Output Stream of Consciousness

For a fan of biology, as well as of puzzle games in general, this is one of the most amazing things I have seen in a long time.

Now, we already have things like Folding@Home, which is a distributed project that attempts to find low-energy conformations for proteins. Basically, the proteins that we are interested in are just chains of amino acids that get spewed out when DNA is transcribed. The protein "backbones" have side chains, which are just the side bits of the particular amino acid, and they vary in their love of or repulsion to water.

Proteins will settle into shapes that are lower-energy. Finding what those shapes might be so that we can deduce a bit about their function has been the aim of projects like Folding@Home.

Well, what if you took that whole concept and turned it into a game?

Not just a half-arsed game, either, but one with tutorials, warm-up puzzles, online teams and a pretty good interface to boot. It comes in Windows, Mac, and now Linux flavours as well.

That's just crazy nifty. Kudos to the folks who came up with that!

(One note: the link to the Windows version just after I signed up was pointing to the wrong place. I had to get the setup from this link. It's correct on the main page)

This is just an awesome baby toy.

We bought this when Axel was seven months old. It was not too long after moving into our new house, and we thought that perhaps having some toys that were specifically "crib toys" might help occupy him when he was going to sleep. We went through the Toys 'R' Us with an eye to letting Axel poke at the toys in question. This was one toy that he figured out and in which he seemed interested, so home it came.

Now, he didn't actually warm up to it as a crib toy for quite some time, but within a couple of months, he would occasionally play with it in the crib when he was just a bit too jazzed up to go to sleep. He also plays with the toy in the morning.

It does have to be said that it is a slightly noisy toy, but not horribly so. There are three handles on it, coloured yellow, red and blue with slightly different textures on them. Squeezing a handle will speak out its colour, play one of the few tunes (like William Tell Overture) and flash that colour on and off in the dome on top.

I get a kick out of some of the other features: squeezing two handles will do the secondary colours (green, purple, orange), and other switches will change the language in which the colours are spoken.

No, we tried squeezing all three handles at once - that doesn't do anything :)

So we have to put up with a little "red... red... red... red.. (music..cut off) yellow (William Tell Overture)", but it really helps him get to sleep when he's a little jazzed up.

Plus, he looks at us with a bemused "what the...!?" face when we say "red... red..." and hum one of the tunes :)

Imagine this scenario: you have downloaded a particular project that has source code, and it's almost exactly what you want, but it's missing a few things, and it's not under version control (for example, the projects on SourceForge) So, you go off and make some updates to it.

Now a new version of the project comes out, and you would love to upgrade... but now there is the matter of those customizations that you did.

So what do you do?

Well, here is one approach that I used to keep my customizations to MWForum, which I used for my Cosmology forums, which fits the description of such a project.

I have made customizations to allow for named quoting and superscripts, etc., and I did not want to lose these. I did, however, want to upgrade from 2.10 to 2.15, and the project is certainly not under version control.

Full story »

Despite all the labels and posturing and rationalizations, when it comes down to why evolution is a particular target for many of the Christian (as well as Jewish and Muslim, though we hear less of those perspectives here), it is relatively simple, and to be found in a few short paragraphs in an exchange on Conservapedia...

Full story »

I have a small passel of graphology books. They were fun, especially when I was younger and wanted to see whether my peculiarities of handwriting were "good" or "bad", and was indeed happy with the bevy of "good" signs.

Revisiting the craft, though, the claims seem puffed up, and worse, in a way, is that it is deeply steeped (the material I have, at least) in simplistic Freudian terms: the upper zone is the superego, the middle zone the ego, the lower zone the id, left-leaning is maternal influences, and lots and lots of sexual issues.

When I went poking around looking for an evidence-based graphology, I got by and large two things: places (e.g. here) that purported graphology to be evidence-based, but that looked quacky (e.g. it's evidence-based, but just for fun you could find out if your wife is pregnant with a boy or a girl?!), and those (e.g. here) that skeptical of the whole enterprise with links to some studies of existing graphology methods that showed them in rather a bad light.

I'm inclined to think that there are bucketloads of chaff in graphological methods. There seem to be some general correspondences, but they are the sort of thing that the untrained eye can certainly see.

If current graphology methods are bogus, it would be nice to be able to start from the ground up and get some evidence-based correlation checks going on.

Not just taking current methods and seeing whether they stack up. Start from scratch.

Correlating questionnaires and measurable writing characteristics may find something, little or nothing.

Either we fix graphology or consign it to the entertainment heap along with the other forms of fortune-telling.

I thought we might escape the Canadian premiere of this poor documentary, having seen nothing of the sort in upcoming movie listings, but I am informed on the theatre locator page of the Expelled! movie site that there are two locations where it will be playing here: Eau Claire and Country Hills. Sad.

