Why I love doing what I do?

If you follow me on twitter or you have spoken to me or just happen to be around you will know
How F***ed up I am currently with my experiments...I am in the phase..yeah PHASE where things just go wrong or don't work for some unknown reasons and all you have is a horrible day/week/month -PHASE in the lab!!!

The irony is...still I want to write or I am in the mood to write yes! about the

"Pleasures in doing Science(biology)"

photos clicked by vidhi patel

I have been blessed by some truly AWESOME ( here even awesome is an understatement) moments for which I LIVE and do SCIENCE.

I may never in my Life win a Noble, I won't! But surely more than once I Win through some moments that make me happy amidst the situations when things are difficult! 

These moments may neither be big events nor be to be bragged about success stories...they are simple and yet they put a huge SMILE on otherwise tensed face!

The moment when-

• the tube inside the electroporator doesn't arc...

• after n rounds of cloning et al the plate shows the clones/mutants the sight of that off-white small tiny-tiny colony! :)

• the gel picture has bands of perfect size (so perfect that the reviewers might suspect it to be Photoshopped)

• positive and negative controls are picture perfect! Specially the negative control!!!

• at one go I hit the bulls eye... pick up the right number of tubes and weigh the right quantity!

• I start with a new project and it looks all interesting and the euphoria of looking at new things is like the one when you are gifted with a new toy!

• I read an amazing piece of literature...listen/read to a logical and well reasoned argument!

• when I talk to a biggie in the field! You always want to meet and talk to the successful well established peers in your field! 

• when after an Eureka moment things START MAKING SENSE

• I am satisfied (though never) and happy as to what I am doing!(mind you very few people fall into this category)

and THE moment for which all of us...every researcher works hard,contemplates,procrastinates 

INVENTION/DISCOVERY/FINDING (peer reviewed :P)

Such moments just "work" they are part of enjoying your job and its just not me it seems it happens to best of us... like my friend working in Computational Biology says 'The kind of joy and satisfaction he gets once he is through a difficult to code Code is surreal'

While we pursue the Questions we ask we also 

Cherish the Moments that lead to it!

And This is part of sharing 'those' moments -

(via twitter)

AndyKraemer Nascent Biologist 

Meetings always re-energize me - they remind me why being a scientist is so much fun! #evol11

 AlecJRoss Alec Ross 

20 years ago today, Tim Berners-Lee published his proposal for the World Wide Web. The proposal http://www.w3.org/Proposal.html

  
 @edyong209 @RogerHighfield
It's about time the public realised science is mainly done by 23 yr olds with hangovers.

  
khedkarsupriya supriya khedkar
1of d reasons I luv Lif sci: it has many best kept secrets waitin 2 be fathomed,each findin addin new dimension 2 ur understanding of life..

   
edyong209 Ed Yong RT ed by khedkarsupriya
MUHAHAHA! I have full individual access to ScienceDirect. (I have no idea how; possibly in response to an email I sent months ago)

   
NeilWithers Neil Withers by khedkarsupriya

Very handy! Bookmarked RT @JonSatriani: My new favourite site: http://copypastecharacter.com/.

khedkarsupriya supriya khedkar
Almost forgot in the middle of the hectic day that was - CSIR AWARD LETTER IS "FINALLY" HERE!!!! :)

khedkarsupriya supriya khedkar
when I say I LIKE discussing science-biology and fundamental questions in biology...I actually LOVE it!!!

What are you working on?

A question that comes to me *too* often these days after the initial greetings and what are you upto these days inquiries!

I truly appreciate the curiosity and I like it when someone is interested in knowing what kind of work do I do?

BUT the point is the people asking this very *interesting* questions are in our common usage terms *layman*

Just to give an example,

If I am working in the depths of Mariana trench, they are at the shore/the beach! And now, how will one at the shore in *unscientific (read sane/layman)* terms understand and if by a very gross mistake understand; appreciate the need, fun and challenge in doing something AWESOME called *RESEARCH* which in the general perception is a boring, insane activity restricted to the nerdy, whimsical minority!

I mean when I was working for my dissertation,

I at least had *circuits* handy- to which if I attach genetic its okay! Cause out of *genetic circuits* people definitely have heard of circuits (I don’t expect them to know what it is, the meaning part, except for those with science background) but it’s okay I mean! SAVER

And then comes *protein* (in my mind- sorry no substitute available here, might give milk protein caesin as an example but no SUBSTITUTE) and then this *protein* (still the person figuring out what I just said) is never produced in constant amount (Why? I don’t allow them to ask or this question never comes to the person’s mind, don’t know! BUT THANK GOD) so, we have designed a circuit which will produce the protein in constant amounts! Tadaa!!!

