Your Daily Dose of Stupid

Every thought about what it would be like to live in a society where murder isn't murder, but just vigilante justice? Apparently this is how it works for Pastor Steven Anderson: killing Barack Obama and executing homosexuals does not actually count as murder, rather a sense of diving justice. In fact, it's been reported that he petitioned his congregation to pray for divine intervention to kill President Obama.

Sequence me up!

Yay! Sequencing technology is getting cheaper and cheaper. A company called Complete Genomics has cut it's price of sequencing a human genome from $250,000 to $20,000!!! Their goal? To sequence 10,000 genomes by 2010.

Only days ago Complete Genomics announced that it had raised $45 million from investors excited by the potential of an economic sequencing technology. By radically reducing the cost of sequencing, Complete Genomics expects to cater to a large field of developers looking for genetic clues to treat disease and identify patients most likely to respond to new therapies.

Dude - forget about genetic disease for a moment ... I just want to know if my ratio of G-C to A-T pairs is above 1 ... or let's see how functional my telomerase is. And what I've really been waiting for - see how many times the sequence GATTACA shows up. Where's 20k when I need it?

Seriously though, this is an amazing economic breakthrough - having more human genomes is awesome so that we can really get data on SNPs and do fine-mapping of disease alleles. Now we just need to get all those people who get sequence to sign release forms to do comparative analysis ... making the world a better place one genome at a time.

Gambling with Religion

This is too good not to share. Via Pharyngula.

Epicurus

After another successful atheist movie night at my house (tonight we watched The God Who Wasn't There) and a vigorous discussion about the personal impact of conversion and the individual (usually intellectual) capacity to undergo the conversion to atheism, this quote from Epicurus came up:

Is God willing to prevent evil, but not able?
Then he is not omnipotent.
Is he able, but not willing?
Then he is malevolent.
Is he both able, and willing?
Then whence cometh evil?
Is he neither able nor willing?
Then why call him God?

Vienna!

I'm finally on my way! Well, sort of. I'm currently on a seven hour layover in Washington-Dulles airport ... yeah, SEVEN hours. Of course this is better than yesterday, when I was supposed to leave but couldn't because my flight got canceled - stupid United airlines. I got rescheduled for today and am excited to be on my way to Vienna, Austria.

Members from four choirs in Durham (Duke Chapel Choir, Duke Student Chorale, Choral Society of Durham, and the NC Vocal Arts Ensemble) under the conduction of Dr. Rodney Wynkoop are traveling together to Vienna to participate in the International Haydn Festival. We're performing Joseph Haydn's tenth setting of the mass, Missa in tempore belli (Mass in time of war), and Ralph Vaughan Williams' Dona Nobis Pacem. These are both very impressive works of musical genius, though the RVW is incredibly moving and apropos for the current worldwide involvement in Iraq, Iran, and Afghanistan.

We'll be performing in the Konzerthaus of downtown Vienna. It is simply a beautiful venue and I'm thrilled to be singing baritone in this monolithic event where we'll be accompanied by the Vienna festival symphony. The RVW music is quite powerful and the texts are taken from the mass, three poems by Walt Whitman, a political speech, and sections of the bible. The most striking of the texts are the poem settings by Whitman. Here is one of them entitled 'Reconciliation':

Word over all, beautiful as the sky,
Beautiful that war and all its deeds of carnage must in time be utterly lost,
That the hands of the sisters Death and Night incessantly softly
wash again, and ever again, this solid world;
For my enemy is dead, a man divine as myself is dead,
I look where he lies white-faced and still in the coffin--I draw near,
Bend down and touch lightly with my lips the white face in the coffin.

It captures the tormented mind forced to deal with the realization of its own mortality through that of his fellow man.

My favorite movement of the RVW uses the text from Whitman's 'Dirge for Two Veterans'. A tribute to my grandfather and any other man or woman who died serving their country, fellow citizens, or free people of the world.

The last sunbeam
Lightly falls from the finish'd Sabbath,
On the pavement here, and there beyond it is looking,
Down a new-made double grave.

Lo, the moon ascending,
Up from the east the silvery round moon,
Beautiful over the house-tops, ghastly, phantom moon,
Immense and silent moon.

I see a sad procession,
And I hear the sound of coming full-key'd bugles,
All the channels of the city streets they're flooding,
As with voices and with tears.

I hear the great drums pounding,
And the small drums steady whirring,
And every blow of the great convulsive drums,
Strikes me through and through.

For the son is brought with the father,
(In the foremost ranks of the fierce assault they fell,
Two veterans son and father dropt together,
And the double grave awaits them.)

Now nearer blow the bugles,
And the drums strike more convulsive,
And the daylight o'er the pavement quite has faded,
And the strong dead-march enwraps me.

In the eastern sky up-buoying,
The sorrowful vast phantom moves illumin'd,
('Tis some mother's large transparent face,
In heaven brighter growing.)

O strong dead-march you please me!
O moon immense with your silvery face you soothe me!
O my soldiers twain! O my veterans passing to burial!
What I have I also give you.

The moon gives you light,
And the bugles and the drums give you music,
And my heart, O my soldiers, my veterans,
My heart gives you love.

To hear these words set to the music composed by RVW simply tears at the heart.

The last movement pulls from multiple texts and more than hints at the great Handel's Messiah. I wish all of you could come hear this concert in Vienna when we perform. If you want a sample of how moving this concert will be, here's a clip of the last six minutes of the RVW conducted by Robert Shaw with the Atlanta Symphony and Chorus. Now, just imagine you're sitting in the audience of the Konzerthaus of Vienna:

Soon I hope to share with you some of my fun experiences in Europe!

