> This image is supposed to demonstrate that the antibody being sold works as intended. (…) Antibodies are near-ubiquitous but notoriously fickle laboratory reagents in biomedical research. For many applications, it is absolutely crucial that the antibodies that you use are selective (i.e., the antibody binds strongly to the target protein) and specific (i.e., the antibody binds to the protein of interest and little else).
Antibodies showing a different picture (Western blot) than what is expected can drastically change the interpretation of the results as well as the conclusion of a study, for example. It may also encourage scientific fraud by authors by forcing them to unknowingly/coincidentally make to a blot image the same (or similar) fraudulent modifications performed by the vendor.
Now I’m curious about how much of the blot photoshopping present in retracted papers can be attributed to these misleading verification data.
I would be more worried if the blotted area was different (the dark blob) - or if data in a datasheet (something like test specificity, level of detection, etc) was wrong
Now, if while preparing the images they needed to do some editorial choices (or it is well possible a person in the editorial group was told to 'enhance the images' but wasn't aware of the details) because of limitations in doing the experiment then this is probably not a big deal
> I would be more worried if the blotted area was different (the dark blob)
Or if more than one blob is present (i.e. blobs at different molecular weights) for a supposedly selective and specific antibody that should show exactly one blob on the blot.
> Now, if while preparing the images they needed to do some editorial choices
Editorial choices on raw scientific data are a big no-no.
> Editorial choices on raw scientific data are a big no-no.
I don't think you can find a picture in an article that hasn't been photoshopped in one way or another (which is mostly ok as long as it is not misleading)
> would be more worried if the blotted area was different (the dark blob) - or if data in a datasheet (something like test specificity, level of detection, etc) was wrong
These images are provided on the datasheet and form the basis for the level of detection / specificity claims
> that structure is as/more important than sequence?
Structure is determined by sequence, so they are equally important. Structure is more conserved than sequence, mainly due to the physicochemical constraints that govern protein folding.
> that "reaction centers" are what matter, and the rest is just "protection"?
Sometimes not even protection. Many enzymes can have plenty of its sequence/structure removed and still be functional. Natural proteins carry lots of evolutionary cruft.
> What do you mean by "reaction center" - surely not physically central within the folded structure
I think they borrowed the term from photosystems/photosynthesis. But, to be more precise, what they actually meant is the active site of an enzyme; the location where the catalyzed reaction takes place.
> (isn't it the surface shape that determines reactivity) ?
Shape is not enough, the chemical nature of the amino acid residues involved is also important. A single mutation in a key catalytic residue will shut down the enzyme even if the shape stays the same.
My PhD thesis addressed a similar question. I did a survey of sub-domain sized fragments shared between different protein folds. It turns out that there are plenty, even among folds considered evolutionarily distant.
This reminds me of structural studies in proteins encoded by de novo genes in eukaryotes. They are usually either intrinsically disordered or adopt a molten-globule-like state.
But if you look at actual proteins where the function is pretty direct, you see ... a total mess. For example, the actual light catcher for photosynthesis, chlorophyll, you see rather suboptimal architecture. There is a central magnesium ion, and the entire rest of the protein is just there to keep it where it is. The only function, in other words, is to create an ion trap a a specific voltage. That's what that massive structure is there for. That's the only reason it's there.
Note: the rest of the protein being so massive has the huge problem that it results in the chlorophyll protein being toxic (even to plants). Several angles of the protein reflect the light ... away from the energy collector (it has sections that are like putting a mirror above a solar panel). Also: it's extremely INefficient. Inefficiency gets solved "the DNA way" (or should I say the Zapp Brannigan way): it's efficiency sucks, but if I just use very extremely large armies of chloroplasts I can compensate for the inefficiency by stacking them ... This sounds totally insane but yes, it works. Oh and the exact right amount of inefficiency can warm op the plant, protecting it (a little bit) from ice ages.
Now I have my suspicions on why chlorophyll + chloroplasts won (it's not actually the only photosynthesis protein or system): it's because by tuning a few amino acids you can change the depth of the ion trap, and so switch to different metals to capture, changing the color (which plants do, even just to have a particular color). It's pretty easy to accidentally adapt to either different metals or different solar frequencies (ie. using natural selection). Plus there was no need to design chlorophyll: plants "stole" the design from bacteria. So it was incredibly cheap in terms of how much computation (ie. generations of plants) had to die to make it. Of course, for the place it was stolen from the length of the protein was a very important factor so the biggest of chlorophyll's advantages (1 big protein, 10 functions that would have required 5x more space in DNA with small proteins) don't actually matter to plants. So why did it win? It was on sale!
So it works. But there has got to be a simpler/better/non-toxic way to create an ion trap using proteins and make plants work better ... I get that part of the problem is that I'm an engineer, a scientist. If one needs a design to catch energy and warm up a plant, I'd expect to create one thing for catching energy, and one plant warmer, both efficient. So there's an expectation problem. But a single mechanism to mostly randomly warm plants and catch energy at the cost of absurd inefficiency (both in warming and in energy production) ... is just not a sane way to go about this problem.
> Natural selection has no analogy with any aspect of human behavior, However, if one wanted to play with a comparision, one would have to say natural selection does not work as an engineer works. It works like a tinkerer - a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him whether it be pieces of string, fragments or wood, or old cardboards; in short it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.
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