Posts By Giorgio

IDA and the media

IDA
Big big fuzz about IDA, today. See here for a rather sensationalistic article on SkyNews or here for one slightly more critical on BBC. I cannot really judge on the importance of the discovery itself; sure enough I can say that the words “missing link” mean nothing at all and I am glad that at least have been left out of the paper. No doubt, though, that IDA is being sold as “the missing link that is proving Darwin was right” — even the name, Darwiniun Masillae, seems to have been chosen for the very same reason.

Now, what really strikes me is the mediatic event that was created around this discovery. Big fanfare presentation in NYC, with opening words of  the city Major; a book, scheduled to appear on amazon on the same day; BBC documentary; a website dedicated with videos, interviews and everything else. Is this appropriate? Not sure.

This is what the authors say about the mediatic event:

The scientific publication of Ida has been carefully timed so that the film, book and website can be launched at the same time. The scientists see this as a new way of presenting science for the 21st century, where a major scientific find becomes available to everyone, wherever they are in the world at the same time. Ida connects to us all, and we can all share in understanding her.

As Jørn Hurum explains, ‘I really like the idea that it’s now possible for people to look at the website or to see the film or read the book at the same time as the scientists read the scientific paper. You can get many different levels of understanding, but you get out the important messages in different ways at the same time. Humans are not special – we’re related deep in time to more primitive mammals. And the best way to tell this story is Ida, and this, I hope, will be the message that will come out.’

The explanation is plausible after all: times are changing and why not use new means for communicating Science? At least authors are pretty coherent: kudos to them, for instance for having picked PLoS ONE for publishing their paper and for advocating OA. From the PLoS Blog:

We asked Dr Hurum about the factors that influenced his decision to publish the article in PLoS ONE.
“Choosing PLoS ONE as the venue for publication was easy,” he explained. “First of all the journal is Open Access. I am paid by the taxpayers of Norway to do research and outreach from The Natural History Museum in Oslo. Why should a large publishing group then own my research and sell it in pay per view or expensive subscriptions to interested people around the world? I feel this is not moral when they have not supported my research at all but wants to make money on my several years of work without any compensation.”
“Secondly PLoS ONE’s lack of restrictions on the length of manuscripts and the number of figures attracted us; we wanted to publish a full anatomical description with lots of illustrations. In other journals this would have been impossible or the page charges would have been enormous.”
“Thirdly, PLoS ONE is the quickest way to publish a large work in the world!”

I still have to decide on whether this was a bit too much. We all know regular media tend to shoot pretty high every time but seems this time is a bit different.

Edit: when the news hits the google doodle you know it is a big deal.

WolframAlpha (only the screencast for now)

Here, an impressive demo of what it promises to be the next big thing on the Internet. Wolfram Alpha is been created by [[Stephen Wolfram]], creator of [[Mathematica]] and it is supposed to become available starting from May 2010. It seems like it could be an amazing example of data mining technology and could prove very useful for bridging technical knowledge to every day curiosities.
And here, a review of a first public demo run.

EDIT [2009/05/17]. Seems the service is online starting from yesterday. You can calculate things like Normality of 37%HCl or your exact age in seconds.

What I Think About When I Think About Manuscripts – I, Editor – Henry Gee’s blog on Nature Network

Perhaps what I am getting at is that scientific papers tend to be static. The best literature – of any kind – has a beginning, a middle and an end, in which the protagonists undertake some kind of journey, whether geographical or spiritual, and are changed by their experiences. In scientific papers, the results often give us no clue to the back story – the reason why the researchers were studying this system or that, and the tale of chances and mistakes and serendipity that led them to that point. The only readable parts tend to be the introduction, in which literature is summarized (a classic case of telling but not showing) and the discussion (in which the new result is integrated into what is already known).

via What I Think About When I Think About Manuscripts – I, Editor – Henry Gee’s blog on Nature Network.

GPG Key

I decided time had come to get a [[Pretty_Good_Privacy|PGP key]].
Here is my public ID:
1024D/DE8D92BF
This is my fingerprint:
6BA6 61B1 A198 8DDF 50BF 7F2A DE7F 773B DE8D 92BF
And from here you can download my public key.

