Done With Life

About a month ago, a colleague in our Department, lost his dad after battling with a debilitating disease for quite a time. From his countenance, I could sense he was harboring mixed emotions. A smile in his face, as I expressed my sympathy to him,  meant he was glad seeing his beloved father relieved of the pains and sufferings he endured through the past years. It must be very difficult for him and his family seeing a moribund loved one day after day. Then as he bit his lip, I felt the grief his heart was keeping, for the eternal loss. But he was quick to regain his composure,  deeply consoled that his dad is done with his mortal sufferings and with the thought, as his faith promises, that he is heaven-bound. A year earlier, another colleague of mine mourned for the death of his dad, three days after which his father-in-law passed away, all succumbed to infirmities which kept them bed-bound for the remaining years of their lives. And all I could gather from him was a sigh of relief, from the painful sight of seeing his dad waging a fight he could not win and for his dad as the end of his sufferings came to pass.

I was thinking about, what if I am in a situation where my life is characterized by nothing but physical pains and afflictions? That after exausting all available modern medical interventions there is, still there isn't  any relief in sight. And the intense physical suffering gets worse every day as it is augmented by the psychological pain  of self-pity generated by the bitter feeling of sheer uselessness.Where I am totally emasculated from doing things I used to, and have to rely on machines with a network of  tubes delivering air and food to, and removing wastes from my body. Then I'd say, I am done with my life. I would sign a waiver seeking a medically-assisted end of my life.

This is euthanasia, also called mercy killing! It is an act of ending a person's life who has been terminally ill by witholding extreme medical interventions. Suicide with consent! This is one of the hotly contested topics for ethical debates. To do or not to do, poses a great dilemma as it creates a divide among many health providers as well as the family members. Euthanasia has also been a subject for long debates in the halls of lawmakers arena. And it has been judiciously argued, with a lot of attention, in the halls of justice, as famously hallmarked by the case of Terri Schaivo.

I offered a course called Controversial Topics in Biology during aWinter Term, three years ago and our class tackled several issues that were, well controversial! I introduced euthanasia through a tear jerking foreign movie titled Done With Life. It's about one man on the way to the peak of his youthful life, which is peppered with feats and accomplishments unusual to any man his age. But he, unfortunately, did not get to where he quite wanted as an unusual accident cut him. He dived in a cliff and he landed at the back of his head, breaking his neck. Becoming quadriplegic was the major source of miseries in his life. After the surreal twists and turns of events in the story,  he eventually ended his life with the help of a medical doctor who prepared the 'drinks'  he had to binge on to kill himself slowly and less painfully.

My students, when asked to give their reactions, as usual were divided close to fifty-fifty. The pragmatists did not doubt taking the same route as the hero in the story. While the conservatives and probably the moralists, on the other hand, were apt to passing their strong disagreement to ending a life which they considered  sacred and given to him by their creator. This scenario reflects a microcosm of  what and how does the society deal with this issue.

Nobody has been incriminated for attempting to commit suicide. But many have been incarcerated for trying to murder a person, pre-meditated or otherwise. One can take another person's life  in the name of self-defense without going to prison. Which means, one's life is really valuable. Just like any valuables, one person's life belongs only to him. And so, I thought, a person is entitled to do anything with his life. For as long as he fully knows the consequences of his action. This is especially so if the person wishes to relieve himself from the pains and burdens he's carrying through for the rest of his life.

For A Dear Sister on Her Birthday!

Every child is a gift from heaven. This is what our parents believed. Getting married at early age, teens to be more precise,  our parents had a long way ahead of them. And so, our first sibling (a girl)  came, followed by another one, then another one… then me, the seventh child. Plus two more after me. .. We thought that was it.  Then, came our last sibling, after a hiatus.

I was about nine when we welcomed our youngest sibling, Berse (she is also fondly called Angging in our family) to this mortal world.  She was the apple of the eyes of many in the family. She was well loved, the privilege she naturally  received being the youngest. But she never grew up a spoiled brat.

In our family, the older siblings were, at times,  charged with looking after the younger ones. And I had my share of babysitting the younger sisters, especially when my older siblings were all at school. This brought me closer to my younger siblings, and Berse, being the littlest always deserved more of my attention. She told me, she could remember fondly enjoying a piggyback ride she got from me when we were heading somewhere.

One thing I could remember so well about Berse is her being an industrious person. As a young child, she would find ways to earn a little  money for herself. I thought this was a trait predicting her success in the future. 

