Cavalcade of Mammals

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


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.

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.”

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!

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!

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.

A compter security hack has appropriated the word nematode to describe “good” network worms. Dave Aitel says

“We don’t want people to think this is impossible. It’s entirely possible to create and use beneficial worms and it’s something businesses will be deploying in the future.”

So much for ever being able to Google “nematode” again! Spoiler! Bastard! And it’s so wrong. Aitel has a apparently heard of Caenorhabditis elegans, everyone’s favorite worm and entirely harmless, and jumped to the conclusion that every nematode is beneficial to humans. So wrong, so sad; a little knowledge is a dangerous thing. If this is the depth of his thinking I certainly wouldn’t take his advice on computer security.

I just read a review on cutting-edge new sequencing technology (Shendure et al., 2004). There are several approaches that were new to me. One that caught my imagination incorporates “polony technology,in which PCR is performed in situ in an acrylamide gel” for DNA amplification. A related technique using emulsion has been developed by the Volgelstein lab.

My idea of developing a method using reversibly terminating nucleotides has also occurred to many other people! Apparently finding a way to do the reversibly termination has been a roadblock. I certainly didn’t have a way to do it. They have worked out approaches to detection of incoration, the other half of the method, and also a part I didn’t develop.

Very interesting tech. According to the paper, even nanopore sequencing is close to working!

The paper talks a bit about using ULCS for personal genome sequencing (PGP, everthing gets an acronym), about the whys and what it will mean. It contain the usual throw away consideration of ethics and consequences. The papers says this “will require high levels of informed consent and security”. In practice, your personal seq info and related disease susceptibility info *will* get spread to interested parties. Just look at who calls the shots; after more than a decade of attention to genetic privacy and overwhelming public support, “no US federal laws that ban genetic discrimination for medical insurance or in the workplace”.

How I would love to seqeunce 1Gb a week!

From PZ Myers, unsourced:

“0.1% of all the species that have existed are currently extant, and the average lifetime of a species is roughly 10 million years”

Bio stats page

I’ve messed with the site’s css style sheets. If it looked OK before, there’s no change. If the layout used to suck, it should be fine now. Css is such a tar baby, I won’t tell you how long it took me.

And I went and downloaded 400+ new mammal pics, should be enough to keep the site in mammals all year!