Introducing FriendFeed

I read quite a lot of blogs, and I do so easily and efficiently with google reader. And google reader also automatically tells me what people I know "share" in their google reader. This is great, I click "share" on blog posts I really like and others do the same. However, even though I know a lot of smart people, only few of them seem to use google reader, and they don't all use the "share" button that much.

Fortunately for me, I have found a way to follow the "sharings" of a lot of smart people who share links and post on FriendFeed. And even more, I can also follow the discussions they have about the links and posts (and participate). I follow a bunch of individual people and I follow some "rooms" where people share stuff with a common theme. Eg.

• The life scientists 
• Science 2.0 
• Python for Bioinformatics
  

This is one step up from blogs in sophistication, I think.

Yes they can. Today we are all american.

We were told they cannot do this by a chorus of cynics. And they only grew louder and more dissonant in the weeks and months that came.

We've been asked to pause for a reality check. We've been warned against offering the people of that nation false hope. But in the unlikely story that is America, there has never been anything false about hope.


For when we have faced down impossible odds, when we've been told we're not ready or that we shouldn't try or that we can't, generations of Americans have responded with a simple creed that sums up the spirit of a people: Yes, we can. Yes, we can. Yes, we can.

Digital restrictions management FAIL (again)

I just read the news that the Blue-Ray Digital Restrictions Management system has been successfully circumvented with a Free and Open Source Software program.

Here is 17 pages of fantastic account of how it was programmed. Those guys are pretty cool, I must say. It seems to be a different group of people, but the same community that circumvented Restrictions Management of the other High Definition format, the (now mostly dead) HD-DVD.

Actually this should be mostly uninteresting to me, as I don't own any equipment or any of the High Definition disks. And as even Apples Steve Jobs admits that Blue-Ray is an expensive pile of crap, I probably won't buy it for as long as I can manage to avoid it.

But the announcement reminds me of what happens when industry lobbyist buy and push through international legislation, that is so at odds with common sense that it has to be reinterpreted. Confusion and non-sense happens.

So is the new software legal to distribute? Or to use? Well, it is hard to say as the Danish Ministry of Cultures interpretation of the lobbyist-law (InfoSoc) leaves something to be desired in the "clarity department". I think the general answer is the sensible "yeah, go ahead, we won't care much what you do inside of your own house". But as that conflicts with the actual wording and intention of the lobbyist law that they support, the ministry just leaves confusion instead.

They have two pages (here and here) that explain that the law doesn't not prevent consumer freedom of choice in operating systems and hardware. Except maybe. So the deal is that even though the lobbyist law says that laws should prevent " the circumvention of any effective technological measures[=DRM]" the ministry of culture sensibly says that circumventing DRM to be able to use eg. a BlueRay dist on a GNU/Linux system is ok. But it is not ok to copy from a BlueRay disk.

This then leaves everyone to wonder what to do when the only way to watch a BlueRay disk on linux involves making a temporary copy...alas!

Great new movie review show on DR2

Denmark has a great new movie review show. Premiere on DR2. The host is really cool - so cool, in fact that his first show was retroactively censured for not living up to political correctness standards (supposedly a case of "Don't mention the war-liars in the Danish government").

And here is an attempt at a transcript of his key points of the movie High School Musical 3

Not since Grease has there been a musical phenomenon like this

 

[...]

 

 looks like a propaganda movie created by reactionary parents and the US department of education.

[...]

The movie is clinically purged of loosers and even people who stand a bit out. It is an example of  motivation that is based on fear. Fear of failure, fear of insufficiency, fear of humiliation.

 

[...]

 

 This is the stuff that annorexia and high school massacres is made of.

[then he cuts to a cool interview with Matt Stone...]


And he then gives the movie one star out of six. For "the occasional reference to better movies". It has sort of a Colbert/Stewart flavor. Seems like TV made for my age group. And people with my tolerance of nauseating Disney movies.

Nice - I wish some Danish politicians had listened...

Christmas comes early

This week is rebate-on-organic-stuff week in my local supermarket, Irma. This week the supermarket is promoting only organic wares, and has announced that it hopes to beat its own record from last year of having more than 29,9 percent of the turnover from organic wares.

Since I already buy all the foods I can get organic, I have planned to do my part by running amok in the organic wines, global financial meltdown be damned.

Nobel laureates publish in PLoS ONE

I have discovered that many scientist don't know about the publishing foundation PLoS, and certainly not about the particular journals. Well, PLoS ONE is the, in my opinion, most exiting of the journals that PLoS publishes. It is a multi-disciplinary journal that publishes any paper that is "is technically sound and worthy of inclusion in the published scientific record" and it has a system for readers to submit comments and evaluations of papers.