The synopsis on the Tribute web site is bang on and somewhat amusing:

This movie follows Ben Stein as he seeks to determine whether religious based Intelligent Design / Creationism is a pseudo-science trying to undermine evolutionary biology or whether it is legitimate science being suppressed by a scientific establishment that is hostile to any deviation from the status quo. Along the way, Stein is told that evolutionary biology is responsible for the Holocaust, Stalinism, and the Second World War, and that only religion based alternatives such as Intelligent Design / Creationism and the intervention of a god can adequately explain the existence of life.

That's about as "in a nutshell" as you can make it. Thanks, anonymous Tribute writer :)

I took a half-day holiday to go to the Calgary Zoo with my wife, my baby and some friends.

At the gate, when I presented our three membership cards, I and I alone was hit with my card 'coming up with an error'. Apparently, when the zoo switched its systems, some of the data "didn't make it" (this was the explanation at both the booth and Membership Services).

Now data migrations can, indeed, be a nightmare, but you test, and you hedge your bets by keeping the old data around somewhere, just in case. It was a little aggravating that it was a "known problem" and they had not gone the extra mile and tried pulling in the data that they missed, but so be it.

What was more unforgivable was that, though it was not my fault, the gal working the ticket booth, despite the membership card trouble not being my fault, despite my other family members' cards working, despite us being in a group, and despite busloads of children arriving in droves, she did not apologetically let me through, but rather, despite explaining the circumstances (and having the other members of our group already in the Zoo), sent me back to the membership services to wait for the better part of half an hour to sort out my card.

People, if you are going to screw up a data migration and decide to just handle the "oops" cases manually, tell your staff not to inconvenience the hell out of the people that you let fall through your data cracks for your own convenience. It's rude.

On a website registered to Lehigh Valley Baptist Church, the "Good Person Test" is a textbook example of that particular kind of monochromatic religious reasoning that just falls down under light dissection. It aims to gently but firmly pinch you by the nose and lead you down a path to a conclusion by following steps a little past the reasonable so that, by swallowing the story in smaller chunks, you might think that the conclusion, in retrospect, was inescapable.

Perhaps people taking the test might mistake their uneasiness at each question for guilt. It's not guilt. It's that same feeling you get when your bus driver has gone off-route, and you are wondering whether they know what they're doing. That's the human cheat-detection apparatus registering a mild alert.

Let's see what's in store for us, shall we?

Full story »

Our new place has a much bigger garden than our previous townhouse.

It did not sink in how much more so until we brought some of our precious plants from the townhouse to the new garden. The chunk of garden at the top of the yard held what was already there, what we brought (minus what we put in the front garden, which was a definite minority), plus other things we bought.

We are in a neighbourhood with a complement of wandering rabbits, so the first thing we were worried about is... what can we put out there without the rabbits eating it? We decided to use this list as a guide, but of course, nothing is totally rabbit-proof. We figure that we will put plants out there as per the guide, as per what's already out there, and whatever we have a lot of that we are willing to risk putting in the front garden.

As it stood, when a rabbit came hopping up to our freshly-planted front garden, it nibbled a dandelion (!), a weedy sedum-looking thing, and then proceeded to just stretch and chill out on the lawn.

Full story »

Not content with letting me in on my European lottery winnings, or being a company representative, or helping ousted generals smuggle their money out of foreign countries, they have now outdone themselves with THE DEATH THREAT.

Full text and very slightly blanked out headers below the fold. Looks like there are a few reports like this with drop boxes pointing at gmail, and the source servers also seem to be in Google. That would seem to be gmail, but gmail itself wouldn't be allowing them to change the return-path: and from:, would it?

Ballsy asses, these folks, aren't they?

Full story »

They are normally fairly timely with moderating comments over on the Expelled! movie blog but, unusually, the moderation has been out of commission there for over a week and a half so far.

Now it could be that there is just one guy and he went on holiday, but in the absence of any news in this regard, I wish to save my one post from moderation purgatory, and post it here instead...

One of the users was posting on the blog, complaining that nobody had answered his seven questions:

Now, I’m going to repeat a few questions everyone seems very comfortable leaving alone. I posted them earlier and it’s just a few of many I could ask you.

Now, he claims to be a "molecular biologist in the medical research area", which makes me wonder what classes he skipped... or where, indeed, he learned his biology, but fair enough :)

I answered him, but the answer is held, at this time, in moderation limbo.

So here it is, albeit in my obscure blog in a corner of the internet :)

Full story »

Based on the misrepresentations in the Expelled! movie, reason tells me that a unilaterally positive review is liable to partake of a number of factual inaccuracies in the movie, and add its own bad conclusions.

Well, one out of one so far.

