Extraordinary Achievement by Michael Phelps May Be Due to Arsenic in His DNA

I firmly believe Nature should consider publishing  (or re-publishing, who cares) this article considering their taste shown on their recently publication of "Why great Olympic feats raise suspicions".

Dear readers, if you like it, please send it around and/or leave comment to support this protest-against-Nature effort.  Thank you! 

Update: Nature has already apologized.  Although I'm not buying it completely (some key points were glossed over), it ended better than I have thought -- kudos to Nature for acknowledging their mistake.
Here's a blog that, to use Dan Patrick's words, goes to the next level on this issue.  Check it out.
Also, thank you Adam for pointing out a typo in the text!

Extraordinary Achievement by an American Swimmer May Be Due to Arsenic in His DNA

Ar U. Kiddingmi¹ and Shamon Neighcher¹

¹World Unsound Allegation Association.

  

The physical and physiological limitations of human athleticism are of great interest for both scientific and sociological reasons.  An efficient method to test such limitations is having human participants compete in sports such as those included in the Olympic Game.  Recently American swimmer Michael Phelps showed extraordinary athleticism in the Olympic Game, winning over 20 medals among which 16 are gold.  This greatness has never been achieved before and therefore is highly likely due to factors other than training, which all previous athletes have undergone.  This seemingly impossible achievement is reminiscent of the robust growth of the recently discovered bacteria GFAJ-1 in arsenic-rich media.  Since the existence of arsenic in the DNA of GFAJ-1 has not been conclusively disproved, it is reasonable to assume, or at least to suspect, that the DNA of GFAJ-1 contains arsenic.  Similarly, we propose that part of the DNA of Michael Phelps consists of arsenic, and that this element strongly contributed to his success.  Although our theory has no evidence, it nevertheless cannot be ruled out.  Our finding illustrates an exciting opportunity to enhance the athleticism among humans, although safety and ethic issues should be fully addressed prior to its worldwide application.

Should we believe in equal opportunity or equal representation? -- A letter to Daily Texan

Dear Editor,

I read the article "Diversity remains issue despite efforts" (http://www.dailytexanonline.com/news/2012/01/27/diversity-remains-issue-despite-efforts
) published on the Jan. 27 , 2012 issue of Daily Texan and have some opinions on this topic.

I agree that it is a noble and admirable goal for UT to help underrepresented minorities improve their high-school education, and I fully support this effort. However, I do not understand why it is the duty of UT President to pursue a student body that "better reflect(s) the state population". As the article rightfully points out, university admission should consider "academic achievement, personal achievement and special circumstances", rather than race and ethnicity. Therefore, the student body of UT should be a natural reflection of college preparedness, rather than the sheer population, of different ethnic groups in the state of Texas.

While UT should play an important and positive role in pre-college education, the obligation to get minority high-school students better prepared for college, however, should fall on the state, the cities, and leaders of minority groups. Without changing the situation in high-school education it is dangerous for the University to impose student diversity because this will inevitably compromise the principle of equal opportunity in university admission.

The core question on this issue, as I see it, is whether we should believe in equal opportunity or equal representation. This is truly a dilemma because it is impossible to believe in both unless students from different ethnic groups are equally achieved and equally prepared for college education and the challenge beyond college. Unfortunately, this is not what the reality is. While on the one hand we should change this reality by making underrepresented minorities more prepared, on the other hand we should be careful not to give up the principle of equal opportunity. This is because equal opportunity, rather than equal representation, is what brings competitiveness.

Let us look at a simple example. If I am not mistaken there is not a single Asian on the roster of UT football team. Imagine what our reaction would be if Mack Brown says we need to have 19% Asian players on the team to reflect the state population. We would think this is beyond ridiculous. Why? Because most Asians are not prepared for playing football! We strictly enforce equal opportunity on the football field because we passionately want to win. Then why do we give up this principle when we want to win on the much bigger field -- the global economy? If we cripple ourselves by excluding the best available players from our team we will do a great favor to our competitors. There is no obvious scoreboard on global economy, but I am sure a loss in this field will be much bitter to swallow than a losing season in the Big 12.

Sincerely,

Xi Chen
Postdoctoral Fellow,
Center for Systems and Synthetic Biology,
University of Texas at Austin

Cloning in the 21st century

It sometimes feels really nice to be old-school. But face it, a first-grader in a new school can out-do you. I'm talking about cloning today.

There are numerous mysterious 'non-traditional' cloning kits out there. One type that constantly gains popularity in recent years is the one that relies on the 3'->5' exonuclease activity of a DNA polymerase (most likely T4 DNA polymerase) to chew out long sticky ends on both the insert and the vector, which then hybridize to form a circular DNA (although not joined by covalent bonds) ready to be transformed. Therefore this procedure is usually called 'ligation-independent cloning'.

A popular example of this MAY be the In-Fusion kit now being sold by Clontech. I said 'MAY' because I don't really know whether the kit is based on this mechanism. I actually came across descriptions like this in literature:

"The In-Fusion mechanism is ligation-independent and while proprietary, likely uses the unique properties of the 3′–5′ exonuclease activity of poxvirus DNA polymerase." [Biotechniques. 2007 ;43(3):354-9, PMID: 17907578]

Now let's get less proprietary.

As far as I know, there are two types of ligation-independent cloning that are widely used. One is called 'LIC-PCR', which stands for 'Ligation-independent cloning of PCR products'. The original paper can be found here: [PMID: 2235490]. The limitation of this method is that at the junctions between the vector and the insert there has to be a long stretch of sequence lacking a particular base -- this is how you generate a well-defined sticky end.

Later it turned out you don't need well-defined sticky ends to do ligation-independent cloning. By optimizing the concentration of T4 DNA polymerase and duration of treatment, one can make roughly 15- to 20-nt overhangs, thus eliminating the sequence-dependence. This method is detailed in this paper: [PMID: 17293868]. The authors called this method 'sequence and ligation-independent cloning (SLIC)'. Unfortunately the method section of this paper is poorly written, and may contains several mistakes. They then clarified their method in Protocol Exchange on nature.com. [Here].

Both methods have gained pretty good reputation. Hopefully they work for you. Happy cloning!