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.

Immortality

I'm currently reading a textbook by Malcom Potts and Roger Short entitled "Ever since Adam and Eve - The evolution of human sexuality". It's quite a good read thus far, and fantastic pictures ... as you can imagine for a book about human sex and sexuality.

I want to share an excerpt with you from Chapter 3, subsection 'The alternation of generations'. This offers a unique and poetic explanation for where we come from and how our posterity will receive us:

Our sex is determined by our gametes. All eggs have one X chromosome, while half the sperm have one X and the other half one Y chromosome. A combination of X and X in the fertilized egg will give a female and X plus Y a male. [... T]he germ cells that will ultimately produce the single-celled gamete (an egg or sperm) are set aside very early in embryonic life. If we are born to a middle-aged mother, we may have lived almost as long as an unfertilized egg as we do in the form of a multicellular organism. In reality, each of us leads a double life. There is the romantic life we know, that of a thinking, moving, feeling individual, and there is that secret life lying dormant within us, the sexual life of our gametes - thoughtless, senseless sperm or eggs, waiting for a rare opportunity provided by their host to meet with a gamete of the opposite sex and produce a new individual, thereby handing down the thread of life from one generation to the next. One world is familiar to us, the other alien and mysterious. One is a brief spark of sentient life, the other tied to thousands of millions of years of slow continuous evolution. For the mature sperm, life is nasty, short and brutish. It lives only for a few days and it is a trillion to one chance that it will fertilize an egg. Few will even make it into a woman's vagina. The vast majority are destined to be washed out of the man's reproductive tract each time he urinates, to be flushed down the toilet, ending their days amongst the detritus of civilization in the sewers of some city, or spilled upon the ground, where they die like stranded tadpoles. A woman begins life with millions of eggs, each unique, but virtually all of them die inside her body and, of the tiny fraction that are released, most go unfertilized and are incinerated with menstrual pads. Our gametes are our birthright, but we are unaware of their presence and accord them scant respect.

This alternation of the generations between a mortal soma and immortal germ plasm has fascinated philosophers, theologieans, poets and scientists for generations, and will continue to do so long into the future. For it deals with the very nature of life, and death, and the transmission of our DNA, from generation to generation. At one extreme, there are those who like to think that a chicken is merely an egg's way of making another egg. Or maybe, as Richard Dawkins would have it, the soma is merely the product of an ageless battle between selfish genes, striving for mastery and seeking propagation through succeeding generations. [...] Our life on Earth has not been a series of discontinuous acts of creation, but is an unbroken thread tying us all to our ancestors and with the potential of linking us to innumerable future generations. We are indeed trailing clouds of glory - the glory of billions of years of continuous evolution. We do not create life: we have only the privilege of passing it on.

Genesis, eat your heart out.

Use Protection

If there truly was a man named Jesus who cared for the sick and poor, I trust that he would have also favored the distribution and use of condoms, particularly in less developed nations with higher rates of STDs. And this video appropriately demonstrates what he'd do to anyone who tried to stop him:

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Religion Kills

How about a handgun with your Sunday morning coffee and salutation in the pews? The NYTimes has reported that Dr. George Tiller was gunned down in the middle of the church he was attending. Why? No one is quite sure, except he is a well known doctor who performs late-term abortions, but always within legal limits.

Where did this take place? Wichita, Kansas ... are you surprised? Probably not. He had been persecuted before, even shot in both arms yet recovered from the wounds. He had also been investigated by a citizen-initiated grand jury, according to the article.

I wonder if we'll see outcry from the catholic or protestant (any denomination) church as to the death of this man. Or will any claim that this is divine retribution for his career choice? If it were in my power I would prosecute the perpetrator with a hate crime. When separation of church and state cannot be maintained because of vigilantism, secular and social judgment should be swift and severe.

Same Difference

What's the difference between being blind and being homosexual? Climbing mountains, apparently:



I wonder what reports on same-vision marriage are like?

Non-smoing Tobacco State

It's official - WRAL.com has reported that today, Gov. Beverly Perdue signed a bill into law making it illegal to smoke in almost all restaurants and bars (private clubs and cigar bars are exempt).

Hooray for finally catching up, and protecting our citizens from about the only thing that the medical profession has definitively shown time and again has major detrimental effects. Of all the medical studies, research assignments, and lab experiments, nothing is as clear cut as the negative side effects from smoking. I understand that our state was built on tobacco money, but it's nice to see that we've caught up and begun to move past it.

Now, if we could just get them to take the anti-sodomy laws off the books ...