And there is SILENCE Golden SILENCE until one of us comes up with a CHANGE of Topic!!!

BTW now I work on expression of stress, cell division and repair related genes in E.coli, which has been evolved for 2000 generations in the lab under Oligophilic low nutrient conditions!

I better not talk about this one!!! STRESS (in cell?) REPAIR (what to repair, in a cell?) and EVOLUTION!!! (BTW almost everyone knows or has heard of Darwin J )

(I wish to appear SANE to the layman’s world, I am no different! I am your kin, your species! )

I think every RESEARCHER/someone doing SCIENCE must have gone through such a dilemma where you are so eager to talk about your work; but even after trying hard, harder and still Hard(btw if you do this you are boring) you are not satisfied with your own explanation and convinced that the other person *layman* has not understood it! I go through this definitely!

Nonetheless, howsoever boring I might sound while I talk about my work to you (which is in the *true* sense, is not boring, you fail to appreciate it due to: still figuring out what?)

I LOVE DOING IT

IT’S AWESOME

NOTHING ELSE MATTERS!!!

            

P.S: All special characters are intended!

On a lighter note...

Location: Pune

Date: 13/05/10

Its 2:16 on clock...it's hot! And adding to it are the mosquitoes sucking a few millilitres of my blood...the blood suckers!

Why don't they jus shoe off...I am bugged, truly!

I wish my blood was poisonous...no no not to me but to these mosquitoes...I wish...aargh got another bite...Losers!

A quick thought chain...People with sickle cell anaemia don't get malaria, are they unbitten by the mosquitoes too? (By at least the mosquitoes carrying malarial parasite)

Reframing it, have mosquitoes developed a strategy...putting it in the right words "evolved" a stratergy wherein atleast for the time being the malarial parasite bearing mosquitoes can avoid sickle celled individuals in whom the parasites future just doesn’t exist??? But then in that case the host mosquitoes are loosing on their hosts (humans)...and that too for a hitchhiker!!!

Can be, may be ...its jus a speculation...can happen too...parasites are drivers of evolution in many scenarios...so you never know…if the logical reasoning goes fine for once…we can at least expect it to happen! Pretty unsure…

For now let us assume that the above mentioned phenomenon of avoiding sickle celled anaemic occurs…it will have to be tested!

And the way of testing the above, makes a hilarious sound! (Unfortunately this comes from a person with average or rather below average sense of humour…so be prepared if it turns out to be lame)

Nonetheless this is how it goes…

Advertisement for volunteers for the “Mosquito Bite Project”

Volunteers required for- being bitten by female anopheles mosquitoes carrying, if your unlucky falciparum and if your super unlucky vivax and if you are super duper unlucky both"

Don't Panic - you will also be bitten by mosquitoes with absence of malarial parasite! It's not all that bad you see.

You can just be a lucky volunteer too...How? Be a negative control volunteer

Or a second chance to be super unlucky - Be a positive control volunteer

All you have to do is stand in a chamber and you will be attacked with n number of mosquitoes for time m (m needs to be calc and for determining n it is necessary to consult a statistician cause the experimenter just doesn't want to “harass” the volunteers with too many mosquitoes; neither wants to repeat the experiment just because the mosquitoes were too less)

* Volunteers with sickle cell anaemia a plus point for you; you will only get bitten by mosquito and no malaria or might not even get bitten in the first place (hoping for the later to happen)! So hurry up! Offer not valid for non-sickle cell anemics for this season. If the above works out... you might be considered for season 2! So keep checking the site for updates.

So hurry up, be the first one to send your consent.

Send in your consent with the answer to the following question:

Why you want to be a part of this "Mosquito bite" project?

a) You care for the Mosquitoes

b) You want to contribute to the cutting edge research on Malaria

c) You have nothing more challenging and exciting to do

d) You have also experienced Mosquito bite n number of times in your life and now want to end it once and for all! And this research according to you is a step in that direction!

2.44 On clock...me still being attacked by mosquitoes!

Leucoderma-HW

There was this study done on a population having Leucoderma in Gujarat and it was found that the alleles involved were in Hardy-Weinberg equilibrium...! The results were surprising because we expect selection to act against the individuals with Leucoderma...because of the so called "mate choices" . But this wasn't the case here... again a study followed to determine the reason for absence of selection! It was found that the symptoms of leucoderma i.e the white patches on the skin occurred or were visible only after the subjects got married... they were totally absent when the mate choices were made...thus selection did not occur against the trait.
(My second encounter with the Hardy-Weinberg law...was with this example and since then whenever i see a person with Leucoderma Hardy-Weinberg law marquee makes an appearance!)
These days more often... I not only encounter quite a few people with Lecuoderma but also these people are quite young! (this is in mumbai) Making my mind wonder of the allele stats...I think the current scenario points towards, selection pressure acting on these alleles cause the symptoms are evident before the mate choice...so selection pressure must definately act, ideally should act and in the future should lead to gradual dilution of this allele from the population.
It's only for someone to study the population of those affected with leucoderma and highlight the allele stats!
Looking from point of view of a science student: Day to day, current, classical example of Hardy-Weinberg law and selection pressure at work.

