How to Fix Blogger's FTP Bug
Posted 7:30 AM

Google is canceling support for FTP in blogger. Fortunately, there's an easy fix and you get to keep your domain, and keep everything working the way it was.

1. Switch to hosting your blog on blahblah.blogspot.com ... but don't finish the migration (read step 2).

2. DONT LET GOOGLE FILL YOUR OLD BLOG WITH REDIRECTS. This will ruin your site's ranking and be, in general, a bad user experience.

3. Use your blogs RSS feed to monitor for changes. Use a script to synchronize the new/altered pages from blogspot domain pages with your real blog. Here's the script I'm using, it works well. I'm running 5 blogs from a cron job.

4. Turn OFF any indexing services for the new blogspot domain (Allow search engines to find this site? NO). You don't want two sets of content out there. Many search engines, not just Google, will punish your site's ranking for having multiple versions.

5. (Rant: I don't believe, for a minute, that the engineers at Google couldn't figure out how to run FTP affordably. I do over a terabyte of FTP crap every month for free at memebot.com ... and I never even look at it.... paid for twice over with cheap ads. They're either liars or they are incompetent.)

6. ADD this script to the HEAD section of your template... so people won't use your blogspot domain:

<SCRIPT language="JavaScript">
<!--
var str=location.href; 
if (str.indexOf('blogspot.com') > 0) {
  var newStr = str.replace('http://YOURBLOGSPOTNAME.blogspot.com','').replace('http://www.blogger.com/blog-preview.g','');
  window.location='http://www.YOURDOMAINHERE'+newStr;
}
//-->
</SCRIPT>

7. I made a form so people could sign up to have their blog sync'ed if they don't know what a cron job is. If you use rsync, I don't need your password. (Why didn't Google use rsync?). I have a bunch of dedicated servers for other reasons, so it's no problem for me for now (not too many people so far):

New Blogspot Site:
FTP Host (aka custom domain):
FTP Path (for example /blog/):
FTP Username:
FTP Pass (optional):
Use Rsync*:

* NOTE: To use rsync, you'll need click here and put this public key in your authority file (~/.ssh/authorized_keys). This way your password doesn't have to be entered anywhere.

Labels: programming

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Catalytic Antibodies Simply Explained
Posted 1:17 AM

Catalysis is the process of speeding up a chemical reaction by lowering its activation energy - the energy hump a reaction has to go over before it can roll downhill. Efficient catalysts of chemical reactions are extremely commercially valuable and widely researched.

Enzyme Catalysis Basics: Biological enzymes are known to catalyze (speed up) chemical reactions, in part, by stabilizing the transition state (halfway point at the top of the hump) of an otherwise energetically-favorable (downhill) reaction. Some catalysts work by moving chemicals next to each other that would otherwise not randomly meet that often. (1) Some enzymes are known to change their shape (conformation) after binding and during the reaction - driving catalysis (2).

The immune system can be stimulated to respond to a incredibly diverse range of molecules by producing antibodies which bind (cling, stick) to these molecules. The theory of "catalytic antibodies" was that if an antibody was purified that bound to the transition state of a reaction, it would, in the same manner as an enzyme (above), stabilize that state (drag it up the hill) and accelerate the reaction. In order to generate such an antibody, a "transitions state analog" (TSA) - molecule that looks like the known transition state of a reaction - is used. Antibodies that are generated (usually by injection into a mouse) to bind to that TSA are then screened until one is found that catalyzes the reaction. Surprisingly, to me, this works very well. (3)

However, these "abzyme" catalysts are never as efficient as enzymes for many reasons. The abzyme may strongly bind to the product of the reaction (not letting go when it's done), greatly inhibiting its effectiveness. Also there is the difficulty of creating a TSA - they may differ in bond angles or polarity, etc. Many enzymes form strong (covalent) bonds during their catalysis mechanism, but this is not known to be possible with abzymes. Enzymes also employ conformational changes, metals and other cofactors to accelerate catalysis.

Abzymes are being aggressively researched, however. For example, it may be possible to engineer abzymes which bind to prosthetic groups to be used in metal-catalyzed reactions. Abzyme reactions which employ several cofactors have already been demonstrated. (4,5)

(1) "Chemical basis for enzyme catalysis", 2000, TC Bruice, SJ Benkovic
(2) "Catalysis by Enzyme Conformational Change", 2004 Jiali Gao1, Kyoungrim Lee Byun, and Ronald Kluger
(3) "Catalytic antibodies" (Biochem. J.), 1989, G. Michael BLACKBURN,t Angray S. KANG
(4) "Pyridoxal 5?-Phosphate-dependent Catalytic Antibody" (1996) Svetlana I. Gramatikova, Philipp Christen
(5) "A cofactor approach to copper-dependent catalytic antibodies" Kenneth M. Nicholas, Paul Wentworth, Jr

Labels: biotech

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Nofollow, Viagra, Google & I told You So
Posted 8:05 AM

When someone links to a website, Google and other search engines have, in the past, considered that a "vote" of confidence for the site linked to. The higher reputation a site has, the more it's vote counts... (sort of, there's lots of other factors).

The idea behind "nofollow" is that you can link to a site, but also mark it as "I'm not voting for it". That way someone who has, for example, a list of comments on their blog, won't simply "vote" for everyone who posts a comment. Presumably that would prevent spammers from posting a million comments in the hopes of getting their discount Viagra ad's search ranking up.

