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Tuesday, 14 February 2012

Thoughts on "Photograph 51"

Posted on 16:49 by Unknown
A few days ago, I and the rest of MIT SPS went to see the play "Photograph 51". It details [and dramatizes] the life and work of Rosalind Franklin, who was the first to see the helical nature of DNA. For all her professional life (which tragically ended rather early due to ovarian cancer), she worked extremely methodically and refused to draw any conclusions or make any models unless there was solid data to support that. By contrast, Crick & Watson, who are traditionally the ones credited with discovering the structure and nature of DNA, went for models even if there wasn't always the most solid evidence to support them. What they did do that Franklin did not (according to the play, at least, which I believe and hope is pretty close to what actually happened) was to model how DNA base-pairing works and where the phosphates are in the nucleic acids.

One of the things that struck me as interesting is just how isolated Franklin made herself even from her colleagues at the King's College in London. I mean, I knew that she was generally reluctant to share her work because she knew that any work she published would be attributed to her male colleagues (even those under her in the research hierarchy), but I didn't realize she was practically antagonistic toward her fellow researchers. I fully understand how she did so essentially to maintain her own dignity and not submit herself to the male-dominated research community, but if she tried that today in a culture where females are quite prevalent (though of course there is still much progress to be made) in scientific research, I would think her actions would be unacceptable as they would be antithetical to the ideas of open science and collaborative research.

On the other hand, though, it's hard to discount just how pervasive the sexism present at that time was. Crick & Watson in the play were both quite patronizing toward her. Her colleague Maurice Wilkins could not really accept her as an equal until around the time when she first fell ill with ovarian cancer. She was segregated from the other male researchers. So of course she had to do everything she could to make sure she would be recognized as an equal to the other researchers rather than as an assistant of some sort.

There's another point to be made regarding open science in this context, and that is in the premature publication of Franklin's data. She didn't want to publish because she felt that she didn't have sufficient data to back up any claims she made (and this is also why she was opposed to making models as prematurely as Crick & Watson did). Ultimately, it should have been left to her as to whether she wanted to publish the data or not. Yet Crick, Watson, and Wilkins were overeager to publish and "win the race" (to finding the "secret to life"), so they managed to get a hold of one of Franklin's photographs without her permission and used it to complete their own work. Consequently, she didn't make it onto their Nobel Prize-winning paper, so the paper she published looked like it simply supported the paper from Crick & Watson. A lot of accounts describe the process as them "stealing" her data. On the one hand, I disagree with this because ultimately it is the results that matter to science more than the personalities behind them. On the other hand, they did acquire that data without her permission, and in the end it should have been up to her whether her own data should have been published or not. There wasn't any doubt that she would publish everything once she got around to it; it's just that she felt that the time wasn't right, and the other researchers violated her prerogative as a research scientist to make that call.

As I think about this more, the whole story really is a good deal more ethically knotty than how it is initially presented. Also, I would encourage you to go and see the play "Photograph 51" if you are in the Boston area; it is playing in the Central Square Theater in Cambridge.
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Posted in DNA, MIT, Photograph 51, physics, science | No comments

Sunday, 12 February 2012

Featured Comments: Week of 2012 February 5

Posted on 09:56 by Unknown
There were no featured comments the previous week because I didn't post anything for that week due to my end-of-IAP business. There was one post this past week that got a couple of comments, so I will repost both of those.

Comparison Test: Linux Mint 12 "Lisa" KDE vs. Netrunner 4.1 "Dryland"

Reader Bart said, "It is a bit.. surprising to see a Facebook shortcut installed on a Linux desktop by default. You write that Netrunner also considers for example Google docs, GCal and Youtube as applications. So in that way it is a sort of a net-runner after all. Thanks for the comparison, I was indeed curious to hear more about Netrunner."
An anonymous commenter had this to say: "Given the web oriented mood Netrunner seems to have ... it would have been interesting checking, as a level of polish, the integration of Dropbox in Dolphin (context menu for Dropbox folders, etc...). On the other hand ... it would have also been interesting knowing a bit more about Blue-Systems, the main sponsor of Netrunner and Linux Mint by now. Good review, but as you can see the curiosity is even bigger. Ps.- Do you really believe they will join together ???"

