Output Stream of Consciousness

Now that is a heck of a mouthful of a word. It's the field of application of the theory of evolution to drug discovery.

Now it's not a matter of making things evolve, but rather taking advantage of the effects of common ancestry and the gene and protein data that comes from that analysis to help with drug discovery, disease modeling, and in some cases to find out the limits of working with other animals.

This article by David Searls is a fantastic, albeit necessarily jargon-filled, summary of the field.

The drug companies are most interested in orthologs, which are gene sequences that are essentially the same gene in two different species. They do not always retain the same functionality, but often they do, and this helps much in analysis.

Since testing in humans is the often the last step, it can be frustrating to bring a drug so far and have the different metabolism of the test animals be the real reason that the drug was failing in testing. From the article:

A strong motivation for the further study of orthology of drug targets is the fact that species differences of various kinds — for instance, in pathophysiology or drug metabolism — frequently hamper the progression of targets and compounds, often after quite significant investment. This indicates that even a marginally improved understanding of species differences could have a major impact on the cost of developing medicines.

This is the practical side of the theory of evolution.

Unless these are males of a different peafowl species, this is my first encounter of peahens, the female counterparts of peacocks, fanning their tales in much the same manner as the males do, only somewhat less spectacularly.

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(NOTE: Update about this story at the end of this post)

There are a number of odd tales in the Bible, but some of them are odder than others.

The tale of Balaam and the talking donkey is an odd one, but not just for the talking donkey. This is a tale of God getting mad when you do what he told you to do.

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Was poking through the Old English-plus-translation version of Beowulf I have, and was intrigued that the first line was:

Hwæt, we Gar-Dena in geardagum

There you go, Dena's in Beowulf!

(Even though it means the Danes, here: Gar-Dena = spear-Danes)

Not knowing where Tolkien got his inspiration, there's an awful lot of homage to Beowulf in Lord of the Rings. Beowulf refers to Middle Earth, ring-givers, and one of the Old English words for king, apart from "cyning" (kewningg) is "þeoden" (the "þ" giving a "th" sound). Theoden King indeed!

There is a site that summarizes many of the proteins that creatures have in common with one another. Most of the creatures listed are bacteria, but there are a few multicellular organisms with respective codes: Microsporidia [E], thale cress [A], a worm [C], the fruit fly [D], baker's yeast [Y], fission yeast [P], and humans [H]. "Coming soon", they have rice, the mosquito, chimpanzees, dogs, mice and rats.

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Dena and I haven't really been posting a ton, with the new baby in tow, but with five weeks and a bit of baby under our belts, I think I'm ready to share a bit of the whole experience :)

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As of right now, their online booking system does not handle infants very well.

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Looks like there's been a small revival in the availability of DRM-free music. No major revolution, but you have the advent of Amazon's DRM-free MP3 collection, which contains quite a number of bands, and even the icon of DRM, iTunes, now has "iTunes Plus" with double the bit rate encoding and DRM-free with the option of upgrading previously-bought songs to this format.

So you want to see a little bit of the tree of life for yourself. Maybe use some of the bioinformatics tools on the Internet to see some of the relatedness of life on earth. Can you do that as a layman? Sure you can, and here's a little introduction as to how.

One protein that's a good one to try is the human hemoglobin alpha chain, a component of hemoglobin, the oxygen carrier in your blood.

Let's do this thing!

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We got a small swack of spam comments today which point at pages on http://meta.missouri.edu/ serialize/tmp/@top/ (I've broken up the link here so the spammers don't get more traffic). I've sent the webmasters off a warning.

UPDATE: Yay, the pages are taken down! :) Take that, spam monkeys!

A commenter at one of the blogs I frequent pointed out in passing this one very cool paper from January 2006 called HOX GENES: Seductive Science, Mysterious Mechanisms in the Ulster Medical Journal.

I love the Hox, or homeobox genes. There aren't too many gene sequences laid out in any sort of order of a body plan, but the Hox genes are. Carroll's book Endless Forms Most Beautiful captures that really well, but this paper has the evolution of the genes in a nutshell.

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I never thought I'd see this in my lifetime. The Canadian dollar is so close to the U.S. dollar. It has actually traded just above the U.S. dollar during the day. From Reuters:

After pushing through the key 1-for-1 level on Thursday for the first time in more than three decades, the Canadian currency hit US$1.0061 overnight, but gave up those gains as the greenback rebounded from record lows against the euro.

Now if they could just change those dang US/Canadian book prices on the backs of book jackets, it would be even better ;)

Arrrrr! At 6:56 pm on September 16, 2007, Axel Duma Annand transitioned from the world of womb to the world of people.

To recap a little bit...

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800notes.com is a simple site with but two purposes: letting people post information on persistent, unknown callers, and looking up such posted information.

It helped me look up our of our persistent nuisances, 1-800-566-8064, which seems to do cold calling as a business from the looks of the various different companies they say they represent when calling (often banks).

There were two posts for how to remove yourself from the list on the last page:

christina wrote:

if you do not want them calling press 1, then they will prompt you for you # area code + 7 digits, this is supposed to take you off their list within 72 hours...we'll see....

UPDATE: I can tell you for sure that christina's method did not work for me - I pressed 1 and someone immediately started into asking for Dena. Mleah.

Rob wrote:

Teresa Engle / COO / TEL 1-800-207-1983 x4500 calling this number will have u removed from this list.

I may look into this, because I'm fed up getting woken up by these people after late nights at the hospital.

P.S. Yes, I will get into details of the new baby and mom - looks like they might get to come home TODAY!

If you're considering using uniqueidentifiers on your tables, particularly as primary keys, then you might want to upgrade your SQL Server or just check your SQL carefully if you're still running SQL Server 2000.

In particular, doing a COUNT(field) on a uniqueidentifier comes up with a bizarre error on SQL Server 2000:

Msg 409, Level 16, State 2, Line 1

The count aggregate operation cannot take a uniqueidentifier data type as an argument.

It's truly a weird error. Why on earth would there be difficulties in counting any field?

Now you can go COUNT(*) without difficulty, or use a different field. COUNT(field) is useful when you're doing cross-database SQL, since it's actually faster than COUNT(*) on some databases, but if you can tune your SQL to the particular database, it helps. SQL Server 2005 also combats this silliness, but this only helps if you can deprecate support for SQL Server 2000.

Just wanted to post this, since there really wasn't anything helpful around the 'Net on that particular error message.