Sunday 13 March 2016

Ten ‘Personal’ Reasons why I am skeptical about Open Access (OA): Thoughts of an Individual Researcher



Ten ‘Personal’ Reasons why I am skeptical about Open Access (OA): Thoughts of an Individual Researcher

Although a great deal of hurdles are overcome with so many ‘models’ of Open Access (OA), I do have a lot of a concerns about it when it comes to Individual research in this collaborative world. Everyone would acknowledge that there are good and bad OA publishers- who have done fairly a great job and those who have largely failed. And this is true for subscription journals as well. I enumerate my personalized opinions on OA, one by one:
1.    Pay to Publish model: This would be my biggest concern as a PI, in future esp. when my Institution would not have OA journal subscription or support. As a PI in a resource limited laboratory, in any given country, I would not be to pay the hefty OA fee of $ 500-$ 2/3,000 and about. In order to make research accessible to ‘all’ why would I pay a commercial business, this is a huge amount. If I wish to contribute a single-authored review of importance, why (and most importantly, how?) would I cough up that huge amount of money? Being asked a few times over survey by new OA models started by research social networking websites, I would shy away for the sheer reason of involved expenses, outreach, limited subscription to these websites by  research area-leaders and so on.  Paying a lot more to sell one’s own work, give away the rights and not to mention a far more complicated system of submission to publication than ever before.
2.    OA vs Predation: Without even going into Jeffrey Beall’s perpetually growing list of subscription or predatory or OA listed journals, it is very much evident that many a times the border between all these three are missing- as experienced as an author. OA advertising as fastidiously as any other predatory counterpart. A great study enlisted next to a bogus one in an OA journal’s index. As long as it is OA, quality goes for a toss and we approve of it?
3.    OA is not blind: That is not all is fair, like any other subscription or orthodox journals, single-blind and open reviews, pre-publication or post-publication reviews can leave a bad taste as an ‘author’ like any other model. It has all the signatures of failures of peer review like any other publishing model. So, why the hype, at all?
4.    What OA makes and what it does: Article submitted, reviewed, OA fee paid; then still why the authors have to format references (the most bogus side of academic efforts which is worthless, least said in terms of efforts and time!), check the galley proof, sign and return this document and that. For that ‘fat money’ would not these be warranted? What is the OA publishers doing with that money- paying their staff (are there enough of them? If not then why not make submission to publishing process faster).
5.    Reviewers are Free, though: No matter when I review for subscription or OA journals, I ‘have to provide free service’ within stipulated time. No incentives for reviewing! This needs a sea change for scientific ‘policing’, serious and honest peer-review, getting rid of junky research papers. Why as a Reviewer I must care if it is an OA journal or not. But, the review days given by the journal office are strangulating, annoying, and unaccomodative most of the times. In addition, no printing charges borne by the journal, no distribution expenses, authors pay and reviewers are free- where all the money goes?
6.    OA models with “NO” rejection: From personal experience, I must say that a bunch of journals in their peer-review process lack a “reject” button altogether for the submitted articles! This is alarming, and the talk of the day for most academicians I meet. From Journals named “P” to “F” (on conditions of anonymity, and for people with learned guessing skills!) all suffer through this syndrome. Some articles are sometimes beyond repair from submission, but end up being “right there” with “a horrendously iterative process of peer review process in place” where the “Editor” is a mere onlooker of the fiasco/ farcical review process. Is OA all about obtaining a digital object identifier (DOI) for $ X? For any quality of research?
7.    OA diluted and contributed to predation?: Form Web-of Science, to DORA, to SCI, to Google Scholar indexing everything seems to say that everything is OA and difficult to perceive as to why everything OA is indexed here and there? Lost among so many of true and fake OA. Where it is being archived to with whom also diluting the intended target of OA? In the name of OA, how many Emails plague our mail boxes every day? Is predation surviving on the OA’s “name-shake”?
8.    OA must publish review comments/ process compulsory “open”: Unless this is done, the tax-payer does not get to see the evolving process of science, publication, peer-review; but only ponders on the final product. This would be another way to make the peer review process serious and responsible. In this regards, retractions-websites and “X”-facts website would not be necessary to enlighten the scientific community on lack of reproducibility.
9.    OA does not ensure robustness/ reproducibility in science: Like any other models, the flaws and pitfalls in the investigation/ study/ met analysis/ experiments/ fraud can exist. Albeit, instead of getting concealed in printed hard copies of journals in some obscure library to hiding behind an expensive pay-wall, they would be glaring in public sights. Does not ensure though the leakage of poor science and bad peer-review process.
10.  OA journals lack the Oomph of Traditional but Elite status: They are the new kids in the block, can make you publish a lot, quickly but then when it comes to matching the grant, funding and tenure- obtaining or career-changing publications in so called “elite” journals, they are no match. Simply put as that. Because still the academic hiring and HR systems run on “impact” and “indices”, those who judge and form committees are from “the-then systems”, and nothing would change overnight even if OA was intended to address it, and not just profiteering. Something is “twitted faster” (aka. Journal house themselves!) does not mean is “catchy, important, crowd-pulling, or sustainable”.
Also, I must wrap up by saying that we do NOT live in a perfect world and everything has pros and cons, but then are we “weighing in a lot”, in exchange of just ‘free access’ to articles!