Thanks to those commenters for commenting on this past week's posts. Depending on my workload this week, I may or may not be able to post anything, but if I do have that kind of time, I do have at least one thing in mind. In any case, if you like what I write, please continue subscribing and commenting!
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Posted in Featured Comments, KDE, Linux Mint, Netrunner, weekly | No comments

Thursday, 9 February 2012

Comparison Test: Linux Mint 12 "Lisa" KDE vs. Netrunner 4.1 "Dryland"

Posted on 07:10 by Unknown
Linux Mint: Main Screen
Both of the latest releases of these particular distributions came out this week. Also, Linux Mint now has a partnership with Netrunner for Linux Mint with KDE; hence, this comparison test may be the last meaningful one between the distributions while they remain as separate as possible, because I think they will converge in the coming months. Finally, Kubuntu just lost its funding at Canonical, so like Xubuntu, Lubuntu, and Edubuntu, after (but not including) version 12.04 LTS "Precise Pangolin" it will be recognized by Canonical as an official derivative but will only be supported by the community. This means that there will need to be a new top dog for Ubuntu-based KDE distributions, and these two distributions seem like the most likely candidates. That is why I am comparing these two distributions now.

Linux Mint of course needs no introduction here. Interestingly, considering that for almost all of its history it has made Ubuntu with GNOME better and more usable, it actually started out in version 1 "Ada" as a KDE distribution, and KDE was still prominently featured until around version 3.1 "Celena" (and that is also around the time KDE made the transition from version 3 to version 4, which caused many users to move away to other DEs). After that, though, GNOME became the really prominent DE in Linux Mint, and KDE has almost become a second-class citizen in Linux Mint; in the last few releases, though the main GNOME edition has received extensive customizations, the KDE edition has been just a lightly-rebranded version of Kubuntu with a few other small customizations here and there. I will see whether or not that continues to be the case.

Netrunner: Main Screen
Netrunner, despite the name, is not a cloud-oriented distribution. It is a traditional desktop distribution like any other, and it aims to provide KDE mixed with useful tools taken from GNOME along with other helpful installed programs and customizations.

I tested both using a multiboot live USB made with MultiSystem. I did not test the installation processes, because both are based on Ubuntu so there is really no need; all I am really comparing are the first impressions created by each distribution (so the whole post may seem a bit superficial), because soon they will more likely than not converge. Follow the jump to see what each distribution is like.

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Posted in comparison, KDE, Linux Mint, Netrunner, Unixoid Review | No comments

Wednesday, 8 February 2012

Fourth Semester at College

Posted on 06:55 by Unknown
Yesterday my fourth semester here started. This semester, I am taking 8.04 (Quantum Physics I), 8.044 (Statistical Physics I), 14.02 (Principles of Macroeconomics), and 18.06 (Linear Algebra). In addition, I am continuing my UROP (though my work will likely change soon) and doing some other work too.
It's going to be a busy semester, but given that I am now used to this kind of workload from last year, I think I will be able to manage it better. Plus, now that my classes start each day no earlier than 11am, I can get more sleep! Yay! That aside, it's going to be an exciting semester, though I can already feel the heat with problem sets and such.
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Posted in college, MIT, semester, UROP | No comments

Sunday, 29 January 2012

Featured Comments: Week of 2012 January 22

Posted on 11:52 by Unknown
There was one post that got a few comments this week, so I'll repost most of them.

How-To: Make KDE Like Unity

Reader decentralist.wordpress.com had a few suggestions for KDE itself: "The main things I want to fix is being able to start a dash/menu/takeoff with just the meta/super/windows key and not need key combinations in KDE. I'm told this would require a change to Qt itself. I also want KDE to be able to use CTRL+ALT+ arrow keys to switch desktops instead of CTRL+Function keys. Don't think this can be fixed currently either."
An anonymous commenter responded to this, saying, "I did this a couple of months ago on openSUSE and Debian. The CTRL+ALT+ arrow keys is in the convoluted UI somewhere, I just don't remember where. I have also have gotten the super key to launch Kicker, I believe I added something to .xinit. Google is your friend, er maybe not. :)"
In the context of KDE being a refuge for people who don't like the Unity UI, another anonymous reader asked, "Why?"

