Thibaut Pinot's training data

[GoodTimes]

I will add though, that I have argued in the past in favor of open access to scientific journals. Two reasons:
1) I (along with other citizens) fund the government. The government funds scientists to do research for me. The scientists publish the research. Then, I have to pay to see the results of the research that I paid for? hmmm.
2) Fundamentally, academia is about furthering knowledge. This is served by widely disseminating research. As such, I applaud colleges like MIT who make their stuff open.

But, alas, the system is what it is, and I don't see any reason to gripe to the authors of this study on an issue that goes far beyond their scope.

 

[Dear Wiggo]

But I am curious... am I to understand that you discount the usefulness of the peer review process on the basis that a bad paper was published?

You started with

Don't you people understand the advantages accrued by the peer review process?

based on the fact that some here are complaining that you have to pay to access the data.

There are probably a number of ways of interpreting this, but it sounds to me like you are saying outright, "You (guys) are ignorant". As if peer review process and its value are the purvey of a select few.

There are 15 studies I have found through my trawling of pubmed et al that I would like to read fully (no, I mean REALLY). And then look at the raw data from said studies. They all cost $30-45 and in my quest for self education, are a much higher priority than the SRM summaries of a single pro rider. You know. n = 1. Kinda boring really.

I don't really care for peer review, no. Give me raw data or gtfo is basically how I feel. I want to get a feel for the methodology followed and the data generated from said methodology and make my own mind up.

The complaint - from me - of having to pay is not based on this single journal article, but the industry as a whole.

And going further down this rabbit hole is not going to further the discussion re: Pinot's data.

I understand the potential for value to be added via peer review, but am also acutely aware of humanity and its flaws. Amen.

 

[Parker]

I will add though, that I have argued in the past in favor of open access to scientific journals. Two reasons:
1) I (along with other citizens) fund the government. The government funds scientists to do research for me. The scientists publish the research. Then, I have to pay to see the results of the research that I paid for? hmmm.

The government aren't the only people who fund research.

2) Fundamentally, academia is about furthering knowledge. This is served by widely disseminating research. As such, I applaud colleges like MIT who make their stuff open.

Books are no different. You can buy them or go to the library and get access to them for free. And books further the knowledge of the non-academic far more than papers do.

 

[Dear Wiggo]

And the peer review process happens post journal initial acceptance, right? So the initial editor review trumps the peer review, right?

You feel me?

 

[GoodTimes]

You started with



based on the fact that some here are complaining that you have to pay to access the data.

There are probably a number of ways of interpreting this, but it sounds to me like you are saying outright, "You (guys) are ignorant". As if peer review process and its value are the purvey of a select few.

...

I understand the potential for value to be added via peer review, but am also acutely aware of humanity and its flaws. Amen.

Yup and yup.

Tone of first post was ott at places and your interpretation is a fair reading -- what was meant was more of a "hey, tell me (honestly) if you understand that there are benefits of the peer review process, as compared to lone ranger internet posts, because it sounds to me like you dont..." sort of a thing.

I already agree re not descending this rabbit trail further. cheers.

 

[acoggan]

And a quick check through a few threads shows more than a few people saying "Coggan defended the study" - so it's pretty much common knowledge you were doing exactly that.

Sucks to be you.

As for grasping concepts - I grasp them fine. You tried to say I was wrong once but that backfired big time.

I hope you are keeping your injection solutions refrigerated these days, Dr Coggan.

As Almesian's confusion (and your allusion) demonstrates, when worthless individuals such as yourself repeat lies often enough, they tend to stick in people's minds.

(BTW, you can't refrigerate albumin, as it becomes pyrogenic.)

 

[Dear Wiggo]

"hey, tell me (honestly) if you understand that there are benefits of the peer review process, as compared to lone ranger internet posts, because it sounds to me like you dont..." sort of a thing.