Saturday 31 October 2015

Updates in Metabolomics Tools and Resources: 2014–2015

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platform (mass spectrometry [MS] or nuclear magnetic resonance spectroscopy [NMR]-based) used for data acquisition. Improved machinery in metabolomics generate increasingly complex data sets which create the need for more and better processing and analysis software and in-silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources – in the form of tools, software, and databases - is currently lacking. Thus, here we provide an overview of freely-available, open-source, tools, algorithms and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table.http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/abstract

Wednesday 28 January 2015

Metabolomics Society Webinar on Thursday 29 January 2015 (7:30 AM - 8:30 AM EST) by Dr. Oscar Yanes

Dear Metabolomics Community,
The Early-career Members Network (EMN), on behalf of the Metabolomics Society, is planning to establish a series of online webinars from January 2015 onwards.
We would like to formally invite you to our first session of our series coming to you live on Thursday 29 January 2015 (7:30 AM - 8:30 AM EST). Session 1 of the EMN webinar series will feature our expert speaker Dr. Oscar Yanes(http://www.yaneslab.com) who will provide a cutting edge 20 minute presentation regarding the complex and multidisciplinary nature of metabolomics. The experiences and research conducted in Dr. Yanes' laboratory will provide an invaluable insight into the challenges faced in modern metabolomics practice. In addition, there will be an opportunity to pose key questions to Dr. Yanes at the end of the session.
Please, register using the following link: 
https://attendee.gotowebinar.com/register/2409752719256762369
The first webinar is freely available for everyone courtesy of the Metabolomics Society and will be uploaded to the society's website. All subsequent sessions from our series will be available for members of the Metabolomics Society only, with the opportunity to revisit live recorded sessions at your own convenience.
We look forward to having you join us!
Sincerely,
The EMN

Friday 6 December 2013

A Date with Alan Dove: Writer (Science), Blogger, Podcaster, Eminent Science Philosopher !

UF had this chance today to have Alan Dove, PhD (for those who are unaware of Dr. Dove: http://alandove.com/content/)  with us for a tete-a-tete. Humility, simplicity, utter wisdom rflected from his frail but active and intelligible physical looks in the formals (not to mention- the baggage he had carried straight from airport to the McKnight Brain Institute to deliver  a talk to the UF Academia). Courtesy- Office of the Postdoctoral Affairs [http://postdoc.aa.ufl.edu/] and Assistant Provost and Director of the Office of Postdoctoral Affairs [Ms. Kim M. Kitagawa Pace] that I could capture this once-in-a-life-time opportunity to hear him LIVE !
[Thank you Alan for the Picture available from your Website!]


I was inspired from the circulating Email in the campus, so was prepared, did not get the snaks that was on offer (to keep me attentive), had a bottle of water and  yeah, a small notebook for notes- and grabbed one of the front line seats to have a  better view of him, his words (no mics there!) and his visions. I never heard about his before, but now feel that he is someone one can look up to- and get messages from his wisdom or follow him to do what he has achieved ! But, being a "average Postdoc" with limited dreams, I believe in doing non-conventional things- and then thinking, why not choose to write, advertise, analyze science and scientists than only doing science in a 4 walled office/ laboratory. Thus, the drive to attend his lecture.

In short, the talk was 'damn practical', full of humor, interesting stories and yes,  a BIG Take home message. And, let me first put the strong take home message first: In his words "The world needs more scientists- is a big BULL SHIT".

One of the first PDF screen shots were showing- the 'well-known' "academic pathways" from "birth, to school, to K2, to undergraduate, to PhD, to Postdoc, and Tenure Track, to Asst. Prof. to Professor, to DEATH! And then just about the time, I felt like yawning to this so-many-times-heard simily of academic perills, suddenly he leaves you with his amazing creations and outright humour ! He  says "and recently to this academic pathway, a SHUNT pathway has been hypoethesized, and discovered, and there exists this ALTERNATIVE career, but that too eventually leads to death, but then by-passes the Tenure, Asst. Prof (= the academic fights!)". OMG ! Reality bi(y)tes ! And, at that time, Alternative Careers in Industry was treated somewhat like "bullshit", but then it is norms  and with a steady increase with !20-30's trained doctorates embarking in the Industry business doing research !