Zooming in: tube light zone!!!

The hundreds of miniature insects on your tube light…or on TV or computer screen in a dark room!!! Always wondered why the hell they are attracted towards light!!! I mean during the day they don’t seem to be moving towards the sun…(real stupid thought!!!)….neither is there some food that they feed on, at the tube light…!

A major question that always aroused…discussed with friends, but we all never got an answer to it!!!

Supposedly many people have tried answering it and the most convincing way out to these widely observed phenomenon is that…usually if you see the natural sources of light they are practically at infinity…e.g.-sun…so all the rays that are coming from the sun are parallel to each other. Now for tracking a linear path the simple logic is to make constant angle with the rays of light…! Now back on earth we have various other artificial sources of light tube lights, bulbs etc. and the rays that are coming out of such sources are given out in all directions and are basically not parallel to each other!!! Now for an insect in order to follow a linear path as it always does…it is constantly trying to maintain a constant angle with the rays…and since the rays are not parallel and radiating from a single point…the angle keeps on changing…due to which they follow a spiral path and finally land up at the source of light!!! The reason our tube lights are full of insects!!!

BUT, since generations of these insects end up at the source of light and seem to get nothing out of it…why don’t they learn to avoid such situations??? Another obvious question…and the reason for this behavior lies in the fact that…it’s a place for aggregation of so many insects…so it might be acting as mating grounds…wherein you can look out and choose for your mates and mate!!!(a very important part of life cycle)

BUT, as I mentioned in one of previous blogs about such areas being feeding grounds of lizards (strategic locations)…there is a risk involved in landing up in such areas from an insects point of view!!!

Again, usually if observed there is just a single lizard at such location …showing territorial dominance and thus benefiting the insects..owing to the fact that the probability of getting eaten by a lizard decreases tremendously when hundreds and thousands of your type are present…to be eaten up! Also..the fact that since there is a single lizard and it has a limited appetite…and the number of insects are always in large excess… such that a lizard is satisfied…much before not more then half of them are eaten up (may be? coz half to me seems a large extrapolation…but still in spite of it the insects seem to be benefited!!!)

Everyday phenomenon…simple observation…logical analysis…complex interactions!

Bio-diversity...

today(23rd Oct 2008) was a knowledgeable day...it changed the way i looked at many things!!!

The topic was Biodiversity and the venue was NCL (auditorium) Pune.
The day was as pleasant as it could be...the air refreshing and the ambiance enthusiastic...greeted with excellent photographic lobby of birds,snails and flowers...they really couldn't have appeared better than these! The auditorium was filled with students, teachers, research fellows and eminent scientists belonging to varied fields...it was the very first encounter with diversity for the day!!!

“you look at that river gently flowing by. You notice the leaves rustling with the wind. You hear the birds’ you hear the tree frogs. In the distance you hear a cow. You feel the grass. The mud gives a little bit on the river bank. It is quiet; it’s peaceful. And all of a sudden, it’s a gear shift inside you. And it’s like taking a deep breath and going….. Oh’ yeah, I forgot about this” (An inconvenient Truth)

The first talk was by Dr. H.N.Gour...he gave an full-fledged introduction to bio-diversity...also impressed the Puneites...with introductory Marathi lines! A very important point that he put across was of GMO's and issues related to them, also truly quoted biodiversity as GLOBAL WEALTH.

The next to come was the best of all I feel...Dr. Hema Sane, she grabbed the attention of every pair of eyes...right from the moment her name was announced and she was on the podium...a real simple down to earth lady she is...in her late 60's may be! A botanist, had focused her lecture on "Wild is Beautiful" part of plant diversity!
Doing justice to the title...she actually showed the true beauty of the wild, excellent pictorial representations and her precise perfect descriptions...completely changed the way i looked at botany as a subject and plants in specific! During her talk she conveyed a very important message...Conserve plants and other life forms not for humanly benefits...but for them..The plants themselves... because you are no one to decide their fate but you need to respect their rights!!!

