And another legend lost...

This Friday, Seymour Benzer passed away. Benzer was a very important person in the history of molecular biology - among his other accomplishments he probed the fine structure of a gene and mapped the rII locus of bacteriophage (I think it was phage Lambda). Every student in genetics learns about his work but most dont know of him by name. It's a shame. The work he did as part of the famous "phage group", along with Luria and Delbruck, eventually lead to Crick and Sydney Brenner to establish the triplet code for DNA translation.

This comes not long after the loss of Arthur Kornberg. Its been a bad winter for molecular biology.

The Republican Youtube Debate Translated

Last week, the Republican party had a little debate on Youtube, and people from the public got to pose questions to all of the candidates. Of course, the susbject of the Bible was brought up:

"I am Joseph. I am from Dallas, Texas, and how you answer this question will tell us everything we need to know about you. Do you believe every word of this book? Specifically, this book that I am holding in my hand, do you believe this book? "

The candidates' replies were rife with sucking up to the religious right and attempts at making themselves look like "good moral, religious people" (the thought of which is humorous; "moral" and "politician" are mutually exclusive) and for those of us not fluent in bullshit, I have taken the liberty of translating their responses into rational English.

Giuliani: "OK. The reality is, I believe it, but I don't believe it's necessarily literally true in every single respect. I think there are parts of the Bible that are interpretive. I think there are parts of the Bible that are allegorical. I think there are parts of the Bible that are meant to be interpreted in a modern context.
So, yes, I believe it. I think it's the great book ever written. I read it frequently. I read it very frequently when I've gone through the bigger crises in my life, and I find great wisdom in it, and it does define to a very large extent my faith. But I don't believe every single thing in the literal sense of Jonah being in the belly of the whale, or, you know, there are some things in it that I think were put there as allegorical."

TRANSLATION: "Just like any other Christian, I like to pick and choose which parts of the Bible I take literally and which parts I think are just symbolism, even though there really is no rational way of determining which parts are the symbolic parts. This way, I can cherry-pick to avoid the inconvience of having draconian beliefs along with the ones that make me a good, moral person! Also, I never read it, but I have a copy on my bookshelf somewhere."

Romney: "I believe the Bible is the word of God, absolutely. And I try I try to live by it as well as I can, but I miss in a lot of ways. But it's a guide for my life and for hundreds of millions, billions of people around the world. I believe in the Bible....I believe it's the word of God, the Bible is the word of God. The Bible is the word of God. I mean, I might interpret the word differently than you interpret the word, but I read the Bible and I believe the Bible is the word of God. I don't disagree with the Bible. I try to live by it."

TRANSLATION: "Lots of people around the world belive in the Bible, so why wouldnt I? I dont always live my life by the Bible, but I am a good moral person nontheless. This is totally completely 100% different from atheists being moral people and not living accoding to the Bible because we all know atheists are souless heathens who will burn in hell. Also, the Bible is open to subjective interpretation, yet it gives us absolute morals we must live by. Please ignore this aparent contradiction. Did I mention that the Bible is the word of God? The Bible is the word of God."

Huckabee: "Sure. I believe the Bible is exactly what it is. It's the word of revelation to us from God himself. And the fact is that when people ask do we believe all of it, you either believe it or you don't believe it. But in the greater sense, I think what the question tried to make us feel like was that, well, if you believe the part that says “Go and pluck out your eye,” well, none of us believe that we ought to go pluck out our eye. That obviously is allegorical. But the Bible has some messages that nobody really can confuse and really not left up to interpretation. “Love your neighbor as yourself.” And as much as you've done it to the least of these brethren, you've done it unto me. Until we get those simple, real easy things right, I'm not sure we ought to spend a whole lot of time fighting over the other parts that are a little bit complicated. And as the only person here on the stage with a theology degree, there are parts of it I don't fully comprehend and understand, because the Bible is a revelation of an infinite god, and no finite person is ever going to fully understand it. If they do, their god is too small."

