Science Time - Molecules and Models

The Magic of Molecular Modeling

"All Art is but imitation of nature." - Seneca
The same seems to be happening in scientific laboratories today.

Life is nothing but a few molecules put together in a certain order. The order is as important as the molecules are. Years and decades of research have brought us the knowledge about these molecules and researchers nowadays are busy determining the order of their arrangement. This has given rise to an extremely important field called molecular modeling.

Molecular modeling is the branch of study that revolves around prediction of structures and functions of various biological molecules by means of models developed on computers.

The study is limited not only to visualizing the structures of molecules, but can range from performing complex calculations related to the behaviour of the molecule to prediction of the functions of the molecule.

Molecular modeling has perhaps been best explored in case of proteins. The vast expanse of the biological world harbours countless proteins. Our hair, skin, stomach, muscles, tears, sweat, diet - everything contains proteins and that too of varied kinds. A detailed knowledge about the arrangement, nature and working of these proteins would definitely be helpful in understanding biological systems.

This ingenious technique allows us to see the desired molecule on a huge computer and further enables us to see its various configurations in static as well as dynamic states just by the click of a mouse. This further helps in predicting the binding sites of the molecule and thus gives an idea about its interaction with other molecules.

This is particularly helpful in drug designing when we are developing pharmaceuticals targeted against some specific molecules inside the body. Reaction mechanisms can be foreseen. Moreover, with the human genome decoded, there has arisen the scope for studying innumerable molecules that could find immense use in molecular biology, immunology or pharmacology.

Molecular modeling is thus basically a computer tool, which also requires a working knowledge of mathematics as molecular structuring on the computer involves handling geometrical figures and toying with them in various dimensions.

Indeed, techniques like this reflect not only the zenith of technology but also a greater understanding of a few pages of the book of life.

-Nivedita M Shori

That's YOU !!

If only you could hit upon that key to unlock the tremendous potential and talents hidden deep within you! How valuable that key must be, isn’t it? Oh, to discover what lies behind this appearance, what you are capable of achieving, what is the reason you are unable to get just that ‘extra’ which someone else whisked away!

Just by a fortuitous chance, that key happened to fall in your own pocket! Rejoice, for all the secrets of the coveted life you always wanted to live can be uncovered by you. Here’s how to use that key-

- Be your own master: More often than not, we are happy or sad because somebody said or did something good or bad. Our emotions should not be subservient to others’ will. If I want to be happy, I will! Smile big, smile with confidence. Right now. Always.

- Self-introspection: All of us need time to wonder, contemplate, speculate. Sit back and think what interests you the most. Give a serious thought to what suits you the best and where is it that you lag behind in perfection.

- Focus on strengths: We all have something in our personality that can safely take us through. That 'something' has to be discovered. We are the best judges of the wealth we possess. It is our own duty to foster our positive points in order to keep at pace with what life expects of us.

- Be thyself: It’s imperative that we cease to be blind followers. Mass mentality is conspicuous but not befitting to all. Have your own style of doing things and be confident enough to abide by it. Who knows, the leader of the next mass movement could be you. So, just get out of that aimless crowd.

- Update yourself: Be a regular taker of the changes that arise in the world. Plunge into all that there is. Don’t let the fear of experimentation or hesitation towards technology grip you. Dive right ahead into anything that can add value to life — economic, mental or personal.

- Don’t bury the inquisitiveness: A child is immensely curious. Over the years, his quest to know more gets ebbed. Never extenuate your inquisitiveness. If there’s something new, catch up with it. Don’t sit there waiting for things to come to you of their own accord.

- Self- acceptance: If you don’t love yourself, nobody else can love you. Figure this — you meet a friend who is continuously cribbing about something, say his car. He keeps considering each one of his car’s features abominable, one more than the other. When you depart, will you carry back a good impression of the car? Some is the case when one keeps dwelling on one’s negative features and keeps hating oneself for the same. Others catch your vibes and start hating you too.

So don't let anything hold you back. Go ahead. Put on that winsome smile and unlock the real “you”.

- Nivedita

Science Time

The Journey of Technology

The first seed of technology sprouted when the cave man invented the wheel. Had there been media in those times, searching the archives today would probably give us an idea that 'Man Invents Wheel' was as important a landmark as 'Man decodes Human Genome'.

Development of technology has been synonymous with the development of man. In whatever phase man has been, there has also been a corresponding state of technology. If the man of 5500 years ago invented the wheel, Bill Gates has given us Microsoft. In 1769, Nicholas Cugnot designed the first car with a steam-powered engine and by 1932, JRD Tata had established Tata Aviation Service in India. From the 'difference engine machine' of Charles Babbage, popularly known as the 'Father of Computer', in 1822, we now have approached the so-called Fourth Generation Computers. In fact, only with the help of computational science can we make sense of the plethora of data that the computers themselves have enabled us to collect.

