True's beaked whale.jpg

Western spotted skunk

Hooded skunk

Yellow-throated Marten

Wolverine

2008 Republican Presidential candidates

May 20th, 2007

2008 Republican Presidential candidates
Evolution question from the first Republican presidential debate, torture question from the second debate. The others believe in evolution (at least to some degree) and did not answer the torture question at the second debate.

VentureBeat understands online journalism

May 11th, 2007

BTW, the previous article comes by way of a link to an article in VentureBeat. Contentwise the article is nothing special, a thinly written industry conference talk/press release. But the author Mark Coker and VentureBeat understand online journalism. The article has what every web news story ought to have but few do–relevant and appropriate links. The article links to a detailed article on the technology, the company, and the conference. This is great!

Unfortunately most news organizations haven’t got this figured out yet. They will report on (summarize) say a report by the FDA without linking to the report. Many/most of these are now on the web–the reporter read it there in many cases–but the article doesn’t link to it. Or to the FDA press release.

Science news never links to the journal article. Or to the less technical journal News and Views summary, or to the non-technical University press release.

It a real opportunity for a news organization. If I knew the McClatchy (formerly Knight-Ridder) news service did this I would seek out their articles over AP’s or the New York Times. I haven’t seen any grab for this brass ring.

Better reading tech

May 11th, 2007

A company has developed a new reading technology called Live Ink (paper here). The idea is to improve the way text is displayed to improve reading comprehension. The way the brain perceives a page of text is as small region at a time. Words from several lines get picked up at the same time. This confuses the parts of the brain that comprehend words and sentences. Live Ink proposed to spread text out to avoid this mental confusion to improve reading comprehension.

There’s a kernal of a good idea there–electronic text allows reformatting to increase comprehension. But their solution sucks. It takes up too much space and it only partially helps with the problem of line confusion. The syntactic breakup may be helpful. Here’s an image of it:
Live Ink example

Computer formatting is a good idea. Here is my idea of how to do it. Fuzz out the lines before and after the current line. This could be done one of two ways. If eye movement tracking is available, follow the eye and only make the line being looked at visible with the others fuzzed out. Without eye tracking make this a timed system (like traditional light bar reading trainers). Start it on a section of text and make one line at a time is visible moving through the text. Controls would be needed to pause and go back a few lines, and flip it off.

By fuzz out the rest of the page I mean alter it so the brain doesn’t think it is text and try to decode it. Whether making it out of focus is enough or if another kind of noise needs to be added would need to be determined by trials. It would be important to leave enough information that the presence of text blocks and formatting is visible. These provide visual landmarks needed for good reading.

Technically, this could be easy–a web browser extension or perhaps as simple as some Javascript added to a page with overlay images fuzzing the text and moving as needed.

Stem cell site

December 3rd, 2006

Well done site that explains stem cells to the public:
http://www.tellmeaboutstemcells.org/

Resetting WordPress passwds

May 16th, 2006

To reset a wordpress password, first generate the hash:

perl -e 'use Digest::MD5(md5_hex);print md5_hex("the_password"),"n";'

then update the password in the database:

mysql
mysql>select * from wp_users;
mysql>update wp_users set user_pass='the_hash_string' where ID=xx;
mysql>exit

Immigration stats

May 16th, 2006

I looked up Jerry Pournelle’s site and he was worrying about the US getting overwhelmed with immigrants. To start with, it looks like he’s using scare numbers, 100 million US immigrants in the next 20 years. The US has recently naturalized 1/2 million to a million immigrants a year (pdf). The base value is about a 1/2 million with the figure doubling during amnesty periods.

So how high was immigration into the US in the past? I recall the last big wave was in the early 1900’s. Googling brought up the census numbers. The 1990 US Census estimates 19.8 million foreign born citizens in a population of 248.7 million, 8.0% of the US population. At the peak of the last wave of immigration, there were 13.5 million foreign born citizens in a US pop of 92.2 million, making up 14.6% the country. And this wasn’t an isolated peak, the foreign-born percentage was 9.5% in 1850, 13.1% in 1860, 13.4% in 1880 picking the earliest figures I found and then the other high points (pdf, pdf).