Aditi Pant took us to Antarctica, she really did!!! With million dollar pics of the Antarctic biodiversity...she explained the food webs there and gave a precept of microbial, fungal, algal, plant, animal and aquatic biodiversity at the Antarctic!
Her good sense of humour was evident during the talk and she convincingly showed "humans are the real problematic creatures on this planet"

Dr.M.V.Deshpande enlightened about the fungal-insect interactions which i never even thought of...the various aspects and the questions posed by him were actually challenging. The journey from pathogenecity to non-lethal parasitism was truly commendable!

Next in line was the topic most hyped these days in microbiology "the unculturables" basically it was “Molecular Approaches for Exploring Uncultured Bacterial Diversity in Extreme Environment” It was an excellent comparison of various techniques used in molecular methods and the boon they are in studying bacterial diversity without culturing!!!(Wow!)

Have you ever thought cockroaches were beautiful...or rather can ever look beautiful? And they show parental care? And insects were the most dominant life forms? This was exactly what Dr. Hemant Ghate shed light on...! He really changed the way we all looked at those creepy creatures!

This was the most impressive man; btw most impressive was his CV...A radiologist by profession and also an ornithologist and photographer!!! Dr.Satish Pande
He had got all his statistics right, right from avian food preferences to their nesting periods to their clutch size to their cultural significance from conservation angle(phew!)
Best were his recommendations for conservation of avian diversity!

Dr. Sawarkar had a collection of excellent quotes...he gave an overall picture of Indian biodiversity and statistics of the endangered one’s and also a word of caution about the wrongly put forward exaggerated figures of the actually non existing wildlife!

All in all the workshop was truly an eye opener..it made quite a few things evident...

1. mimicking is a very successful strategy employed by diverse life forms!
2. presence of mind is the most important facet of life everyone should adorn(all speakers had excellent presence of mind and related their talks to fellow speakers quite well)
   

Something to think on...
“Darwin gave us the first glimpse of the origin of species. We know now what was unknown to all the preceding caravan of generations: that men are only fellow voyagers with other creatures in the odyssey of evolution. The new knowledge should have given us, by this time, a kinship with other fellow creatures; a wish to live and let live; a sense of wonder over the magnitude and duration of the biotic enterprise” -----Aldo Leopold

An intresting evolutionary finding...

Completely forgot, the existence of the following pile of words...
i stumbled upon this while going through my desktop folder...
reviving an older creation...

Evolving Evolution…


Evolution the magic word
To me it first sounded absurd…

Apes, Neanderthal and Sapiens
By heart I learned…
Cranial capacity, physiology and backbone
This was the evolution I was made to know!!

Thank god Darwin did not face this
Otherwise he would not have proposed the natural selection thesis!!!

Evolution I know is a brainy business
But works according to one’s interest!

Darwin and Lamarck with their theories start
And you think both are equally right on their part!!!
(though darwin most of the times and the later rarely)

Many questions keep hovering around
Archea, bacteria, virus, eukaryotic cell
Tell me which one has evolved well???

Understanding, learning, imbibing it
Evolution for me is evolving bit by bit…

Evolution can sometimes be confusing…
One might seem to understand what he’s actually not understanding!!!
To understand the point I mention
Try answering this question

Is perfection evolution’s intention???
OR
Is evolution unintentional perfection???

the smarter one's!!!

just a few old observations...

mosquitoes..! they are a real menace in India...cause of malaria and its dangerous types!
so in every household you generally employ one or the other ways of taking care of them...
at my place we have got nets on the sliding windows...which prevent them from entering in...!
so in the evenings when usually they take a tour at your place,you put on the netted sliding...

now one fine evening at around 8pm...I was at the window and noticed one lizard on the net...
it was,i thought lazing around there on the outer side.
frankly speaking i being really scared of lizards and wanting to zero on the chances of it entering the
house...i just gave a jerk on the net...and it fell off!!! ooh...how relieved i was!
this sequence of events took place for few more days that followed...
sometimes it was me or my bro otherwise on the remaining days...!
one day i was at the window for quite sometime then...completely bugged of doing this core everyday to find the lizard again there after sometime...was really curious...

y? the hell was the lizard always there only in the evenings???
...was she trying to terrorise me???
she wanted a breakthrough into the house??? if it was so y? was she doing it only in the evenings???
did she give it a shot, of trying to enter the house from other ways???

the answers to all this were just there...
OK...this was the time in the late Aug..when you actually experience attack of variety of insects at
your tube lights!!!
so here was this lizard strategically located at a checkpoint from which every damn insect attracted towards light would go...and she would easily feast upon them...those innocent notorious creatures!!!
wow!!! Wat a strategy...you feast...by just lazing around at the right place at the right time!

