SWITCH Conference, Coimbra: Science [en]

Running notes from the SWITCH conference in Coimbra. Are not perfect. Feel free to add info in the comments, or corrections.

José Pereira-Leal

Human genome: internal representation of our building blocks (assembly plan). Reading that “book” is an operation that has been going on for more than 10 years, and is an ongoing battle between public and private initiatives. Thousands of people involved, billions of dollars. Halfway through the process, somebody decided it was going nowhere, and went “private” => do this **and** make money in the process.

Public: taxpayer money goes into research, research is public, made available, and not owned by a corporation.

Genome: 3G letters (A, C, T, G)– 1 human cell = 1.8m of DNA in a space < 0.00001m. Very compact! Today, we know that less than 5% (probably less than 2%) actually means anything. Each cell reads a different part of the instructions.

Bioinformatics is at the crossroads of biology, computer science, maths, physics… Breakthroughs in computer science (e.g.) can dramatically speed up the process of deciphering the genome *steph-note: I think that’s what he said*.

Malaria: mass murderer => in the cell of the plasmodium, there are the remnants or an engulfed algae, and bioinformatics predict it should be possible to kill the parasite by using stuff that kills the algae, without harming the host.

For a proposal like that (fosmidomycin) to go into clinical trials, it would take 10 years. With bioinformatics, 2 years *steph-note: if I understood correctly*.

What else? Breast cancer. We need markers for disease prognosis and response to chemotherapy, and we need to know how well they predict. Approach: take an oncologist and a computer scientist, and data integration tools (bioinformatics) + data. *steph-note: something about HLA-G*.

Other thing: bacteria who live in human cells. Bioinformatics discovered that these bacteria lack copy redundancy (no spare tires) and we can predict which drugs will kill them.

From academia to commercialisation: need a business-friendly environment.

Archon Genomics Prize.

**Monica Bettencourt Dias**

PhD on cell biology of heart regeneration.

Cell proliferation. Mutant drosophiles (fruit fly).

Seeing is believing: with a microscope you look at fixed cells, but now it’s possible to actually see live cells. *steph-note: photo of jellyfish, reminds me of my trip to the Oceanarium on Monday ;-)*

Cell cycle. If you lose part of the genome in the process, you can lose very precious proteins. Two important moments for us: chromosome duplication, and mitosis (where it can go wrong from the DNA point of view).

*steph-note: Monica is showing us some video sequences of cells dividing, etc. — pretty cool! Nuclei tugging away from each other to separate the chromosomes. tug-a-war!*

Centrosome helps distribute the genetic material equally between the two cells.

Interesting questions: How are the centrioles formed, and what is the role of the different structures in development and disease?

SAK/PLK4 is a centrosomal protein needed for centriole duplication in flies and humans. Does SAK-dependant centrosome duplication rely on a template? What happens if there is too much SAK? *steph-note: oops, the science has lost me — very interesting but I must have skipped a bit here and there*

Of course, all this has a link with figuring out cancer cells…

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Ada Lovelace Day and Backup Awareness Day: Today! [en]

Completely accidentally, Backup Awareness Day collides with Ada Lovelace Day in March. And it’s today, March 24th.

So, I’m going to ask you (yes you, faithful readers!) — if you have a blog — to write two blog posts today, as I will. They don’t have to be long. They don’t have to be perfect. L’essentiel, c’est de participer — taking part is more important than performance.

I would also be very grateful if you took a few minutes to spread awareness about these two events amongst your friends and network. Post a link on Facebook or Tumblr, tweet about it (hashtags are #ALD10 and #backupday), send an e-mail or two, mention them to your IM buddies.

Thanks a lot for taking part and helping spread the word.

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A Month From Now: Ada Lovelace Day [en]

A month from now exactly, on March 24th, it will be Ada Lovelace Day. I urge you to sign the pledge to participate and to spread the word around you so that we can reach our ambitious target of 3072 bloggers writing about a female role-model in tech or science on that day.

