Monday, May 23, 2016

The degradation of mitochondrial research

Does everyone remember this?

Most especially this bit:

Control is using pyruvate at 5 mmol/l and the ATP synthesis shut down is generated using palmitoyl carnitine at 10 micromol/l. Got that?

Try this one too, plots of pyruvate against palmitoyl carnitine:

And how about this one, increasing doses of palmitoyl carnitine alone, showing self destruction of ATP synthesis with rising doses of palmitoyl carnitine:

Is everyone convinced that allowing anything over, say 5 micromolar palmitoyl carnitine anywhere near a mitochondrion is going to crash ATP synthesis? Lots of experiments, lots of evidence.

Now, this is pretty basic science. What happens when a lab takes their basic science and goes clinical? This is the same lab:

Chronic Reduction of Plasma Free Fatty Acid Improves Mitochondrial Function and Whole-Body Insulin Sensitivity in Obese and Type 2 Diabetic Individuals

Here is the key statement, from the methods:

"Mitochondrial ATP synthesis rate was measured ex vivo with a chemiluminescence technique as previously described (16)".

Reference 16 is the one from which all of the above graphs have been taken. The isolation, washing and feeding of the mitochondria have not been changed. Yet now, in a clinical study showing the wonders of free fatty acid reduction, we get this:

We can ignore the acipimox groups and use the pre treatment open columns. Look at ATP yield from Pyr, this is pyruvate 2.5 mmol/l. Now look at PMC 0.5 and PMC 1. Here we have palmitoyl carnitine being added at either 0.5 mmol/l, ie 500 micromol/l or even 1000 micromol/l, giving comparable rates of ATP synthesis to pyruvate 2.5 mmol/l.  That 1000 micromol/l is one hundred times the concentration used in their first paper to shut down electron flow and collapse delta psi.

Where did the inhibition of electron transfer from reduced CoQ to complex III by palmitoyl carnitine go to? What changed?

They went from basic science to a clinical application. Was the basic science correct? Is the clinical paper correct? An interesting set of changes. Makes me thing of the degradation we see so commonly in research, from something which looks sound to something which looks incomprehensible.



Gretchen said...

It would help some of us if acronyms were defined at first mention. Well, maybe not ATP, but the less common ones.

Peter said...

Will see what I can do!


Stan Bleszynski said...

Hi Peter,
It got me so curious I tried to find a difference in methodology to explain that, by reading thru those papers. Nothing obvious! How come mitochondria shutting down almost completely on FA metabolite in 2008, somehow completely recover showing no effect at hundred times the dosage in 2014? Very weird! The same analytical techniques was used, even have the same two of the co-authors. Did you try to ask them for explanations?


Peter said...

Stan, I've just butchered their copyright graph and dished their logic and probably their integrity. I might not get a polite reply. DeFronzo, the corresponding author of the diabetic/acipimox paper is group leader for that study and group leader for the earlier basic science paper. If anyone would like to try a polite query, unassociated with Hyperlipid, feel free to do so and update us on the ensuing silence! As group leader he might not actually know how they wash the mitochondria!!!! One big down of being group leader is you don't get in to the lab much.


Unknown said...

If you want good mitochondrial research just look at Dr. Doug Wallace before you look anywhere else.

DLS said...

hey peter, i though you might find this old pic interesting

Peter said...

That's another one to try down the garden! Just ender where I might find any margarine...


karl said...

This is exactly what Richard Feynman warned about - cargo cult science . It looks like science - but it is not.

Today, it is worse than the oil-drop slowly changing numbers.

I think there are 2 things at the center of the trend of bad science. One is the grant-money-machine - the goal is to get the money - or to get the degree - not to further science.

The other is the infection of the universities with irrational philosophy - post modernism in particular. No longer do graduates actually learn and master the scientific method - I remember an old college level textbook on the scientific method (couldn't find it to share the in my stacks of books for the exact name (but found a second copy of Hecht's Optics!)). At some place students spent a whole semester pouring over this book - examples of how to set up experiments, where the pitfalls were. Lots of clever tricks for designing experiments. But today I've not seen students working on such a course. Instead there seems to be constant confusion between the 'stamp-collecting' step and the testing step. Correlations do not show causation.

This postmodernist philosophy basically says that it is really easy to be biased in doing science (which is true), but their solution is to give up on being objective. Doing real science is really hard - apparently too hard for many, yet they still get published - don't get retracted even if the experiment step fails to isolate things down to a single variable.

It is frustrating to be constrained by science, but it is the only tool there is to expand technology and our understanding of the world. We are surrounded by a sea of computers that remind us that we are living in the future - yet computers don't replace the discipline of thought needed to expand what we know. Computers may even be shortening the attention span needed to do careful thinking.

Even in physics there has been a problems with thinking a computer simulation equated to an experiment. ( I've worked with simulations in electronics - and fooled myself at times. Simulations can help save time, but in the end you absolutely need to test reality - with out such a step you are basically writing science fiction).