Human Genome Ten Years After It's Been Mapped

I voluntered to deliver a talk covering  a certain topic in Genomics in an upcoming Friday Science Seminar which is regularly sponsored by our Department of Natural Sciences. We have a Spring Break this week and I was supposed to be relieved from the usual school tasks. But I was glued most of the time to my laptop gathering materials for my talk. The good thing is that, unlike during my student days when I had to dig up the card catalogs in the library and spend countless hours leafing through the pages of journals,  I just have to type the topic and let the search engine do the searching!

Turns out, this year marks the 10th year after the draft of the human genome was reported. Two drafts actually, one done by the government-sponsored International Human Genome Sequencing Consortium, the other one by a Biotech Company, Celera Genomics. Each used different mapping strategy and both came up with comparable results.

Mapping the human genome was an ambitious project conceived in the 1980s under the Clinton Administration. It officially took off as a 15 year- and 50- million dollar project in 1988, as a collaborative undertaking by participating laboratories in the US, UK, Japan, Italy, China and somewhere else. This project had an initial rough sailing while presented to the  government for funding. Fears were mounting that most of the research budget would be siphoned to this audicious project.  Tauted as a big science, many scientists were abhorred of the idea at the get go. Being a non-hypothesis research was also a major issue.

Anyway, in the month of February 2001, two leading highly authoritative scientific journals, Science and Nature, trumpeted to the whole world the first drafts of the human genome project. The project was completed two years ahead of schedule and at $3 billion bill.  Among the salient findings:  (1) about three billion  bases (A,T,G,C combined) or 3.2 Gigabases  was estimated to compose the human genome; (2) only 1.1 to 1.4% of the sequence actually encodes for proteins; (3) over half of the total DNA consists of repeated sequences; (4) about 1.42.million single nucleotide polymorphisms (SNP) were unearthed to be distrbuted throughout the human genome. Simple translation - there are fewer genes annotated than what most scientists were expecting! For it was believed with the complexity of human beings and being on top of the evolutionary ladder, at this time, humans must have accumulated a comparably higher number of genes. The question that crops up with this finding is: what is most of the DNA (the non-genes)  in the genome doing?


Hope springs eternal. With the human genome sequenced, it was hoped that information about every base in the human DNA could provide benchmark to the development of personalized treatment of certain disease/s tailored to every individual's genetic profile. The genetic clues could be mined from the individual's SNPs pattern. In the same manner, preventive treatments could be given to individuals whose SNPs patterns reveal predictable late onset gene-based diseases.

But medicine is  not quite there yet! Ten years after, the beginning has just started. The art or science of medicine has yet to take off incorporating genomic information to the treatment regimen. In response,  a few topnotch medical universities in the US are beginning to re-write their curriculum considering the direction of personalized treatment of human diseases. While humans are genetically distinct from our close furry relatives, every individual has a distinct set of SNPs. This unique genetic identity explains why different individuals having similar symptoms and nature of disease would respond differently to the same treatment. And this is when personalized treatment becomes an invaluable tool.

Personalized medicine brings forth to life pharmacogenomics! That is - developing certain drugs or treatment plans based on the patient's  DNA sequence. Which means, a patient should have his entire DNA sequenced.

Sequencing the human genome for the first time was very costly, took a long period of time (13 years), and quite labor intensive with  hundreds of DNA nerds spending countless hours in the laboratory , in over 20 laboratories worldwilde! But through their journey, technologies evolved. Automated DNA sequencers were developed, and the processing capability of computers has been improved beyond one's imagination! We learned that some who's who in the human genome project ,and rumors have it that few celebrities, have their own genomes sequenced, to a tune of a million dollars a piece.

But mortals like me and everybody else, may not lose hope. With technological advancement occurring in quantum leaps,  genome scientists sing in unison that soon sequencing one's genome could be inexpensive, and therefore, become affordable to many! Save a thousand dollars and drop your mouth swabs in the mail. In one week,  receive your DNA sequence!  This will then mark the era of the start of personalized medicine... when a patient's genomic sequence has become a part of his medical records!

The Day The Earth Moves

I was watching the raw video footages posted on the internet taken while the 8.9 magnitude earthquake  was in progress in the Sendai Prefecture in Japan. I could not believe what I saw!! It was terrifying. Inside the grocery, workers were uselessly trying to keep the tall aisles still to prevent the displayed items- wines, canned good, boxes and what-have you, from falling. Inside an office, computers, monitors, wall decors, even desks were falling. There was a footage in a  lobby which reminded me of my first trip to Manila, decades ago, on board the M/V Dona Marilyn (before it sunk) while navigating through the unusually rough waters off  Romblon island, where bottles rolled from side to side of the huge ship. In that footage, I thought the tall building must be swaying!!! Indeed, it was swaying!

What was even more gut wrenching was the aftemath of the strong earthquake, the tsunami which flowed in multi-story high waves of rushing waters raging the coastal areas up to 3 kilometers to the mainland. I watched the dark mound of water picking up yachts and small boats from the shoreline and cars and trucks parked in the streets bringing them  to who-knows-where, knocking down weaker structures (homes and bridges) along the way The eerie sight sent a chill to my spine! In the airport, I saw few airplanes swarmed around by drifted cars and trucks.

I thought I was watching the thriller of the futuristic movie, The Day After Tomorrow. Some scenes were so surreal that most people think would happen only in the silver screen. It did happen for real, caught  in people's not the director's camera! The magnitude of the damage seems incomprehensible, as thousands of lives are lost or missing, massive infrastructures damaged including the nuclear power plant facilities and power is out for who-knows how long!

This powerful earthquake occurred in Japan earlier today while rescue and recovery operations are still underway in the rubbles of Christchurch, New Zealand after it was rocked by 6.3 magnitude quake less than a month ago. Elsewhere, tremors shook and caused significant damage to buildings and loss of lives and limbs in Southwest China, and was felt in Bali, Indonesia. Unfortunately, the tremor which shook Japan was estimated to be 800 times more powerful (and hence more destructive) than the one which shook New Zealand.

With this string of calamitous events, the self-proclaimed soothsawyers out there are apt to quickly remind the people the end of time is near. That humans have caused so much displeasure to god. And that god is punishing the earth!

Truth to  reckon is that the earth has been a harsh environment to live in. This planet was born out of unimaginable disaster if we try to contend with the Big Bang Theory. After it's formation, the earth's environment has been so hostile, even before the first life was formed.  Volcanic eruptions, powerful earthquakes, meteorites invasion and some other forces described the cataclysmic nature of the earth. Ironically, it is believed that through the energy generated from these activities, chemical reactions occurred which in the course of time, the first life was formed.

Life in this planet just come and go. According to scientific estimates, more and more living forms were present in the past (and are now archived in the layers of rocks in the earth) than those that live at the present. This is just how things go. We heard about fish kills, bird drops, and massive loss of lives. These are tell-tale signs of  natural selection. It's part of the dynamics of the Gaia, the earth being likened to an organism. Where there are continuous interactions between the various components of the earth's ecosystem (the atmosphere, the oceans, the land and the bedrock beneath)  in order to keep the earth healthy.

And so catastrophes are part of our existence. Sometimes we are lucky.. others are not!