There are many brilliant and inspiring women in the traditionally male-dominated scientific and technical fields who often do not get as much attention or “screen time” as they might deserve. This is a real shame, all the more because women need to see female role models more than men need to see male ones, as Suw Charman-Anderson, the initiator of Ada Lovelace Day, explains very well in last year’s kick-off post. Ada Lovelace Day is a direct solution to this, by inundating the blogosphere with posts about inspiring women over the space of a day.

I took part last year by writing a post in French about Marie Curie. Ada Lovelace Day 2009 was a big success, with around 2000 people participating, media attention, a comic which took on a life of its own to become The Thrilling Adventures of Lovelace & Babbage and even a T-shirt, and the drive to organize Ada Lovelace Day 2010, complete with a higher target for people participating, and offline events.

We need your help to make this happen and reach our target of 3072 people participating. What can you do?

  • sign the pledge and blog about a woman in tech you admire on March 24th (please read the FAQ for more information about the why and how)
  • write about Ada Lovelace Day on your blog, and tweet about it to spread awareness
  • talk to the people around you: if you know any bloggers or influential people, ask them to participate too and spread the word
  • join the Ada Lovelace Day group on Facebook and invite your friends to join too
  • organize an offline event in your town!

I know that for many of you who think the event is a great idea and want to participate, the big question is “who should I blog about?” — particularly if you already took part last year. Here are a few thoughts to help you out:

  • you can write about any woman, be she alive or dead
  • the woman you choose to write about does not have to be famous — but she can
  • you can write about more than one woman if you like — or just about one
  • think of the women who have influenced or inspired you in some way or another throughout your life (teachers? family members? public figures? historical figures? friends? colleagues?)
  • “tech and science” is a pretty loose field, on purpose
  • if you are in the field of science or tech, look around you: are there women you know (or know of) who are not getting as much recognition as they would deserve?
  • your post doesn’t have to be about “the woman who most inspired me” or “my absolute top role-model, and she happens to be a woman” — go for “a woman who inspires me, or whom I admire”.

“Blog”, here, is shorthand for any kind of publication: video, podcast episode, web comic, newspaper column…

Thanks a lot for being part of Ada Lovelace Day!

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Journée Ada Lovelace: Marie Curie [fr]

L’hiver de mes quinze ans, je me suis plongée dans des ouvrages scientifiques écrits par Isaac Asimov. De fil en aiguille, j’ai emprunté à la bibliothèque d’autres ouvrages, et fait mon éducation dans les domaines de la physique des particules, l’astrophysique, et la chimie.

J’avais jusque-là une vague ambition d’être prof de maths. Mais après ce contact avec le monde de l’infiniment petit et de l’infiniment grand, c’était décidé: je serais physicienne, chercheuse, scientifique — comme Marie Curie.

Du coup, je suis partie en section X au gymnase (ça n’existe plus, mais à l’époque, c’était une spécialité vaudoise qui combinait les programmes des sections latine et scientifique) et en chimie à l’université.

Aujourd’hui, c’est la Journée Ada Lovelace: et la femme admirable dont je veux vous parler, c’est Marie Curie. J’ai longuement hésité entre vous parler d’une figure historique ou d’une des nombreuses femmes contemporaines et plus proches de moi, et je me suis finalement décidée pour Marie Curie.

Je crois que le role qu’elle a joué en tant que modèle dans mes aspirations d’adolescente est une démonstration parfaite de l’importance d’avoir à portée de main des modèles féminins, et par conséquente de la pertinence d’une journée comme Ada Lovelace Day.

Si j’ai entrepris des études scientifiques, c’était donc parce que je me voyais chercheuse. L’image que j’avais dans la tête, c’était Pierre et Marie Curie dans leur labo — et cette femme, prix Nobel du tout début du XXe siècle… j’avoue qu’elle m’impressionnait.

En général, on mentionne “Pierre et Marie Curie”. Le couple un peu romantique de scientifiques découvrant la radioactivité, la main de Marie photographiée aux rayons X par son mari Pierre… Dans de tels cas de figure, on a vite tendance à mettre la femme un peu dans l’ombre de l’homme. Remettons l’eglise au milieu du village, si vous voulez bien.

