Friday, July 29, 2011

Aerobic endurance

Today's post is about endurance. Physiologically, endurance is about energy delivery. In many ways the muscles are machines that can keep up a given amount of work for as long as there is sufficient energy. Chemically, fuel and oxygen is converted to carbon dioxide and water, which releases energy. This is the same thing that happens in a fire, but since we don't want to burn up, the energy release is very closely controlled by the use of the energy currency: adenosine triphosphate (ATP).

New ATP is produced through three basic mechanisms: nonaerobic metabolism, anaerobic metabolism and aerobic metabolism. The mechansims are listed in order of speed, that is the rate at which they can replenish ATP, which corresponds to the maximal level of effort that can be sustained by them.

Nonaerobic metabolism is the conversion adenosine diphosphate (ADP, with two phosphate groups), into ATP using creatine phosphate (CP). This is very fast and provides almost all energy the first 8-10 seconds of any exercise, and can produce around 1200 watt (Guyton & Hall, 10th ed.). It is limited by the intracellular stores of CP, which aren't that large.

Anaerobic metabolism is the breakdown of glucose or glycogen into lactic acid. The process is very fast, producing about 650 watt and can keep going for much longer than the CP-ATP conversion. However, it is limited by the acidity of lactate. All enzymes, including actin and myosin and the metabolic enzymes, have an optimal pH. When the pH varies from this they get less effective, and after about 60 seconds of pure anaerobic exercise the muscle pH will be far enough below the ideal for the process to be severely impaired and the muscle becomes fatigued. In judo, the combination of these first two kinds of metabolism is what provides energy during the intense parts of the workout.

Finally there is aerobic metabolism where glucose/glycogen, proteins, fat or lactate can be used to produce ATP through the Kreb's cycle, which requires oxygen. When burning glycogen, which is the most efficient, aerobic metabolism can produce about 280 watt. In judo this is what allows us to keep going for a full two hour session, and importantly what happens between the short periods of attack and defense to keep fatigue at bay. In the low intensity periods between bouts lactate can be removed from the muscle.

So, the most important part of endurance for judo training, and thus for keeping up with young elite athletes, is the aerobic capacity. The demands aren't as strenuous as for pure endurance sports like running or swimming, but you have to be fit enough to continuously recover from fatigue for a full two hours of training. Going back to our definition of endurance as energy delivery. This means the rate of oxygen consumption, which can be measured in ml/min. In order to be able to make comparisons between different athletes this in often normalised to body weight so that the most commonly used unit is ml/(min*kg).

According to the only english-language, judo-specific book on sports science I know of: "The sport science of elite judo athletes" by Wayland Pulkkinen, the maximal rate of oxygen uptake, or VO2max (that's "V" with a dot over it indicating volume over time, "O" with a "2" subscript as in oxygen, and max, as in max.), of judoka is around 60 ml/(min*kg).

The question then is: How do I measure up? To find out we have to find a way to measure VO2max, but actually measuring VO2max is impractical outside of a physiology laboratory. What remains is estimation from parameters we can easily measure. There are a number of more or less well validated methods to estimate VO2max. You can find them through your friendly, neighbourhood search engine (PubMed, not Google). Uth and co-workers presented their method in 2004 (Eur J Appl Physiol, 91(1), 111-115), so fairly recently, and they used well-trained men aged 21-51 years old by running while measuring their pulse.

The method by Uth et al calls for a resting heart rate, which I found to be about 50/min and a maximal heart rate which I found to be about 200/min. You then divide your maximum heart rate by your minimum heart rate and multiply by 15.3, let's say 15. That gives:
200 / 50 * 15 = 60 ml/(min*kg)
In conclusion, I can not blame my aerobic capacity for any of my shortcomings, but I did find out that I need to work on my running. My calves are killing me.

Fitness for judo

Physical fitness is a complex parameter that is not easily caught in any one number. As any role-playing gamer knows, there are three basic physical characteristics: constitution (CON), strength (STR) and dexterity (DEX).

In addition, judo competition is divided by weight categories so that each of the stats have to be optimised in relation to body weight. Some judoka have, apparently, rolled the perfect 18, 18, 18 and can beat everyone, but the rest of us will have to do with stats that aren't as stellar, and hopefully, bodies (and opponents) that aren't quite as large.

