Saturday, November 3, 2012

This is how it is done!

You know what is the best thing about science, the way it is done! The way scientist think is logical, the way they work is very practical.Remember its not a perfect world though, specially when it comes to academic publications in Science, you are not sure which  peer-review  model is the best?

Before we judge the peer-review process we step back and find out who needs the peer-review process and why?

Well scientists as you might know are these set of boring geeks who invent cool stuff! 
So generally scientists are on this quest to find answers to the most interesting and intriguing questions,they are passionate about. The fact of the matter is that, a particular scientist is not alone he has peers other scientist who seek answers to same or similar questions (will be evident towards the end of this post)

Say there is a scientist.He has a very interesting finding/an answer that he reached to after a lot of hypothesis testing and experimentation! But that amazing finding of his is not enough. It is necessary that his peers also agree with his findings, not only that they should agree with the experiments he did to get to his finding. So its necessary he describes his findings in a particular format called research paper which  not only states the finding but also mentions the ways, the means, the methods he used, basically everything he did to arrive to the new finding.So, this research paper also called as manuscript he submits to a journal which takes the responsibility of peer-reviewing. Now the whole process of peer review takes a month at-least. Trust me usually it takes a lot more time than a month (6 months - 1 year). And scientist to say the least are restless and desperate to get their work published ;)

Google Images: Science publications

The publication process described above is pre-publication peer-review since the work is first peer-reviewed  (considered appropriate for publication) and then actually published (made public)

There is an alternate model of peer-review which is followed by arXiv.

So what is arXiv?

As stated by arXiv website: (formerly is a highly-automated electronic archive and distribution server for research articles. Covered areas include physics, mathematicscomputer sciencenonlinear sciencesquantitative biology and statistics.

So basically arXiv allows post publication peer review. You get a platform to publish your work while the pre-publication peer-review goes on and takes its own sweet time. Your work is read by peers and criticized and commented on.The greatest advantage of this model and arXiv of-course is not only that your work is quickly out in the public domain but also you start getting immediate feedback. ITS OPEN ACCESS.

arXiv is if I am not wrong a general rule in the fields of Physics and Mathematics. Biology is relatively new to this model of post publication peer-review.

In biology, the way post publication peer-review goes ahead is, the scientist receives feedback to his paper mostly via blogs wherein other scientist,PhD students, possibly anyone expresses their view either in support or against his finding! In real-time scientist can engage with the other scientists and discuss their work, which is frankly speaking a huge plus not only to the scientist but to the field.

Personally though I was aware of the existence of arXiv for a longtime only recently I got a chance to experience the post publication peer-review at work via axXiv.

So back in April 2012 this year there was this paper published in Nature(pre-publication peer review) titled
Evidence of non-random mutation rates suggests an evolutionary risk management strategy

Link to the abstract here.

This paper challenged the belief that mutations that occur in an organism's genome are random and essential genes in the genome have lower mutation rates.Indicating some sort of risk management which prevents organisms from the deleterious effects of mutations in essential genes.

A paper with such general belief challenging claims obviously got a lot of coverage by popular science press where scientists discussed the paper in details.

In September this year 2012 a paper challenging the above mentioned findings was published in arXiv, titled
Horizontal gene transfer may explain variation in θs

In this paper the authors find that there is no significant difference in the rate of mutations across different genes and hence mutations are random and not non-random as the previous paper claims.

Now in an non-awesome world these papers would have been published, read and may be discussed among small groups in the respective labs from where both these papers come and end of story!

Thanks to Haldane's Sieve which believes in increasing the exposure to interesting papers, published a blog on both these papers and one thing led to another and now we have the the lead authors of both the papers discussing their science and we know what reasons Inigo has to believe mutations are non-random and why Rohan thinks otherwise! Eavesdropping on the comment section of the above mentioned blog tells us a lot more about this study from the authors themselves, which is supercool! Check it out and you would know what I am talking about!!!

A win win situation for science!

P.S: An update posted by Inigo and Nick on Haldane's Sieve (5th Nov).

Friday, June 15, 2012

My Marathon Story!

✔ Marathon

When I ran the TCS Open 10K marathon on 27th May 2012 it was a surprise to many who know me! In-fact it was a pleasant surprise for me too because for me it meant that I had been loyal to my routine and I practiced about 4-5km every evening for about 6 months!