Tout d’abord, c’est Marie qui entame ses recherches sur le rayonnement de l’uranium pour son doctorat. Un an plus tard, Pierre abandonne ses propres recherches (sur la piézoélectricité) pour la rejoindre dans ses travaux sur la radioactivité (c’est d’ailleurs elle qui a inventé ce terme). Ils obtiennent en 1904 avec Henri Becquerel le prix Nobel de physique. Elle est la première femme à recevoir un prix Nobel, et également la première femme lauréate de la Médaille Davy.

Pierre Curie meurt accidentellement en 1906. Marie vivra jusqu’en 1934 — en fait, la plus grande partie de sa carrière scientifique se fera sans son mari à ses côtés.

Elle reprend le poste de professeur à la Sorbonne de son mari décédé, devenant la première femme à enseigner dans la prestigieuse université (professeur titulaire en 1909). En 1911, deuxième prix Nobel, de chimie cette fois-ci. Elle est la première personne à recevoir deux prix Nobel pour ses travaux scientifiques, et la seule femme à ce jour.

Elle dirigera ensuite le laboratoire de physique et chimie de l’Institut du Radium (futur Institut Curie), passe son permis de conduire en 1916, et participe à la création d’unités de radiographie mobiles (les Petites Curies) pour pouvoir directement prendre des radios des soldats blessés au front, sur place. En 1925, elle crée avec sa soeur l’Institut Radium à Varsovie.

Si la vie et l’oeuvre scientifique de cette femme extraordinaire vous inspirent (j’ai mis des heures et des heures à écrire ce billet, finalement, parce que je me suis plongée dans des lectures de biographies que je n’avais pas prévues!), les articles Wikipedia en français et en anglais sont de bons points de départ (n’hésitez pas à utiliser les liens cités en source à la fin de chaque article… il y a de la lecture!)

Et vous? Qui sont les femmes scientifiques que vous admirez? Choisissez-en une, qu’elle soit célèbre ou non, et parlez-nous d’elle pour la Journée Ada Lovelace. Je me réjouis de vous lire!

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Today is Ada Lovelace Day [en]

Today, March 24th, is Ada Lovelace Day — an occasion to celebrate outstanding women in technology.

I’ll be publishing my post later in the day — I look forward to reading yours!

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Twitter Metrics: Let's Remain Scientific, Please! [en]

[fr] On ne peut pas prendre deux mesures au hasard, en faire un rapport, et espérer qu'il ait un sens. Un peu de rigueur scientifique, que diable!

10.02.2011: Seesmic recently took its video service down. I have the videos but need to put them back online. Thanks for your patience.

Video post prompted by [Louis Gray’s Twitter Noise Ratio](http://www.louisgray.com/live/2008/04/whats-your-twitter-noise-ratio.html). I’m still [somewhat handicapped](http://climbtothestars.org/archives/2008/04/24/the-neighbours-cat-won/) and [used up my typing quota this morning](http://climbtothestars.org/archives/2008/04/27/diigo-i-think-i-like-the-idea-bonus-content-conversation-fragmentation/). corrections: measure time, measure **distance** (not “speed”) My graphs: Louis Gray's Twitter Noise Updates/Followers Ratio Zoom in to the beginning of the graph: Twitter Noise, extremes removed Attempt to spot trends: Twitter Noise Updates per Followers, annotated Not conclusive. See also: [Stowe’s Twitterized Conversational Index](http://www.stoweboyd.com/message/2008/03/scoble-on-the-s.html) — interestingly, Stowe became much more “chatty” on Twitter lately 😉 **Update: The Problem With Metrics** — a few thoughts on what metrics do to the way we behave with our tools. Confusing ends and means.

