Zientzilaria

Covering the bioinformatics niche and much more

Books 2010

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1 – The New New Thing: A Silicon Valley Story

2 – What Do You Care What Other People Think?: Further Adventures of a Curious Character

3 – Days Between Stations: A Novel

4 – A Bridge Too Far: The Classic History of the Greatest Battle of World War II

5 – The Man Who Smiled: A Kurt Wallander Mystery (4) (Vintage Crime/Black Lizard)

6 – Silence of the Grave (Reykjavik Murder Mysteries, No. 2)

7 – What Mad Pursuit: A Personal View of Scientific Discovery

8 – Seed of Light

9 – American Psycho

10 – Glamorama (Vintage Contemporaries)

11 – Eats, Shoots & Leaves: The Zero Tolerance Approach to Punctuation

12 – Slaughterhouse-Five: A Novel

13 – Bellini e os Espíritos

14 – Drop the Dead Donkey (A Channel Four Book)

15 – The Girl with the Dragon Tattoo

16 – Vascones

17 – A Cidade Ilhada

18 – The Girl Who Played with Fire

19 – The Girl Who Kicked the Hornet’s Nest

20 – Caught

21 – WAR

22 – The Big Short: Inside the Doomsday Machine

23 – Survivor: A Novel

24 – Presumed Innocent

Best and Worst of 2010

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  • Movie: Inception, not the best one, but highly entertaining, worst: none
  • Book: The Big Short: Inside the Doomsday Machine, worst Days Between Stations: A Novel
  • Website: Kissing Suzy Kolber, worst: Mendeley
  • Software: Things, worst Mendeley, by 1000 miles
  • TV: best Walking Dead and Modern Family worst: any TLC show
  • Purchase: snow tyres, again
  • Money-grabbing-scheme: Global Warming or Climate Change, again
  • Politician: no best in the category, but the worst is the Brazilian President.
  • Music: most of the things I listened to were great, but the new Superchunk takes the cake
  • Best programming language was still Python, worst, still Java
  • Best operating system was Snow Leopard, worst, any Windows (including XP)

Interview With Rosie Redfield

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I haven’t received so many visits on one of the interviews I run some years ago, like this time with Rosie’s. So, if you are looking to know her a bit more here’s the link for the July 2007 interview.

You’re Quite Wrong, NASA

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NASA slammed Rosie Redfield’s assessment (or review) on the new form of life that was found:

When NASA spokesman Dwayne Brown was asked about public criticisms of the paper in the blogosphere, he noted that the article was peer-reviewed and published in one of the most prestigious scientific journals. He added that Wolfe-Simon will not be responding to individual criticisms, as the agency doesn’t feel it is appropriate to debate the science using the media and bloggers. Instead, it believes that should be done in scientific publications.

To say the least, it’s hypocritical to call a press-release to tout about your new discovery and then say that the debate shouldn’t be in the media. Peer review is wrong, bad and broken, and without a 180 degree fast turn it will die a slow death, being surpassed by what NASA calls “the media”. Being published on Science is not a badge of quality; nowadays it’s a badge of connections (most of the time), a badge of who do you know and who knows you. The worst papers I read in my life were published in Science and Nature, and they were not high impact papers either to the public or the field.

If NASA didn’t want to bring the discussion to the public realm, let Science (not the journal) take its due course and correct the paper. Maybe Science (the journal) is losing ground and relevance to Nature, maybe there were no peer-review of this paper, who knows, and they needed the exposure (NASA is losing budget too). But if it’s a bad paper and there’s no PR, scientists will try, check, re-analyse data, write more papers about the issue and then, maybe in five, ten years, we will have a final answer. “The media” always existed: scientists wrote letters when there were no emails. There were always been conferences, meetings, where things were discussed, checked and re-checked. Were there mistakes? Obviously, but time took its course, and things were slower and sometimes quite wrong, sometimes really right.

That’s the problem of the Generation Mendeley®: they want things now, in this exact minute. There’s always a final and definite instantaneous answer. They have the social sites on their side, but don’t accept when the same hand that feeds them, bites them. Software with major bugs is the next saviour of citation. New life form is proof that aliens are out there. And I will have sushi for lunch. PR, PR, PR, always the now, the now, this exact second. No wonder that so many people come to Science now in order to “cure cancer ASAP”.