Creation

The words of JBS Haldane have inspired me today:

My practice as a scientist is atheistic. That is to say, when I set up an experiment I assume that no god, angel or devil is going to interfere with its course; and this assumption has been justified by such success as I have achieved in my professional career. I should therefore be intellectually dishonest if I were not also atheistic in the affairs of the world.

Some claim that science has no implications for religion or for the nature of god. I disagree; and I'm in good company. Not only is science not a democracy, but it consistently rules against the ignorant and the stupid. While the god 'hypothesis' is not a scientific hypothesis at all because it can't be completely disproved, science has aptly moved the notion of god into the same drawer as belief in santa claus ... belief in the ridiculous.

This year we celebrate the 200th birthday of Charles Darwin, and the 150th anniversary of the publication of his book 'On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life'. This paragon of reason gave full foundation to the wrecking ball that would begin to deliver shattering blows do the dogmas of religion all over the world. It became no longer necessary to implicate a god to explain the existence of life. This marked a new enlightenment.

In commemoration of these events, a movie depicting the life of Darwin and his discoveries will be coming out soon and I'm very excited about it. It's called 'Creation'. I have a feeling this is going to be one of my favorite movies for a while. Be sure to stay on the look out to find when and where the movie will be coming out near you.

High school party

This is too good not to share. Bo Burnham is one of my heroes. He's a comedic genius and a talented musician ... it also doesn't hurt that he's hot and makes fun of everything. We listened to his EP from iTunes in lab today, and so I thought I'd share a music video from one of his songs. Enjoy!

I'm an enzyme!

Being a science nerd means you get to have fun alll the time. We get joy out of many different activities and discoveries. For example, writing out mad libs but instead of words and letters, using the chemical structures of amino acids and their one letter substitutions as code. Other times it's fun to see who can read a long sequence of DNA the fastest, and then who can read the antisense mRNA the fastest ... without writing it down!

But today, I thought I'd share with you the joy of having my own restriction endonuclease named after me. Well, not exactly named after me, but it has the same initials as me - elevating me to cool status. What restriction enzyme do I share my initials with???

Answer: MscI

If you're not aware, restriction enzymes are like scissors, but in chemical form. They take long strings of DNA and cut at sequence specific sites. For example, if you had the DNA sequence 5'-GATCTAGGAATTCTCTAG-3' then at that bold spot, the restriction enzyme EcoRI could cut that DNA, separating it into two pieces. Cool, huh? But remember, DNA is double stranded; so when it cuts, it looks like this:

Those leftover sticky ends want to bind again, and will, if they're given other pieces with complementary sticky ends. So think about it ... if we can harness the power of these enzymes, then we can cut and paste different pieces of DNA together in any order we want! This is what scientists discovered in the 1970s and ultimately lead to the era of genetic engineering. We've come a long ways since then, but that's basically the gist. Using restriction enzymes we cut up pieces of DNA and insert in pieces that we want and then put the whole construct in an organism of interest to be expressed. Shazam! You've got a genetically engineered organism.

These enzymes were originally discovered in bacteria as a defense mechanism against foreign pieces of DNA from invading viruses and other sources. Remember, if bacteria exchange genetic information then they're having a form of sex and they don't want to do that with just anything. There are many of these enzymes out there that have been discovered, and each one cuts only at its sequence specific site. Interestingly, all restriction enzyme sites are palindromes, or they are the same sequence forward as they are backwards. So using our host of enzymes, we can cut and paste our way into the genetics of the future.

I wonder what properties I share with my restriction enzyme ... ? According to New England Biolabs I work at 75% in Buffers 1, 2, and 3, and at 100% in Buffer 4. I'm not sensitive to methylation or CpG methylation, but with dcm methylation I am blocked by overlapping. You can heat inactivate me at 65 degrees Celsius for 20 minutes but I work optimally at 37 degrees Celsius. I'm an isochizomer of BalI and if I'm not working well, just give me a little more KCl and I'll get the job done.

Does that turn you on?

Happy Birthday Stravinsky! (and my sister!)

My sister happens to share a birthday with one of my favorite composers of all time ... Igor Stravinsky! Can't you see the resemblance?

In celebration of both birthdays, here's a clip from 1965 when Stravinsky was 82 and conducting Lullaby and Final Hymn from the Firebird Ballet Suite (1945). Hope you enjoy it as much as I do! (thanks for sending, Andy)

Show me on the map where religion touched you

Who would have thought that dogmatic celibacy could be a bad thing??? Well, when people use it as cover for sexual deviancy, perhaps it could at least be re-evaluated as a practice. Unless you're the catholic church.

Deliver us from evil is a movie that explores the depraved indifference the catholic church has for the ill-effects its pedophile clergy has on parish members and their children.

You should visit the website. It's replete with a US map indicating the number of catholic priests accused of sexual misconduct. It's quite shocking to see. Makes you think twice about leaving your child at an after school day care run by a religious organization. The poor assumption that it's safe to leave your son or daughter with a man of the cloth simply because they are a member of the clergy is shown to be an incredibly poor assumption in this movie.



And if you're feeling particularly good about the human race and need to be brought down a couple of notches, you should hear what head of the catholic league, Bill Donahue, had to say about the recent atrocities reported out of Ireland, perpetrated by clergy of the Irish catholic church.

Fortunately my morals do not come out of religion, so I am able to see how inhumane these acts are, even if Bill Donahue cannot.