However when I explain about PLoS ONE, the newness, the multidisciplinarity and the criteria for publication that favor "soundness" over "importance" often does not sound appealing to scientists.

Therefore it is great to notice that the newly awarded Nobel Laureate Françoise Barré-Sinouss recently chose to publish in PLoS ONE. If it is good enough for her ...

How to use Google Reader

Some time ago, I tried to write about how RSS feeds and blog-reader programs makes it much easier to keep up to date with blogs.

Now some cool people at http://www.commoncraft.com/  have made a nice video explaining Google Reader, which happens to be my favorite program to read and share blog-posts. Enjoy.

Managing online communities

A really interesting article about the censors/community managers on the photo-sharing community site flickr.com

http://www.sfgate.com/cgi-bin/article.cgi?f=/g/a/2008/09/29/onthejob.DTL

Neo FreeRunner

I recently got the chance to play with an OpenMoko Neo FreeRunner. It is a small linux computer made as a phone. With a touch screen and lots of fun hardware. GPS, WiFi, Motion sensors - and of course, mobile phone antenna.

However, my initial impression is that it is much more a toy than a phone. It can actually make phonecalls, but many things are wrong with the software that comes with it by default. It is slow, and misses programs for all the fun hardware. And this warning is really scary:

Can't boot with discharged or missing battery

Issue: Neo FreeRunner requires battery power to boot, because Neo FreeRunner consumes too much current while booting to boot with only a charger. Since charging isn't enabled until the Neo FreeRunner has booted, this means that a discharged battery can not be charged. One manifestation of this problem is a kernel panic (red LED flashes constantly) when trying to boot using the power button.

 
Fortunately the FreeRunner can be upgraded with a bit of effort. I'll try that soon. There is hope:  This guy is way ahead of me and seems to be enjoying his FreeRunner now.

Linus Torvalds reviews new flash based disk drives (SSD - solid state drive)

Here.

I want one too.

Mythbusters with helium and SF6

Lise and I are huge mythbusters fans. And incredibly, given our anemic TV channel selection, we have a channel that shows episodes quite frequently.

Here is a favorite clip

Smart Energy Homes in Barcelona

I wonder where they will be built? Poble Nou? I missed the session about Smart Energy Homes at the ESOF in Barcelona.

http://www.guardian.co.uk/environment/2008/jul/21/greenbuilding.ethicalliving

Catholics and crackers

This post reminded me of mess in Denmark about offensive drawings of Muhammed.

And this post (with back-ground story) exactly mirrors my opinion on the drawings (although I think much, much better of PZ Myers than I do of Flemming Rose).

Google docs - for web-polls

I just completed this questionaire - because all the cool kids are doing it. And I noticed that the poll was done with Google Docs. Cool! I haven't bothered to find out how, but I still find it cool. So, Google Docs, and doodle.ch has me covered with all the polling ability I can imagine needing.

PLoS and the future of publishing - as framed by Nature

There has been many good comments about the recent opinion pieces on PLoS from Nature employees (you can find the link via the comments - here is the second).

One perspective which has been overlooked a bit, as far as I can tell is that Nature has managed to frame the debate. Intentionally or not.

The framing can be summarized as "the problem is that top tier journals can't be profitable as open access - author pays, in competition with Toll-Access journals". This framing is advantageous to Nature as it implies that "the author-pays principle must generate all revenue for OA journals - subsidies are not ok". Equally advantageous is it when "top-tier journal" is defined not only as "high rejection-rates" but also "high overheads". Nature has an interest in making the two things seem inseparable.

For society and everyone who is not Nature (or other Toll-Access, high overhead journals) the framing does not make sense. The debate is part of a broader debate of the future of scientific publishing. And it is unreasonable to assume that a future of efficient digital publishing must be hobbled to serve to needs of businesses adapted to the past of high cost of paper distribution. Or that it must be measured by the same criteria of success (high profit from monopoly priviledges) as old businesses.

For society the question (obviously) is "how do we maximize society-gain from published research". There is no question that the enormous subsidy that is coorporation held monopoly priviledges via copyright can make publishing of popular content profitable for some publishers. But since this arrangement maximizes monopoly profit for select organizations and not gain for society, society should look at other arrangements. Other arrangements, which secure access also for those that value the access below the monopoly pricing but above the neglible cost of digital reproduction. And in no area of publishing is the fairness of society interference with current buisiness models larger than science, where the producers of content are mostly publically financed and the consumers also.