It all began towards the end of January 2012 probably the effect of Mumbai Marathon that had just taken place! I think I got inspiration from my friends who had been part of the Mumbai marathon!

The practice session, well that time I did not know I was practicing for the marathon, began every evening at about 5.30pm. (I am not a morning person and more than that not motivated enough that I can manage both getting up in the morning and then going for a jog!)

I think the most important factor towards sticking to the routine is the GKVK campus. Its green and beautiful! I must say I was blessed with such a beautiful campus which definitely is more interesting then the treadmill in the gym! Best part is if you get bored with a route you can take alternate routes and still manage to cover upto ~8kms! GKVK campus(google maps)

While I ran/jogged every evening it was in the company of my friend and many walkers/joggers who came to GKVK campus for what it offers for a perfect run outdoors! 

And it was only serendipitously we came to know about the TCS marathon that was going to take place in Bangalore this May. We thought we should go ahead and experience a marathon! That was when we were really were worried whether or not we should register for a 5.7km or a 10km! 10km looked far fetched but advice from two of my very good friends

"Register for whatever you want to do "
"Don't think if you will be able to do it or not" 
"Its very easily possible. Dont worry about that part."

... and we registered for 10kms!

While the 5km daily routine continued so did stretch exercises and cross-training begin.There were a lot of things that were to be known and read about following links were a saver

How to train yourself?

What to eat?

Best for everything under the sun...
Practicing for marathon was not just about running but also a lot about appreciating the evening breeze and the perfect climate outdoors! On very few occasions when we did the morning just felt great...mornings are AWESOME too ..if only someone can drag me out of bed everyday!

27th May was fun but before that the timing chips and the number Bibs were perfect kick starts and  the Goodie bag made me smile all that day! With a early start on a Sunday morning we headed towards Kantirava Stadium the  starting point! The whole area in and around the stadium was energetic and fresh, dominated by young adults and with impressive representation from all other age-groups.

 The race began sharp at eight and in five minutes we took the road to AWESOMENESS. A sea of people making their way from the Heart of Bangalore. I must say the event was well organized with water to hydrate ourselves at regular intervals to helping us keep track of distance covered and good music to cheer! A very special mention and thanks to fellow Bangloreans who where cheering and motivating us to go ahead and just do it! The random high-fives,the smiles, the energy and the enthusiasm that morning are one of my most priced possessions that I brought back home!

Successfully completing 10km was just wonderful! It was a feeling I fall short of words to describe all I know I had achieved a goal and grabbed the Finisher medal and it felt FANTASTIC :D
Nothing else matters!

Friday, September 9, 2011

(I) It never happened to me before...

Pre-planned for a change...Expectations where high
Packing was quick and different 
Group was large and varied
One Man One Place made it EPIC!!!

Day 1 in Lab  (yeah Day1)
Its been 11 days I was not part of this WORLD and my 1st Day here... I don't know what to do literally my twitter updates ->
DO I belong here??? Everything seems so different...It's a new's a new place... 
It was the time when neither the REAL nor VIRTUAL world made any SENSE!!!
To my realization "I got Leh'd" 'I did' "I got Leh'd" That's what its called...Truly Leh'd!!!

Here I RELIVE those MOMENTS those Days again...

"An early morning wake up call on 5.8.2011 made sure I boarded my flight to Srinagar On Time!
A sleepy flight journey from Benguluru to Dilli took care that I wasn't bored at the height 45,000ft speed of 800mph and a temp of -45 Degree Celsius outside!Dilli to Srinagar flight was good mainly due to the scenic beauty outside and a Kashmiri co-passenger with whom had a nice talk about Kashmir-Srinagar and the SITUATION there!
On Srinagar airport I had the unexpected HEAT SHOCK ( I can bet even Bangalore and Mumbai were colder that day)On the airport two locals had come to receive me on behalf of Isha tours and one of them Muzarraf delivered a dialogue I won't forget Madam 
                   "Bambai ka fashion or Kashmir ka Mausam kab badale koi keh nahi sakta"
Muzaraff's houseboat is where I met the GROUP rest 34 of us! Yes! in total we were 40 of us on the trip to the 'Top of the World'"

Evening in Srinagar

"6.8.11 and the Road Trip on NH-1 began...
We knew we had to cover Zojila today and let me just introduce what Zojila is...