Maybe that's why some PhD recipients like to post here where they have no peers and can dismiss anyone's disagreement by reiterating lack of peership...

Peernicity?

 

[acoggan]

And the peer review process happens post journal initial acceptance, right? So the initial editor review trumps the peer review, right?

Not for most journals, no. That is, unless the paper is completely off-the-wall and/or well outside the journal's scope, most will send it out for review w/o any editor's input.

That said, editors have the final say regardless of what reviewers might think.

 

[GoodTimes]

The government aren't the only people who fund research.


Books are no different. You can buy them or go to the library and get access to them for free. And books further the knowledge of the non-academic far more than papers do.

1) My point is in reference to research that is funded by government--I think that this research should be the property of the people who paid for it (ie you & I). Conversely, I work at an engineering firm, that uses private sector money to do for-profit research. This should be the property of my firm exclusively.

2) IMO books are different. People write books to make money. Academia is done to further basic knowledge. If you disagree, that's ok... not going to take this point any further.

 

[Dear Wiggo]

As Almesian's confusion (and your allusion) demonstrates, when worthless individuals such as yourself repeat lies often enough, they tend to stick in people's minds.

(BTW, you can't refrigerate albumin, as it becomes pyrogenic.)

Well leaving it on the bench for 10 days isn't much chop either, is it?

"Defend the study" is the same as "defend the results of the study" - and you already admitted to doing that.

 

[GoodTimes]

Maybe that's why some PhD recipients like to post here where they have no peers and can dismiss anyone's disagreement by reiterating lack of peership...

Peernicity?

Or do the PHDs (i'm not one, less anybody by confused ) complain of a lack of persnickety ...

 

[acoggan]

Well leaving it on the bench for 10 days isn't much chop either, is it?

For tracer studies that's actually SOP to this day.

"Defend the study" is the same as "defend the results of the study" - and you already admitted to doing that.

No, I defended (explained) the process that led to its publication, then attempted to educate people when they have criticized it improperly. I have also described how I think its publication has moved the field forward, despite any issues with the original paper.

As for the study itself/data themselves, I've always been in the camp that thought it was a bit "meh" (but then again, I never have been one for hero worship).

 

[GoodTimes]

For tracer studies that's actually SOP to this day.



No, I defended (explained) the process that led to its publication, then attempted to educate people when they have criticized it improperly. I have also described how I think its publication has moved the field forward, despite any issues with the original paper.

As for the study itself/data themselves, I've always been in the camp that thought it was a bit "meh" (but then again, I never have been one for hero worship).

sounds pretty persnickety to me

 

[Dear Wiggo]

For tracer studies that's actually SOP to this day.

And fatty acids? Is it SOP to store them on bench tops too?

 

[acoggan]

And fatty acids? Is it SOP to store them on bench tops too?

Yes - see "Handling and Storage":

http://shop.isotope.com/supplyimages/MSDS012/PALMITIC_ACID__1_13C__99___CLM_150_GHS.pdf

 

[Almeisan]

As Almesian's confusion (and your allusion) demonstrates, when worthless individuals such as yourself repeat lies often enough, they tend to stick in people's minds.

(BTW, you can't refrigerate albumin, as it becomes pyrogenic.)

I got my info reading what Tucker wrote on Science of sports website.

I must admit, I haven't read the paper myself(and why would I read a decade-old trash article in a field that neither does unimportant science, sports is entertainment after all, nur is my field, when there is a large volume of articles in my field I haven't the time to keep up with.


Why don't you ask Coyle to retract the article? People in your field are still galled by the idea that there is a paper out there, accepted by their peer-review system, that suggests Armstrong's cycling legs have some property about them that seemingly make them get around the second law of thermodynamics.


BTW, don't take this as criticism of your, or Coycle's world, we are way past that point and the both of you are unimportant. The criticism is of those that let it slip through the peer-review process and of the journal that never retracted it.