I was off to college when Berse was starting grade school. Away from home for 8 years, the only times I could see her were during short visits  at Christmas or summer vacation. In 1985, job brought me back close to home and about that time, Berse was starting college. This was the time Berse and I were closely associated again, as she went to the school where I worked as a professor.  Through the years, I saw her transformation into a very responsible person. I even teased her as 'sipsip', showing extreme loyalty to one of her favorite college professors. We parted our ways again after her graduation from college as she started teaching in a high school somewhere.

Fast forward.... today Berse, our baby sister, turns 42 years old. And yes, she lives a simply full life. She is blessed with a nice family, intelligent kids and a very successful career. There is one thing I admired so much about her, being the caregiver to our octogenarian mother. Living alone like a single mother since husband Roger is working overseas, I thought it was difficult for Berse to lead a normal life, with our frail and ailing mother,  three  kids with two teenagers, and acting as head teacher in two elementary schools. I thought she has so much on her plate. But I have never heard her complaining. On top of that, she seems to be the go-to person when a sibling or two are in need of something, especially financial matters.

I am greatly indebted to Berse.  She has done the greatest job which nobody else in our family has ever done, caring for our dear mother. Words are not enough to express my heartfelt thanks and appreciation to our baby sister. 

Now I realized why heaven sent her, the youngest sibling in our family.  Because if she did not come, who would take care of mother? If the older siblings were to take care of the younger ones, then the youngest will take care of the old folks! LOL..

Happy birthday dear sister! We wish you with continued success in your family and in your career! I owe you something... a trip to the US with a stop over in Canada someday soon!

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!

Symbiogenesis

A couple of weeks ago, I was in a room with privileged people - students, professors and researchers, listening to a talk which dealt with  the topic on Symbiogenesis. The speaker, Dr. Lynn Margulis,  was a not an ordinary person as she has been credited for the widely-accepted  endosymbiotic theory of the origin of eukaryotic cells. She is currently a distinguised professor in the department of geosciences at the University of Massachusets in Amherst.

It was about 6 years ago since I knew about Dr. Lynn Margulis. I was a member of a large delegation of biology professors from all over the US grading the 2006 Advanced Placement test in Biology (APBiology) in the University of Nebraska -Lincoln. No, she was not one of us. But her name always popped up in almost every page of the test booklets I read. The question was about the origin of the first eukaryotes and many students unnecessarily mentioned her as the proponent of the theory.

In that lecture, I paid particular attention on how she talked and how she relayed the wealth of information within a limited period of time in a presentation. For people like her, I thought,  are exceptional mortals and are endowed with the unique critical skill in weaving a major  scientific concept which makes it to the college textbook. And all I wanted was to emulate her wits and style.

Symbiogenesis, the merging of two entirely different organisms to form a new organism, is not really new. This idea was synthesized in the 1920s by a famous Russian botanist in a book titled Symbiogenesis: A New Principle of Evolution. Symbiogenesis was considered a major driving force in evolutionary biology along with Darwinian's natural selection. This treatise on symbiogenesis however, suffered the same fate as Gregor Mendel's theory of inheritance,  gathering dust in the library's bookselves over a long period of time as they were ignored by the scientific community. In just about a year ago, The Harvard University Press published a English Translation of the book where Lynn Margulis was one of the co-editors. The re-discovery of symbiogenesis has begun an exciting era in evolutionary research.

We share this planet with a gazillion of other living organisms. We share our bodies to tons and tons of other living organisms. Lice in our heads or pubes; worms inside our guts; fungi in between our toes, armpits and yeasts in the vagina; and of course the truckloads of bacteria and protozoans which call our intestines their abode, others invading every inch of our skin, eyes, nose, mouth and not to mention the genitalia. These are part of who we are. They make vitamins for us! They make us stinky! Many of the them form our normal biota where they offer themselves the 'military' protecting our bodies from invading 'alien' microorganisms.   

Similarly, in bodies of other organisms live tons and tons of living hitch-hikers.Symbiosis, the close association and coexistence of different forms of organisms, therefore has become the way of life. Symbiosis causes different consequences to the parties involved, parasites get 'fat', hosts nutrient-deprived, commensals mutually benefited. When the host becomes immunocompromised, the opportunistic pathogenic endosymbionts (those who live within our bodies)  are out there to defeat the host in a disease. In short, both the endo- and ecto-symbionts make our either bodies better or bitter.

