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Archive for the ‘Scientific progress’ Category


A discussion today with a student asking about the use of the Royal “we” in a report about his work. I agree, this is wrong. My suggestions were the first person singular and the passive. The passive gets a bad press in places, but it does work; the repetition of “we” or “I” grates, the latter particularly so because it can convey a strong sense of ego. Though as I pointed out, this depends how it is used. It was common in single author papers for the author to use “I”. The practice has disappeared due to multiauthorship and the urge to make scientific observations look objective. We finished by joking about the feudalism implicit in the use of ‘my laboratory’, as if this was some sort of sentient being, and then I wondered out loud whether one might not, in a multiauthor paper state:

“In experiment X (Fig. X), blogs demonstrated that….” And then later “In experiment Y (fig. Y) Doe indicated….”

Tonight a tweet from @UtopianCynic

UtopianCynic tweet

reminded me of my earlier conversation. Indeed, why bother with all the rubbish associated with authorship position? Why not have a list of authors and in the paper report who did what and who thought what?

It would then be clear (i) who pulled together the original hypothesis; (ii) who did the experiments; (iii) who thought up the interpretations of the data.

I think I might try this out.

This also solves the long-standing problem of blaming whoever is at the bottom of the pile when a paper is found to have manipulated data. Someone will be explicitly on watch and someone else will have done a particular measurement under that person’s watch.

It will be obvious who should walk the plank, and reaching for lawyers will only result in keel hauling, because it will be all written down and signed off.

 

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A recent article on bioarchiv “Amending published articles: time to rethink retractions and corrections?” puts forwards ideas on how we might change the way we deal with retractions and corrections. (more…)

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This is a question raised at the end of the excellent article by @Amy_Harmon regarding Open Access and preprints is can biomedical scientists evaluate each other without journals?

The short answer is a resounding yes.  Physical scientists and mathematicians have been posting much of their research as preprints on arXiv for a few decades, with no prejudice to their ability to evaluate the quality of work or of individuals.

The counter argument raised by many in biomedical sciences, from scientists to some journal editors can be boiled down quite simply: We are special and cannot possibly do this.

Various arguments are put forward, from competition (=fear of scooping) to intellectual property. These arguments are heard in many biomedical/biology departments, sometimes leading to quite heated discussions. It is also interesting to note that the defenders of the status quo are not necessarily the older members of the community.

There is a simple answer. Yes you are special, but not in the good sense of the word. (more…)

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This post assembles various comments I have posted and other thoughts on sci-hub and access to the scientific literature. It finishes with some ideas about what we should consider keeping and some of my better experiences, as a consumer and producer of the scientific literature.

Some time between clay tablet and the PDF

Once upon a time manuscripts were hand written, double spaced (fountain pen as ever outperforming all other tools), graphs transferred to tracing paper using a rotoring pen and Letraset (also alive and well) used for symbols. (more…)

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During a quick scan this morning of the “recent” comments on Pubpeer, an activity that I pursue regularly, as part of my reading, there seemed to be a lot more author responses.  So I counted.

70 articles featured with comments.

10 of these had an author response.

This is progress. I have no data, but my impression is that a year ago author comments were far rarer, maybe 1% or thereabouts. Now we are at 14%. Let’s hope this is not an anomaly, but a trend, and maybe in a few years papers without author responses will be in the minority.

Regardless of arguments about anonymity, etc., post publication peer review is growing, which is a sign of health in the scientific enterprise.

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Much has been written about the peer review process and its flaws. Richard Smith, a former editor of the British Medical Journal has stated that since peer-review doesn’t work, we shouldn’t do it

I have recently come across another example of the flaws in peer review. I reviewed a manuscript last year and identified what I believed to be technical problems and suggested at least major revision. The other two reviewers agreed; the three of us had homed in independently on the same technical issues.

Move forward a year and the paper is published in another (equally “prestigious”) journal, no changes.

So I will now amend my New Year resolution (still holding firm) from 2014 and 2015.

In addition to only reviewing for open access journals, I will from now on only review for journals where the review is open and published or where I am free to publish the review. That, at least, will avoid the ethical tension between participating in anonymous peer-review and then wanting to publish the critique when nothing has changed in the paper.

Why Groundhog day? This is not the first time I have had this experience.

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Of nanoparticles, cells and polyanions

It is the end of semester 2 so it’s marking season. Since we double mark (a good thing), the final year research projects are marked by both supervisor and an assessor, a member of staff who is not involved in the project. One of the projects I marked was Gemma Carolan’s on “How do SmartFlares RNA detection probes reach the cytosol? Available are the PDF of report, and posts here and here.

I had a sense of déjà vu while reading the project – the clear endosomal location of the SmartFlares, regardless of the DNA sequences brought me back to the days when antisense was the technology of the future for medicine.

While evaluating new technology it is useful to go back and look at other high flying technology. The reality is that it takes decades before we know whether the promise (and hype) were justified; this is true for any hot topic from stem cells to nanoparticles and graphene.

Antisense effects can be mediated by RNAse H, an enzyme that specifically cleaves RNA-DNA duplexes and which protects our cells from RNA viruses. There are other mechanisms, e.g., interference with splicing or translation, but the RNAse-H mediated transcript degradation should be central to many antisense effects. There were many papers reporting specific effects (evidenced by differences between sense, antisense and scrambled oligonucleotides sequences). These certainly contributed to success of individuals and of institutions, e.g., in UK Research Assessment Exercise and grant awards.
(more…)

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