June 13, 2008

Sad Day

Tim Russert, a giant in the field of political journalism and the longest-running host of NBC's "Meet the Press" in history, has passed away today. Apparently, he collapsed due to a heart attack at NBC's Washington Bureau this afternoon.

A strong voice for reason and integrity in both politics and media, he will be missed. Via Thinkprogress.org

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John McCain is a Dumbass

Too funny not to post. Via Canuckoo at DailyKos.com:

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WoW, I Can't Believe I'm Doing This

If you're anything like Dean you'll probably enjoy this video, the new release from World of Warcraft

'Warcraft' Sequel Lets Gamers Play A Character Playing 'Warcraft'

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School Prayer Causes More Cancer Deaths

You see what I did there. It is really easy to do and the intelligent design and denialists (of all sorts, evolution, vaccines, science based medicine) have become very good at it. Let me continue a little.

Back in 1962 (Engel v Vitale, 370 U.S. 421) the Supreme Court said teachers and other public school officials may not lead their classes in prayer, devotional readings from the Bible, or other religious activities. This essentially started the path toward eliminating prayer from schools. By 1992 the Supreme Court had pretty much put the wraps on school prayer (Lee v Wiseman, 505 U.S. 577, 599) saying officials couldn't attempt to persuade or compel students to participate in any religious activities.

At the same time this was happening cancer had become a national problem. Scientists were working on treatments and cures but nothing was really working and we still don't have a cure for cancer. But nonetheless this is what happened.

That's right, as our Supreme Court continued to chip away at the religious stronghold in our schools the probability of surviving a childhood cancer rose by over 80%! Obviously its about time we start eliminating prayer from other aspects of our life as well. If children benefit so well from removal of prayer, maybe we should ban prayer from church, there are a lot of old people there and they tend to have a lot of cancers.

Ok, that almost made my head explode, but I think its a pretty good example of how to misuse science. Data is just data, numbers mean nothing without context. That's what scientists are there for, and it's why some guys make a whole hell of a lot more money than others. The ability to read into the data and determine the significance of certain trends, design further experiments to elucidate unknowns, and combine this new data with the old and make sense of them is truly what science is. Honestly anybody can sit in a lab and repeat procedures and fill stacks of notebooks with data, but if you can't find out truly what that data means then you have done bad rather than good.

Hence the argument I made earlier, that declining school prayer has led to a better survival rate among children, is a logical fallacy. I combined two unconnected sets of data into an overreaching statement about how the two data trends are causally related. Some people have become really good at doing just this thing (I'm looking at you Creationists and anti-vaxers), but in much more subtle and non-inflammatory ways. There are some pretty good theoreticists (they aren't scientists) who work for creationist institutions (The Discovery Institute), scouring the literature to find two points of data which will prove that Darwinian Evolution has failed as a theory. But these guys do exactly what I did to make my earlier argument.

I had previously decided that school prayer causes cancer deaths. Now I know that cancer deaths have declined for most cancers due to effective treatments and therapy, but that is irrelevant to the argument, because I am choosing to dismiss the rest of the body of cancer literature stating our social evolution has had little to do with the rate of cancer deaths. Creationists are great at this, finding two simple data sets and saying they connect to prove the theory they already believed. Here's the difference between a belief and a scientific theory; A belief doesn't need data and discovery for you to accept it, which is why creation by a god or the denial of evolution, is simply a belief. There is no data needed for people to believe this. But evolution is an idea that was borne out of data. An idea that did not exist prior to the years of observation and idea synthesis that has led us to where we are today. It is easy to state the opposite of science, by definition science is the exploration of the unknown, so at some point science will always struggle to define every detail and question. But it is much harder to understand the provided data and the holes in the data to come up with the correct theory, which is why the guys who push the hardest for core ideas such as evidence based medicine and Darwinian evolution make the big bucks.

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June 12, 2008

20 Years of Evolution in a Flask

ResearchBlogging.orgUpdate: This experiment has picked up a lot of attention. Unfortunately some are claiming this experiment is evidence of creationism. Many of them haven't even read the paper because its behind a subscription wall, but the researchers have posted it on their website to be seen by everyone, very cool.

Ok guys, we're gonna try something for the first time here. I've reported on some pretty serious science stuff but I finally got my new toy today (thanks researchblogging.org) and I'm anxious to use it. When you see the "blogging on peer-reviewed research" icon you know I'm going to be writing about some recent professional science happenings. But don't let it scare you, the goal is to present the article in a way that is accessible to the general public (so let me know what you think). Alright, enough with my rambling, let's get to it.

In 1988, Richard Lenski filled 12 flasks full of identical E. coli colonies and put them on a gentle shaker. Inside that Michigan State University lab the bacteria have continued to swirl undisturbed except when Richard would stop to refill spent nutrients and take a small sample from each flask. Those samples now fill a freezer with a genetic snapshot of 12 isolated strains of evolution. Just like the birds of Galapagos that Darwin studied over 170 years ago, each flask had separated the colonies into islands, each sent on its own evolutionary trajectory. And since Lenski paid such close attention to those 12 flasks they have offered up some very unique and compelling insights into the mechanics of evolution.

