Synthetic life. Biochemistry. Genomics. And my ignorance of it all!

"Life's like a box of chocolates, you never know what you're gonna get" said the philosopher Forrest Gump.  Well, I never know what I will get on the television.

I flicked to ABC.  It was the last quarter of the USC-Stanford game.  With the Cardinal's football ranking competing with the university's academic status, and the Trojans still reeling from the NCAA sanctions, it was a surprise that the game was tied at 17.  Every once in a while, a match is that way--it still has to be played out for the win, and the higher ranked player or team is not guaranteed a victory.  For a while, it appeared that neither team was able to breakthrough, until USC played for it all with a gamble on a fourth down. The rest, as they say, now belongs to the fabled Trojan history.

Oh, did I mention that I earned my graduate degrees at USC? ;)

After pottering around for a while, I returned to my favorite weekend channel: BookTV.  One of the best channels ever in the lineup.  The number of hours that I have logged in front of BookTV!

It was Craig Venter talking about his research work.  I watched it as if I was a registered student in a course that Venter was teaching.  I made mental notes to myself. I learnt a lot.  I thought about them.  And then went to the BookTV website and even extracted a 15-minute video clip and tweeted about it.  I was that pumped up!

Here is a clip from the Book Discussion on #Venter's "Life at the Speed of Light" that I watched thanks to @BookTV http://t.co/3USBLw2ItH
— sriram khe (@congoboy) November 17, 2013

It was only thanks to Venter's lecture that I understood how urea, and synthesizing it--back in 1828--was itself an important and revolutionary step.  In the slide that Venter put up was this sentence:

The Wohler synthesis is of historical significance because for the first time an organic compound was produced from inorganic reactants.  

I am confident that we never got to know this from high school chemistry, when we spent those couple of months on organic chemistry.  What is worse is this: we lived in a town where a fertilizer factory produced urea; how could they have missed out on conveying to us the significance of urea synthesis from such a perspective too!

Venter and his team of researchers, and other scientists all over the world, have now come a long, long way from that first step of organic chemistry.  His talk was mostly about the key steps over the years, which finally led to the publication of their research in Science, on "providing proof of principle for the production of cells from digitized sequence information," which was the cover story as well in July 2010:

Source

When Venter got into talking about the applications, it felt like it was science fiction.  But, some are already underway.  Some are already happening--like creating vaccines from the digitized sequence information.  Essentially to cook up the vaccine based on a recipe.  No need to wait for months for the egg-based vaccine production process that we now have!

The futuristic scenarios were impressive, and a tad scary as well.

Similar to how in 3D printing we can send the details as electronic ones and zeros and then print the object wherever, Venter offers the possibility of vaccine production labs spread all across the world, which will produce the vaccine from the digital information that will be delivered to them.

Even better was his description of the possibility (though it might be highly regulated) of us sitting at home by our computers and medical dispensing machines--like how we have printers now--and prescriptions like insulin or vaccines will then be sent over to the machine, which will then create them for us at our homes.  (Check out this video clip from his talk)

Or how it might be possible for something like a Curiosity Rover to digitize a life form on Mars (should it find one there) send across the sequence to the ground-station here on Earth and we then assemble it--a biological teleportation!

Even more reasons for me to wonder what it means to be human.

Those were all over the weekend.  This morning, I read this in the news:

Frederick Sanger, the British biochemist who twice won the Nobel Prize, has died at the age of 95.

My first thought was this: there was a British scientist who was awarded the Nobel twice?  In the same field? How come he is not a highly celebrated figure?  Why isn't he a household name?  Ballplayers get venerated as gods, and this scientist was condemned to obscurity among the public?

Turns out that his work is intimately connected to the Venter research stories; what a coincidence!

The first came in 1958 for developing techniques to work out the precise chemical structure of proteins.
Proteins are made up of amino-acids. Dr Sanger was able to determine which amino-acids and in what order were used to build the hormone insulin.
He then turned to DNA and its building blocks, bases.
Dr Sanger's group produced the first whole genome sequence, made up of more than 5,000 pairs of bases, in a virus.
He was awarded his second Nobel Prize in 1980 for developing "Sanger sequencing" - a technique which is still used today. 

How fascinating!

But, even more impressive was this:

"He remains the only person to have won two Nobel Prizes in Chemistry - recognising his unique contribution to the modern world.
"Yet he was a disarmingly modest man, who once said: 'I was just a chap who messed about in his lab'.

What an old-fashioned virtue--modesty!

Destroying "Intelligent Design" into single-cells :)

I wish I had more time to read up on science articles that are not too complicated for me.  I am glad with this recommendation that Ron Bailey had.  This article, in the Journal of Eukaryotic Microbiology that offers a lit-review of the evidence that punctures the argument of the Intelligent Design folks.  And the evidence is all from the single-celled world! 

While it is true that I will not be able to comprehend the finer details of the terms used, I was blown away by this paragraph in that article:

When one considers the tremendous diversity of protistan forms (see Adl et al. 2005), the array of body plans among the Cambrian metazoa pales in comparison. In terms of biological diversity it can be argued that no group approaches that of the protists, especially if one considers that all the plants, fungi, and animals, including the famously diverse Coleoptera, are merely sub-groups of the protistan clades Archaeplastida and Opisthokonta (Adl et al. 2005). Even with the exclusion of the multicellular ‘‘higher’’ eukaryotes, the morphological and physiological diversity among protists is staggering. The major clades of protists contain everything from photosynthetic autotrophs to amitochondriate flagellates and are found in virtually every habitat on Earth (Foissner 2008). The extant diversity of the protists should therefore be seen as the ‘‘background radiation’’ of the eukaryotic Big Bang, with the Cambrian radiation of the metazoa being a subsequent event within a specific group.

I had no idea that there was such a tremendous diversity of those tiny single-celled critters.  The metaphor of the "background radiation" before the biological big bang also really, really appeals to me
And when I read the following paragraph, I thought how cool it will be if the DNA had some kind of a time-stamp on it!!!  I mean, that time-stamp alone can come in handy in everything from crime-scene-investigations to solving the puzzle of when life originated.  Hey, maybe it is encoded somewhere and we are yet to figure it out :-)

As readers of this journal know, DNA sequences are not like birth certificates, stamping an organism with the time and place of its origin. Ancestries inferred from DNA-based methods are founded on comparison of sequence or genomic data, evidence-based modeling of how DNA changes over time, and calculations of the most credible relationship between genetic sequences or patterns. This is just as true for variable number of tandem repeats (VNTR, or so-called ‘‘DNA fingerprint’’) analysis, which is broadly accepted in courts of law, as it is for deep phylogenetic analyses encompassing hundreds of millions of years of evolutionary history. For that matter, acceptance of ‘‘written geneaological records’ requires confidence that the records are not false or misread. Therefore, all methods for determining the history of an organism (except for the direct observation described in the previous section) require theory and well-grounded inference, just as stratigraphic analysis does; they stand or fall together.