'Zoji La is 9 km (5.6 mi) from Sonamarg and provides a vital link between Ladakh and Kashmir. It runs at an elevation of approximately 3,528 metres (11,575 ft), and is the second highest pass after Fotu La on the Srinagar-Leh National Highway.'(Wikipedia)

 Zojila is the place where people with motion sickness had their worst times but then by the evening we were in Drass the Second coldest place in the World obviously not so cold when we went there!

Now that we were at Drass 'The Gateway to Ladakh'

"We knew we were under Enemy Surveillance
 We knew we are at the place where Kargil war was fought
 We could see Tiger Hill from where we took a halt
 We could see the Tololing range at the backdrop of the War memorial built in Kargil
 We could see the walls built by Indian Army in a single night to protect NH1 D from the Enemy
 But we couldn't see into the eyes of the BRAVE WAR soldiers (yes!we met them they are now once again posted at Kargil after the war in 1999)who spoke out of their hearts about the war times! "

And even when I write this I get emotional... I literally cried that evening...Life is difficult and weird and in war times more so difficult and weird!

But as NH 1 goes on so does Life :)"

"Night well spent at Kargil we left for Alchi on 7.8.11 conquering Fotu-la pass having a nice time at Lumayuru monastery and Moonland!

This day this patch of NH1 D got me high yes! I got High!

Best of NH 1 I would say...

The mountains-the inseparable river alongside the road-the valley-the colors-the blind turns-the rocks-the trees-the melted snow marks from the previous season...

Alchi  is gem of a place had the Best night here...

Pitch dark 'Shooting Stars' and 'Milky Way' what more can I ask for!

(At Alchi we met sporty bunch of guys who took NH1 on CYCLES yeah!!! That's so COOL Dude types! All we wanted to do that night was to know their story! I don't know if anybody else thought so but they where not the same guys whom I knew before... faces content and happy and minds filled with recently experienced AWESOMENESS of a different and EPIC kind!)"
L to R: Subhash-Aditya-Anni-Ravi-Akshay-Ashwin
 "Next morning the guys left ahead of us Cycling to Leh form Alchi and what the road had to offer cannot be described but only seen in the picture below I just LOVE such roads and now you would know why the mention why the words of praise and why hats off to BRO...

And finally on the EPIC road that it is we reached the other end of NH 1-> 'LEH'"

What happened next needs another post...
What we experienced on NH1was as we say just the Trailor
Awesomeness continued to achieve new levels and heights in the coming days...

Monday, July 25, 2011

What you say DOES matter...

Bandra station
1st Incidence: Time :       Sunday morning 7-7.30amLocation : Bandra station ticket line
 There is a believable but given the time and day unbelievably long queue for suburban (local) train ticket. I am one of those unfortunates standing in the line. Just one person ahead of me is a Cool guy(soon you will come to know why I refer to him as Mr.Cool) standing in the queue with his friend (I prefer not referring her as his girlfriend)Next what the girl asks is exactly what I was thinking about at that moment( which is pretty obvious given the above details) -
Girl: Why is it so crowded at this hour on a sunday?Cool guy: looks like all the people out here just want to get out on a Sunday morning and explore the suburban train network out there...waiting to get itself explored!Girl:laughsI : smile  2nd Incidence  Time :       Monday evening 7.45pm (today)Location : somewhere in Bandra A guy tweets about the insane traffic in Bandra@b50 Bombay AddictAvoid Bandra. Word's out that it holds the portal to leave this world which ends tonight at 8pm. Everyone's here.I: smile and it reminds me of the first incident and one thing common to bothHow it REALLY does matter what you say... When you are helpless there is nothing you or anyone else can such situations a little sense of humor does much more than just letting it go it brings that unexpected smile and gives you a stress relief :)

Wednesday, July 6, 2011

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 
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)
    Nascent Biologist 
    Meetings always re-energize me - they remind me why being a scientist is so much fun!

      Alec Ross 
    20 years ago today, Tim Berners-Lee published his proposal for the World Wide Web. The proposal