What Lenski knew was that in each generation, some of the bugs would have a mutation. Most of these would be harmful and kill the bacteria, cause them to grow slow, or keep them from creating progeny. But others would offer benefits like faster growth or the ability to breed faster. These microbes, that were the fortunate recipients of beneficial mutations, eventually would grow to dominate the population, at least until the next more suitable mutant arose. And this is how the experiment went, with the microbes now breeding at a rate 75% faster than the original colonies. This is good enough experiment in itself, but Lenski threw in a few details that makes this one of the more elegant genetic experiments conducted.

The E. coli colonies were grown in a glucose limited environment which also contained citrate. Glucose is a sugar that E. coli shuttles into its cell membrane and uses to extract energy. Citrate, on the other hand, cannot be taken in by E. coli in the presence of oxygen, this failure is a distinguishing characteristic of E. coli. In Richard's well oxygenated lab the citrate went unused, but the glucose had to be replenished daily. For over 33,000 generations this trend continued; a sample was collected, a limited amount of glucose was added, and the cells continued to shake. But one day a flask was cloudy, meaning a huge explosion of growth had taken place. As a microbiologist I know that as soon as this happens you assume contamination, a microbe that got in your flask that could use a previously unused nutrient (in this case citrate), takes hold and with the abundance of an unused resource breeds fast. The huge increase in population turns the flask cloudy.

But this flask hadn't been contaminated, the E. coli was the organism using the citrate. After being placed in pure citrate the microbes continued to grow with no other source of carbon. The researchers then traced the history of the citrate eaters and found that they appeared first in generation 31,500, making up a whole 0.5% of the population. For the next 2,500 generations the citrate eaters battled with the glucose eaters for dominance, almost being eliminated at generation 33,000. But eventually they came to dominate the population, suggesting that only after further mutations was the citrate absorption mechanism efficient enough to overtake the other populations.

The advantage Lenski had over nature was that he could replay evolution with the frozen samples he had collected. And he did just that, growing new populations from 12 time points in the 33,000 generations of bacteria that didn't eat citrate. And out of those new colonies only a small amount of bacteria had the ability to use citrate. And only individuals who had come from after the 20,000th generation were able to develop the ability. This meant that something happened around generation 20,000, specifically in a population dubbed "Ara-3", that allowed for a later mutation to becoming a citrate user.

That is the biggest implication of this paper. Lenski explains it eloquently:
The long-delayed and unique evolution of this function might indicate the involvement of some extremely rare mutation. Alternately, it may involve an ordinary mutation, but one whose physical occurrence or phenotypic expression is contingent on prior mutations in that population...The evolution of this phenotype was contingent on the particular history of that population. More generally, we suggest that historical contingency is especially important when it facilitates the evolution of key innovations that are not easily evolved by gradual, cumulative selection.

If the citrate-eating was the result of a very rare mutation you would expect that at any point you could restart the colony and each would have an equal likelihood of producing the citrate-eating mutation. But this isn't what Lenski saw, only those progeny from generation 20,000 or later (and population Ara-3) evolved the ability to use citrate as a carbon source. Stephen Jay Gould once claimed that if we replayed life we wouldn't get the same result. In fact, if we replayed it 100's of times we would get 100's of different results. This experiment is demonstrating just that, that each step in the ladder of evolution is dependent on the history that preceded it. As Lenski states in his title, historical contingency is the true meaning behind the data he collected. Some quirk that happened around generation 20,000, which didn't alter fitness or affect survival, allowed for a combination of mutations (all equally likely) which resulted in an advantageous citrate characteristic.

This is evolution as we should understand it, the combined effects of many mutations which eliminates those who struggle and rewards those who develop the most efficient means at conveying DNA to the next generation. This is probably the first definitive experiment showing historical contingency through natural evolution, but even science as clear and illuminating as this can be misconstrued.

To tell you the truth I really wanted to cover this paper but knew it was big enough that everyone in the blogosphere would write about it. I have restrained so far, but today I happened upon Michael Behe's blog at Amazon and now I can't hold back. His last sentence probably sums up best what he wrote:
"If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did."
Behe would like you to believe in his "irreducibly complex" belief, which conveniently disguises for 'someone had to make it so because it's too complex'. Here's the problem with his argument that multiple mutations are "beyond Darwinian" evolution. Richard Lenski's experiment was just that, the course of Darwinian evolution which showed multiple mutations developed to allow E. coli to use citrate. Behe uses a rather weak argument here to try and push his intelligent design agenda, especially in the face of overwhelming praise from the science community. It is irresponsible for those in science to place an agenda behind their research, especially one that clashes so fundamentally with all legitimate science. But it is stupid to continue to throw out tired lines on public forums that even the most untrained of scientists can debunk. This isn't even an attempt at true science as much as it is a commercial for a book, one that claims to "extensively" speak about Lenski's experiements. So save up from those book sales Michael, cause your credibility isn't going to get you into the afterlife.

Lenski, R.E. (2008). Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences, 105(23), 7899-7906.