TRANSLATION: "I believe that it is 100% fact that you either believe in all of the Bible or none of the Bible. But some of it is allegory. And some of it no one understands. But, even if we dont understand it, we should belive it anyway! Beliving in something you dont understand and not questioning it is the key to being a good Christian. All that confusing stuff we can ignore for now anyway, because we should focus on The Golden Rule. What was that? Atheists have been saying that The Golden Rule is all that matters for years? And you can be a good moral person without the Bible? Poppycock! My life partner campaign supporter, Chuck Norris, and I are the only ones who can talk about the Bible because I have a theology degree! Your god is puny!"

I think no further comments are necessary.

Dover part 2: Polk County, Florida

Hot off the heels of the NOVA doccumentary on the Dover trials comes something that will probably give you that eerie feeling of deja vu: the school board in Polk County, Florida has had a majority vote to include intelligent design as part of the school science cirriculum. The board has voted 4 to 2 on teaching intelligent design along with evolution. The currently proposed standard for Polk county schools lists evolution and biological diversity as one of the "big ideas" that students should know to have a well grounded science education, and 4 of the board members are in direct opposition to this.

Quote board member Margret Lofton (emphasis mine):

"If it ever comes to the board for a vote, I will vote against the teaching of evolution as part of the science curriculum," Lofton said. "If (evolution) is taught, I would want to balance it with the fact that we may live in a universe created by a supreme being as well."

""It crosses the line with people who are Christians," according to her. "Evolution is offensive to a lot of people." Let me paraphrase this for you: "It doesnt matter if something is true, some people find it offensive so we shouldnt teach it." What complete idiocy.

Thankfully, the scientific community in Florida is up in arms about this decision and strongly supports the current scientific standards proposal.

I dont know if these people are ignorant of the whole Dover case or what. This all seems like the same situtation all over again. Im just waiting for the Discovery Institute to get involved.

Mysterious protein of mystery

I'm writing this from the computer lab in the botany wing of biosci waiting for my lab to start. We're going to be down here trying to determine what gene our original cDNA came from and what organism it belongs to. I thought Id go ahead and try it out myself before the lab begins but Im running into some problems.

I aligned my sequences last week but I was a little wary of the results because my sequencing reactions didnt work out all that well. The chromatograms showed a really weak signal all around so it was tough, if not impossible, to determine the correct bases where I got a string of N's. This meant that alot of spots in my sequence were really unknown. The resulting consesus sequence was a little suspect because of this.

I saved the consensus sequence anyway and used it to run a Blast search on NCBI. I should have been able to figure out what the gene was (I know its a form of actin but what form of actin?) and the organism it came from. Except, this didnt happen. I have a whole schwack of results, and about 10 of them all have the same Query coverage, total score, max score, E-value and max identity. Unfoturnately, theyre all from different organisms so I dont know which one is the "right" one. The query coverage and max identity are 83%, which means that my sequence is about 83% identical to these sequences...which isnt all that great. If my sequence was the same as a sequence in the database, then the values should be like 95% or more. This means one of two possible things: either the sequence isnt in the database and the closest thing to it is only 83% identical or my sequence is wrong. I think the latter is more likely. They all are beta-actin genes, though, so at least this tells me my gene is probably a beta actin.

Hmmm

You know how Dr. Bruce Banner turns into The Hulk when he gets angry? And how The Hulk's massive green body is like twice the size of Dr. Banner? Isn't that a violation of the first law of thermodynamics?

Just how big is the universe?

This big. And that's just the VISIBLE universe. These maps only show the distances to galaxies, clusters, nebulas and the sort that are relatively close to the Earth. Most galaxies are so far away that their distances cannot be accurately calculated and aren't included. Use the zoom-in buttons to see how the Solar System compares to the immense vastness of the universe. Just consider the Earth's place in all of this: a infinitesimal speck amonst a plethora of other infinitesimal specks. The sun is one star in an estimated 30 billion trillion (3x10²², or 30000000000000000000000). I challenge you to find a thought more humbling than that.