In judo constitution, or endurance, means that you have to be able to do two things: Control your opponent for at least five minutes, and launch your own attacks. The former is an inherently aerobic task because of it's length, but it is broken into shorter intervals by all sorts of breaks. At the same time the latter is anaerobic on the verge of nonaerobic. That is, during a match you use enormous amounts of energy very quickly, when attacking or defending, and then you have to re-coup this oxygen debt time and time again in the lulls of the fight.

For any given technical level, the stronger judoka always wins. The easiest way to get stronger is to increase muscle size, this increases the number of motor units and makes you stronger. It also makes you heavier. That's the reason for weight categories. Another way to become stronger is to learn how to activate as many muscle fibers as possible at the same time, while relaxing the opposing muscles as much as possible. This is an important reason for building strength using the movements that will actually be used in judo, and not only by lifting weights.

Dexterity can be separated into speed and limberness, where speed is the most important. It is important to be limber enough to perform all techniques, but there are always techniques that require less flexibility. However, if you are faster than your opponent, he will be hard brought to avoid your attacks. Speed in judo means how quickly you can step and turn into your technique or out of your opponents. It also means how quickly you are able to notice and react to an opening in your opponent's defense. Both require very specific training, which is why years of recreational judo has surprisingly little impact on the ability to beat competitive judoka (not to mention that they have higher CON and STR as well, or do they?).

Next up will be a more detailed look at CON. How do competitive judoka perform, and how much do I have to catch up?

Wednesday, July 27, 2011


I did include judo as something that the Nephrophysiologist blog would be about, but there hasn't been much about that. Actually, there hasn't been any judo here at all. It has been hard to find something sufficiently interesting to write about, something where I also feel I have enough to say that someone might find interesting.

So, what has changed? you might ask. My answer would be that my sights have been raised for me. As I moved home to Uppsala and changed labs and hospitals, I also changed clubs. From a small club with recent recruiting difficulties and therefore a clientele of slightly older, non-competetive judoka, to a large, competitive club with some recent successes. Anyway, while it is a lot of fun working out with the youngsters, they are in better shape than I am. It would be more fun if that wasn't the case.

To remedy the situation (so that I'm not that embarrassingly winded older guy) I started doing some supplemental training. At first I had the basic philosophy that anything is better than nothing (which is true). However, being a physiologist it's hard not to have a quick look at what the science says. The judo posts will try to handle the science of judo performance from a practical perspective as I play catch-up with elite judoka more than ten years younger than me.

Monday, July 25, 2011

Using the OS X clipboard in R

One annoyance with using a command line based statistical system, i.e. R, is that if you use a spreadsheet program to handle your data (as most of you do) you have to incessantly export to csv and import to R. For big data sheets and complex calculations this generally a Good Idea(tm). It improves reproducibility and readability when going back to the project at some later time. However, the complexity of that is enough that you often, at least I, end up doing statistics in Excel. This is generally a Bad Idea, and often entails much more work in the long run. In order to make importing and exporting data easier R can handle the clipboard directly, which is what this post is about.

In OS X the clipboard is easily accessed through the command line programs pbcopy and pbpaste (pb means "pasteboard" but everyone knows it as the clipboard so that's what I'm going to call it). These are easily scriptable programs that can be used with any unix command in the shell or scripts (enter "man pbpaste" in the terminal to learn more). "pbpaste" pastes the current clipboard to std-out (that is where you call it from), while "pbcopy" copies std-in (what you put there) to the clipboard. An important quirk is that they only handle plain text, RTF and EPS, that is formats that are transferred as plain text. This is because unix is a text based system. What it means is that you can't copy stuff from formatted text, e.g. word, but with spreadsheets you are OK.

As command line programs they can be handled through the R command: pipe(). Pipe does not produce the current clipboard contents, just a description of the pipe as such. You have to use a read command to get the actual contents.
> readLines(pipe("pbpaste"))
which will produce one string per line (completely useless as data, but often useful to see how a given copy is formatted). To format it for data you use the same as you would any import, using one of the higher level read-commands: read.table(), read.csv(), etc.
> x <- read.table(pipe("pbpaste"))
This will put your copied excel table directly into the table "x" in R. Often you will be forced to tweak the function a little to get a usable table.
> x <- read.table(pipe("pbpaste"), header=TRUE, sep="\t")
That should be able to read your copied Excel data ("header" specifies that the first row is the header, and "sep" specifies the separator which defaults to tab or "\t" in excel).

