Tuesday, March 30, 2010

The Values We All Stand For

Last week, project reason announced its winner for its video contest. The winner was a well constructed video on the incorporation of religious symbols and phrases in federal programs to the exclusion of other groups (namely atheists).

I didn't realize it at the time, but the person that put it together is a KU student named Chris Redford that was in SOMA with me the last few years I was there.

In addition to his entry in this contest, Chris has also been working on putting together a documentary on his de-conversion. I've watched all the parts out there so far and it's exceptionally well done and worth a watch.

The first segment is below. Make sure to watch, rate, and subscribe!

Sunday, March 28, 2010

Netflix streaming on the Wii = WIN

I got my Netflix streaming disk for the Wii in the mail the other day. When I first heard about it, I was interested, but not hopeful. Streaming video to a computer monitor is one thing. But blowing that up enough for a 30" TV while still having decent resolution is more difficult. And with the challenges from movie companies to limit online content, the selection is bound to be limited.

But I went ahead and plopped it in and checked it out.

So far, I'm very impressed. I've watched a few movies and the quality has been superb. The Guild was nice and shiny. Angles & Demons was perfectly clear. Ghost in the Shell, a bit fuzzy, but then again, it's an older anime series and they tend to look that way anyway. So we'll go with it faithfully reproducing the quality of the source material.

In what I've watched so far, there hasn't been even a second of lag once the movie has buffered. Speedy servers on Netflix's end.

As far as the selection, 14/94 items on my original queue have online streaming available. Some of it is anime, which only streams as the dubbed version, so I'll probably get the disks on that.

However, I flipped through the items available from the menu and found several more things I probably wouldn't have added to my DVD queue, but would definitely stream episodes of here and there. For example: The first four seasons of Mythbusters! Epic. Dr. Who? Got it. Carl Sagan's Cosmos? Yeah, it's there.

Overall, the streaming to Wii (and other systems) is awesome. Limited, but hopefully it will continue to grow.

Monday, March 15, 2010

Kawa Kon Wrap Up

Another month, another con. This past weekend I hit up Kawa Kon here in St. Louis.

Kawa's a fairly new con and only has about 1,000 attendees. But this was actually one of the better cons I've been to. As usual, I volunteered myself in any way I was needed. This meant I helped run the game room which, for the most part, was just donating a fistfull of equipment, assisting in the setting and running of a Smash Brothers tournament, and just hanging around to keep an eye on stuff.

This generally works well for me since there's rarely panels at cons I find worth attending. I can't stand panels that are too much attendee generated discussion. It inevitably becomes about 1 or 2 people grand standing while everyone else sits around. I much prefer lecture style panels which are generally far more organized with less grand standing (assuming the host actually knows what they're talking about). But such panels are uncommon at cons around here and typically on topics I'm not interested in. So panels don't usually interest me.

There were a few other events I did want to attend. The first was the Vampire Ball. This was a formal type ball with a vampire theme. That theme wasn't apparent anywhere except the name though. Naka did a similar event which was fun, but ultimately proved to be awkward since no one (myself included) knew much about formal dancing (despite me taking lessons at KU for a semester; it's all gone now). So it ended up being the stand and sway dance while people without dates sat around the edges. At Kawa's ball, they had a few designated people teaching the basic waltz steps and going around to help people and pull them off the walls. This greatly helped the atmosphere although I was disappointed that the dress code wasn't enforced. Guys in jeans and a tee just didn't cut it. Meanwhile there was an amazing Jareth from Labyrinth hosting it who I chatted with for a good long time the next evening (after she did the Dread Pirate Roberts from The Princess Bride).