It's a solid concept, but in practice it has backfired because it was coupled with a "punishment" system for linking to spam sites.

This punishment system has led sites like Wikipedia, which are, for the most part, extremely reputable, to put "nofollow" on every single link in an attempt to prevent spam. These links are, usually, extremely well-vetted votes of confidence for the site in question. Wikipedia, despite its problems, remains one of the foremost authorities on "link quality".

Other quality sites that have adopted "nofollow" on every link include Digg and Twitter.

You see where this is going. Rather than rely on top authorities with quality information, like Wikipedia, Digg, etc. Google now has to rely only on links originating from people who don't know or care about their link voting/ranking, etc. In other words, generally less knowledgeable or lower quality votes are the only votes used for ranking.

This ultimately harms Google's page ranking system. What Google needs to learn is that "open" is not the right way to go for search rankings. Heavy use of personalized and regional results is the only thing they've done to halt this trend. Here's the next step: allow someone to mark another Google user as "trusted" for search results. In other words, I should be able to mark friends of mine as "trusted" (on a scale of 1 to 5 maybe), for personalized search results.

That way personalization will dominate the results, be highly relevant, and impossible to game.

Google, the last time I emailed told you to track clicks you listened...and it helped. But you never thanked me! Get back to me when this multilevel personalized trust system is done.

Labels: google

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Myoglobin Pov-Ray
Posted 9:34 AM

One of my assignments from biochem class was to play around with VMD and Pov-Ray. It was fun. The red sphere is supposed to be an oxygen.... (I know it's not that big, or shiny, or red and there's no heme prosthetic to bind it with.)

You can click on the image to zoom in.

Labels: biotech

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Google Code Scripted Upload
Posted 9:43 PM

When you want to upload a file to google code in a script there are several options. IMO, send2goog is the best one. In addition to command-line args, it has an interactive mode that auto-saves your config info in ~/.send2goof.conf on both a global-default level and per-file-name level... so you don't have to remember pesky labels, retype usernames, etc. Much nicer than using google's web UI.

Reminder to self as much as anyone else.

Labels: programming

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Apple Says Killing People is OK, Bikini's are NOT!
Posted 10:11 AM

Apples new move kicks 5000 apps off its system, rather than merely rating or categorizing them.

Conspicuously they are leaving on apps which depict graphic beheading, allow kids to play the role of a terrorist sniper, and one that encourages adultery through social networking.

Welcome to the Apple morality lesson. Boobs are really bad. Everything else is fine. I wonder if they'd kick a nursing mother out of one of their stores?
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Gnu Programs on Win32
Posted 8:27 AM

Because I keep forgetting, I'm posting this as a reminder to myself that you can get nearly all the best GNU tools running on Windows. I use MinGW, G++, and gdb as my compiler suite of choice... but there's also programs like "calc", which I go rooting around looking for on Windows.

But this list is more than comprehensive, continins full binaries and works on every old, wonky and new, fancy version of Windows out there.

Labels: open source, programming

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Stop Calling it Global Warming
Posted 8:33 AM

I wish pundits and politicians would cease, as of this minute, to refer to the human-caused exhaust poured into our atmosphere as "global warming".

It's not an accurate description of the problem. Increased carbon in the atmosphere might result in "cooling" in some models. Everyone agrees CO2 levels are lowering the PH of the ocean. And CO2 isn't the worst of our problems. Levels of hundreds of industrial pollutants are skyrocketing globally.

We could be headed for a mini ice age because of a carbon-induced thermohaline cycle change. "Warming" is a derivative term that may, very soon, prove wildly inaccurate and set the politics of this issue back for many years.

Responsible management of the millions of tons of industrial gas byproducts and car exhaust that we pour into our atmosphere has nothing, at all, to do with "warming".

Our atmosphere is a globally shared resource and must be globally managed. There can be no sovereign exceptions to the rules, or those countries will be able to spew their industrial filth upon the rest of us.

Is it socialist to manage shared resources in this manner? Not at all. Feeding and educating people is a social agenda that may be relevant indirectly (after all, if you're family is starving, why should you care about climate models), but for some reason is often "tied" to atmospheric pollution issues by deniers.

Protecting the Earth's atmosphere is an issue of survival, not socialism.
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Virtual Chat Room for Google Talk
Posted 2:57 PM

I created a Perl program that allows you to create a "virtual chat room". It works with Google Talk, AIM and any chat client that works with AIM.

Please see: http://code.google.com/p/vcrbot/

Let me know what you think
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Caffeine, Cancer and Gray Hair
Posted 3:41 AM

We're exposed to DNA damaging, age-accelerating radiation every day. And caffeine might make it worse... or better. (Click on links for references).

Caffeine can accelerate the division of cells, speeding up repair, but also it appears to inhibit the activation of "ATM", a gene responsible for DNA repair. This makes cells more "radiosensitive" ... in other words, more likely to have damaging mutations.

Caffeine is fully absorbed about 45 minutes after drinking coffee. However, it stays in the body for up to 10 hours (5-10 hours for most of us, but 10-20 or more hours for people over 55, women who are pregnant, children and women taking hormone (oral/patch/etc) contraceptives).

So how does this add up? Basically, it means, don't drink coffee up to 10 hours before you go out in the sun for any extended period of time... unless you want your hair to prematurely gray. (Graying hair, and overall aging, has been directly linked to DNA damage and the mediation of this damage by pathways such as those involving ATM kinase.)

Labels: biotech, science

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