And yet another reason to hate Chuck Norris

As if those asanine "Chuck Norris Jokes" that are all the rage with mush-minded frat boys and his vapid, plotless, doldrum-inducing action movies weren't enough for you to despise Chuck Norris, I've uncovered some facts that might make you hate him even more.
Last night, on G4TV's Attack fo the Show I saw the clip below:

Yes, that is Chuck Norris, and yes, he is endorsing a presidential candidate. If any of you dont remember who Mike Huckabee is, he was the governer of Arkansas who was featured on Talking To Americans - the one that congratulated Canada on our "national igloo".

It seems that Mr. Norris is a staunch supporter of Mike Huckabee. That alone might not arouse your ire for Chuck Norris, but get this: Huckabee is (not surprising for a politician from Arkansas) a rightwing fundie. He has been quoted (I'll find the exact quoute later) with saying that, if science and religion were at odds with one another, he would pick religion because "science changes constantly with new facts, and religion never changes". He obviously have little understanding of the scientific method and how the constant revision of facts upon being presented with new evidence is what makes it so powerful. Anyway, after realizing that Norris is endorsing someone who would likely turn America into some draconian theocracy, I began to do a little research on him. What I found was disturbing.

Firstly, he is an outspoken critic of evolution, and supports creationism. If that were not bad enough, he holds the theory of evolution responsible for school shootings, commenting:

"We teach our children they are nothing more than glorified apes, yet we don't
expect them to act like monkeys."

Basically, he thinks that evolution tells us that humans are nothing more than "glorified apes", and kids are going to act like wild animals, shooting and stabbing each other in the schoolyards. No doubt, Huckabee also shares this view and would try to get evolution thrown out of schools were he to become president.

Aparently, Norris also belives that there is an "atheist conspiracy" in the United States that is working to make Christianity illegal. Not only is he ignorant but he's delusional as well! Futhermore, to stop the growing "threat of secularization", he said that,were he to become president, he would tattoo "In God We Trust" on the forehead of all atheists, and even deport all liberals from the country (and "force them to listen to Bill O' Reilly every day for five years", but this must be a misquote, because the US doesn't torture, right?)

Mr. Norris is a contributing writer to the site WorldNetDaily (aka WorldNUTDaily for the outrageous conservative drivel the site publishes) and I took a look at a few of his articles. In one, he complains about abortion and how evolution has lead to "human degredation" and "fetal devaluation". He claims that "life begins at conception" - his evidence for this, you ask?

"Before our embryonic twins were surgically placed into my wife Gena, the nurse
told her, ''I want to show you something.'' She wheeled Gena to the incubator
where they were kept and gently opened the door. The incubator was bathed in
warm light and soft classical music. Gena later told me it was the most incredible sight she had ever seen. ''It was like looking at something from heaven,'' she explained.
That was only 2 days after conception! Whether or not Gena had become pregnant,
we were fully convinced at that moment that life begins at conception.
Thirty-two weeks later our twins were born."

He looked in an incubator at two embryos which had been fertilized only days before and, because it was "beautiful" it MUST constitute a human life. Real convincing, there, Chuck.

Other articles he's written go on and on about how terrible it is not to teach the Bible in schools (as if it were literal truth) and how the media is so liberally biased.

After finding all of this, I am convinced that Chuck Norris has the intelligence of a sponge cake. I couldn't stand him when he was only making crappy movies, I REALLY couldnt stand him with morons began telling those lame "jokes" about him and now I utterly detest the man. It's a shame that he's so popular, and it's disgusting that he has been using his fame to promote his backwards conservative beliefs.

Responses to PBS "Judgement Day" program

Last Tuesday, PBS ran a two hour special on NOVA about the infamous Dover School District "Evolution vs Intelligent Design" trials. Jessica and I watched it and we found it to be a very well put together program, which explained in a very easily comprehensible way what science is, why intelligent design IS NOT science, and how the members of the Dover school district were religiously motivated when trying to teach students intelligent design as an "alternative to Darwinian theory". It was one of the better episodes of NOVA I've seen and was greatly pleased that PBS stood up for science cand didnt play the "Christian apologetic" card. Many other people, it seems, were not so pleased. The PBS ombudsman has released an article publishing some of the emails and letters they recieved from viewers; many of which were complaints about the "one sidedness" of the show.

