MedWorm.com provides a medical RSS filtering service. Over 5000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Fourth Floor Studio' source. Sat, 16 Aug 2008 14:42:17 +0100 http://fourthfloorstudio.wordpress.com/2007/10/25/the-great-and-the-gaffe/ James D. Watson, cantankerous Nobel prize winner, proves that no cow is too sacred. Even Lord Jim couldn’t withstand the furore over his latest round of bigoted comments in the Sunday Times magazine on Oct 14th: He says that he is “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours – whereas all the testing says not really”, and I know that this “hot potato” is going to be difficult to address. His hope is that everyone is equal, but he counters that “people who have to deal with black employees find this not true”. He says that you should not discriminate on the basis of colour, because “there are many people of colour who are very talented, but don’t promote them when they haven’t succeeded at the lower level”. He writes that “there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of humanity will not be enough to make it so”. I had been waiting to see whether he would have been able to weather this storm, although his suspension from active duty at CSHL on Oct 18th didn’t bode well. There is a fine line between having the courage to drag out sensitive topics so we can look at them, and being a bigot. Apparently, this time Jim was caught on the wrong side of that line once too often. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=979176 Thu, 25 Oct 2007 15:59:28 +0100 979176 http://fourthfloorstudio.wordpress.com/2007/09/29/extra-special/ I have just noticed that the fish sauce in my kitchen cabinet is “first press” and “extra virgin”. wtF? (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=915040 Sun, 30 Sep 2007 02:33:19 +0100 915040 http://fourthfloorstudio.wordpress.com/2007/09/26/damn-you-weak-dollar/ A hostile exchange rate is a budget’s worst enemy. These days, if you count in US dollars, this implies that only the most impoverished of third world countries are desirable conference destinations. I have barely managed to secure accommodation in the UK within my per diem reimbursement range - we are naturally expected to make our own arrangements as the conference centre does not accommodate all -  at considerable cost, which I must carry forward until the check arrives from Central in 6-8 weeks. I happen to have some money stashed away for rainy days and stupid conference setups, but really! How do they expect post-docs to lay their hands on a spare couple of grand for a booking? (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=904522 Wed, 26 Sep 2007 04:25:39 +0100 904522 http://fourthfloorstudio.wordpress.com/2007/09/13/giving-up/ How many times do incarnations of a paper need to be rejected (outright!) before you lose hope in it? This one has been doing the rounds for >3 years in 5+ versions. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=869509 Thu, 13 Sep 2007 21:20:21 +0100 869509 http://fourthfloorstudio.wordpress.com/2007/08/24/newbie-python/ I’ve finally hit a problem requiring multidimensional data structures, mathematical grunt, and speed, coupled with good DB bindings and text/file handling. Normally, I would use a perl script to fetch data from the db and process it with R (as I’ve been having trouble with the R DBI library). However, processing 31K chunks of data for 13K variables each just won’t work in R. So I’m delving into python as a one-stop shop for all my woes. I’ve been procrastinating about learning the language, because, let’s face it, why write bad code in a new language when you can write ugly code in your long-term favourites. Some resources I’ve found are: a python tutorial, the NumPy library for data arrays, SciPy and the python DB-API module. I’ll also have a look at StatPy for statistical computing in python. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=821331 Fri, 24 Aug 2007 15:12:09 +0100 821331 http://fourthfloorstudio.wordpress.com/2007/08/23/furniture-pr0n/ My absolute favourite chair is the Eero Saarinen womb chair. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=818779 Thu, 23 Aug 2007 21:21:34 +0100 818779 http://fourthfloorstudio.wordpress.com/2007/08/13/outage/ *cough cough* The dust here is rather thick, isn’t it? I’ve been rather busy being unproductive at work, and I’m about to go on holiday for a while. So here are some random-ish snippets: Nodalpoint facebook group My thesis is up at the Australian Digital Theses project The ADT site sucks big-time, so I can’t get a link just yet A question to the audience - how do you feel about blogging on current projects, particularly collaborative ones where you are not the primary mover? Spilling others’ beans doesn’t seem very polite now, does it? (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=797043 Mon, 13 Aug 2007 18:35:19 +0100 797043 http://fourthfloorstudio.wordpress.com/2007/07/18/graceful-rebooting/ When things go wrong, there are more options than the hard reboot. