Nobel winner declares boycott of top science journals

Randy Schekman says his lab will no longer send papers to Nature, Cell and Science as they distort scientific process

Ian Sample, science correspondent he Guardian, Monday 9 December 2013 14.42 EST

Excerpt: “I have published in the big brands, including papers that won me a Nobel prize. But no longer,” he writes. “Just as Wall Street needs to break the hold of bonus culture, so science must break the tyranny of the luxury journals.”Schekman is the editor of eLife, an online journal set up by the Wellcome Trust. Articles submitted to the journal – a competitor to Nature, Cell and Science – are discussed by reviewers who are working scientists and accepted if all agree. The papers are free for anyone to read.

“My comment: Open access is a great way to ensure peer reviewed materials are available to a wider audience. Comments on articles help to ensure discussion of new information. Unfortunately, my comments on an eLife article were first accepted, then moderated, then removed. There is no other record of the following exchange with regard to How keeping active pays off in the olfactory system.

Excerpt: “Importantly, this model provides an elegant balance between plasticity and adaptation; although the potential to detect a wide range of odours, afforded by the exceptional number of genes for receptors, remains intact, the sensory organ becomes ‘tuned’ and sensitized to odorants relevant to its habitat.”

I asked: “Is what’s being elucidated the bottom-up epigenetic effects on stochastic gene expression via chromatin remodeling, which is controlled by the top-down epigenetic effects of pheromones on reproduction in species from microbes to man?”

Lomvardas replied: “The article elucidates how the environment can broadly influence gene expression through an epigenetic effect chromatin – the way DNA is package and organized. This allows the environment to influence sensory function, to tune the olfactory sense to better suit the surrounding environment, because these environmentally regulated chromatin changes are coupled to cell longevity. This results in a change in the distribution of cells in the tissue that have made particular stochastic choices, where the stochastic choice is which olfactory receptor to express, without affecting the mechanism of stochastic gene expression.”

Lomvardas reworded what I wrote about epigenetic effects from the bottom up, and ignored what I wrote about their top-down control.

My response to him was blocked:

“Thank you. In my model, the bottom-up epigenetic effects on stochastic gene expression are largely dependent on adaptively evolved glucose uptake and the top-down epigenetic effects on stochastic gene expression come from the metabolism of nutrient chemicals to species specific pheromones. The honeybee model organism best exemplifies this epigenetic tweaking of immense gene networks and how the epigenetic effects of food odors and pheromones on the glucose-dependent secretion of mammalian gonadotropin releasing hormone that also links genes to behavior and back. The additional information about the histone core and fine-tuning of the required plasticity appear to attest to the control of chromatin remodeling by the microRNA / messenger RNA balance. It would interest me to learn if others agree with that proposal given the extreme technicalities of the issues addressed by Santoro and Dulac.”

per editor a.collings@elifesciences.org on 1/8/13

Dear James,

Thanks for your comments on ‘How keeping active pays off in the olfactory system’. Comments are checked by a moderator (and/or an eLife editor) before they appear. Comments should be constructive, relevant to the article, conform to our terms and conditions, and include any pertinent competing interests.

We posted your first comment along with a response from the author but we have decided against posting your latest comment (below) because the discussion deviates away from the article in question. We also think it would be have been appropriate to declare your involvement with https://pheromones.com/.

Best wishes,

Andy

I added this comment with a link to my figshare model on 2/21/13

I have since modeled nutrient-dependent pheromone-controlled adaptive evolution and uploaded the text and diagram, which are available here: https://dx.doi.org/10.6084/m9.figshare.155672 I was advised I should have previously declared ownership of the domain Pheromones.com and my commercial involvement in marketing products based on animal models of common molecular mechanisms in species from microbes to man.

I attempted to add this comment on 7/8/13

I own the domain Pheromones.com and recently published Kohl, J.V. (2013) Nutrient-dependent/pheromone-controlled adaptive evolution: a model. Socioaffective Neuroscience & Psychology, 3: 20553. This article details the bottom-up epigenetic effects on stochastic gene expression via chromatin remodeling, which is controlled by the top-down epigenetic effects of pheromones on reproduction in species from microbes to man. Across-species examples of nutrient-dependent pheromone-controlled adaptive evolution include a human population that arose in what is now central China during the past ~30,000 years. With other examples from model organisms, the human population helps to refute mutations theory, especially any theory about the role of ‘random’ mutations, because adaptive evolution is so obviously experience-dependent and controlled by nutrients from the bottom-up and controlled by the metabolism of nutrients to species-specific pheromones from the top-down.
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The moderator/editor at eLife prevented information dissemination at the level of pre-publication comments that might have facilitated more rapid scientific progress. Instead, we have since seen publication in “Nature Neuroscience” of The missense of smell: functional variability in the human odorant receptor repertoire. However, there is still no mention of how the de novo creation of olfactory receptor genes is controlled by the epigenetic effects of food odors associated with nutrient uptake and the metabolism of nutrients to species-specific pheromones that control reproduction in species from microbes to man.

Thus, while I agree that “…science must break the tyranny of the luxury journals” I am not sure that will happen at eLife. Although “Nature” blocks my comments on their articles, “Science” does not. That makes eLife more like “Nature,” a journal that Schekman accuses of distorting scientific progress.