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

Algae for Biofuels

Another article crossed my desk that was all about algae for biofuels. This one quoted a figure: Algae absorbed roughly 20% of all venture capital invested in biofuels last year. I think that’s pretty impressive. That’s about $180 million. Also impressive: an article over at Green Car Congress talks about a 91 octane gasoline derived from algal a biocrude.

Here are a few of the companies looking into algae biofuels:

Sapphire Energy

Petrosun [edit 3/9/14, defunct]

Imperium Renewables

GreenFuel Technologies [defunct]

AXI, LLC – this one is was cooperating with my Alma Mater [defunct]

-Peter

Geoengineering – is it possible to really engineer our ecosystem?

Today is the start date for a program in which iron based fertilizer will be seeded into a swath of the southern ocean. That will cause a massive algae bloom, and (in principle) soak up carbon dioxide. The notion is that, I suppose, it will stay in the ocean end up as sediment.

The Science short news article is not heavy on the details, but I at least wonder about the possibility of harvesting that algae. But it’s a secondary interest. The bigger issue is: we can certainly inadvertently cause unintended effects on the climate; can we really hope to create intended consequences as well?

I saw a TED talk on that a while back, and thought it was great.

Hope you enjoy.

-Peter

Breaking News: Cellist disease a hoax

Cello Scrotum is a hoax! Hypochondriac male musicians inclined toward large stringed instruments will have to find a new problem with which to afflict themselves. Guitar nipple, however, is all too real.

Alert reader Jason brought this L.A. Times article to our attention. It seems that in or around 1975, a mated pair of physicians cooked up the idea of Cello Scrotum despite the fact that a properly operated cello does not, in fact, come in contact with the genetalia. The paper got published anyway. It’s an early example of a parody in the scientific literature being taken literally.

It reminds me of a more recent iteration of this phenomenon: Alan Sokal published a computer generated gibberish paper in Social Text. He tells why he did so in his book, Beyond the Hoax: Science, Philosophy and Culture.  Another instance occurred more recently: an MIT student got a conference paper accepted that was pure gibberish. To be fair, conference papers are not held to the same review standards as journal papers. Nonetheless, The Register sums up thusly:

Perhaps because of the atomization of the disciplines in both arts and science, the quality of published academic papers appears to be at rock bottom.

And these days, simply being published means you’re an authority. The MIT pranks illustrates all it takes to be published, is to submit a paper.

Maybe that’s true for Social Text, but it’s another matter for, say, Analytical Chemistry.

-Peter

We will restore science to its rightful place

I’m “reporting” from Ukraine today. I’m not as well-connected to the ‘net and to the doings of Science, so I don’t have much in the way of news for you.

I said before at some point that I wanted to avoid politics in this project. But I think I will skirt that line again today.

The New York Times wrote up a little thing headlined “Scientists Welcome Obama’s Words.” I think the article quite decently summarized the attitude of the scientific world, at least as I’m familiar with it.

Party loyalty and the scientific world’s liberal lean aside, I think it’s fair to say that the Bush administration was pretty hard on the scientific community. Back a few years ago, when the U.S. had money, they did some good things for the science budget. But when push came to shove, those were not fleshed out, and programs that got a good start had to struggle for the last few years.

It’s a funny thing: when the NIH budget doubles, more then twice as many people show up to ask for money. And even more strange: if they get it, they are hoping for more next year, too!

Obama said in his in his Inaugural Address: “We will build the roads and bridges, the electric grids and digital lines that feed our commerce and bind us together. We will restore science to its rightful place, and wield technology’s wonders to raise health care’s quality and lower its cost. We will harness the sun and the winds and the soil to fuel our cars and run our factories.”

Well, that might be rhetoric, but it’s refreshing, anyway.

-Peter