Slide: 2: In 1973, after finishing a PhD most (~50-60%) were assured of Tenure Track Positions, and this stats have fallen to as low as 10% only in 2006 (the data based on NSF/ NIH studies), with another 10 % into "out of labor force" (the worse part!), while the %age of Postdocs have risen significantly since them from an odd ~10% to about 40-50% at our times. Alarms- in my head, in many grads in the lecture hall, but truth rings louder, is not it ? He was spot on and hence, convincing with this statistics. In this slide, he reaffirms the fact that in ~early 2000s when we had the NIH funding "doubling", had NO EFFECT on  increase/ rise in TT positions. Hmmm, a fact reflecting saturation in "that are being trained" and "deserving positions for the trained".


The out-of-labor force (the worse situation to face after unsuccessful stints as grad students and myraid of Postdocs!) can be beneficial to the concerned individual in realizing "parenthood" is not it ? This was convincing to some extent. 

In the Alternative Career options I was more convinced about moves to professional Schools as Lawyer (Intellectual property rights- Patent attorneys) or for an MBA for a more demanding industry needs. But then he emphasized that, in "industry as you get promotions, you get less and less into research" is not that obvious ?

He draws attention to the fact that "there are people who are immersed (excelling) in science, but are poor in communication" and he himself, was the opposite prototype and honed his skills to be in there, where he is right now. He, in a nutshell, described, how he started his life in science media after a PhD, followed by a paid internship at New York Office of Nature Biotechnology for the news sections and then moved on.  He did say about his initial NY city shared apartment deals and so on.

The image and dimensions of media has changed from "old to new" where Podcasts, peer review, "Science Fans" (people who are NOT trained in science, but are really really into it: his words!), public relations (journals  and universities have them equally). I would have never know what "science fans" meant until he explained this to us, and that a virology related story being followed by a "long distance trucker" as a science fan.

He then underscores some of his own recent achievements (rather highlights) in  terms of what he has written recently- in Science "Microbiomics: the Germ Theory of Everything", "one of his written piece from New York Academy of Science (Academy eBriefings)", "his writings in "This Week in Virology" and by this he shows us how the "advertiser supported models are more viable in longer runs than the subscriber supported models". An anecdotal example that he cites  is Nature Methods (supported by the industrial partners for maintenance and publishing). His examples, showed, how the modern world of science journalism amalgamates different aspects of an event into one "web-news" (by merging of pictures, write-ups, Podcasts, links, social networking, iTunes, RSS feeds onto one platform) leading to wider and more active audience participation than we had ever before.

Then he quickly says, the "print world of science journalism has moved to the WEB".

Coming to the self-raised question on "how much money' does he make, he explained in terms of "adjusted profit", much smartly, than anyone anticipated in the audience, to come out successful, without answering it directly and still answering it to the smart ones !

He concludes, that he did not have a "formal journalistic training, but now has 15 years of vast experience", but the science journalism now has various forms such as - news and web editors, audio/video producers, PR folks, research editor, staff writer and so on. So, opportunities are ample, but one has to find the suitable one.

Finally, he says, "writing is not art, but a craft" and should be honed gradually with passing time- not to be worried too much about writing skills, abilities and forms in the beginning. He said he loves to work on "1-3 assignments" at a time, but can sometimes painstakingly be 5-7 at a particular point of  time". And to write well, his 'gem of a advice'" "be a loner" (keeps repeating). Also that "self-discipline is required for free-lancing' and one "has to set hours to be able to do writing as a profession in a successful way".

I tried to ask him a question, unsure, that probably, I did not put it in right context/ wordings- "I am tempted to write all the time- but how to determine if what I am writing/ about to write qualifies for a good scientific review, a commentary, a letter to editor (all technical writings), a  blog post, or simply a comment to a bigger scientific article, a popular article or stays forever on my desktop" ? So, I followed it up with the clue- "if the themes rules or the structure is more important than the outcome". His terse reply was "it would be  a blog, as long as none is willign to pay you"- to a muffled laughter from the audience, but I wished he answered me more (I understood the 10s of curious raised up hands for other questions!). But, even that would have been my take-home-message as long as I was trying fit myself in his shoes/ similar profession. But, seems I am not yet ready. Earning by writing ? NAH. I am far from it as of now. But, yes, I do love to write on various aspects of "science, scientists, inventions, discoveries, updates" and so on.