Dr. Margulis used the sea slug, a close relative of the squids and octopuses, as one example that seems to exemplify the process of symbiogenesis. Many different species of sea slugs obtain defense structures, like the nematocysts from the deadly jellyfish, portuguese-man-of-war. Instead of being destroyed, these stinging cells are kept by the slugs for their own defense. There is a certain species of sea slugs which feeds voraciously on algae. Instead of being broken down as food, some algae stayed infact and remained functional within the animal body, as endosymbionts. The slug, which is shaped life a flat leaf, looks green because of the presence of the algae which carry on photosynthesis inside the slug body. So here is an animal that, through its of endosymbionts, is capable of photosynthesis. Examination of the eggs produced by the slug showed the presence of chloroplast genes in the cytoplasm. 

This could just be the tip of the iceberg. There could be many animals out there whose close contact and  strong association with other organisms, may result to the formation of an entirely different organism in the long run. In here, missing links will not be an issue. The scientist may just have to look closely which other organisms that are associated. And by looking at the different DNA fingerprints, the identity of these associated oganisms can be obtained  by blasting their DNA sequence with the extensive database that are available.

Here is a nature's way of making transgenic animals!

The Faces of Morality

A religious couple, who has been married for over ten years, patiently kept on trying to have a baby. When they were about to surrender their childlessness up to their god, the wife found out she was pregnant. That was the best news ever for the couple. As the wife's pregnancy  progressed, she noticed something seemed not right. She developed pregnancy-induced hypertension (preeclampsia) due to mother-fetus serologic incompatilbility, putting hers and the fetus' life in danger. Sonographic examination and amniocentesis reveal the fetus suffers lethal genetic malformation and the chance for  survival is very nil. The physician recommended for immediate termination of  pregnancy for her safety. The couple did not heed the physician's advice for they don't want to  murder their unborn child!

S. P. is an intelligent, outgoing, happy-go-lucky teenaged girl who simply enjoys life. She has a boyfriend her age. They love  hanging-out and chilling with other teens, their age. As many curious teens would do, they experiment on stuff like pot, alcohol and sex. S.P. got impregnated and was in a dilemma. She did not want to inform her parents about the pregnancy, and she certainly was not ready for the daunting responsibility of raising a child as a single mom. The boyfriend deserted her after finding out she got impregnated. S.P.  terminated the pregnancy! To her, it was the best thing to do!

To kill or not to kill? There are only two answers, neither is  right nor  wrong!

Morality is a very delicate yet a very subjective topic. Just like beauty, being moral (or immoral) lies in the eyes of the beholder! That's because there is not a single standard to measure morality. It is looked at differently by different groups of people.

This bring us to the question on what serves as the basis for morality For christians, morality stands on a solid ground rooted in the Bible. Any act done against or in contradiction with the doctrines of their church could be hailed immoral! The Mosaic Law provides a long list of Dos and Don'ts for christians to observe. But even among the different christian groups, people are divided as to what acts are considered immoral, which ones not! In the two cases presented earlier, is killing considered an immoral act? The ultraconservatives would say yes outrightly! For the act itself is in defiance of the Mosaic Law 'thou shall not kill.'  But killing people were rampant in the days of the bible just as the present days. Even god himself caused massive killing of people, the highest form of genocide, when Noah refused people to let them in in their ark during the Great Flood. Innocent babies were killed as consequence with the parents  not painting their  front doors with the sacrificial lamb's blood for the Passover!

The muslim religious extremists hold on to their belief that killing people who they consider as 'infidels' would merit them great rewards in the afterlife. What motivates a young and just-after-puberty suicide bomber to sacrifice his earthly life in killing people is the reward of being with 42 virgins in the afterlife! Killing is not regarded as immoral, in this case!

The non-believers got their system of calling morality. Being not under any church doctrines makes their notion of morality a little more pragmatic and more than philosophical.

Morality has been invented by man. Whatever it is based on, morality deals with what is the right thing to do! It is laced with elements of subjectivity. For there is no clear cut black- and- white in morality,  many things are in the gray zone.