The main event I was wanting to attend, however, was the cosplay competition. This is always the highlight of cons to me. Halloween is my favorite holiday simply because I love costuming. So getting to see the costumes of others and show off my own is great. For this competition, I took my Sesshomaru costume from Inuyasha. I started this costume in late 2008 and finished it for Ohayocon in Jan 2009. Rabid fan girls destroyed some parts of it there and I made a few quick fixes for Naka 2009 where I wore it as the host of the cosplay competition there. But it's been in need of some serious overhauls for a long time. Namely, the armor hadn't turned out as well as I wanted and didn't work. It was made from cardboard and pleather so it sagged and had unsightly creases. The spikes around the shoulder had all been broken off (thanks to the fan girls) and needed to be made from stronger stuff and more securely fastened. Additionally, the bow was falling apart and needed to be hand stitched to really keep it together.

I fixed these things by completely redoing the armor using thick, heat-formed styrene and putting it all together with bolts and rivets instead of glue and duct tape. Additionally, I asked a friend of mine to come do my makeup since she was a costume design major for a time and does fantastic work. The new work I did on the costume added another 20+ hours to the already 100+ that had gone into the costume and the makeup took another 1.5 hours just before the contest. But it paid off. The applause was easily the largest of the entire show and I walked away with the top prize: Best in Show.

That night I went to the dance party for awhile and danced with a friend I made while standing in line for the costume competition and then went and chilled at Karaoke. After that closed up, I hung in the game room with some people and played a nice game of drunken Apples to Apples.

Sunday I ended up sleeping to noon thanks to staying up playing + the time change and didn't have much time to hang around since the con was ending. So I grabbed my equipment from the game room and walked around a bit more. I chatted with a few people and won a prize at closing ceremonies (by being the first person to pull a $2 bill. I always carry one around in my messenger bag for some reason).

Overall, it was a wonderful time and I can't wait to start a new costume and hit up another con.

Wednesday, March 10, 2010

I might have to care again

Two years ago, I was really into Battlestar Galactica. Then the last season happened. It was pretty bad and the final episode was one of the worst endings of anything I've ever seen. I swore off the series at that point and haven't even popped in my DVDs from the first season since then. It was that bad. So bad it made Jar Jar look like a decent character choice.

But now I hear there's going to be a BSG MMO.

This sounds promising so long as it leaves out the horrible deus ex from the series.

Monday, March 08, 2010

Dear Biologists: You're All Crazy

In my Bio II class, we're working our way through the various classifications of life. We started off with the prokaryotes. They were all right. Talking about all the nasty ways viruses and bacteria can destroy you was great fun for the students.

Next up is "protists". And I gotta ask...

What the hell were you guys thinking on the classification on this one?!

The definition is a pure anti-definition: It's everything eukaryotic except plants, animal, and fungi. That only leaves (according to one source) about 30,000 species left to classify into some kinda sub-groups. So how do you do it?

I have no damn clue. Why? Because I've seen no less than five different methodologies for doing so. Miller and Levine uses one. Wikipedia uses a different. John Kimball (the author of another Biology textbook) uses yet another!

Yes, I get that the classification is a messy business and these little buggers go so many different ways that it's a nightmare for you, but trying to teach this in any logical, digestible manner is impossible. Every classification scheme has exceptions in every category. I try to define something only to find a list of counter-examples!


Someone let me know when protists make sense. Until then, my students will get another fun section of memorizing all the ways protists can do whatever it is each one does with no sane categorization to tie it all together.

Saturday, March 06, 2010

Top 50 Online Videos for Space Geeks

I was clearing out my inbox today and found an Email from last month pointing me to this site which contains a list of cool online videos for space geeks.

There's a lot of stuff on there that is more about spaceflight than science but still a very fun list that will easily consume your afternoon if you let it.

Click at your own risk.

Pseudo-scientists Failures at Math

Over at Dealing with Creationism in Astronomy, Tom has a post up explaining how math is the language of science (especially physics and astronomy) and how pseudo-scientist supporters visiting his site often ask him to town down the math to a simpler level. This very strongly reflects on just how intellectually sophisticated these people are as are their leaders (who Tom has repeatedly requested mathematical and numerical predictions from instead of post-hoc "my theory predicted that" claims).