To conclude, I did learn BIG TIME. I did learn about the alternative paths a lot. Especially, when he drew similarity between the "bacterial growth [same media, small population of bacteria grow to a log and then flat curve followed by death" with PIs/ Positions", and then he says, as money is limited, and so are positions, so does not matter how much PhDs and Postdocs we have trained, all are not going to be successful. The competition is tough in the present day and many many are BOUND to MISS OUT from positions and opportunities.   I immediately correlated this to my PhD supervisors statement that "publishing quality is also suffering from this cut-throat competition to find positions". It was a memorable experience with Alan, one that I can cherish for a long time, a true "philosopher" (esp. when he shares a  poignant family pic of his, showing his wife and daughter- that the checks he had been paid were all for his "adjusted profit" and how much is enough for a life?") in his own world, and been able to affect and touch the lives of a diverse number of scientists and a "science fan" like me.

There is a funny note as we were about one in the audience- Sofia (that is how she introduced herself at the meeting) and had noted some questions in a snacks plate ! To this end, Alan cunningly quipped "so you do in fact have  a plateful of questions" ! In fact, the questions were very practical and good ones that were eventually answered.

Owing to hectic Postdoc schedules, I was bound to miss on the following dinner meeting (on offer from UF) or lunch meeting (the next day) with him ! Beyond the meeting, I had to run to my laboratory back, to see my protoplasts are ready to be subjected to mass-spectrometry analyses or not ! But, i swear, I would again be in his audience sooner and would not miss that chance again for a one-to-one exchange of ideas in order to learn more on my shunt-pathway of life.

Note: Sorry Alan, if I have misquoted you anywhere, or have lingual/ spell mistakes. But, it is all in good spirits, that I have tried to summarize what I could gather during the talk, and re-write them the next day, based on the small notes I had taken and some unforgettable memories and mental-images".


Thursday 26 January 2012

The Genome Lost It's Organelle: Lynn Margulis (1938–2011): In Fond Memories of 1 Of My Idols !

Well...Not a New News, but Enough Dreadful ! Remorseful, as always...these great losses to science are !

Cut2: Back in the Summer of 69...well, in 2003, during 1sy Year's of Master's in Botany, while going through the "Biochemistry by Stryer" or one of those classical books, I came across this name for the first time in life.

"Lynn Margulis"


Why ? Simple...1st person on this earth to concieve the greatest, "our organelles like mitchondria and plastids were free living prokaryotes out-side eukaryotic cells, and during course of evolution have been integrated to us, symbiotically"...and what was famouly known as "Margulis" hypothesis/ Endosymbiotic Thoery ! Awesome.


ENDOSYMBIOTIC THEORY


I felt, shattered, when I read the hypothesis ! Why ? Because, I felt, why this did not strike to any one, until she did it, not all those Biology greats, not to my Professor, or for that matter me !

And thats what most commoners like us, miss out and specials make it even more special, their ways !

And then with her sad demise, was again shattered [this time to more profound effective loss!].

Always used to ponder, to go for the Sigma Awards that is named after her, and in a life time may be see/ meet/ Email her, but not to be, missed out !





And since that day, I was one of her zillion admirers in the sciencitific world.

Why ?

To Quote her: "“If an organelle originated as a free-living cell, it is possible that naturally occurring counterparts still can be found among extant organisms".


Please find more: http://www.nature.com/nature/journal/v480/n7378/full/480458a.html [Nature's Own Dedication]...
And for the Naive's in Science: http://en.wikipedia.org/wiki/Lynn_Margulis [Guess, no BlackOut this time !]

And yes, also here: Schaechter, M. (2012). "Lynn Margulis (1938-2011)". Science 335 (6066): 302.

HAT'S OFF



For those, who like it with a bit of spice, once she said she does it: “tell bullshit from ... real authentic experience”, and imagine a Professor in Geosciences, untrained in molecular sciences, giving this once-unacceptable "so-called" "radical" hypothesis.


Ok ...then.....dear fellow-scientists,

Have to go off to hypothesize, something more "sense-making",  well and  a very simple hypothesis.................."Will me proteins denature if I donot store them in glycerol tonight ! Or, go back and start working tomorrow ?"..Awesome ! Lolz!


Catch ya, soon after I get my answers to the "hypothesis".

Ur Science-O-Nomist !












Raise a Toast in 3-Dimension for "Ankylography": New Kid on The Block !

