There has been substantial recent lamentation concerning the nature of scientific publishing, and the perceived requirement that experimental results “tell a story” in order to be published in the peer-reviewed literature. For example, The Bean Mom recently stated the following:

The data that’s confusing, that doesn’t fit a paper’s hypothesis, usually isn’t published. No suprise–why would any author include data that contradicts or confuses the story she/he is trying to tell? Negative results usually also aren’t published. That transgeneic mouse with no phenotype? Will probably languish unknown. But if the experiements were rigorous and carefully controlled, then even puzzling and negative data is valid data. And when that data is not communicated, it can be to the detriment of the whole scientific community, as researchers waste time and money heading down blind ends . . .

Read the rest of this entry »

Science Blogging San Diego

November 22, 2008

Are you a scientist in San Diego who blogs or (duh) reads blogs?

Time to tribe up my friends.

Why let all those nutballs in the North Carolina Research Triangle area have all the fun? Are we really lamer than the Minny-soooooootans?

email bikemonk at the google mail or drop a comment. let’s plan some stuff…on blog and IRL.

Recent discussion of the way papers should be presented and comments on the way papers were written in the good old days when Uncle Sol was a wee scientist motivated me to repost something I put up on the old blog July 11, 2007.

First, I’ll tip the hat to Shelley at Retrospectacle for starting a “tour of the vaults” with the classic LSD in elephants study. Today, I’m reaching way back for “A study of trial and error reactions in mammals” by G. V. Hamilton, Journal of Animal Behavior, 1911 Jan-Feb 1(1):33-66. This study is worth reading because it provides an often hilarious insight into the conduct of science at the turn of the past century but also because this study is a root (perhaps the taproot) of a relatively current subfield on spatial working memory and spatial search.

Read the rest of this entry »

Friend of the DoucheMonkey blog Sol Rivlin had the following to say in response to other friend of the blog Isis the Scientist’s query to her minions regarding how to handle unexpected or unplanned experimental outcomes when writing them up for publication:

As to the unexpected results. My suggestion for you is to be truthful about your intial intent and expectations and to tell the story as it happened, including the unexpected. In reality, that is exactly what happens to many of us, but too frequently, we are tempted to appear smarter than we really are, pretending that the unexpected outcome was actually very expected and that we knew exactly what will happened long before we did the experiments. Most scientists tend to lie in this way, we know they lie because we have done it ourselves and yet, we continue doing it.

That ranks among the absolute stupidest gibbering dumbfuck advice concerning manuscript preparation I have ever seen or heard.

Read the rest of this entry »

How To Read A Retraction II

November 21, 2008

Here’s an interesting retraction just published in the Journal of Neuroscience:

Retraction for Ma et al., Glucagon-Like Peptide 1 Stimulates Hypothalamic Proopiomelanocortin Neurons
Retraction: At the request of the authors, the following manuscript has been retracted: “Glucagon-Like Peptide 1 Stimulates Hypothalamic Proopiomelanocortin Neurons” by Xiaosong Ma, Jens Bruning, and Frances M. Ashcroft, which appeared on pages 7125-7129 of the July 4, 2007 issue.

This is it, the entire text of the retraction. There is absolutely no mention of why the paper is being retracted. People who have relied on the retracted manuscript to develop their own research conceptually and/or methodologically have been given no guidance whatsoever on what aspects of the manuscript are considered unreliable, and/or why.
Is this ethical behavior? Do the authors have an obligation to the scientific community to come clean with everything they know about the whats and whys of their retraction?
Please discuss.

The Marijuana Potency Data

November 21, 2008

You may have heard a relatively sustained drumbeat in the mainstream press reports in the past few years regarding the content of current illicit cannabis products. It has been promulgated in a PR campaign which attempts to convince baby boomers that today’s marijuana is more dangerous than that of their own misbegotten youth because it is “stronger”. In other words, higher in the concentration of the major psychoactive constituent, Δ9-THC. The subtext, I assume, is to alleviate the boomer parents of today’s teens of any guilt related to communicating seemingly hypocritical anti-dope messages. If the pot today is more dangerous, then it is not hypocritical that Daddy and Mommy used to smoke in the seventies, right?
I have an objection to one of the fundamental concepts here* which explains my laziness in never bothering to track down the data on which the assertion rests. Happily, I stumbled across the relevant source.

Read the rest of this entry »

With the announcement that Tom Daschle has been selected as the Obama administration’s Secretary of Health and Human Services speculation about the down market appointments has accelerated. For this audience, of course, everyone is nattering on about the next Director of the NIH. My nattering sources are moving in the direction of Elizabeth Nabel, M.D. current Director of NHLBI, but that’s just vague speculation.
One of my correspondents reminded me of a non-HHS appointment that is VERY important for NIDA funded scientists and indeed everyone interested in drug abuse issues.
Who will be the next Drug Czar?

Read the rest of this entry »