Among "other arrangements", one obvious extreme is lump subsidy and no access restrictions. This gives maximum society benefit at a fixed price.

Other arrangements are "some subsidy + other revenue" which is exactly the model that PLoS explores. And which should be explored. And which does not need to be successful by the same measures as Nature was successful in the past.

And as a personal opinion on this - I think that what will (and should) happen is that the market (lead by initiatives like PLoS) will drive costs of top-tier publishing down. Future top-tier publications will simply have to have unbundle, have less costly content, and less costly procedures - and will consequently look different from today. I see an obvious analogy to newspaper-publishing which was discussed at the Becker-Posner blog recently: Posner - Becker

And as Greg Laden relates, Nature supplied somewhat opaque answers to the UK parliament on Nature finances. But from those, to me, there seems to be plenty of costs to cut.

(Updated: fix link, clarify last sentence)

Shucks, real nature needed.

Apparently the nice pictures of bounty islands and pretty scenery that I sometimes put on as background on my computer desktop is not as effective as I hoped. I might as well just stare at the wall.

http://www.sciencedaily.com/releases/2008/06/080610154746.htm

Someone I know on TV

Seat has a new advertisement on TV (Spanish and Catalan - and even Dutch TV). And they have put real Seat employees in the spot. Yay for Seat - it always seems idiotically fake when models pose in company promotional material - especially if they pose as employees.

A fun detail about this advertisement is that the owner of the flat that I live in is in it. He works for Seat.

Danish patent office messup

Some weeks ago I saw a post (on slashdot probably) about a new copyright treaty being negotiated in secret, basically by industry lobbyists.

http://wikileaks.org/wiki/Proposed_US_ACTA_multi-lateral_intellectual_property_trade_agreement_(2007)


The great copyright jurist William Patry blogged additional details here, here, and here.

So I decided to ask on the weblog of the Danish patent office who is representing Denmark in the negotiations, and by which mandate he is negotiating.

First the patent office blogger replied that he would look into the case and then get back to me, but then later both his comment and my subsequent comment was deleted. Well, the comments can currently be found in googles cache - so here they are for reference.

Current blog-post

Google cache from the 11. july before posts were deleted.

Intersting posts on scienceblogs

I normally share interesting blog-posts simply by sharing them from google reader. See the box on the right of the main page of this blog.

Scienceblogs is a wonderful site with blogs about...science (mostly), but unfortunately there are simply too many post that I want to have them in my reader. So I can't share them the usual way.

So here is an interesting post about SAD - "winter depression".

http://scienceblogs.com/corpuscallosum/2008/05/serotonin_transporter_changes.php

And here is one about blogging being good for people

http://scienceblogs.com/evolutionblog/2008/05/blogging_is_good_for_you.php

On being a vegetarian

Andreu from work sent me a link to a story about how one guy feels about being a vegetarian.

The story is well written and funny and I agree. Go have a look here. It is from Slate magazine.

Google Appengine

Last tuesday I was at a meeting in the local python-interest group in Barcelona. We discussed http://appengine.google.com/ - the new service from google that allows people who know just a bit about programming to make their own internet programs.
How is that different from the blogging service that google already offers here on blogspot? Blogspot lets you type text, and then displays the text. Appengine allows you to create a program that lets you input data (directly or indirectly) and then have those data processed and displayed in a structured manner.

Why is this great? Because "activation energy" is a dominant obstacle to creativity, and Appengine lowers the activation energy of making internet programs drastically. With Appengine, you just need to program. The easy and fun task. You don't need to buy a domain name, buy hosting or set up a server, install stuff and look out for the server.

Appengine is the kind of tool that allows the internet to run on love (see below about the internet running on love).

Nuclear winter?

Reading mostly biology papers it is not that often I see a scientific paper with the keyword "nuclear winter".

However, here is one:

http://www.pnas.org/cgi/content/short/105/14/5307?rss=1

Unfortunately it is not open access and I can't find it on arXiv , but I guess the paper shows that nuclear war is an even worse idea than previously recognized.

An honest R&B song

Hat-tip: Mailund

Uh oh, I'm trapped by evolution

I was not made for unlimited information on the internet

http://online.wsj.com/public/article/SB120527756506928579-3wNdJRXhkpLqY4EDBt4j3ly1foo_20090312.html?mod=rss_free

Fun with 3D

PyMol is my favorite program for protein structure visualization. It is Free Software, and I just saw a video about how some people from the University of Toronto have used PyMol to make a module to implement "Head tracking" for giving a 3D feel to looking at the proteins.



The video doesn't give such a great impression of how it will be. But it is really nifty if the head-tracking-by-webcam works.