He makes an excellent point, saying
Most physics-related pseudoscience is communicated not by the rigorous language of mathematics, but by nuanced re-interpretation of terminology and rhetorical tricks. Pseudoscience is communicated among its supporters more like politics than science.
When asked if he could simplify the material more Tom responds that he could but "such explanations would be of little scientific value."

There's another danger that builds on this that I think should be mentioned as well:

Although concepts can often be expressed in simpler terms it must often be done by analogy or a generalization. These analogies can be wonderful teaching tools, but without being able to see the mathematical sub-structure at some point to explore the limits of the analogy, pseudo-scientists will often take the analogy as the true idea and extrapolate from it wildly.

A prime example of this is the horribly common abuse of the Second Law of Thermodynamics by Creationists. To scientists, it's a statement about the statistical filling of available energy states (often from quantum mechanical statements with are mathematical in and of themselves) which can be expressed in numerous mathematical forms depending on how you're using it. To Creationists, it's a statement about "order" and "disorder" and think that the "order" of keeping your room clean is somehow the same "order" as structure in the universe.

The irony is that, while pseudo-scientists frequently do this wild extrapolation through twisting words, which is boundless as long as you can twist the language enough, they turn around and moan that scientists make unjustified extrapolations through the rigorous math which isn't so flexible. Not that pseudo-scientist hypocrisy is in any way surprising any more.

So I completely agree with Tom's point that if pseudo-scientists can't get the math to back up their position (and I mean real math; not the multiplication of a bunch of numbers to make bigger numbers to scare people with math that Dembski and other Creationists use for their "tornado in a junkyard" analogies) they should be left sitting on the curb.

Friday, March 05, 2010

Book Review - Galileo's Daughter

Galileo's Daughter has been on my reading list for almost four years now, ever since I stumbled across it in the KU library while doing research for one of my term papers. I stumbled across a copy of it while at the bookstore last month and decided to pick it up and bump it to the top of my list.

The book is a biography of Galileo, told partially through letters sent to him from his oldest daughter, Sister Maria Celeste. Although there was a large correspondence between them, only 124 of the letters sent to Galileo survive and none of the ones sent by him are known to exist.

The narrative frequently does not involve his daughter at all, for much of the first part of the book because she had not yet been born and even after her birth, not until she had joined a nunnery and was no longer at home to correspond. Even after, there are long stretches when there is little to no mention of the Maria, so although the book presumes to approach Galileo from that angle, it is not overwhelming.

Much of the early part of the story is dominated by Galileo's novel uses for the telescope and discoveries resulting from it. Namely, the numerous new stars he observed, sunspots, and the moons of Jupiter. From these, Galileo began to support the Copernican, heliocentric model, of the solar system. Even the publication of these first discoveries caused controversies.

I have often seen it argued that Galileo did not truly come under fire from the Church, but rather from fellow scientists* who then pressured the Church to condemn Galileo. This book makes it very clear that this was not the full extent of the case. While other scientists were certainly critical of Galileo and did indeed pressure the Church, there was much vitrol from the Church at the outset as well. One of the first signs Galileo received of possible trouble came from the painter Ludovico Cardi da Cigoli, who warned him that meetings were taking place at the home of the archbishop in Florence of people
in a mad quest for any means by which they could damage you, either with regard to the motion of the earth or otherwise. One of them wished to have a preacher state from the pulpit that you were asserting outlandish things.
The letter does not detail who these "ill-disposed men" were, but the fact that they were entertained by the archbishop shows the complicity of the Church from the very start. Whenever other scientists did complain, they did so not on grounds of the merits of the evidence, but relied on arguments from authority because they accepted the Aristotelian, geocentric model as the only one authorized by the Church.

