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).

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