Hello...

Well, for those who are caught unaware of Prof. John Miao, a physicist at the University of California, Los
Angeles, must take a note of "ankylography". Not a revolution in image science, but a method, to "pull out a rabbit in 3D, from a 2D Image of a Hat".

Yes, those of you get it right ! A technique that, according to its creators, could reveal the
structure of scientifically important subjects such as complex proteins that can be glimpsed only once before they are destroyed by the high-powered lasers used to image them.

Raines et al.  have proposed ‘ankylography’ as a three-dimensional tomographic modality with a single monochromatic beam.

For those, who are "dealing in depths", please follow here:

Non-uniqueness and instability of ‘ankylography’: http://www.nature.com/nature/journal/v480/n7375/full/nature10635.html

and here:


Fundamental limits of ‘ankylography’ due to dimensional deficiency: http://www.nature.com/nature/journal/v480/n7375/full/nature10634.html

Raines et al propose a method, which they call ‘ankylography’, for three-dimensional structure determination using single-shot diffractive imaging (SSDI).

and here as well ! http://arxiv.org/ftp/arxiv/papers/1112/1112.4459.pdf


"Ankylography is definitely an emergent advantage for X-ray technology called diffract and
destroy, which would use X-ray lasers.......take images of objects using a dose of radiation high enough to destroy them, forming an image from the X-rays scattered in the few dozen femto-seconds (10−15 seconds)
before the object explodes !!! The ideal application would be imaging biological samples such as proteins, viruses, cells or tissue that are very sensitive to radiation. Ankylography would allow researchers to extrapolate 3D structures."


 Am no Crystallography-Geek, but still can tell, it would help science, than those who think, otherwise. I am UP for anything, that grows ! Always, positive and to embrace newer technologies included into the mainstream science, without any double thoughts, as tools help grow our ideas with fresh Angles !

Well, and I would not mind loosing the structure of my "pullulanase" burning into pieces, after it's 3D has been exposed ! Huh !


Ok...That's it for now !

Got to stop a few running tools to rest and pack-up for the day !

Your science-feeder, gotcha feed himself !

Science-O-Nomist
















Tuesday 10 January 2012

Indian science in need of overhaul...BUT, BUT, BUT !!!

Hello,
Back to Bog you !
Came across this story [most of you must have been!]:http://www.nature.com/news/indian-science-in-need-of-overhaul-1.9750
Indian Science in Need of Overhaul !
Question is: How ?
Points to Ponder:
1. Funding of whole R & D of the country is 1/3rd of what and USA University's Good Biological Sciences Laboratory gets.
2. Do our PM/ Politicians/ Establishment have enough time, resource thought for any Improvisations in the Scheme [with Annaji, 3G, Kolaveri, Scams lurking around !].
3. When will the agencies STOP FUNDING for projects like "Exploration of effect of Silicon on Rice yield" or "Biodiversity explorations in Similipal Forests"!
4. Until when our InBred Indian Post Docs will be keeping paid: INR 18-25,000 PM ?
5. When will our Publications not be evaluated by Impact Factor but by real IMPACT ?
6. When the Bosses will grow up, not promote wrong deeds, produce TOILET papers ?
7. What does CSIR/DBT/DST/INSA/ISC do to bring the TRAINED INDIAN back home ?
8. When will the B. Tech [Biotechnology] NOT BE OFFERED with a IT Sector JOB or an M.Sc. [Biology] looks for a BANKING PO/CA/RAILWAYS Job ?
9. When will the PARENTS/ PEERS STOP thinking that POST-DOC is NOT STUDYING and also is not a PERMANENT JOB ?
10. When will the NORMS / GUIDELINES be established for a COMMON CRITERIA for PH.D. ENTRANCE/ TIME FRAME FOR IT'S COMPLETION ?
11. When will the PI/ STUDENTS NOT WASTE CONTIGENCY in FLYING TICKETS/ LAVISH STAYS-DINNERS/ HARD DISKS-PENDRIVES ?
12. When will the CENTRALIZED UNIFIED RESEARCH INSTITUTIONS come into a single umbrella for collborative research ?
13. When will CONTACTS/ BUDDIES/ COUSINS of SCIENTISTS will STOP getting the coveted JOBS/ OFFERS from their own relatives ?
14. Above all how to discard BIAS IN SELECTION [REGIONALISM, Q-FACTOR etc.].
Any ANSWERS ? NO- RIGHT !
So we stop BOTHERING !
Time to grab BREAKFAST and be prepared for a Day's bench Work !
Catch ya soon,
Science-O-Nomist