We have simplified the cumbersome process of bill payments, banking and other financial dealings. Automated systems finish things within half of the earlier time. Book hunting in libraries is no longer tiring with the advent of electronic cataloguing. Kilos of paper have transformed to bytes and megabytes of diskette space.

The sentience of distance is no more, thanks to the technology of electronic postage. And with the advent of the Internet, there's no topic under the sun that remains out of the reach of man. With the help of search engines, we can find almost any word hidden somewhere in the huge information labyrinth.

To beat Graham Bell's invention of the telephone that mockery of distances, there came the mobile phones. Spirited brains are racking to usher the world's first lip-reading cellphone. All you have to do is move your lips silently and the technology will decipher the electrical signals being sent out around the muscles of your mouth .

Cybernetics in Biology has appeared with the name of Bioinformatics combining the tools of Mathematics, Computer Science and Biology. Medical technology has come up like a growing plant extending its branches near and far and coming out with the ingenious Gene therapy that encompasses a broad range of technologies that may eventually be applied not only to cancer but also to a diverse group of other genetic disorders. Laboratory wonders reflect the zenith of technology.

We have gone and explored the rest of the universe. In fact, George Stephen's train of 1825 is being dressed up for a journey to the Moon. Technology is definitely soaring. The higher we go, we realize there is scope for still high. For here, sky is not the limit!

NO TIME FOR ... STRESS !

It's all in your mind. If you want to forget it, you can! If you think you can't, you won't. That is the basis of stress.

Very often we think we can't afford to disregard a particular situation or issue. We insist on not changing our mind and on continuing to torture ourselves with the agony of it. Writer and author, Natalie Goldberg quoted the realistic words in O Magazine (Oct 2002), "Stress is an ignorant state. It believes that everything is an emergency. Nothing is that important."

When we refuse to digress from a heated subject, we succumb to stress. We allow tension to grip us. And before we know, it spreads its roots far and wide.

Certainly, some things are important. But nothing in the whole world could be more important than your own life! Even the worst troubles of men have been known to have passed. "Why should something as alien as stress claim my peace of mind?"

Those questions of "Should I", "Shouldn't I", "Will it", "Won't it", "What now", "What if"... just let them alone for a while! Of course, if they're important you'll come back to them again. But not right now! Let them linger on a bit. Give everything a chance. Nature has a wonderful capacity of sorting itself out to the last fibre, only if wise humans care not to interfere.

Even if you don't have answers to the troubling questions that had been boggling you, when you let things loosen up a bit, at least the mind becomes more capable of resolving complex matters in a more facile manner.

Did you know your stress isn't a part of you? First thing, it isn't yours ! So, it doesn't have to necessarily stay with you. You won't appear any less influential in its absence! Shut the door in its face and it might be so upset with you that it doesn't show up again.
What else could one want?

- Nivedita

Science time: Radiation talk

Electromagnetic pollution - a biohazard

Is the air really as calm as we see it or does it hold some invisible demon in its folds?

The environment in which we live and the pace with which we are advancing our technology ensures our constant interaction with electromagnetic radiation. Since it is inevitable to be out of its path, it would be beneficial to be aware of the biological effects of exposure to such radiation.

Physically, there are two types of eelectromagnetic radiation - Ionizing (X-rays, g-rays, neutrons, b-rays and a-rays) and Non-Ionizing (extremely low frequency, radiofrequency and microwaves). It is the latter type that we encounter in our daily lives.

Until about a century ago, the sole source of human exposure to electromagnetic radiation was atmospheric electricity and geomagnetism. Various human activities involving the use of electromagnetic fields have now led to widespread presence of fields of low frequency in the environment - the main sources being electricity distribution systems, household electrical appliances, radiofrequency heaters, television broadcasting waves, radars and portable radio-transmitters.

Now since the living body is electrochemical in nature, any force that alters the normal electrochemical phenomena occurring in humans will affect the physiology of the body. The effects depend on the age, sex and pre-existing stress conditions of the exposed individual, besides the srength and duration of the exposure.

Exposure from high voltage power lines can cause lymphoma and leukemia. Electrical workers, in addition, are also prone to pancreatic cancer too. The tumor promotion action is attributed to the alteration in the immune defence system as well as in the enzymatic functioning in the body.
Prolonged exposure to extremely low frequency fields can cause hormonal imbalances, due to which growth might be affected.