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=741428 Wed, 18 Jul 2007 04:11:21 +0100 741428 http://fourthfloorstudio.wordpress.com/2007/07/06/australian-undergraduate-teaching/ […] universities are taking in students to study science who do not have the preparation, and possibly ability, to complete courses of proper rigor[…] In Australia, the pressure to combat declining science undergraduate enrollment has resulted in dumbed-down courses with lower standards enrolling many unprepared  students (a worldwide theme, mind you). Whilst keeping the departments afloat - at least temporarily - the long-term damage to education and science is huge. The other logical extension, recruiting foreign students, has lead to interesting, if flawed, experiments in foreign campuses. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=718014 Fri, 06 Jul 2007 16:30:36 +0100 718014 http://fourthfloorstudio.wordpress.com/2007/06/27/did-he-deliver/ These are exciting times. Science continues to push back the frontiers of knowledge, finding new areas of which we were previously unaware and making discoveries that add novel twists to the world views we were taught as children. I intend to ensure that the United Kingdom continues to foster excellence in scientific and technological cooperation. Our success will help realize the creative potential of the next generation. Blair, T, 1998 Science  281, 1141. See commentary by Robert May in this week’s Nature. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=700695 Wed, 27 Jun 2007 19:08:25 +0100 700695 http://fourthfloorstudio.wordpress.com/2007/06/27/a-just-review/ Ken Miller’s review of Behe’s new book: “It would be difficult to imagine a more breathtaking abuse of statistical genetics.” (Sub required) (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=700696 Wed, 27 Jun 2007 18:43:52 +0100 700696 http://fourthfloorstudio.wordpress.com/2007/06/14/nature-wades-into-the-religious-debate/ Comments by US Senator (and presidential candidate) Sam Brownback prompt an editorial in this week’s Nature: … the suggestion that any entity capable of creating the Universe has a mind encumbered with the same emotional structures and perceptual framework as that of an upright ape adapted to living in small, intensely social peer-groups on the African savannah seems a priori unlikely.    Brownback’s NYT opinion piece is littered with the usual flotsam of non-overlapping magisteria, micro- vs macro-evolution, a priori belief in a creator, and of course the requisite “many biologists believe in God” argument. He concludes with this gem:  Man was not an accident and reflects an image and likeness unique in the created order. Those aspects of evolutionary theory compatible with this truth are a welcome addition to human knowledge. Aspects of these theories that undermine this truth, however, should be firmly rejected as an atheistic theology posing as science. Enlightenment, what enlightenment? (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=675260 Thu, 14 Jun 2007 11:50:34 +0100 675260 http://fourthfloorstudio.wordpress.com/2007/06/12/the-utility-of-arrogance/ Here’s something that has begun many a bar conversation: why are (some) scientists arrogant? From the grand old men of our time to first year graduate students, science seems enriched with people sublimely convinced they are all right, all the time. Here’s a couple of reasons why this might be a selected trait: Survival. Don’t kid yourself - academics is a cut-throat business. A certain self-confidence is required to navigate the heady political heights of grantsmanship, institutional funding, and policy making. There are many ways of making yourself heard, and it seems that shouting loudly is one of them. Science (unlike the humanities) is fortunate in that eventually data can objectively show who was right, so this doesn’t get too out of hand. Sanity. Have you ever pinned your career on a five-year project that you have no evidence is even possible? Welcome to science! Given the likelihood of failure, it takes a modicum of self-inflation to even get out of bed in the morning - especially after you’ve just received a vicious, cursory review of your latest paper. Feeling like a twelve-year-old with red ink all over their homework is not something many people continue to face throughout their careers. Blazing your own trail. Research is essentially a process of making things up as you go along. It involves challenging current wisdom, scrutinising others’ findings, and, at some level, thinking you can do things better. It does take a certain arrogance to do all these things: it’s enshrined in the belief that you can add something to human knowledge. Now, I’m not saying that arrogance is good, or even excusable. There are plenty of good (and quite a few great) scientists who are modest, kind, even demure. But don’t kid yourself - there’s a little seed of arrogance deep in their souls somewhere. They just don’t let it get out of control. