Re: [AMBER] accuracy of FEW free energy calculation

From: Robert Molt <rwmolt07.gmail.com>
Date: Sun, 21 Jun 2015 12:43:10 -0400

1.) The better idea would be

a.) Make a real incentive to review articles well. People don't take
reviewing seriously; they just accept papers quickly (because it's fast)
or reject (because it's fast or the reviewer feels threatened), not
examine a paper carefully. We need to have either a requirement or
monetary incentive or something. The reviewing system *is *broken; there
is very, very little incentive to review papers other than to squash a
competitor.

b.) Remove the single blind system; make all reviews public or double
blind (it makes NO sense that the reviewers see your name but you cannot
see theirs). Right now, if you disagree with a previous author, they
reject your paper outright and there are no repercussions (can't prove
it was him/her).

I say this on the back of a paper being rejected with CCSD(T)/CBS
calculated transition state barriers giving a qualitatively different
result than prior B3LYP/6-31G* studies, but the reviewer said "Nope,
problem's already solved with B3LYP/6-31G*, nothing new here, reject."

2.)

"If someone gets away with falsifying a study, it's because that study
wasn't worth repeating and disproving. So who cares? If someone
falsifies something important, others will try to reproduce it and the
study will be eventually disproven (see Wakefield et al., 1998)"

The "who cares" part is that those people get funding, others do not.
Resources are wasted on terrible studies. The "who cares" is that
misinformation gets spread and becomes fact. My favorite example is the
"cult of 1 kcal/mol." Curiously, every method, quantum to force field,
always claims to be accurate to 1 kcal/mol. This certainly has been
going on since the 90s, perhaps further back. They never claim to be
some number other than 1 kcal/mol...never 2, never 3 kcal/mol...always
1. It's a marvelous coincidence that all methods just so happen to be
accurate to this one particular number out of all the possible numbers.

Or you can take it as a sign of a problem in our fields.

On 6/21/15 12:30 PM, Jason Swails wrote:
> On Sat, Jun 20, 2015 at 6:54 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Jiri,
>>
>> I agree these days a lot of people are scared to say things controversial
>> - it's a shame and in my opinion science is suffering because of it. A lot
>> of the issue with the quality of papers though I believe comes because
>> these days the peer review process is more or less at breaking point, if
>> not already broken.
>
> ‚ÄčI'd love to hear a better idea.
>
> In the big picture, science evolves via natural selection. If someone gets
> away with falsifying a study, it's because that study wasn't worth
> repeating and disproving. So who cares? If someone falsifies something
> important, others will try to reproduce it and the study will be eventually
> disproven (see Wakefield et al., 1998). Sure, the peer review process
> isn't perfect. But it's better than any alternative I can think of and
> science has a built-in correction mechanism that has proven that it works
> for centuries. I think the current rate of scientific progress is rather
> exciting (and that it proceeds despite all its problems is rather
> encouraging).
>

-- 
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
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Received on Sun Jun 21 2015 - 10:00:03 PDT
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