Secondary effects: Stress, inflammatory responses, heating of the tissues on the surface or deep within the body, production of new, unwanted proteins or change in protein quantity.
Effects of chronic or occupational exposure: Reduced metabolic heat production, lowered skin temperature, altered vasomotor thresholds and augmented sweating rates.

Keeping in mind the hazards of continuous exposure, certain safety standards have been prescribed in terms of the Specific Absorption Rate (SAR), restrictive limits being the human resonance frequency of 30-300 MegaHertz.

Some specialists think it is high time we shelled out large sums on making major changes in the designs, operation and use of electric systems. Efforts are on to investigate more vigorously the multidimensional aspects of electromagnetic pollutants and find ways to strike a balance between minimizing of radiation and technological progress. Devices like Trifield meters have been introduced to measure the levels in houses.

Nevertheless, as long as radiation cannot be out of our way, we have to be careful not to fall into the arms of its hazards by indiscriminate and ignorant use of technology.

- Nivedita M Shori

LOSS

As a little child when, I used to lose my pencil

Panic would overcome me,

with despair my heart would fill

I wouldn't rest till I found it and in case I did not

I couldn't concentrate on a thing,

unless I got it or (in the rare case) forgot!

I remember that feeling of emergency but I also remember

that the true emotion of loss,

the episode did never usher

Things go harmlessly, some never to be found again

For who knows if that pencil was

in the flowing stream or on rough terrain.

Harmless absence of little things

would've perhaps been my closest encounter

With the meaning of loss, until it was time for destiny to flounder!

When I had moved from school to university,

and from crayons to pens

When I had got myself a career and graduated from dolls to friends

Lightning struck and the clouds were overcast,

the truth of loss I was to find

My shelter and haven, the epitome of wonder, only one of a kind

A mother so great, a woman so gentle,

my friend so close - that's what she was

Away she was taken never to be returned to teach me what was loss!

Things are created in all their glory to be savoured to the last drop

But once they're gone, you've got to move on,

even if you want to, you can't stop.

Yes, the memory comes back to you, brings with it the tears of ache,

Yet if you would realize - it's a test by heaven,

to see how much you can take!

Everything teaches something and my loss taught me how to lose

For winners are they who take their losses

just the way they choose

I did lose a jacket two days ago but now I know what loss meant

Greater things had been taken from me,

several others will continue to be sent!

I won't despair, I won't panic,

the greatest lamenting brings no fruit

My loving Creator watches me, sends bountiful joys for me to loot

In the vast scheme of things, my own loss is but a miniscule

I appreciate His presence and

understand now there's no time to drool.

With a heavy heart I remember my loss, with a glad one I thank it

What it taught me is a comfort when it's hot,

in the cold my blanket.

Things will come and things will go, never be fluttered O soul

The journey must continue unabated, I must reach my goal!

Yes the journey must carry on, I must reach my goal!

- Nivedita

Science Time - From Laboratory to Office

BIO-INFORMATICS – Cybernetics in Biology

Powerful data management tools are now required more than ever to store, share, study and compare the burgeoning library of biological information. Bioinformatics combines the tools of mathematics, computer science and biology and serves as a platform for all aspects of the acquisition, processing, storage, distribution, analysis, interpretation and display of biological information.

Once primarily a word processor and graphics aid, the computer has evolved into an all-purpose scientific tool. It is essential for collecting and analyzing data, for reading and searching the scientific literature and for sharing and discussing the data with colleagues around the globe. Studying the processes of various biomolecular interactions is difficult and time consuming. Computation simplifies this through ingenious modalities like the chip-based ‘Surface Plasmon Resonance Technology’ which claims to reveal significant information about molecular dynamics.

People working in the field of bioinformatics in most cases have a training in either biology or computer sciences. As a consequence of the large amount of data produced in the field of molecular biology, most of the current bioinformatics projects deal with structural and functional aspects of genes and proteins. The major investigatory topics include sequence alignment, biological database design, geometric analysis of protein structure and macromolecular simulation.

First, the data produced by thousands of research teams all over the world is collected and organized in databases specialized for particular subjects. The basic idea is that these databases should enable the scientific user to get a quick idea about the current knowledge that has been gathered about a particular subject. In the next step, computational tools are needed to analyze the collected data in the most efficient manner.