Ooh, and the problem of course is defending bad science badly, not defending a cheater-athlete. No one in the scientific community cares about TdF results.

You're confused: I wasn't a coauthor on Ed's study of Armstrong.



And yet you opened your mouth and inserted your foot because...

I am perfectly qualified to attack you or attack peer-review when it obviously failed to operate as intended.

Coyle was your PhD supervisor. Since he is a fraud, you should give up your PhD and redo it properly, if you have the ability to do so.

I don't know if it could have happened timeline-wise, but based on the impression you give online, if Coyle had asked you to be a coauthor, you would have been.



I do agree though that case studies of one person can have some scientific value and are worth publishing. Every study or experiment has it's limitations.

 

[acoggan]

I got my info reading what Tucker wrote on Science of sports website.

No comment.

Why don't you ask Coyle to retract the article? People in your field are still galled by the idea that there is a paper out there, accepted by their peer-review system

Lots of people have, and yes, there are some still upset about the paper. The editors of JAP, though, decided that this was the most appropriate way of handling things:

http://jap.physiology.org/content/114/10/1361

, that suggests Armstrong's cycling legs have some property about them that seemingly make them get around the second law of thermodynamics.

Hyperbole: although Coyle reported that Armstrong's efficiency improved over time, at no point was it exceptionally, much less impossibly, high.

The criticism is of those that let it slip through the peer-review process and of the journal that never retracted it.

I agree, if anyone has issues with the paper that's where their attention should be focused...so why are you attacking me, when I had nothing to do with it?

Ooh, and the problem of course is defending bad science badly, not defending a cheater-athlete. No one in the scientific community cares about TdF results.

Again, we are in agreement. Well, all except the bit about "defending bad science badly"...there I would argue that I've done more to highlight the best "point-of-attack" for undermining Coyle's paper than anyone.

I am perfectly qualified to attack you or attack peer-review when it obviously failed to operate as intended.

Do you really think that's a legitimate statement, when you clearly didn't even know that I wasn't an author on the paper in question?

Coyle was your PhD supervisor. Since he is a fraud, you should give up your PhD and redo it properly, if you have the ability to do so.

Well, you be the judge:

https://wustl.academia.edu/AndrewRCoggan/CurriculumVitae

I don't know if it could have happened timeline-wise, but based on the impression you give online, if Coyle had asked you to be a coauthor, you would have been.

See, again you reveal your ignorance of the issue-at-hand. I had graduated from UT-Austin before Armstrong was ever tested there, and didn't know Ed had turned his abstract into a paper until I saw it in print. Even if he had asked me to be involved, though, I would have turned him down...I've never really been one for hero worship so the fact that the data came from Armstrong wouldn't have mattered to me, and I have very high standards for myself in terms of what I need to do to earn co-authorship on any paper, as well as very high standards for the quality of the data themselves. I would submit that this is why ~25% of the papers I've published have reached Citation Classic status.

I do agree though that case studies of one person can have some scientific value and are worth publishing. Every study or experiment has it's limitations.

Again, we are in agreement. What's interesting to me in this case, though, is how publication of a case study with such obvious limitations has still seemed to move the field forward significantly. In the big scheme of things, then, you could argue that its better that the paper was published, flawed though it might be.

 

[Almeisan]

We already know more about you than we'd wish to know, I think I don't only speak for myself.

I am amused about why you step in this hornet's again and again. You must surely believe you get unfair criticism here, but somehow you get a kick of out it.

Indeed, if in a decade or two my publishing record in my field, one much more rigorous, looks at glance as yours does right now, I would be satisfied.

But yes, Coyle's paper did suggest that there was something amazing at work, increasing efficiency though some undiscovered system. Of course it wouldn't outright contradict the law, but there was something 'magical' about it.
In fact, it seems Coyle still believes somewhere efficiency can suddenly change and does so apparently only in elite athletes only after years of training.

