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Dec
30

Journal editors add more balance than needed – provides marketing windfall

Just when you think the year is going to end without having to get drawn into some additional discussion on publishing.. well it happens..

I get an email today that the article a (very nice) journalist, Vivien Marx had written for Nature Methods “Pouring over liquid handling” was now published.

Lets get this straight at the outset, yes I am very honored to have been asked to interview. Yes I know that rarely does an interview actually lead to an article I agree with. Yes I know that the interviewee has basically no control other than saying yay or nay to their specific pieces of text, in the best circumstances. Yes being taken out of context, being used as the contrarian viewpoint etc often happens…got it, fine, OK!

Backstory: I was contacted by Vivien a few months ago, then I met her for 30-40 min during a brief trip to San Diego. She asked me good questions about the PLOSONE dispensing paper. I was brutally honest, independent in my views that were not of course not influenced by others / companies etc. I had a good feeling about what was to be written, someone was to take on the cause and try to get different perspectives. Maybe some experts would chime in on dispensing and present some fresh ideas. Of course I live in a fantasy world.

Vivien’s article is good (she is a pro) but I get the impression it morphed massively from what we discussed when I was interviewed. The article was no longer about dispensing. It was basically an opportunity for vendors to discuss their wares if I am honest or blunt. Eppendorf* got to plug their “additive free tips”, their “LoRetention tip” and even discussed manual pipetting techniques in detail. TTP Labtech got to plug their positive displacement instrument. Labcyte got to plug their acoustic method, but then again this was the method described in the paper. The tip-based dispensing technology in the paper was not one from Eppendorf or TTP Labtech. Even TTP Labtech plugged an Artel device for multichannel verification which I think is totally superfluous to the article. In addition HP got to plug a digital dispensing technology they collaborate with Tecan on. Yet oddly it was also mentioned that the same system cannot be used to dispense aqueous solutions (is that a typo). Anyway this “inkjet type” technology also was not in the PLOSONE paper and still they get significant column inches. My overall concern here is that in the interest of “balance” everyone and their cat had a pedestal to tout their wares. This was a marketing bonanza. There was minimal discussion of why comparisons had not been performed and why the manufacturers were not ensuring we understood their respective pros and cons.

Several scientists commented on the paper itself..e.g. “the paper did not offer detail on the AstraZeneca tip-based dispensing used” – well we cited exactly what was in the patents from AZ  – – tip-based dispensing (Genesis, Tecan Ltd, Weymouth, United Kingdom).  But it appears Tecan did not get to address the data from the AZ patents.

A number of well known “factors” are cited as examples for explaining the difference between dispensing techniques. e.g. precipitation, inter-batch variation, the number of times tips are changed. Perhaps we could have added the phase of the moon too for good measure? Surely one would expect AZ to have been aware of these. But then again really how many papers do you see where any scientist describes this level of detail on how they dispensed a liquid.

I was kind of surprised with one of the interviewees from BMS who questions that “we provided little detail on the computational methods used for both sets of dispensing data”. Well we actually do describe in the paper the methods used and the data from both dispensing methods were treated identically. BMS may not have noticed dramatic differences between  dispensing methods but clearly AZ have and probably other companies too. Actually we cited in the PLOSONE paper examples where BMS and AZ scientists had seen dramatic differences in dispensing methods which kind of contradicts the statements made in the Nature Methods article.

The one voice that really I heard loud and clear was George Rodrigues..suggesting the key was to find the “root cause”, “the physical cause” of the dispensing variability.

I was astounded that Eppendorf were given the last quote and basically say that acoustic systems will not oust pipette systems from the market. Honestly I just will refer the reader to the wiki site of incorrect predictions on that one. I am not going to make any predictions myself because I really have no interest in the matter other than to say that one day, a better  method (without tip-like issues) for dispensing will displace pipettes as we know them now.

As a P.S. Three papers are referenced but only 2 are mentioned ..the 3rd appears to have been cut, which makes me think the editors at Nature Methods may have wielded a few big cuts.

After reading the article, I then went back to one of my Xmas presents, “Bicycle Diaries” by David Byrne, p97 which in turn quotes the Jared Diamond book “Collapse”. To (badly) summarize; people develop cultural affinities for many things we take for granted like food, travel etc which become ingrained and people persist in maintaining these habits to the point of driving themselves  or a whole civilization to extinction. I see a parallel here. As scientists that dispense liquids by pipette, have we too become set in our ways such that a technique is ingrained, we persist in using a method which we know to have failings.  We take it for granted and is it slowly causing a sort of destruction by sending us in the opposite direction to where the data should send us. While we do not want to believe that something so simple could be the root cause for many of our failures, could it be staring us in the face.

I am kind of a little sad that the article in Nature Methods really did not delve more deeply into dispensing, but then perhaps it reaffirmed that perhaps also so few people are thinking about the big picture. They just want to sell their dispensing device or their tips, or they want to do their job, which could be screening millions of compounds regardless of the best method for it (or even not considering if the data will be correct/ meaningful). I will say it one more time. IMHO there needs to be an unbiased, large scale comparison of different dispensing methods and we need to really understand what is happening at the physical level too. Otherwise we are wasting too much time and money on pretty meaningless data generation (that includes all NIH funded studies that use pipettes  – low throughput or high throughput dispensing). Civilization may depend on how me move liquids in the future.

*Eppendorf also happened to be providing an application note in this month’s Nature Methods, any coincidence?

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