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=675261 Tue, 12 Jun 2007 15:01:06 +0100 675261 http://fourthfloorstudio.wordpress.com/2007/05/24/maths-for-biologists/ I’ll break radio silence briefly to catch a meme wave from Neil (via RPM, Deepak and Keith). I’ve disguised my rant as answers to Sandra’s questions (evil chuckle). Usual grain of salt provisos apply… (more…) (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=637914 Thu, 24 May 2007 15:53:49 +0100 637914 http://fourthfloorstudio.wordpress.com/2007/03/31/rules-for-collaboration/ The latest installment of the PLoS Computational Biology “10 Rules” series focuses on collaboration. The rules deal primarily with people skills, rather than explicit guidelines for collaborations. One thing that strikes me is that they are written around a passive assumption, geared toward cases where one is either considering an offer of collaboration, or beginning to pursue one. It may be my bias, but there’s almost an air of “wait until someone more senior approaches you” to the rule-set. With that in mind, I offer these pro-active corollaries: Rule -1: don’t wait; find a suitable problem and offer it to potential collaborators. You are much likelier to begin collaborations with people if you take a problem to them, particularly if they are more established than you are. I think one of the problems for people just starting out is exposure: no-one really knows you or your capabilities, so they are unlikely to come to you with a collaboration offer. Find a problem, write up a research proposal (even a blue-sky one), and then start approaching people with skills complementary to the problem. You can’t fish without bait… Rule 0: beware of farming-out. Some “collaborators” may simply expect to farm out a portion of their work to you, rather than admit you as an equal in an ongoing effort. Unless you feel that being absorbed under someone else’s umbrella would be advantageous, steer clear. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=514493 Sat, 31 Mar 2007 19:21:42 +0100 514493 http://fourthfloorstudio.wordpress.com/2007/03/20/rip-john-backus/ The creator of Fortran is dead. “You need the willingness to fail all the time,” he said. “You have to generate many ideas and then you have to work very hard only to discover that they don’t work. And you keep doing that over and over until you find one that does work.” (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485227 Tue, 20 Mar 2007 03:04:17 +0100 485227 http://fourthfloorstudio.wordpress.com/2007/03/15/aggregation-and-meta-blogging/ The food world is at it, too. Of course, we’ve been doing it for a while. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485229 Thu, 15 Mar 2007 05:28:03 +0100 485229 http://fourthfloorstudio.wordpress.com/2007/03/14/mind-mapping-and-outlining-tools/ I like the idea of mind mapping: a graphical, non-linear representation of connected stuff appeals to me (perhaps I’ve been looking at biochemical pathways for too long?). As an on-again/off-again google search, I’ve stumbled across several implementations of this concept: bubble.us vym kdissert gjots2 (my favourite outliner atm) gnome-think (outliner) notecase (outliner) See a more comprehensive article. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485231 Thu, 15 Mar 2007 00:37:17 +0100 485231 http://fourthfloorstudio.wordpress.com/2007/03/14/a-helpful-bsd-login-tip/ Welcome to FreeBSD! If you accidentally end up inside vi, you can quit it by pressing Escape, colon (:), q (q), bang (!) and pressing return. $ All you need to know about vi. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485232 Wed, 14 Mar 2007 23:53:50 +0100 485232 http://fourthfloorstudio.wordpress.com/2007/03/14/recent-r-version-on-ubuntu-64bit/ Something that’s been bugging me lately is that CRAN doesn’t seem to have recent (ie v2.4+) versions of R ubuntu packages for 64 bit architectures. So I finally bit the bullet and added the debian/ stable/ source path to my sources.list, and voila! Instant goodness. You’re not really supposed to cross-contaminate like this, but I haven’t even broken anything - yet. Trivial, but annoying. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485233 Wed, 14 Mar 2007 20:46:40 +0100 485233 http://fourthfloorstudio.wordpress.com/2007/03/12/was-this-on-the-job-description/ He was inebriated, his hands were tied and he was gagged with a rubber ball in his mouth. In spite of his drunken state, the naked figure was reportedly able to identify himself by his full name and job title. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485234 Mon, 12 Mar 2007 14:08:35 +0100 485234 http://fourthfloorstudio.wordpress.com/2007/03/11/life-organisation-and-the-war-against-entropy/ I hate the second law of thermodynamics. The one that trashes my desk, dirties my apartment, and reduces my life to a disorganised mess. Barring a complete breakdown in standards of hygiene and work, I am doomed by the universe’s freakish sense of humour to constantly enter energy into aspects of my life that should Just Work. Unlike Sisyphus however, I have two choices: I can either wait until “stuff” accumulates until I have to do something about it, or I can try to rework my habits to keep everything going on a day-to-day basis. So far, I’ve taken the first approach, and although periodic spring cleans of mind and space are good, they really don’t seem to cut it any more. I’m lost in my workload, depressed by my apartment, and bemused by my life. I’ve experimented with aspects of the second, and I feel they’ve given me quite a lot of mileage. So, over the past few months, I’ve gradually come to the conclusion that the second mode of continuous operation may be worth a shot. Now, the death-knell of any resolution is its requirement of massive change at an arbitrary time-point. However, at some point there comes a time where systems must be switched, habits realigned, and behaviours reordered. Mine was a couple of weeks ago, when I switched over to Getting Things Done. I’ve since lapsed, of course, but this time I feel determined to stay on top of things. My difficulty here is two-fold: I’m not a natural list-maker, and my work is largely data driven, in the sense that one analysis will then engender material for the next, without a priori knowledge of what the second should be. Trying to implement a system based on lists of next actions therefore poses a challenge. Nevertheless, I’m giving this a whirl: the prize of comfort, productivity and lack of clutter are too much to resist. Let’s see where we go. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485235 Sun, 11 Mar 2007 22:41:38 +0100 485235 http://fourthfloorstudio.wordpress.com/2007/03/06/the-case-of-the-leaking-memory/ I’ve been having memory issues on my server/cruncher box [1]: available RAM seems to disappear. At first I thought it might be the well-known Firefox memory leaks, so I did a little (unconscious) experiment. I rebooted yesterday and never fired up FF. Today, I notice: bobo% free -m total used free shared buffers cached Mem: 3943 3673 270 0 161 3253 -/+ buffers/cache: 257 3686 Swap: 6000 110 5889 Something appears to be caching to buggery. It turns out to be the kernel. The trick here is to interpret the second line, which tells you what programs “see” when asking for memory. In this case, it’s 3686M free, so all is well. A little scary there for a second… I shall have to be a little more sanguine next time. [1] dual amd64, 4G RAM, Ubuntu Dapper clean install. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485236 Tue, 06 Mar 2007 20:32:01 +0100 485236 http://fourthfloorstudio.wordpress.com/2007/02/27/working-with-databases/ DbVisualiser is a nice tool to view large, complex databases graphically. It’s a Java-based GUI client with built-in sql query composer and nifty tricks. Good for us Oracle newbies who (i) hate sqlplus and (ii) want a quick rundown of a complex database to write perl::DBI scripts for. You’ll have to provide your own drivers, though, which in Oracle’s case are downloadable after registering and swearing to uphold the constitution. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485237 Tue, 27 Feb 2007 21:07:20 +0100 485237 http://fourthfloorstudio.wordpress.com/2007/02/24/enabling-firefox-plugins-on-amd64/ It appears that proprietary plugins (Adobe Flashplayer, RealPlayer, JRE etc) are generally built against 32-bit architectures. So, you have to cheat and run a 32 bit version of FF. Details on the Ubuntu fora. (Source: Fourth Floor Studio) Fourth Floor Studio blogs http://www.medworm.com/rss/comments.php?id=485238 Sat, 24 Feb 2007 17:46:22 +0100 485238