Thus, we are trying to bring simplicity to the complexity that is being continuously discovered. Areas particularly beneficial to this field are pharmaceutical research wherein the display of the entire protein pattern facilitates better drug designing, analyses of sequences of DNA and proteins, listing of Single Nucleotide Polymorphism (SNPs) on all chromosomes, bacterial/viral classification, forensic investigations and analysis of complex inter-relationships in gene expression data. Moreover, features like data mining and navigation guidance provide ease of information access from among a variety of heterogenous databases.

However, many scientists complain that it is getting increasingly difficult to find useful data on the web that is becoming more like an ‘information labyrinth’ due to more and more information scattered over wide ranging resources. Software experts are on the lookout for computational tools that integrate the scattered information in new types of web resources.

With the help of search engines, we can find almost any word hidden somewhere in this data labyrinth. Moreover, technologies like ‘supercomputing’ and ‘quantum computers’ are also being contemplated as the ever-smaller computer chips approach a physical limit.

It is certain that bioinformatics will lead us from research laboratories to offices where we can actually explore and understand science. Scientific work is no longer a task of a handful of us but relies on the expertise of specialists from various fields to exploit the actual worth of research.

(Originally published on Oct 21, 2002)

- Nivedita M Shori

SOMEWHERE, SOMETHING OCCURRED...

Somewhere along the way
When life was pulling away
When I was busy being free
When the world seemed so full
When there was nothing to worry me

Somewhere along the road
That went up the way to my abode
When I tried to count the colours in the sun
When gathering flowers in my little basket
Was my heavenly idea of fun

Somewhere along the path
That led to the woods so dark
When I held my mother’s hand
And laughed the perils away
Amidst dangers I had the courage to stand

Somewhere along the years
That were spangled with smiles and tears
When I did not know what it takes
To face the wide world beyond
To hold on when the storm shakes

Somewhere along the way
Somewhere along the road, something occurred
Somewhere along the path
Somewhere along these years, I grew up!

-Nivedita M Shori

Science Time

The Ethics of Human Cloning

The first woman created by God was Eve, says the Bible, and the first woman created by cloning is … Eve again, say scientists! This news, true or not, confirms that science has thoroughly permeated into our routines. Mere speculations have turned to reality. Today, the aspects of human cloning, what human clones actually are, the misconceptions we hold about them and most importantly, its ethics are worth understanding. The debates for and against the technology emphasize that human cloning is something we cannot afford to miss notice of.

Human cloning can be used for both therapeutic and reproductive purposes. Therapeutic cloning is popularly called ‘Stem Cell Therapy’, whereby embryos are created with the purpose of mining out the stem cells. This medical breakthrough of the century will be a boon for a number of disorders and organ transplantation.

There are misconceptions regarding human cloning. People believe that it will become possible to produce hordes of Ladens or Hitlers or retrieve a beloved person who has long been dead. However, scientists wave off this suggestion as purely irrational. They say that cloning requires ‘live DNA’ and it is impossible to produce a clone of the deceased unless the corpse was preserved by some means and some living cells are still available and usable. Moreover, the clone is a unique person with unique talents, nature and intelligence and in some rare instances may not even physically resemble the original cent per cent, as researchers have observed that the genetic expression is influenced by environment and experiences.

The million dollar question is – ‘Is clone an offspring or a sibling?’ Such ambiguities as ‘father or brother?’, ‘mother or sister?’ will embed people in a sea of controversies regarding individuality – the primary characteristic of a human. Dr. Patrick Dixon, a leading expert of the ethics of human cloning says that people are obsessed with their own right to have a clone without any regard to the welfare of the child. Human cloning is ethically unnecessary and immoral and is described as tinkering with nature.

Does this mean we should lock up our cloning laboratories? Not so. The merits are too good to be ignored. Technologies like cloning have to be harnessed for good ends. And if we could balance both sides, we can reap rewards not imagined. It is going to be a boon for science and society.

The world of human cloning lies before us. Only, we should know the rules before stepping in.

(Originally published on Feb 10, 2003)
- Nivedita M Shori

TO LEARN OR TO EARN - That is the question !

The early years of life are the ones most often thought to be meant for studying and learning. After that it is considered to be time to apply all of that learning for earning!

However, I sometimes wonder: Isn't learning in itself a form of earning? The knowledge, experience and wisdom that one gathers through learning is something that has been permanently acquired and that will in fact, be one's asset forever.

Is cash flow the only form of earning that this world wishes to recognize? All that cash might be gone without a moment's notice if, God forbid, calamity strikes! And that is the time when the actual earning that was collected through learning will help one rise over and above the helplessness of time.

Never cease to learn even if it doesn't give you an opportunity to 'earn' in the material sense of the word. As the US philosopher George Santayana puts it: The wisest mind has something yet to learn!