple PowerBook G4 and my Lumix TZ3 camera. They got the job done in terms of covering the presentations, but live blogging from poster sessions was practically impossible.

I have now put on my thinking cap to come up with a live-blogging platform that would work for poster sessions. You generally have too little time for too many posters, so it has to be very fast to snap a photo and post it. The light is often poor and people tend to use too small fonts on their posters, so you need a good camera to get a readable result. Finally, the lack of space and tables prevents you from using a laptop. The Eye-Fi Card  might be a solution as it would enable me to upload images directly from my camera to, for example, a Picasa web album or Flickr. Please let me know if you have any ideas, experiences, or thoughts on this.

Editorial: No intelligence involved

You may have heard about the controversial movie “Expelled: No intelligence Allowed” by Ben Stein in which people behind the intelligent design movement whine about being suppressed the scientific community. The truth is obviously that intelligent design is not a falsifiable theory and hence simply does not qualify as science.

However, the movie is also controversial in other respects. To start with the producers conned both Richard Dawkins and fellow blogger PZ Myers into participating in the movie by interviewing them under false pretense.

Richard Dawkins and PZ Myers thus both registered for participating in a public screening of the movie. But while queuing up for the movie, PZ Myers was identified by security officers and told to leave the premises – immediately! Oh the irony, oh the double standard. They make a movie about suppression of views, they call it “Expelled”, and then they expel a person whom you conned into participating in the movie because you disagree with his views.

But it gets even better. The very same security officers were apparently oblivious to the fact that Richard Dawkins was standing right next to PZ Myers and thus let him enter to watch the movie. PZ Myers immediately wrote a blog post about it, while the movie was still being shown to the audience – including Richard Dawkins.

After the movie, Richard Dawkins (of course) stood up and asked why PZ Myers was not allowed to see the movie. The answer? Because he did not have a ticket and was thus a gate crasher! Very interesting explanation since it was not a ticket event – you simply had to register a seat, which PZ Myers had done.

The two gentlemen have now posted an interesting little discussion on YouTube in which they humorously describe the incident as well as just how bad the movie really is:

Richard Dawkins also reveals that Expelled includes one of the beautiful movies produced by the multimedia team at Harvard. You really have to wonder if they actually got permission for that, if they conned the people at Harvard as well, or if they just resorted to plain old plagiarism. In any case, this has to be one of the biggest PR disasters ever made by the intelligent design movement.

Expelled from Expelled: no intelligence involved.

Editorial: One month anniversary

When I launched this blog just a month ago, I wrote that it was an experiment and that I would later evaluate if it was worthwhile to continue. I am very happy to already now be able to declare the experiment a success. With over 2000 views during the first month and around 50 subscriptions to the RSS feed, Buried Treasure is certainly worthwhile writing – I hope you also find it worthwhile reading.

In the near future I plan to experiment with live blogging. The idea is to provide coverage of the conferences and meetings that I attend. To avoid polluting my blog with dozens of short posts consisting of just one or two sentences and a photo, I have setup an associated Picasa web album. This is where the main action will happen – I plan to post only highlights and summaries here on the blog. You can find the RSS feeds for the album and the blog in the sidebar.

Editorial: Why “Buried Treasure”?

I’m a computational biologist who tends to work on way too many projects at any one time. Many of these result in observations that I find interesting – but not interesting enough to bother writing up a manuscript and sending it to a peer-reviewed journal. In other cases the results were simply negative and no conclusions could be drawn. My disk may thus contain “buried treasure”.

My primary goal with this blog is to make my never-to-be-published observations openly available. As I don’t plan on continuing these projects, anyone is welcome to pick up a project and continue where I left off. I also plan on reporting negative results on this blog so that others can hopefully avoid repeating analyses that would lead them nowhere.

Please note that this blog is an experiment. Over the next few months I will try to write up a number of posts on various projects. After a test period, I will make up my mind about whether to continue or not. This depends on how many people read and comment my posts vs. how long it takes me to write the posts. Like for all other experiments, time will tell if it becomes a success.