Here's a few choice excerpts from some of the letters (emphasis mine):

"I realize that PBS has always treated the neo-Darwinian theory
of Evolution as sacred and beyond question but last night's dose of
Darwin-worship was so strong and so contrary to any genuine search for truth
that I can no longer consider support of public television a
morally defensible practice."

So, basically, because PBS, on a show dedicated to science, chose to support the science and not the religious rhetoric, supporting public television is now immoral? You've got to be kidding me.

"After tonight's program on Intelligent Design it proves that
PBS has a "design" of its own — it's one that is driving the country to
destruction — your bias is completely counter to history, to the very foundation
of our nation and history of nations. Every part from beginning to end
had its own objective; completely counter to the Truth which is proven in the
rise and fall of nations."

Aparently, countering "the Truth" (id est the Bible) has been the cause of the collapse of nations throughout history. I'd bet good money that this guy slept through history class. This letter also displays the sickening misconception that the United States was founded as a Christian nation. Perhaps the study of the founding fathers and reading the Decleration of Indepenance should become mandatory in American schools. Maybe then the myth that the US is a "Christian nation" would be dispelled.

"It doesn't take a "Rocket Scientist" to figure out that if we,
as humans, evolved from monkeys . . . THEN WHY? . . . Are there STILL Monkeys???
We were "Created" by God!!! Pull up AOL now and you'll notice the Gov. of
Georgia praying for rain, (No Doubt to GOD). When 9/11 happened what did every
good neighbor do? PRAY. Not to monkeys . . . To our "Creator"!!! It shouldn't
take tragic and desperate circumstances for people to realize this fact!!! GOD
BLESS AMERICA!!! In GOD We Trust!!!"

Yet another example of the painful ignorance people have of evolution. It gives me a headache trying to figure out why some people cannot grasp what it is that evolution teaches. Nowhere does it say that we evolved FROM monkeys. Humans and monkeys both evolved from some other common ancestor. Apes are not our ancestors but theyre more like our cousins. Also, because people prayed to God after 9/11 doesnt prove his existance. That's a complete non sequitur. I also find it amusing that people are still using AOL (there's something to be said about the intelligence of fundies and AOL users but I'll let you draw your own conclusions).

"I measured the time from the beginning of the program to the first
time an idea from ID theory was even presented (25). If I had time I could make
a chart of how many times a positive statement was made pro evolution
(uncontested) vs. pro ID statement (each contested or refuted). "

Hmm perhaps this is because Intelligent Design is false and evolution is our current best understanding of the natural process of speciation? The one major point of the Dover trial was to show that ID was not science, so why would the doccumentary give a "pro-ID" stance at all? Of course it was "pro-evolution" - that was the outcome of the trial! If the outcome had been reversed and evolution pronounced baseless mumbo-jumbo while ID was the Gospel truth (pardon the pun) then things would have been different. But that is not the case. ID was presented as a refuted non-scienctific religious idea BECAUSE IT IS A REFUTED NON-SCIENTIFIC RELIGIOUS IDEA.

"I am glad I have not donated any $ to KQED for many years since I would not want to contribute to the propagation of the false, erroneous, illogical theory of macro-evolution. If evolution were true and man "evolved" from apes, why do we have apes and monkeys co-existing with man? Why have the apes not all turned into humans? Then, there's the immoral implication of evolution. "Survival of the fittest" follows from evolutionary theory. Evolutionists, to be logical and true to their faith (it takes faith to believe in it since there is no clear, unimpeachable physical evidence for macro-evolution) should see nothing wrong with what Hitler, Stalin, Pol Pot, etc., did in the genocides of millions of people."