Here is another video that gives a great impression of how head-tracking (by Wii-mote) works.

Quote of the day

“I’ve reluctantly discarded the notion of my continuing to manage the portfolio after my death—abandoning my hope to give new meaning to the term ‘thinking outside the box.’”

Warren Buffett in his annual letter to the shareholders of BERKSHIRE HATHAWAY, 2007

Link from the Economist

Organic shoes

I spent last week with Lise in Copenhagen. I usually remember to pack all important stuff for my travels, but this time I forgot my indoor-shoes. In order to avoid catching a cold I had to get some. Fortunately Lise remembered that the supermarkets were selling some inexpensive indoor shoes.

Wow. Organic!

Only when I went to the shop and had the shoes in my hand, did I discover that they were all organic. Yay.

An objection to organic farming (and products) I hear somewhat often is that "it cannot feed the world". Well a group of researchers from University of Michigan, Ann Arbor believe it can [non free link :o(]

Here is the news story http://www.ns.umich.edu/htdocs/releases/story.php?id=5936


And on the same subject - a nice story of how to make organic mango, from the Economist http://economist.com/science/displaystory.cfm?story_id=9468901

New apartment

For the last 7 months I've been living with some very nice people in a large apartment in central Barcelona. However, my room is very small and not suited for sharing with Lise when she joins me in June.

In January Lise then started looking at the websites that advertise apartments in Barcelona: loquo.com, idealista.com etc.

The first one she found on loquo looked really good. It is in my favorite part of Barcelona; Poble Nou. And it is close to the beach, the lab, and the main street of Poble Nou. It is also a nice apartment. With a kichen/living room in one. The only thing it misses is a nice balcony with afternoon sun.

The kichen. Nice and new. And with room for a dishwasher (oh joy!)

The only other apartment we actually went to see had afternoon sun in copious amounts. But it had a small kitchen and was expensive.

So the decision was not too difficult. And I didn't even have to take it alone. I went to see the apartment the weekend of the week that I contacted the owners. Lise came for a weekend visit the next weekend, and we were given a second look.

The living room (TV not included, regrettably)

We will rent it from April, and I will move in, even though Lise arrives in July. As there is a nice guest-room visitors are welcome anytime. Yes, that means you!

Prenzlauer Berg

Photo is CC-By by Mishkabear

Since visiting Berlin on a vacation some years ago, I have been dreaming about a flat in Prenzlauer Berg. It is just sooooo, trendy. Apparently others agree, and Henning Sußebach has written about the place and the people. "Too trendy for their own good" seems to be his sentiment. I would still love an apartment there.

(Once again a link I got from Luftskibet )

Stieg Larsson in English

Stieg Larssons crime stories, seem to have been read by half the Danes I know. And now I can mention them to English-speakers too.

The first book in his trilogy has been translated, and it gets a favorable review in the Independent.

I got this news at the blog of Information. Information is easily the best newspaper in Denmark, and "Luftskibet", the collective blog of their journalists fantastic. Is almost better than the newspaper.

Blogging advice for me

I didn't blog from September until after this new year. Or so I thought...

In this nice list of tips for new bloggers one of the original bloggers, Jorn Barger, emphasizes the idea that a blog is mostly about sharing what you find interesting on the web.

I actually did this a bit by posting links on Facebook. Which is really easy, because you can just bookmark a link in Firefox, and press it whenever you're on an interesting page, make a short comment, and then it appears in your "Facebook mini-feed"

Ok. Now I will try to post these links on this blog instead. I'm sure that somewhere there is some software that will make it easy....

Skiing in Masella

Saturday I went on a one day ski-trip to Masella, with a couple of colleagues from the lab.



To me, who grew up in Denmark, and therefore had to travel far to find either nice weather or (skiable) snow it is always amazing that other places it is not so. Masella is less than 2 hours drive from central Barcelona.

The skiing was fine, and so was the weather. But it was a bit expensive. Probably around 100 Euros for the day (transport, ski-rent, lift-pass etc.)

Two things I noted: 1) The car sharing scheme, we used as transport seems really cool. I need to find out more (and maybe blog about it). 2) When we got back to Barcelona, it was striking how polluted the air seemed. Yuck!

New years resolutions

This blog has been dead for a while unfortunately. But as part of my new years resolutions it will be revived. Yay!

Without further ado here are some New Years resolutions:

• Blog at least a couple of times per month (preferably once per week)
• Run ca. 10 km once per week (in preparation for a half marathon in May)
  
• Get to work around 9 am instead of 10 am
• Participate in Open Science