This was largely due to Galileo just being born at the wrong time. After the split of Protestants thanks to Martin Luther, the Church was working hard to explicitly reinforce its position and came down unusually hard on those that would dare question its teachings. The council of Trent in 1546 (the same year Galileo had been born) had declared
no one, relying on his own judgment and distorting the Sacred Scriptures according to his own conceptions, shall dare to interpret them.
Another charge against Galileo had asked him to explain how the Earth could move when scripture clearly stated in the book of Joshua that God had stopped the Sun which required that the Sun be the object which was moving. Additionally, Psalms stated
O Lord my God, Thou art great indeed ... Thou fixed the Earth upon its foundation, not to be moved forever.
Galileo responded to these by saying that, although scripture could not err, the interpretations of it could. He could then accuse his critics of misinterpreting scripture, but so too, could they accuse him.

By 1614, Galileo was being denounced from the pulpit in Florence. When in 1618 three comets appeared, challenging the immutability of the heavens, Galileo published a series of thoughts on these and was challenged, not by a fellow scientist, but by Father Grassi.

Although there were many challenges to Galileo, none of these were especially escalated. A friend warned him from delving too much deeper into supporting the heliocentric universe and Galileo backed away turning to other topics for a time. However, when his friend Maffeo Cardinal Barberini became Pope Urban VIII in 1623, Galileo felt the time was right to attempt to support his favored model. In 1624 he traveled to Rome to seek permission to write his book supporting heliocentrism and was warned that an outright support was forbidden, but treating it as a hypothetical model, for use in calculations and the like, would be permissible.

Galileo rushed to publish this work, entitled Dialogue on the Two Chief World Systems: Ptolemaic and Copernican. When it neared completion, Galileo had to submit it for censorship since another Church doctrine required that all publications be approved by Church appointed officials. Galileo went through the proper channels and it was approved and eventually made its first print run in 1632.

When it reached Rome, in 1633, Galileo was almost immediately summoned before the inquisition by a group of advisers to the Pope. It was argued that his earlier warning by a friend had been an explicit prohibition to write on, or even discuss Copernican models. Galileo produced a letter showing that it had never been worded so strongly, but the inquisition then argued that Galileo had argued too successfully for the Copernican model. For this, they forced him to repent and ultimately put him under house arrest. Again, this may have been due to Galileo being alive at precisely the wrong time. Urban came down hard on Galileo, perhaps due to, in part, his failure to end the Thirty-Years War and a need to make an example of his decisiveness. Additionally, Urban became paranoid of attacks on him and very well could have interpreted Galileo's works as mocking him.

Through the entire ordeal, his correspondence with his daughter lifted his spirits and while he was stuck in Rome, she managed his affairs from the convent. Although the letters do not add anything to the actual story, they flesh out Galileo as a character and showed how much he cared for his family and his work. She would eventually die before him.

The book also does a wonderful job of showing how Galileo was a true skeptic. He had remarked on "how the prophecies of astrologers could most clearly be seen after their fulfillment." He also challenged his opponents saying they would be prone to error,
when they would base themselves always on a literal meaning of the words [in the Bible]. For in this wise not only many contradictions would be apparently, but even grave heresies and blasphemies wince then it would be necessary to give God hands and feet and eyes, and human and bodily emotions such as anger, regret, hatred, and sometimes forgetfulness of things past, and ignorance of the future.
Obviously, Galileo was no literalist.

Galileo noted the vague and intentionally distracting terminology used by his detractors saying, they were commonly
employed by some philosophers as a cloak for the correct reply, which would be: I do not know.

That reply, is as much more tolerable than the other as candid honesty is more beautiful than deceitful duplicity.
Galileo could teach the ID/Creationists of today a thing or two.

Ultimately after many years under house arrest, Galileo perished and due to the continued wrath of the Church, he was denied the burial he had requested. However, a succession of friends vowed to move his tomb. Finally, in 1737, permission was granted to give Galileo the interment he deserved. A sculpture was designed to show him presenting a telescope to the muses of Astronomy, Geometry, and Philosophy although the last was removed, likely due to his challenges to religious philosophy.