So the rate of immigration into the US is not near the historical high. And in context and with regard to assimilation I would expect current immigrants are easier to assimilate. Typical immigrants today come to the US knowing quite a bit about the country, and already familar with many aspects of the culture from the movies, TV, and books that the US exports around the world. The immigrants coming from Southern and Eastern Europe in the early 1900’s knew much less about the US.

Ecologist’s doggerel

December 12th, 2005

Old doggerel, but new to me:

“Let’s consider the concept of niche-
If I knew what it meant I’d be rich.
Its dimensions are n
But a knowledge of Zen
Is required to fathom the bitch.”

RAID1 recovery

December 8th, 2005

One of the MA database systems went down. It wouldn’t boot, so we put in the install disk, ‘linux rescue’ at the prompt, and it booted into rescue mode. The system is set up with the system files on a pair of RAID1 SATA drives. Drive /dev/sda was gone–fdisk found no partition. /dev/sdb was fine. I looked around for hacking traces but found nothing. /var/log/messages indicated the system had shutdown for reboot two days before. We hadn’t done it, so how/why?

First, I re-partitioned /dev/sda to look like /dev/sdb using the same ‘fd’ RAID partition type.

To bring it back up, I shut down, switched the sda and sdb cables so we could boot off the good drive and then have RAID restore the second drive. The original /dev/sdb didn’t have grub installed on the MBR, so I had to reboot with the rescue disk and reinstall grub.


/mnt/sysimage/sbin/grub
grub>root (hd0,0)
grub>setup (hd0)

I had to use grub because grub-install wasn’t available from the rescue environment and /mnt/sysimage/sbin/grub-install couldn’t find /sbin/grub.

Then reboot, grub comes up, the system boots. The root /dev/md1 RAID1 is degraded as this shows, so add /dev/sdb back:


mdadm --query --detail /dev/md1
...degraded...

mdadm --add /dev/md1 /dev/sdb

And 20 minutes later the array is clean!

vnc to linux vncserver

October 26th, 2005

Figured out how to VNC from my laptop to my linux server. Forwarded X conections were too slow so I gave VNC a try. It was harder to set up than I expected. I googled around and after many tries found a post online that worked.

Here’s the stiuation. I need to connect to my lab computer from my laptop at home. The lab computer is behind UK’s firewall. Run vncserver on the lab computer–that’s the easy part. It runs on display :1 by default:

elegans.uky.edu> vncserver

Turns out I need to enable port forwarding on the lab computer’s sshd:
As root add this line to /etc/ssh/sshd_config

AllowTcpForwarding yes

then restart sshd:
/etc/rc.d/init.d/sshd restart

Then forward the ssh connection. On my laptop I run this command from a terminal:

ssh -L 5901:localhost:5901 me@elegans.uky.edu

And run the VNC client. My laptop runs OS X, so I downloaded “Chicken of the VNC. By default it uses port 5900, enter display 1 (so it goes to 5900+1 = 5901) and the host is localhost. Starts up and runs fast!

Oldest noodles

October 14th, 2005

Archaeologists push back the date of the invention of noodles to 4,000 BP:
BBC NEWS

The 50cm-long, yellow strands were found in a pot that had probably been buried during a catastrophic flood.

Radiocarbon dating of the material taken from the Lajia archaeological site on the Yellow River indicates the food was about 4,000 years old.

Scientists tell the journal Nature that the noodles were made using grains from millet grass – unlike modern noodles, which are made with wheat flour.

The discovery goes a long way to settling the old argument over who first created the string-like food.

Professor Houyuan Lu said: “Prior to the discovery of noodles at Lajia, the earliest written record of noodles is traced to a book written during the East Han Dynasty sometime between AD 25 and 220, although it remained a subject of debate whether the Chinese, the Italians, or the Arabs invented it first.

Great science writing too–packed with detailed information yet succinct. I’ve never read a molecular biology news article as good.

noodles