Category Archives: Uncategorized

Amazing first decade, futurists, and suffering

The Jester has has his time for long enough. Once he crosses the line into flagrant paranoia, I have to step in.

It’s a new year and a new decade. The decade might have been better for Science (still no flying cars) but all-in-all, I’m pretty happy. We’ve seen tissue engineering come a long way including grow-your-own skin and grow-your-own hearts. We’ve seen metamaterials with negative index of refraction and a lower thermal conductivity than vacuum, both of which I grew up believing were physically impossible. We seen bona fide proof of evolution (as if we needed more).

Basically I can’t even begin to touch on all the cool things in that happened in the last ten years. It’s enough to have give me a glimmer of faith in the vision of the futurists’ utopia: we may conquer death and scarcity and create a world of never-ending exploration. But maybe human nature needs scarcity and death to be whole. Maybe ten years is a good time for reflection on what we all want for ourselves and for each other. Facile suggestions that ‘happiness’ is what we want miss the point: If we knew what would make us happy, we would have it by now.

Ultimately, and strangely, I’m not sure that conquering death and scarcity will make us any kinder. I think we’ve made some real progress toward doing those things, and I’m not alone in that thought.

Yet, even so, I think a lot of otherwise crazy-seeming people might be sane in the light of this statement: abundance does not necessarily engender generosity. People who think we’re better off without public healthcare may be right up to a point: the threat of true suffering can be motivation for good. Don’t get me wrong – I don’t hold with people who would sell others’ welfare for the sake of an abstraction. The Free Market is all well and good until Henry Frick has you killed because you want fair pay. Yet, we only have the opportunity to be truly charitable in the face of true misfortune. Would we cheat ourselves of this sorrow?

If we could truly alleviate human suffering on a large scale, would we be neutering humanity?

Cheers,
Peter

New generation of drugs, and the next things for TBU

Occasionally, I get asked what I do. Here’s a little introduction to the kind of technology I’m working with. Aptamers are short bits of DNA that bind to whatever target of interest you might be interested in. Why is that useful?

Here’s one good reason, from a TED talk by Kary Mullis. He won the Nobel prize for inventing PCR. Now he is making aptamers that act like the tape on a big note on a bacterium’s back that say “EAT ME” to the immune system.

I’m going to take the Big Upshot in a new direction. From here on out, I’ll be doing my best to make posts relevant to current and future medical students and biomedical graduate students. We’re going to talk about the periphery of a scientific education that might otherwise get missed.

Cheers,
Peter

Firefox shortcuts

I’ve found a few shortcuts in Firefox that I love.

Ctrl-tab : switches among open tabs
Ctrl-w : closes the current tab
Ctrl-shift-t : re-opens the last tab you just closed

I also found a shortcut that I hate:

Ctrl-q : quits the whole program instantly
Ctrl-shift-w : closes the current window

I keep reaching for ctrl-w and hitting ctrl-q by mistake

This little plug-in, keyconfig, lets you fix that:

http://forums.mozillazine.org/viewtopic.php?t=72994

Enjoy.

-Peter

New computer hotness: Fedora kills Vista

I bought a new Presario C700US laptop recently. I purchased it from Newegg, the place I like most for these sorts of things. It came with Vista on board. I bought my fiancee a computer about 4 months ago and spent 2 months getting all of the bloatware off and another month trying to make Vista stop “taking walks” while I’m working. I disabled all of the annoying visual “features” that I could in an effort to free up processor cycles for things like music and movies and (god forbid) word and data processing. I didn’t want to do that again, so I installed Fedora Core 10. I have my student version of Mathematica, and experience tells me that it generally gets about twice the available memory in Fedora compared to XP. I don’t even want to guess at how little is available in Vista. It is amazing to me that free software is now more functional than software I can’t avoid paying for. This article will be pretty detailed (read: boring) so that anyone who wants to repeat what I did can get some help.

For people in the academic world who are considering Linux, I suspect the big hurdle is MS Office. Microsoft Word is the mainstay of the academic establishment, so  that had to work. I actually bought Office 2003 a few years ago, and it turns out that it installs really well under WINE. So that’s great. Unfortunately EndnoteX, my reference manager, is not so amenable.

I found a much better solution. Zotero is the new hotness when it comes to reference managers. It manages a searchable database of references along with associated files like the PDF, captured fulltext HTML, notes, links to other references, abstract. It also builds a smart bibliography, formatted to whatever specification you want, it makes MS Word compatible citations and also integrates into OpenOffice Writer… basicaly it does everything but massage my feet.

I had about 2 days of frustration with Fedora. Compared to 90 days of frustration with windows. There are still some bugs. If I plug my USB headset in, Skype doesn’t automatically switch its input and output over to the new device. But I can do it manually, and Skype works fine. Alas, my Dino-Lite AM311S does not work at all.

Here are some things I managed to get fixed.

I had some trouble with audio skipping, but a quick google search told me that I can fix it by updating /etc/pulse/default.pa and changing

load-module module-hal-detect

into

load-module module-hal-detect tsched=0

I had an issue with the power icon not updating sometimes, so I turned SELinux to permissive mode… since I don’t have any server services running, hopefully that will be OK.

Another thing I like to do with my computer is to enable multiple monitors so I can have lots of desktop space. Unfortunately, Fedora comes preconfigured to support a desktop of only 1400×1400 pixels. So when I would try to use the desktop resolution applet to change to dual monitors, it would just not do it. No error message, just nothing. So after some digging, I found out that I needed to create an xorg.conf file (it didn’t exist at first as, evidently, defaults were OK) using an automatic configurator then add  “Virtual 2048 2048” like this:

SubSection “Display”
Viewport   0 0
Depth     24
Virtual 2048 2048
EndSubSection

I also managed to get my unlocked cell phone with AT&T’s GO Phone (pay as you go) service to dial like a modem and connect to PPP internet; that was not too hard following the settings in a buried protocol on AT&T’s website: “Create a Dial-Up Networking Connection…“. I also needed to update my unlocked Nokia 7610 phone to be able to talk to the data network. AT&T is calling their data product MEdiaNet… so all of my searching for GSM and GPRS turned out to be in vain. I just needed to google “nokia 7610 medianet” and I found what I was looking for. It was impossible to find with the ATnT support pages.  I also called their  611 service number and bought 1 mb of MEdiaNet service. I was pleased that they didn’t charge me for the call. I don’t know if that helped or not… it seemed like the contract indicated that MEdiaNet was there by default, but who knows.

Getting the phone to connect to the MEdiaNet was actually harder than getting linux to dial the phone’s modem.  Fedora comes with wvdial already installed by default, and although I had to write the configuration file myself, that was easy given some examples I googled. Once that was done, I just execute wvdial as root. This is the wvdial.conf file that I got to work:

[Dialer Defaults]
Modem = /dev/ttyACM0
Baud = 115200
SetVolume = 0
Dial Command = ATDT
Init1 = ATZ
Init2 = ATQ0 V1 E1 S0=0 &C1 &D2 +FCLASS=0
ISDN = 0
FlowControl = CRTSCTS
Modem Type = Analog Modem
Username = WAP@CINGULARGPRS.COM
Password = CINGULAR1
Phone = *99#
Stupid Mode = 1

So, if you are struggling with any of those, I hope this was useful for you. Have a look at our archives! We aim to please.

Cheers,

Peter