 

[acoggan]

Coyle's paper did suggest that there was something amazing at work, increasing efficiency though some undiscovered system.

No, it did not. Specifically, he hypothesized that the changes in efficiency were due to changes in myosin expression, something that is known to occur with increased chronic use of muscle, e.g., electrical stimulation.

Of course it wouldn't outright contradict the law, but there was something 'magical' about it.

Only in the eyes of those who mistakenly believed, e.g., Ashenden when he presented cycling efficiency as something that is immutable. In-point-of-fact, the earliest study (that I have been able to find, anyway) showing an improvement in cycling efficiency (actually, economy) with training dates to the 1930s. There are also studies showing changes in response to, e.g., chronic hypoxia, dietary nitrate ingestion, aging, etc. Although such changes tend to be small and aren't found in all papers, it is incorrect to claim that such a change would have to be "magical".

In fact, it seems Coyle still believes somewhere efficiency can suddenly change and does so apparently only in elite athletes only after years of training.

Take out the "suddenly" and the "apparently only in elite athletes" and you'd be right. He's also not the only one.

 

[Almeisan]

Myosin use ATP. If more Myosin is expressed, more is used, then more ATP is needed.

By definition, only factors that don't depend on oxygen can have an effect on efficiency.

And apart from that, we know from research that, besides the Armstrong-Coyle, every study has shown that improvements in cycling efficiency is not why good riders become elite riders.

Of course you may still believe that Coyle has shown that Armstrong has this freaky genetic makeup that codes for a system that, under extreme endurance training, allows his body to cook up new novel variations of pyruvate dehydrogenase or myosin that have a different amino acid sequence.

We know that in other organisms there are enzyme-variants that are more efficient then the ones we have. But we have this theory that explains the origins of enzymes, among other things. It is called the theory of evolution, (the neo-Darwinian version of it). Endurance training isn't an alternative to a 1000 generations of natural selection.

Gene expression can change, but that doesn't explain 18% improvement in efficiency 'because of more myosin'.

 

[acoggan]

Myosin use ATP. If more Myosin is expressed, more is used, then more ATP is needed.

Not quantity, type: muscle is most efficient when contracting at ~1/3 of its maximal shortening velocity, so changes in the type of myosin that is expressed could impact efficiency.

By definition, only factors that don't depend on oxygen can have an effect on efficiency.

Huh?

And apart from that, we know from research that, besides the Armstrong-Coyle, every study has shown that improvements in cycling efficiency is not why good riders become elite riders.

The primary take-home message of Coyle's article was how Armstrong apparently improved over time.

Of course you may still believe that Coyle has shown that Armstrong has this freaky genetic makeup that codes for a system that, under extreme endurance training, allows his body to cook up new novel variations of pyruvate dehydrogenase or myosin that have a different amino acid sequence.

See above. Also see the scientific literature re. changes in myosin expression with chronic changes in muscle use.

We know that in other organisms there are enzyme-variants that are more efficient then the ones we have. But we have this theory that explains the origins of enzymes, among other things. It is called the theory of evolution, (the neo-Darwinian version of it). Endurance training isn't an alternative to a 1000 generations of natural selection.

Gene expression can change, but that doesn't explain 18% improvement in efficiency 'because of more myosin'.

Clearly the topic-at-hand is outside of your area of expertise (or else you would have realized what I meant by changes in myosin expression).

 

[Almeisan]

When we move into biochemistry, we are actually moving into my specialty. I may be too young to have my PhD and it may be 50/50 if I actually get it and I am not one to brag about what I have, but surely you are wrong.

Whatever nuances there may be found in individual studies about myosin expression in different type of muscle fibers, the types of muscle fibers that may be classed aren't defined by myosin expression. Most of the myosin genes aren't even associated with muscle fibers anyway. We don't have so many so muscles can adapt to TdF or 100m sprint efforts in elite athletes.
Those mysosin change carry vesicles along cytoskeleton in cells, help macrophages change their cell membrane to eat up bacteria, help cells maintain microvilli, etc.