Additional notes:
Quick notes for GPG syntax (here)
Creating SSH keys (here)

Project GREAT: General Relativity Einstein/Essen Anniversary Test

This is kind of old (goes back to 2005/7) but fascinating. This guy got 6 atomic clock. He left 3 at home and he took the other three to a weekend outing on Mt. Rainier (~1500 meters above) – along with his three kids, of course. All this to test one of most famous Einstein’s postulates. Here’s the link.. Don’t miss the family pictures section.

Videocapture for linux

If you did some hacking with a webcam and python, you probably ended up using the Videocapture module by Markus Gritsch. Unfortunately, the module does not work on any operative system other than windows, which could be a problem if you wish to make your application platform independent. So, here you will find a linux version of Videocapture. It has been tested on ubuntu distributions. It will run as long as you have installed

  • python 2.5 (maybe others too)
  • PIL – the python imaging library
  • opencv

You can download it here. Some functions are actually not active (namely those that would call the configuration panels). It should work on mac too. Please, if you try it on a mac, let me know how it went.

Enjoy.

WinGooglizer

If you are a Linux user you probably already know and appreciate that (amazingly) simple piece of software that is googlizer. If you don’t know what I am talking about: googlizer is a tiny gnome applet that sits in your taskbar; everytime you click on it, it will start a google search using the text in your clipboard as query. Just select the text using your mouse to copy it in the clipboard, then click on the G icon of googlizer and voila, your google search is already waiting for you in your favorite browser.

Being myself a ubuntu user I love the googlizer but sometimes I need to work on computers running windows OSs. I decided to invest 20 minutes of my time (while waiting the confocal to do its work) to make a windows clone of Googlizer.

You can dowload it from here (it’s free, as in free beer of course). To completely emulate X copy&paste functions you may want to consider using True X-Mouse Gizmo as well.
Is written in Python then compiled to exe using py2exe and the installer is build using Inno Setup. In case you are interested in the source, here you’ll find the python code for wingooglizer, the py2exe setup file and the iss inno script.

WinGooglizer works fine on windows xp, sp3. I guess it will work on any Windows OS. Enjoy and let me know how it works for you.

pySolo: a complete suite for sleep analysis in Drosophila

Bioinformatics. 2009 Jun 1; 25: 1466-1467
pySolo: a complete suite for sleep analysis in Drosophila
Giorgio F. Gilestro, Chiara Cirelli

pySolo is a multi-platform software for analysis of sleep and locomotor activity in Drosophila melanogaster. pySolo provides a user-friendly graphic interface and it has been developed with the specific aim of being accessible, portable, fast and easily expandable through an intuitive plug-in structure. Support for development of additional plug-ins is provided through a community website.
Availability: Software and documentation are located at http://www.pysolo.net. pySolo is a free software and the entire project is leased under the GNU General Public License.
Go to pubmedDownload PDFlink to the website

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From this page you can easily interrogate the PubMed database by restricting your queries to only certain journals. This feature is not available on the Pubmed site. Check the box next to the group category to include all the journals belonging to that category or select the journals one by one.
The list is currently restricted but it will grow and eventually it will be possible to customize it with per user settings. This page requires javascript and it has been tested on Firefox and Internet Explorer. Please let me know if you encounter problems with it or just drop me a line if you want me to include new categories and new journals.   

Widespread Changes in Synaptic Markers as a Function of Sleep and Wakefulness in Drosophila

Science. 2009 Apr 3;324(5923):109-12
Widespread Changes in Synaptic Markers as a Function of Sleep and Wakefulness in Drosophila
Gilestro GF, Tononi G, Cirelli C

Sleep is universal, strictly regulated, and necessary for cognition. Why this is so remains a mystery, though recent work suggests a link between sleep, memory, and plasticity. However, little is known about how wakefulness and sleep affect synapses. Using Western blots and confocal microscopy in Drosophila, we found that protein levels of key components of central synapses were high after waking and low after sleep. These changes were related to behavioral state rather than time of day and occurred in all major areas of the Drosophila brain. The decrease of synaptic markers during sleep was progressive and sleep was necessary for their decline. Thus, sleep may be involved in maintaining synaptic homeostasis altered by waking activities.

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