This one has three pathetic points. First, this guy also says that macroevolution is "illogical". I'd like to know his reasoning for this. Macroevolution is possibly one of the most logical ideas I can think of. Animals with genes that make them more fit have more offspring. More offspring with this gene means a change in allelic frequencies. Over time, the more fit gene is kept and the less fit gene dies out. What's so illogical about that?
Secondly, this guy also displays the ever-so-present lack of understanding of how evolution works. Again, we didnt evolve "from monkeys", we evolved along side of them. Apes have not "turned into humans" because that's not how evolution works! Why can't people undersand this!? The third thing he says is the often used "Evolution = survival of the fittest = killing off weak people = OMG HITLER MASSMURDER" argument. He combines this with the claim that there is no physical evidence for macro-evolution (there is. Tons of it.). Hitler (and Pol Pot, and Stalin) did commit genocide, there is no denying that. But what people have to understand is that "fit" and "weak" do not mean the same thing. Survival of the fittest DOES NOT MEAN survival of the strongest or fastest, biologically or socially. Fittest = better chance at producing offspring. From what I know, Hitler didnt exactly send the Jews to Auschwitz because they were having more kids. This disgusting misconception that "survial of the fittest" ammounts to killing off socially weak people is rampant in creationist thinking and ammounts to little more than extreme Social Darwinism, a concept that has long been abandoned.

"Surely you could have interviewed prominent scientists,
philosophers and theologians who could explain how the two theories are actually
one and the same. Typical humanistic, lefty propaganda staged to move the feeble
mind to a certain point of view. Garbage, really. You should fire the writers
and producers."

The two theories are NOT one and the same. Evolution is a naturalistic process that occurs over immense periods of time. Intelligent Design is when a magical entity sneezes and POOF you've got another living thing. The two ideas are almost antithetical. Once again, the point of the program was not to compare and contrast Evolution and ID; the point was to tell the story of the Dover trial, during which ID was shown to be a flimsy psuedoscientific religious argument. Why are people surprised that this is the idea expressed in the show?

"It was fascinating to see those dipstick high school teachers,
bolstered by the heir to the Darwin fortune explain the impossible and to the
great lengths that these . . . will go to deny that there is a greater power
than some . . . that passed teacher's college in some backwater . . .
state."

Yeah, because Darwin totally made it rich off of his ideas. I'm pretty sure I saw him on the 1888 Forbes 500.

There are a ton of other letters but it would take a century to write a full response to all of them. Read them if you like but I take no responsibility if your blood pressure skyrockets due to the sheer ignorance that most of the letters wallow in. There are a few letters commending PBS on what was truely an accurate and well presented program, but the vast majority of them are drivel from fundies. Be warned.

Interesting

While just browsing the internet I came across a couple of facts that I found rather interesting:

The first is about the infamous fugu pufferfish (Takifugu spp.) It's a well known fact that a great majority of the human genome is comprised of so called "junk DNA" (regions of DNA that has no aparent function, for those of you who dont know). What's interesting about Fugu is that it has pretty much no junk DNA whatsoever.

According to Daniel Rokhsar, "within each taxonomic grouping, there can be wide variations in genome size that are not necessarily related to the complexity of the organism. These variations appear to be due to differing amounts of 'junk' or 'selfish' DNA, often dominated by the remains of ancient viral-like genomic infections that left hundreds of thousands of repetitive elements littered throughout the genome. The Fugu genome seems to have avoided these events and sequencing it will therefore allow us to obtain a complete vertebrate genome extremely rapidly."

It may be that Fugu represents a pristiene "primitive" verterbrate genome, since it's been untained with retrotransposons or pseudogenes. It would be interesting to find out how the species has been able to avoid this. Maybe it's genome will shed some light on the divergance of verterbrates from inverterbrates some 530 million years ago.

The second interesting thing I came across was a paper on an experiment done in 1989 by Diane Dodd (Reproductive Isolation as a consequence of adaptive divergence in Drosophila pseudoobscura 1989 Evolution 43(6) pp. 1308-1311). This experiment is awesome because it shows speciation in action. What she did was raise one strain of D. pseudoobscura which, obviously, could breed with each other. She then seperated the population in two groups. One group was raised using a starch-based food, and the other was raised on a maltose-based food. These groups were reared for several generations (I think it was 8), and after were combined into one larger group again. What resulted was the maltose group only mated with the other maltose group flies; the starch flies only mated with other starch flies. There was reproductive isolation - in other words, speciation - between the two groups that started off as one interbreeding population.