In a credulous and blithering post entitled Ben Stein is the Rosa Parks of Darwin Skeptics, Kevin Wirth lays out a positive review and some commentary on the Expelled pseudodocumentary.

Years ago Rosa Parks got on a bus and sat where she shouldn't have - a form of protest letting the world know she'd had enough. Ben Stein, about as unlikely a candidate as Rosa for similar notoriety, has now done much the same thing, only this time the issue isn't about racial prejudice, it's about prejudice against those who question any aspect of evolution.

Well, for an easy objection, Ben Stein is no Rosa Parks. He's no Ghandi, Galileo or Martin Luther King, Jr., either, lest someone be trying to reserve any more pedestals that Stein is most unfit to occupy.

The larger claim, though, "prejudice against those who question any aspect of evolution" is bullshit, unless you modify the phrase to have "by using the already-disproven Second Law of Thermodynamics argument".

Kimura's Neutral Theory did not get him Expelled, and neither did Gould get ejected for Punctuated Equilibrium. The most aggravating thing about this, of course, is that intelligent design luminaries know this, in part because they are constantly quoting these sorts of working evolutionary scientists.

(Instead of doing their own damned research, I might add!)

Full story »

If you go throw a function into Oracle, and it's wrong, e.g.

CREATE OR REPLACE FUNCTION Banana IS -- Oops, no return!
BEGIN
RETURN SUBSTUR('Banana',2,5); -- Oops, misspelled!
END;

You will get no warnings about this in most tools until it comes time to call it:

SELECT Banana FROM DUAL;

(If Banana were a procedure, we would use CALL Banana; instead)

You will get the error ORA-06575: Package or function BANANA is in an invalid state.

So how do you find out what's wrong? SHOW ERRORS; only works for SQL statements, not the contents of a stored procedure.

This is what you have to do:
SELECT * FROM USER_ERRORS WHERE NAME='BANANA' ORDER BY SEQUENCE, LINE;

It is important to put the name in uppercase.

You get:

BANANA, FUNCTION, 1, 1, 17, PLS-00103: Encountered the symbol "IS" when expecting one of the following: ( return compress compiled wrapped, ERROR, 103

If we add in the RETURN VARCHAR2 before the IS, and select the user errors again, we get:

BANANA, FUNCTION, 1, 3, 10, PLS-00201: PLS-00201: identifier 'SUBSTUR' must be declared, ERROR, 201
BANANA, FUNCTION, 2, 3, 3, PL/SQL: Statement ignored, ERROR, 0

Nice, rich error messages, but what a way to have to get them!

If you are using PL/SQL Developer, take a look under Functions or Procedures. Any stored procedures in error show up with a little X on their icon. The errors will show up if you right click->Edit. Creating the stored procedures from right-click->New on these items will save you a lot of hassle.

If you are stuck with a bit of a "manual" tool, however, the USER_ERRORS technique is your best bet.

From a more recent episode of the "Why do people laugh at creationists?" series, Stein is shown being interviewed by Paul Crouch, Jr. on Trinity Broadcasting Network.

The episode is here.

Now, a lot of this particular episode is not all that interesting, dealing with somewhat contradictory wishes Stein has on the military versus how you should treat people, and on the rule of law versus being a lawyer, but I don't see those as terribly beyond the pale.

I've transcribed a couple of quotes from Ben Stein's opinion on science below:

Stein: ...mother's already been gassed, so they would take a child and give him or her an overdose of barbiturates to kill 'em, and that's... that was horrifying beyond words, and that's where sci... in MY opinion, this is just an opinion, that's where science leads.

Host: That's right.

Stein: 'cause love of God, the[?] passion and empathy lead you to a very glorious place. Science leads you to killing people.

Host: Good word, good word.

Charming.

The entire original interview is on TBN's site here, if you want an extra helping of ignorance.

Someone reposted a Kent Hovind video about the dangers of evolution. There was one slide that just caught my eye, because it was sitting in the freeze frame, ostensibly showing the evil population control that will be foisted upon us all:

Reduce birth rates w/
* abortion
* RU486
* birth control
* homosexuality
* lower cholesterol
* high cost of living=smaller families
* eugenics
* 1 child/family-China

Wow, so homosexuality is now not only somehow voluntary for people, but being promoted to help control population! Who knew!

It was the "lower cholesterol" that made me blink a couple of times, though. Oh no, it's not about your heart health, it's about infertility. From Truth Radio:

Low cholesterol and its link to infertility. Keep in mind the big picture. Satan hates God. And Satan and God have been at war for 6,000 years. God's plan is fill the world with kids. [...] Satan, of course, wants the opposite. He wants to reduce the world's population to zero as soon as possible. And so Satan is going to work towards reduction of the population and lowering cholesterol is good way of doing that.

In keeping with the worldview of "there are only two choices", Kent Hovind: delusional or two-faced? :)