Thanks to all those who commented on this past week's posts. This coming week, I don't really have much planned, but I'm sure I can think of something to write about. In any case, if you like what I write, please continue subscribing and commenting!
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Posted in Featured Comments, KDE, Unity, weekly | No comments

Thursday, 26 January 2012

How-To: Make KDE Like Unity

Posted on 18:14 by Unknown
I was going to do a review of PC-BSD, but unfortunately, that didn't work out (more on that later), so I'm doing this instead, though I had planned this for next week.

Vanilla KDE
Many months ago, I did a post on how to make KDE look more like Elementary OS. It was just one way of showcasing KDE's power and customizability. Now, I'm doing the same with regard to the Unity UI present in recent versions of Ubuntu. I know that a lot of people online have expressed displeasure with Unity along with the intention to use KDE instead. But what if you like the Unity UI but want the other features of KDE as well? Then this article is for you.

If you are using Kubuntu, this post is technically moot, because it is possible to use all of Unity 2D under KDE in Kubuntu without any issues; that is because Unity 2D is made with the Qt libraries, which also underlie KDE, so there's some compatibility there as far as I can tell. If you aren't using anything Ubuntu-based, though, then you're out of luck in terms of trying to use Unity 2D, so this is for you. I did this using a Chakra 2011.12 "Edn" live USB, so all my instructions will be based on that. If you are using another distribution, you may have to search online to see how some steps are done. Follow the jump to do it.

Read more »
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Posted in Chakra, How-To, KDE, PC-BSD, Unity | No comments

Sunday, 22 January 2012

Featured Comments: Week of 2012 January 15

Posted on 09:30 by Unknown
There was one post this past week that got a whole bunch of comments, so I'll repost a few of them.

Review: Fuduntu 2012.1

Reader Fewt, who is the main Fuduntu developer, clarified reason for the issue that I was having: "There is a problem with our LibreOffice package (my fault) that causes it to use a lot more space than normally necessary (over 1GB). I'm working on a fix, but you probably saw your system run out of memory and oom killer ate some of your running processes. Sorry about that."
Commenter enrico said, "[I]nstall software in a live environment is a nightmare, in every distro you can try there are some errors, or at least glitch that cause every error you can imagine... A good review is made when software is installed in a real or virtual machine, live cd are a good thing, but some software and the stability of the distro is only a matter of luck... even sabayon has a live dvdfull of software, really good, but if you try to installa anything in live session,there are always crashes... in a virtual setup, there are no such things.. the same occur using a opensuse live cd...and the setups of this distros are stable as debian is."
An anonymous reader had this to say: "Perhaps this should have been named a "live" environment review because basing it totally off of that experience only covers a small portion of a distro's capabilities and character. Thanks for the effort of writing one up though. Hopefully you can try Fuduntu in the future and give it a fair chance."
Another anonymous commenter had these bits of advice: "Not related to fuduntu, but I want to share. I remember reading a live cd review where the author recommended installing distro x. i asked about package manager and he didn´t know. He said he never bothered because he just uses the vanilla distro and doesn´t install anything new. Yet I think it´s kind of unfair not mentioning and not looking at methods of installing new software. Yet a fuller review, where one installs and uses the distro for about a week as his main system and really tries everything he/she normally does, is rare. Understandable. Because Linux still sucks that much. It´s great but it sucks that much that You have to face these hickups.  I installed Kubuntu on my laptop and thought it was great. Updated to latest KDE SC...ah. And then my girlfriend was unable to set up wireless. And she was right. The issue is now fixed but I can not blaim her. Sometimes You really need another PC to google Your problem. So, it´s easy to say: write a full review. An I agree that some reviews are really, really shallow, often barely more than a summary of the release notes and screenshots (not PV´s though). This is all free. Open a blog, download the distro and start writing."

Thanks to all those who commented on that post this past week. This coming week, I intend to have another review out at least. In any case, if you like what I write, please continue subscribing and commenting!
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Posted in Featured Comments, Fuduntu, weekly | No comments
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Blog Archive

  • ▼  2013 (63)
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      • Featured Comments: Week of 2013 September 8
      • Featured Comments: Week of 2013 September 1
      • Seventh Semester at College
      • Review: Elementary OS 2 "Luna"
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