BTW, without googling it, what were the names of the cold fusion guys?

http://www.wired.com/wiredscience/2010/12/the-wrong-stuff-nasa-dismisses-arsenic-critique-because-critical-priest-not-standing-on-altar/

Secure OS

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Tyring to download a file from Microsoft.com on Internet Explorer 8, under Windows 2008 server.

The New “Form” of Life and the Generation Mendeley

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I’m quite late jumping on the bandwagon, but after reading this and visiting this site, both related to the new “form” of life found recently, I can only say a couple of things:

  • I don’t know if young scientists (this included my generation and me) need to do this kind of PR to achieve something in their careers

  • Based on the quality, and lack of, of the paper, as assessed by Rosie Redefield, it’s very sorry that Science and scientists accept this kind of publication in their journals. For one, this only reinforces my feeling that most of the things that are published on Nature and Science are just things that will sell more paper, and reinforces my will to not read most of the papers from these journals

I would expect in the coming years to meet students that will fall in both categories: ones crazy for PR and with a website full of pictures showing how connected they are, others will read a paper and like Rosie Redfield will have the necessary intelligence to actually read the Science behind the PR. The latter will be the ones I will admire and will teach and learn from. The ones from Generation Mendeley will be just an empty shell, maybe with a good job.

Preview of Best and Worst of 2010

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I have received several emails about my coveted Best and Words of 2010. So, to placate the hordes and get some email relief, here is a short list of the worst of 2010:

Worst software: Mendeley

More next week, or the following.

Why I Left Biostar

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About eight months ago I started using Biostar as I saw it as a great opportunity to exchange some ideas, concepts, tips in biology and bioinformatics. I even mentioned the website in this space, trying to bring more people to the mix; at the time the community wasn’t big enough, and some days went by without any question being posted.

But a couple of months ago my interest started to go down the drain. I don’t know if it was the constant next-generation sequencing barrage of questions every day, if it was the infantile blog/twitter posts from members competing for points or maybe the lack of votes for some answers that I posted (that’s selfish on my part, I admit). But at some point it seemed that the website turned into a competition of CVs or knowledge, very different from what I could see in different Stackoverflow spin-offs or in the main site. I guess the turning-point, or the moment I realized that the scientific community (at least in bioinformatics and related fields) will never the be the same as the programming and statistical ones, was the time I gave an answer that had less votes that the one saying “it’s not possible”.

Maybe the problem is myself, I don’t like cliques, don’t mind helping people for nothing, don’t care about reputation. I didn’tt care about how many points I had, and used the down-vote to actually vote down answers that I didn’t see as pertinent (if you never used those sites, every down-vote removes one point from your score). I still think that Biostar is a great idea, and I wish it becomes a great resource for all the bio fields. Maybe if the community gets big enough, maybe if don’t see the same group of people that you see every where else it might become a better place to hang-out online. But right now, I’m over it.

Why I Left Biostar, but I Still Like Stackoverflow

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About eight months ago I started using Biostar as I saw it as a great opportunity to exchange some ideas, concepts, tips in biology and bioinformatics. I even mentioned the website in this space, trying to bring more people to the mix; at the time the community wasn’t big enough, and some days went by without any question being posted. But a couple of months ago my interest started to go down the drain. I don’t know if it was the constant next-generation sequencing barrage of questions every day, if it was the infantile blog/twitter posts from members competing for points or maybe the lack of votes for some answers that I posted (that’s selfish on my part, I admit). But at some point it seemed that the website turned into a competition of CVs or knowledge, very different from what I could see in different Stackoverflow spin-offs or in the main site. I guess the turning-point, or the moment I realized that the scientific community (at least in bioinformatics and related fields) will never the be the same as the programming and statistical ones, was the time I gave an answer that had less votes that the one saying “it’s not possible”. Maybe the problem is myself, I don’t like cliques, don’t mind helping people for nothing, don’t care about reputation. I didn’tt care about how many points I had, and used the down-vote to actually vote down answers that I didn’t see as pertinent (if you never used those sites, every down-vote removes one point from your score). I still think that Biostar is a great idea, and I wish it becomes a great resource for all the bio fields. Maybe if the community gets big enough, maybe if don’t see the same group of people that you see every where else it might become a better place to hang-out online. But right now, I’m over it.