However, the author notes that although only two females are noticeable, there is, in fact, a third. When Galileo's tomb was opened to move his remains, a second coffin was discovered in his tomb. Only one of the skeletons could have belong to Galileo. The second was that of a younger woman; Galileo's Daughter, who remains by his side.

* - Notice how the Creationist site just says "Many historians" without bothering to even cite them? Yeah. I'm wondering who these "historians" are too and whether they any better than Creation "scientists".

Tuesday, March 02, 2010

Book Review - Your Inner Fish

Your Inner Fish by Niel Shubin was yet another book that wasn't originally on my reading list. But I had some Barnes & Nobles gift cards and I'd heard good things about this one so decided to pick it up. Then after finishing Breaking the Spell, a random dice roll determined this would be my next book.

So far, of all the books I've read on evolution and related topics, Finding Darwin's God has been my favorite. Your Inner Fish comes in a close second if it doesn't tie.

For those that haven't heard of this book, Inner Fish is written by the guy that was one of the lead researchers on the team that discovered the tiktaalik fossil.

The book starts off by explaining how the fossil was discovered: Scientists knew that in the early Devonian period, there weren't any tetrapods, but by the end there were. This left a window in which they must have evolved (assuming evolution were true). Thus, they looked for exposed surface rocks dating from that era. One of the best unexplored sites for it ended up being on Ellesmere Island near Greenland. Sure enough, Shubin's team discovered exactly what evolution had predicted (something that shouldn't have happened if Creationists were right).

What Shubin then spends the majority of the rest of the book discussing is how many features we have in our bodies today are remnants of developments like the ones tiktaalik went through. Specifically, much of our arms and hands were developed and their basic plan laid out by species like tiktaalik and then modified through evolution to suit new needs.

Shubin points out that this is spectacularly revealed when we look at other features in the human body which make no logical sense, such as nerves and arteries which take the oddest detours to reach their intended targets. He likens it to a new research facility in his university:
I had been given space for a research laboratory in a hundred-year-old building and the lab needed new utility cables, plumbing, and air handling. I remember the day when the contractors first opend the walls to get access to the innards of the building. Their reaction to the plumbing and wiring inside my wall was almost exactly like mine when I first opened the human head and saw the trigeminal and facial nerves. The wires, cables, and pipes inside the walls were a jumble. Nobody in his right mind would have designed a building from scratch this way, with cables and pipes taking bizarre loops and turns throughout the building.

And that's exactly the point. My building was constructed in 1896, and the utilities reflect an old design that has been jury-rigged further with each renovation.
Similarly, to understand the design of a species, you must understand its history, just as one must understand the history of a building to understand the wiring.

The next several chapters deal with numerous other components of the human body and how we can find structures that preceded them still intact in other species today. Namely, he skims into embryology and discusses how homologous components in the embryo develop into wildly different structures in different species. He goes through Hox genes and development of the olfactory, visual, and auditory systems.

But so what? A Creationist could easily claim (and do they ever) that these similarities due to a common designer. But in all of these, Shubin emphasizes that all of these ways of relating species give a nested "Russian Doll" structure. And that's really the key. This picture of groups within groups (taxonomy) fits perfectly with the evolutionary model and should not in any way be expected if a designer was popping out species here and there, even if similar designs were used! Additionally, on top of all this amazingly self consistent family tree from taxonomic grouping, it can all be checked against the fossil record and by making more classification trees from genetic evidence (such as ERVs).