I see the evolution of practical morality in the future. Where terminally-ill patience with nothing but hopelessness on top of their constant suffering  and excruciating pains can openly opt for physician-assisted end-of-life care without the fears and apprehensions of not going to heaven (for those who believe!) and with full support by their church. For doing so seems to be the right thing to do if only to make their sufferings a little less unbearable. Furthermore, I see a society that recognizes and embraces people's diversity. As it is now, morality digs that  deep and big gap which divides the people. Self-proclaimed moralists are easy to render judgments, and cause indignation among others.  Living in harmony seems to be the right to do, and that implies being tolerant instead of judgmental to others. This means respecting and accepting other people for who they are,  regardless of race, creed and belief systems, and most importantly, sexual orientation!

I see this coming! But probably not in my lifetime...



As the Earth's Land Area Is Shrinking

Global warming is blamed for the rising of sea water levels which sinks islands under water. Droughts and rampant forest denudation choked watershed areas and aquatifers  slowly killing the lakes, rivers and streams. More and more areas are slowly becoming deserts. With urbanization and industrialization, large areas of tractable lands are converted into residential areas,  developed into recreaction facilities or commercial establishments. These are causing the earth's land surface to keep on shrinking.

Food production hinges largely on how much land area is available to grow crops and raise animals. Menaced by the shrinking acreage of arable lands and the ever increasing demand for food due to the ever-increasing human population worldwide, scientists are left with the only option of producing more food within less available land. This was the major driving force in the so-called  'agricultural revolution'!

I could still remember, when  I was a young, farmers used to plant traditional varieties of rice in their fields. The rice grew tall, and the winds could easily knocked them down to the ground especially during the booting stage when the grains started to fill. This explained why traditional varieties yield way too low per acreage. In the 1970's, the International Rice Research Institute released new rice varieties, one of which was dubbed  the 'miracle' rice. The rice plants grew up to only knee high, and were resistant to shattering. Being stout and short, normally the plants were able to support the grains at booting until up to harvest. True to its name, a huge increase in yield,  amazingly up to 10 times, were enjoyed by the farmers.

Scientists have developed ways to close in the gap between food production and the increasing global demand for food. They developed genetic engineering or recombinant DNA, a tool which radically changed the way scientists develop new and superior varieties of plants and animals. This technique cuts short generation times needed in the conventional breeding methods. In a nutschell, through this technology, scientists can source out good genes from different plant or animals species, and have them pieced together in a new breed, just like a designer jean. These newly-designed plant or animal varieties will go to the farmers' field or ranch for mass production. A visit to the produce aisle in any huge grocery, one could easily admire the good-looking red, green and yellow bell peppers, huge bright red seedless watermelon, huge ears of freshly-picked sweet corn, and a wide variety of potatoes and tomatoes. Many of them are designer products, now known as 'genetically-modified' crops.

In addition to designing high yielding varieties of crop plants, agriculture is taking a second look at promoting 'hanging gardens'. Vertical structures are built,  on each side, layers of  horizontal 'plots' are planted with crops. Growing some vegetables hang upside down is another practice in consideration.

It's not only the planting of crops that is affected by the shrinkage of agricultural lands. Raising cattle, lamb or goat suffers the same fate as ranches and grazing lands get smaller. As such,  animal breeders came up with rather grain-feeding instead of mostly grazing kinds. In the news lately, a scientist is trying to grow meat in the laboratory. Cultured meat, anyone? Why not?

It has become common practice now using stem cells  to replace certain defective adult body part.s On the same premise, one scientist is using myoblasts, the embryonic stem cells which give rise to the muscles in the body, to start with his meat culture. Pork myoblast for pork, beef myoblast for beef, lamb myoblast for lamb. A beef myoblast made to grow around a T-shaped streak of osteoblast (the stem cells for making bones) , given the right mix of growth substances.... voila, a T-bone steak!  So why raise a whole cow when one needs only the meat? This is called tissue engineering!

Engineering has infiltrated and significantly re-designed the architectural lansdcape of  biological science. There is genetic engineering, protein engineering, food engineering, tissue engineering... Engineering will continue to adulterate the minds of biologists in response to the increasing challenge of life sustainability  amidst the different adversities.

An image in my crystal ball, I see  'green' humans and animals in the future. No, am not thinking about Shrek or the green-haired ompa lompas! Another brave-new-world scenario is predicted where humans and other animals are engineered to contain chlorophyll in their skins instead of or in addition to the usual melanin. This seems very interesting and, apparently, a win-win situation . Imagine, our body producing food through photosynthesis as we walk or jog under the morning sun! We won't go hungry then! Probably thirsty, as the body's demand for water may be doubled - in photosynthesis and perspiration!