moreover...y? the hell she would bother..when creatures like me were trying to shoe her off...
i mean you don't leave your feast for such silly reasons...naah..never!
the lizard had a smarter way of taking care of us...!
when she would feel our presence by the jerk we applied...the lizard was intelligent enough and would go and hide herself in between the steel non-netted region of the slide....from where she was not visible to us from the inside...in short she pretended that she was off her way home after our act...making us fell happy and relieved!!!

would come back after a while and continue with her feast!!!

from that day i never even tried to shoe her off from there...i really did not mind her being there coz she was even benefiting me from her act...the number of insects that hovered over my tube light and were quite troublesome,reduced because of the lizard's presence!!!
had it not being for this observations...i would have missed a real smart and intelligent strategy which was employed right at my window!!!

http://scienceblogs.com/loom/2008/06/02/a_new_step_in_evolution.php

summary of work carried out by richard lenski... just chk out his web page...its really awesome and the work carried out by him is mind boggling..!!!

http://myxo.css.msu.edu/index.html

chk out AVIDA...!

my first paper ppt...

had my life's first paper presentation...!!!
have given many ppt before this...but this one was really special one... was waiting for this since my B.Sc years...and really wanted this to happen in my M.Sc....and here it was on 30th Aug 2008...

i have already posted the abstract here...and if anybody interested in reading the paper its freely available online(just type the title on Google...!!!)
OK this paper was on evolution....and it is "the" thing for me.... so the excitement of presenting it was, i seriously cant explain at what levels...!!!
actually looking at the paper...i was cautioned to take a simpler one...this one being interdisciplinary and this being my very first paper ppt!
but was quite adamant on this particular paper...after all it was on evolution and RNA!!!(ribozyme)

btw all the things required for the seminar i.e the abstract and the actual ppt... as usual did it at the 11th hr....mind well not at the 11.59th....
for a change wasn't tensed at all about the whole thing...was the first one in the whole batch of the first yr M.Sc students to present...
And let me tell you the whole thing went really well....i mean right from the intro....till the concluding line...it was just too good...at least i was satisfied...after the ppt!!!
Still the most dreaded part of the seminar was left...the viva questions and let me tell you there were real intelligent questions asked by both the teachers in the panel and also by my seniors!!! real good questions...and i was most delighted after answering all of them....convincingly!!!
i mean i presented for 20mins and was there at least for another 10-15mins answering the audience...it was fun!!!

hmm...was really happy about the whole thing...it went so well...really wasn't expecting it to be this way...really cool...a wonderful experience....a lifetime experience i would say!!!
now eagerly waiting for my next paper ppt...in the next sem...that time there will be many expectations too....!

abstract to my seminar ppt...

Darwinian Evolution on a Chip

Brian M. Paegal, Gerald F. Joyce

PLoS Biol 6(4):e85. doi:10.1371/journal.pbio.0060085-

Abstract

Darwinian evolution in nature has led to development of many sophisticated enzymes. Recapitulation of Darwinian evolution in vitro has emerged as chemical tool for optimizing functional ribozymes in the lab. A ribozyme that catalyzes template-directed ligation of oligonucleotide substrate was made to evolve continuously under the selective pressure of reducing substrate concentration. A micro-chip based automated serial dilution circuit was developed which carried out serial 10-fold dilution after exponential growth phase, this was repeated for 500 log-growth iterations. Evolution of the ribozyme was observed during the 70h evolution process on the chip. The ribozymes adapted and achieved progressively faster growth rates over time. The final evolved ribozyme contained 11 mutations which conferred 90-fold improvement in substrate utilization, coinciding with the applied selective pressure. The constellation of mutations that aroused during this evolution process and the corresponding phenotypic changes that were responsible for the adaptation were analyzed. The system thus, aids in accelerating evolution and also allows the experimenter to observe and manipulate adaptation.

References-

1. Joyce GF (2004) Directed evolution of nucleic acid enzymes. Ann. Rev. Biochem.73:791-836

2. Bartel D. P., Szostak J. W. (1993) Isolation of new ribozymes from a large pool of random sequences, Science 261: 1411-1418

3. Cadwell R. C., Joyce G. F. (1992) Randomization of genes by PCR mutagenesis. PCR Methods Applications 2: 28-33

http://www.allaboutthejourney.org/theory-of-evolution.htm

a good read...(continue for the next pages...)

gaia hypothesis

http://en.wikipedia.org/wiki/Gaia_hypothesis

sounds weird....
guess...got the fact-reason relationship all wrong..very difficult to digest!