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Oh My, You Took Pictures of My What?

Here it is in all of its life-giving glory. The actual act of ovulation caught on camera in humans for the first time.
Here's the article from the BBC describing how Gynaecologist (Brits spell funny) Dr. Jacques Donnez spotted and filmed the act of ovulation for the first time during a routine hysterectomy. Pretty incredible stuff.

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June 10, 2008

NBA Finals Update

by: "Sporty Spice" Drewsky (wow)


The NBA Finals kicked off full throttle with the Celtics claiming two home victories, putting enormous pressure on the Lakers. It'll be interesting to see how LA responds to this early deficit. In the NBA Finals game format of 2-3-2, only 2 teams have come back to claim victory; Detroit in '04, and more recently the 2006 matchup between the Miami Heat and Dallas Mavericks. In this series, Dallas took a commanding lead (2-0) and had a comfortable lead in the 3rd game before imploding and allowing Miami to win 4 straight to hoist the coveted Larry O'Brien trophy. However, this postseason has been disparate than most, showing such a drastic home/road divide in performance.

LA, undefeated at home this postseason (8-0), has the daunting task of needing three straight in the Staples Center. If LA were to lose any at home, the proverbial fat lady would leave the buffet and begin to warm up her vocal cords. However, if there is any team capable of winning three straight on their home surface, LA is the candidate. As we have seen throughout the playoffs, the bench/role-players on each team are more energized and effective at home, almost appearing like entirely different players. Their shots fall with much more prevalence, their close-outs, transition game, and help defense is far quicker, and the intangibles they provide are much more noticeable.

In the opening two games, we see that the Boston defense is shutting down LA's honed triangle offense. LA's cutters are always accounted for, Kobe's iso's have been far less effective than in previous series, and LA's outside shooters collectively haven't been getting many wide open shots. That team defense is absolutely stunning. Another thing we have witnessed is Pau Gasol is incredibly soft. Being an international player, usually it is difficult to transition to the physical, in-your-face mentality of American ball; as witnessed by Kevin Garnett mopping the floor with Gasol's scruffy beard and shaggy hair. Additionally, Lamar Odom has looked like a turkey in the cornfields in the first games, however he too plays more skillfully at home.

On Boston's side of the coin, there aren't many negatives in how they played (the only exception being giving up a 24-point lead with 7+ minutes remaining in the 4th quarter allowing LA to cut it to 2 with 30 seconds left). The big 3 looked solid, Rondo looked like a poised point guard capable of freakin' em with the okie doke, everyone was aggressive at taking it to the hoop, and the bench play was stellar and absolutely dominated LA's bench. It will be interesting to see if Boston's bench shows up on the road. Equally important, Boston outrebounded and out-free-throw-lined (I'm copyrighting that antic) LA for the series thus far 83-69, and 73-38, respectively. Obviously, these stats are crucial since these games were decided by 10 or less points. When LA gets defensive rebounds, they can play a transition game with the best of them, as seen in that huge comeback (LA hit an NBA Finals record of 7 3-pt field goals in one quarter, most of which in transition). The disparity in free throw attempts provoked a verbal assault from Phil Jackson on the officiating crew, and perhaps rightly so. However, credit Boston's D with this differential. LA has become complacent with contested jump shooting instead of the usual aggressive mentality. Even Kobe has gotten apprehensive about driving the lane, shooting a mere 20-49 for the series.

One thing that amazed me was Ray Allen's effect on the Celts. Before the Finals, Ray Ray looked like a complete scrub with no confidence; causing Boston to play horribly inconsistent (going to 7 games with Atlanta and Cleveland). However, with Ray Ray running on all cylinders, Boston has become a wrecking machine. Note: This is a flat-out digression, however there seems to be a correlation here.

Clearly, something must give for LA to continue their unprecedented flawless record at home. Expect Phil Jackson to light a fire under some arses and for LA to play like an actual team in their backyard.

Something I found interesting was the Boston Globe's renowned sports writer Bob Ryan claiming Paul Pierce was the franchise's most potent and prolific offensive threat. Personally, I think that is insane since I would dub the Birdmeister that label, however if the Celts are to win the series, the Boston faithful probably wouldn't mind that statement too much.

In this quintessential matchup of unstoppable force vs. the immovable object, so far the immovable object has prevailed.



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Best of...Tuesday Links

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June 8, 2008

Human Rights Watch: Cluster Bomb Update

Human Rights Watch has released a video describing the very real danger cluster bomb munitions pose to civilians all over the world. The these weapons, currently used by the US Military, effectively create undocumented mine fields when a percentage of the "bomblets" they release fail to detonate and lay dormant until disturbed by a footstep, vehicle tire, or child's hand. Over 100 nations have signed an international ban on these weapons and agreed to implement programs to deal with the unexploded munitions already scattered around the globe, but as of this posting, the US and several other major militarized countries have refused to sign the UN ban, claiming it would impair their ability to kick ass effectively. Merely another facet of the standing US policy of "To hell with the brown people" I guess.

Previously blogged about here.

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