Shubin doesn't hammer this point home as well as he could have, and that's my main problem with this book. Instead of reminding the reader of all these additional, consistent pieces Shubin skims over them. However, he does at least nod in their direction (without explicitly stating them) by saying
Some groupings are so strong, that for all intents and purposes, we consider them fact.... Our fish-to-human framework is so strongly supported that we no longer try to marshal evidence for it - doing so would be like dropping a ball fifty times to test the theory of gravity.
Overall this is a fantastic book and I'd recommend it to anyone. It's very approachable even without much science background. There's a few parts that get more in depth and would require a more methodological reading for someone not at least passingly familiar with genetics and embryology. But then again, those are some of the coolest parts in the book. One of my favorites was the discussion of the hedgehog genes. It's a great example of gene regulation during development and I'm doing more reading on it (and other such traits) since we just finished talking about gene regulation in my Bio I class.

As a side note: There's a few versions of this book out there. The one I see most often in book stores is the "Vintage" edition. I have the January 2009 one and this one contains a nice afterword which follows up on a few of the developments with tiktaalik since the first printing of the book. It gives another perfect example of how tiktaalik is a stunning intermediate fossil. When they dissected the skull, the team found a bone wonderfully proportioned between a larger ear bone from earlier, aquatic species and the later smaller bone of more terrestrial ones.

Monday, March 01, 2010

Not So Privlidged Planet

Oh, poor Creationists.

One of their favorite claims is that we live on a Privileged Planet that is just right for us. Thus magic man done it.

Unfortunately, science keeps coming along and showing that our egos are misplaced. We're special, but not magically so. We evolved big brains capable of deep thought, but it shares a common ancestor with all life.

Even our planet is a pale blue dot in a vast and inspiring universe. But Creationists constantly try to claim that this solitary orb is so amazingly perfect that it must have been made that way.

But even this claim is contradicted by the evidence. A new paper on arXiv takes a look at just how habitable planets similar to Earth can be.

The authors modeled Earth clones and varied numerous components of the system from the amount of ocean, to the eccentricity of the orbit, to the spin rate of the planet and looked to see just how far they could push them before the planet either froze into a snowball or became prohibitively hot.

Oh, the poor creationists. Their "privileged" prediction fails (not that this is surprising since previous work of Kasting et al. (1993) have shown the "habitable zone" is at least 0.95 to 1.37 AU).

The new paper suggests that eccentricity isn't an overly prohibitive constraint for planets. This is good since "40% [of exoplanets with measure eccentricities] are on more eccentric orbits than Pluto (e = 0:2488) and ~10% are on orbits with eccentricities >0.5." Surprisingly, for "planets with eccentricity 0.5... [the] greatest habitable semimajor axis can vary by more than 0.8 AU (78%!)"

This would be like Earth moving in as close as Venus and as far as Mars every orbit! According to Creationists this would be certain doom! Shame on reality for spoiling all the fun.

Ultimately, the most important factor of all the ones they simulated was the amount of ocean. Thanks to the high specific heat of water, it moderates the temperature even under large changes in eccentricity.

Regardless, the Creationist claim that Earth is so perfect for life just took another blow.

Perhaps one day the Creationists will actually notice.

The Drama Llamas Strike Back

Apparently the Obama administration been meeting with some nasty "hate groups" and "activists".

Who were these evil people out to destroy America?

Atheists from the Secular Coalition for America.


Bill Donahue is throwing a fit, saying,
People of faith, especially Christians, have good reason to wonder exactly where their interests lie with the Obama administration. Now we have the definitive answer. In an unprecedented move, leaders of a presidential administration are hosting some of the biggest anti-religious zealots in the nation.
Not "anti-religious zealots"! How dare they talk to the administration (not even Obama himself)!

What dastardly things did they have on the agenda?

The deadly effects of "faith-healing" and religious harassment and proselytizing in the military.

Oh how evil! How dare they suggest that religious parents not be allowed to murder their children by denying them decent medical care.

How dare they complain that the military is violating the constitution they swear to uphold by acting as a religious outlet and promotional tool!

So much hate....

...And all of it properly placed. Murder and flagrant violation of the foundational document of the nation is not something we should stand for.