Yes, heart muscle, skeletal type I and type II muscle have different myosin expressions. But we know type I muscle fibers don't readily change into type II or the other way around.
We don't understand everything about myosin, or most of our genes/proteins yet. Especially the complexity added by splicing and gene expression and epigenetics/chromatin structure. But nothing suggests an extreme level of plasticity.
But all this has nothing to do with the Armstrong study. The data was wrong, Coyle knew that at that time and he surely knows it now. If not, he could have won a Nobel prize researching Armstrong's freaky genetics and oddball gene expression mechanisms.
And even so, there would still be needed and explanation about why this change in gene expression occurred so late in his career(about the time when WADA taught him how to beat the EPO test). He had been a triathlete throughout his childhood, had matured as a man and a pro rider, and then did something never shown again in any athlete anywhere in the world (while he was doping), at least according to the almost certainly faulty data.


Yes, you have some expertise. But the embarrassing thing is, you have been losing internet debates to laymen for the last 10 years. Why? Because you just want to defend this no matter how wrong you believe it is. Pretty sure most people don't think you actually believe this stuff.
So what does your expertise actually amount to? And now you dare to insult real scientists as well? Haha...

I would have realized what you had meant to say, but didn't? I guess that's your usual defense in academics as well...

 

[acoggan]

When we move into biochemistry, we are actually moving into my specialty. I may be too young to have my PhD and it may be 50/50 if I actually get it and I am not one to brag about what I have, but surely you are wrong.

I'm not.

Whatever nuances there may be found in individual studies about myosin expression in different type of muscle fibers, the types of muscle fibers that may be classed aren't defined by myosin expression.

In point-of-fact, when push-comes-to-shove muscle fibers are "typed" entirely based on the (primary) form of myosin they express. This is why, e.g., the most popular nomenclature system has changed from Brooke and Kaiser's original classification as type I, IIa, and IIb to type I, IIa, and IIx.

Yes, heart muscle, skeletal type I and type II muscle have different myosin expressions. But we know type I muscle fibers don't readily change into type II or the other way around.

That depends on how you define "readily". While it remains a point of controversy as to whether significant changes occur as a result of "normal" endurance exercise training, there is at least some evidence that it can. (Of course, such changes are well-established with more extreme interventions, e.g., chronic electrical stimulation or denervation.)

Regardless, the point is that this was Coyle's hypothesis for the reported improvement in Armstrong's efficiency, and one that was plausible enough that the paper was accepted. IOW, you were flat-out wrong when you said that Coyle didn't offer any explanation.

 

[Almeisan]

I rather be wrong like that than be wrong like Coyle&Armstrong.

 

[Dear Wiggo]

I rather be wrong like that than be wrong like Coyle&Armstrong.

Almesian: the entire training protocol espoused by the big 3 is based on endurance training converting muscle fibre types. I am quite pleased to see some light shone on this.

While it remains a point of controversy as to whether significant changes occur as a result of "normal" endurance exercise training

Apparently you have to electrocute yourself 24x7 to get guaranteed changes. There are some scientists who I would like to see prove that on themselves...

But I digress.

My question to you, Almesian, is this: approaching it from an analytical, "correlation is not causation" POV. If muscle fibre types are determined via myosin expression and a change in myosin expression is used as evidence of change in muscle fibre type, is it possible to change myosin expression without changing the fibre type?

Is is possible angiogenic etc manipulation (?) via EPO usage, not to mention testosterone and HgH could also have an impact on myosin expression without any corresponding muscle fibre type changes?

Is it possible that the evidence cited in

there is at least some evidence that it can.

comes from equally dodgy studies of doped up elite athletes?

Can you determine muscle fibre type without consulting the god of myosin expression, to corroborate the hypothesis that the fibre type in an athlete had changed?

Thanks!