Comments on: The Nature paper that required three corrections

By: Edy

Edy — Wed, 28 Nov 2012 22:08:42 +0000

This paper never made sense in the first place; it makes if even less sense now.

By: DefendSmallScience!

DefendSmallScience! — Wed, 21 Nov 2012 01:03:55 +0000

Very interesting story and comments. I suspect AMW’s remarks above are very close to approaching the truth of what happened.

On another note, does anyone know what happened to the “abnormal science” blog? It was deleted. http://abnormalscienceblog.wordpress.com

It had extensive postings about the Aggarwal debacle at MD Anderson. I wonder if outside forces prevailed in shutting it down? By my count, only RW and science-fraud.org remain as publicly-accessble watchdogs on scientific miscreancy.

By: Motard

Motard — Tue, 20 Nov 2012 19:43:59 +0000

I have to agree with these replies.

Even for well-validated monoclonal antibodies, with known specificities, the likelihood of off-target binding and interaction can be nuts. The *point* of Western blot is to get around those specificity issues.

ELISA can most certainly be useful, and it would be to many investigators’ benefit to consider using it instead – but as a quantitative supplement. Western blot will answer questions of antibody specificity that ELISA (and other similar sorbent assays) simply cannot.

In the end, even the most well-characterized ELISA antibodies are still validated by Western.

By: JudyH

JudyH — Tue, 20 Nov 2012 16:59:36 +0000

Agreed. If corrections to most of the figures have no effect on the conclusions, why were those figures in the paper to start with? Figure 4g must be entirely irrelevant, since neither the correction nor the correction to the correction of this figure changes the conclusions. And if the researchers made detectable mistakes in their figures, I expect that they made mistakes elsewhere in their procedures and in their data collection. I get that the publication means a lot to them. They should have thought about that back when they were doing the research and preparing the manuscript.

By: Dave

Dave — Tue, 20 Nov 2012 16:42:41 +0000

I hate to beat a dead horse, but how about a quantitative imunoassay instead? Is that a joke? Why do you need a quantitative assay when a semi-quantitative assay does the job perfectly? WB are not and never were quantitative; by nature they are semi-quantitative so I don't understand what point you are trying to make or why you are making it. The quantitative (or not) nature of WBs has little to do with why WB misuse is detected more frequently. An undergrad can develop a home brew ELISA for relative quantitation... Really? An undergrad can design and manufacture and ELISA-grade antibody and then develop and standardize the ELISA assay itself? I don't think so. But the better question is: why would you bother when WBs work perfectly? I wouldn't want to be your student. Don't make the common RW mistake of assuming the WB is fundamentally flawed because some people abuse them. It is not. Move on. ELISAs are Photoshop-proof. ... And you can't "edit" the data in Excel at all, right? Ah yes, the solution to the "WB problem" is to hide ones data in and Excel spreadsheet. [face palming right now]. Laughable comment.

By: Schmuck

Schmuck — Tue, 20 Nov 2012 16:24:22 +0000

Call me old style, but I cannot understand how a scientific paper can stand when you have to correct almost half the initial figures.
In my own, and admittedly closed mind, if you a problem with any figure, the house of card has already crumbled. THe peer review process is built on absolute trust. We trust what our colleagues tell us and their figures/data. Once that trust is broken once, it will be very hard for me to trust the same people again.
It is bad science and we all know it and if the scientific community does not stand up to that, I am sure other people will be hot on our heals soon.

By: Physician Scientist

Physician Scientist — Tue, 20 Nov 2012 14:43:44 +0000

Don’t be silly. Antibody specificity isn’t good enough to switch entirety to ELISAs. Most antibodies don’t detect a single protein and as such, and ELISA will give you total protein detected, not specific protein detected. Western blots help with this problem by adding a separate layer of specificity – the molecular weight of the protein detected. The problem is not with the technique – the problem is with the interpretation and/or manipulation of the technique.

By: pharmapawn

pharmapawn — Tue, 20 Nov 2012 13:46:12 +0000

I hate to beat a dead horse, but how about a quantitative imunoassay instead? An undergrad can develop a home brew ELISA for relative quantitation, and ELISAs are Photoshop-proof.

The way most labs run them, ECL Western blots are at best quasi-quantitative, and more often are effectively qualitative. Li-Cor data can be better, but how many properly run Li-Cor blots (with standard curves and other controls) have you seen published? IMO, Westerns are so antiquated that they barely warrant inclusion in the Supplemental Materials section.

I suspect that this addiction to Western blots is here to stay because most academic labs are either ignorant, scared, lazy, or deluded about the cost of properly working up a plate- or bead-based immunoassay. It’s amusing to me how many labs will gladly spend $250 a pop for IP/Western antibodies, then waste weeks running gels, when they could run 60 samples in an afternoon with an ELISA at about $0.60 per well.

It’s the 21st century. BAN THE BLOT!

By: Robert Fagan (@RobFagan)

Robert Fagan (@RobFagan) — Tue, 20 Nov 2012 13:23:20 +0000

Producing perfect western blots doesn’t require any particularly high level of skill – completely green undergrads in our lab can usually produce usable data after only a few tries. There is no more excuse for image manipulation in western blots than with any other form of visible data representation. I think that western blots are taking as lot of unfair flak at the moment.

By: Neuroskeptic (@Neuro_Skeptic)

Neuroskeptic (@Neuro_Skeptic) — Tue, 20 Nov 2012 13:06:42 +0000

Is the paper JNK science?