This is evolution in action, folks! If anyone ever doubts that evolution is true because "no one has ever observed it", kick 'em in the shins and point them to this paper. Not only can we see the beginnings of evolution, but we can see it in as few as 8 generations.

Painful Ignorance

I dont know how familiar people may be with Joseph Farah, but he's one of the bigwigs over at WorldNetDaily, a megasite for rightwing conservative nonsense. Alot of the articles wirtten there are rife with religious propaganda and unscientific garbage, but one article written by Mr. Farah has sent my bullshit meter off the charts.

In this column, he writes about the problem of global warming, or the lack thereof. Now, I do not agree with alot of the "conventional wisdom" surrounding global warming (Al Gore and his Inconvienent Truth is bunk if you ask me) but I will not deny that the Earth's climate is changing and rather quickly (whether this is caused by us people or is more of a natural occurance I'm not quite convinced). Joseph Farah has taken an alltogether different stance. He says that global warming, or more specifically, "global cataclysmic flooding" caused by global warming will never happen. Why? Because "God said so".

"First of all, in Genesis 8:22, we're told of a promise by God never to use global floodwaters again as a means of destroying life on Earth. In that promise, the Bible explicitly states: "While the earth remaineth, seedtime and harvest, and cold and heat, and summer and winter, and day and night shall not cease."
In other words, no more cataclysmic floods – the result Al Gore promises in the near future as a consequence of global warming."

Basically, he thinks that because "God told us that he wouldnt flood the world again", rising sea levels cannot possibly occur due to global warming. He goes on to support his argument by saying that it's pointless to even bother worrying about the climate because God is the one that controlls it, and not man:

"It is so presumptuous and haughty of believers and non-believers alike to think man is in control of the destiny of the planet God created for us.
If it were so, would he not have warned us? With all of the prophecies in the Bible, should we not expect to be told that such matters are actually in our hands? Why would we be told exactly the opposite throughout scripture?"

Of course, the only "support" he uses for his absolutely ludicrious view is taken straight from the Bible. "This verse or that chapter says this or that" should never be used as support for an argument. It's all based on one very flawed assumption - that the words in the Bible are true. The veracity of the bible is incredibly dubious and all scientific evidence points that it's nothing more than ancient fairytales - so any argument solely based on "the word of God" is void.

In fact, as has been pointed out by Ed Brayton, Farah's claims disprove themselves. As of writing this, there is extensive flooding in Mexico, with 80% of the state of Tabasco being covered in water making an estimated 800,000 people homeless. It is in every sense of the word catastrophic. If Farah is correct in saying that the Bible "promises no more catastrophic flooding" then he's proven the bible false. I guess that means the rest of his arguments fall apart since theyre based on the same book he's just shown to be rubbish.

Farah also writes one thing that points to his lack of congnitive abilities:

"It's not that the Bible tells us there are no consequences for our actions on the planet. In fact, it quite explicitly does. But it is not the production of carbon dioxide that God finds offensive. It is the commission of sin. Nowhere in the Bible does God ever suggest that producing CO2 is sinful. "

Allow me to paraphrase: "The bible doesnt say that making lots of CO2 is a sin, so we dont need to worry about how much we produce. Nothing bad could come of it!" What a load of crap. Like Brayton put it, "The Bible doesn't say that dumping toxic waste into your drinking water supplies is a sin either, but it's still a bad idea."

This idea that global warming is not a problem simply because God didnt say it would happen is absolutely insane. It's this kind of thinking that leads people to think that global warming is nothing to worry about because "Jesus is going to return in the next 50 years anyway" (Astonishingly, 25% of Americans seem to think he's going to return this year!) How anyone could ignore scientific evidence, or even direct observation, for the word of a two thousand year old book is beyond me.