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LIFT08: Kevin Warwick, the "Cyborg" [en]

*steph-note: live blogged notes, may be incomplete, etc. Kevin is exploring where the machine starts and the human stops.*

Two things:

– chips in humans
– rat brains in robots

LIFT08 139

Working with Parkinson’s disease — deep brain scans to try to detect the illness before the tremors begin.

Research partly to help people, partly for enhancement. Eg. man who lost his arm to cancer, and has a robotic hand, but must use his exiting hand to control the robot arm. A bit silly! Would be better if he could control it directly — that would require an interface between the arm and the brain/neural system.

Increase sensory range.

Kevin has a chip with 100 electrodes implanted (fired!) in the nervous system of his left arm. 4mm in diameter.

*steph-note: wondering if that hurt?*

For three months had his nervous system partly out of his body. (Had to be careful to not short-circuit it when taking a shower). Part of this was to experiment stuff to help people with disabilities.

*steph-note: not sure I quite understood what the thing sticking out of his arm was — something to link him to the computer — and also if the chip was removed after three months or not.*

When Kevin was connected to the internet, if you had known the IP address of his nervous system… But what they did is not tell anybody what they were doing until they had done it. Careful not to get your nervous system spammed or hacked!

Highlights from the experiment. Output from the sensors fed to his nervous system (fancy thing on his wrist).

LIFT08 141

When an object came closer, his brain received and increased frequency of ultrasounds (?). So basically with a blindfold on, Kevin was able to move around and detect objects pretty accurately. Not what they were, but where they were.

“It felt like something was coming close to me.” Extended the sensory range. Like “what does it feel like to see something”?

LIFT08 142

*steph-note: showing a short video clip. It makes Kevin sound like Terminator! Will add link if somebody gives it to me.*

Experiment with his wife: when his wife moved her hand, he felt it. He could actually feel her movements.

*steph-note: Daleks in the video!!! I find it hilarious — the angle this video takes.*

Jewellery his wife wears, and the colour changes with his excitement: blue, calm, flashing red: excited. “What is he doing? and with who!?”

Through the internet, made a robot hand mimic what his hand did, with feedback. Objective: hold an object. Good news for people who have been amputated. But also, stretching Kevin’s body across the Atlantic.

His wife had wires pushed into her nervous system from the outside. Very painful! But no anesthetic, because the doctor said he needed to see if he made good contact. It hurt!!

Linked their nervous systems. When she moved her hand, his brain received pulses. Worked very well. Vice-versa: “like lightening running through her hand” when Kevin moved his.

Kevin’s research is now moving from nervous system to the brain directly. Brain to brain communication! Telepathy. Ideas, codes, concepts, images. Upgrade these humans. Communicate in a respectable way!


The implant was taken out because the wires coming out were starting to break, it was an experiment — a lot of practicalities.

Kevin’s experiment changed the way people look at things medically. “Cyborg” is not anymore a purely SF term.

Lots of things could have gone wrong with the experiment, but as a scientist, it was tremendously exciting! Discovered stuff about the nervous system that nobody knew, because nobody had done this before. Scary but really exciting. Rollercoaster.

It took Kevin’s brain six weeks to recognize the electric pulses it was receiving as a “distance radar”. Boring time, but it took that time to train his brain, and it adapted — he actually “felt” how far things were.

What next? Research on Parkinson’s, by analysing deep brain scans to predict tremors. Also with epileptic patients to try to see when the fit is coming. Parkinson’s: can predict tremors 15-20 seconds before they happen! With epilepsy, 25-30 **minutes**! *steph-note: wow.* This can change the patient’s lives!

Cultured brains. After a week, a rat’s brain starts having some “neural firing” (activity), and after a month it’s starting to act like a brain. All the brain knows is that it drives the robot. Not good drivers! Now, trying to teach these biological brains how to drive the robot better. Lots of philosophical questions. *steph-note: so, from what I understand, they don’t remove brains from rats, but grow them.* Cultured neural networks. Artificial intelligence. *steph-note: Cylons!*

Watch the video:

Watch a [shorter video excerpt about extending his sensory range](http://www.viddler.com/explore/steph/videos/33/).

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