To write to the clipboard you use "pbcopy". It is a bit more involved, but not much. First you connect a variable to the pipe from pbcopy.
> osxclipboard <- pipe("pbcopy", "w")
Now you can write to the variable "osxclipboard" and it will turn up on the clipboard so that you can paste it into another application. You have to remember that it is a pipe to an external file, which means that you have to use "write()" to put data in the clipboard. If you just assign some data to "osxclipboard" it will be changed from a pipe to that data. Thus:
> write(x, file="osxclipboard")
where "x" is your data, will to the trick. Then you just have to clean up using:
> close(osxclipboard)
In the same way as with copying from the clipboard, this will not format your data optimally. so you have to add some formatting command for Excel to read it properly.
> write(x, file="osxclipboard", sep = "\t")
There we are, but that is rather alot of code. Not really that much easier than a regular export from excel and then import to R. So here are two simple functions to do it all at once, with the most used arguments (I'm sorry for the code, I haven't figured out how to get indenting to work properly in blogger).

Simple readlines from the clipboard:
clipboard.readlines <- function (
clipboardname = "pbpaste",
n = -1L) {
readLines(con = pipe(clipboardname),
n = n)}
Read table from the clipboard. I have only included the most commonly used arguments to read.table(). You could easily add all the rest if you need them:
clipboard.readtable <- function (
clipboardname = "pbpaste",
header = FALSE,
sep = "",
quote = "\"'",
dec = ".") {
read.table(file = pipe(clipboardname),
header = header,
sep = sep,
quote = quote,
dec = dec)}
Write to the clipboard:
clipboard.write <- function (x,
clipboardname = "pbcopy",
sep = " ") {
osxclipboard <- pipe(clipboardname, "w")
write(x = x,
file = clipboard,
sep = sep)
That was it for now. I hope someone finds it helpful. I'm probably not putting any of this into a formal extension, so you will just have to run the code to use it. Consider the code GPL-licensed, although the text is under regular copyright.

Monday, July 18, 2011

MD or PhD

Let us return to the discussion about combining research and clinical work. Specifically starting a new group in a physiology lab and working as a junior doctor at a university hospital.

I have now finished my first spat of full time research in the new lab after a year as a clinician. I have been able to do most of what I set out to do this semester, but I will probably have to work as much next spat of research to make it work then too. The reason for this is that none of the senior PIs are directly behind my project, therefore none of them thinks that I should encroach on their space. At the same time they are all very supportive and positive to me being there. Just in a more theoretical way. What will happen is that in a year or two (hopefully sooner), there will have to be a centrally controlled reallocation of the lab space at the department, until then I will probably have to continue on borrowed space.

Funding wise, it is going alright. With a couple of minor grants I have had enough production of preliminary data to be able to apply for some real grants. Career wise, the next step will be a docenture, which is kind of like the Swedish version of tenure. You need a number of original publications and you need to show that you are independent as a scientist. On top of that you have to have taught a minimum number of classes. In combination with clinical work it is a chore to get it all done as quickly as possible, but nothing much happens until it is done.

Clinically I have spent the first year in medicine, which is my home field, so that has been good. Now I am going to rotate out into psychiatry and surgery this autumn, and while that may be interesting and possibly good for something, it is also a bit of a waste. Especially as I am just picking up speed in the lab again after moving back to Sweden. I know, it was my choice to try to combine the clinic with research and rotation is a necessary part of a junior doctor's life, but I can still complain. There is surprisingly little time over when working clinically, but I hope to spend the autumn revising and submitting some new and exciting manuscripts, and writing even more grants.

But now for my last week of vacation.

Tuesday, July 05, 2011

Advice for a Young Investigator

Santiago Ramón y Cajal was a 19th century neurophysiologist. I'm told he is well known, though he seems to have ignored the kidneys completely. Strange.

Any way, he wrote a book - "Reglas y consejos sobre investigacion cientifica" translated as "Advice for a Young Investigator" - to help budding scientists through their first years as researchers. While some of his advice is dated, such as the section on how to choose a wife, most is well worth the $14. What follows is a brief summary and some comments on the 1999 MIT Press pocket edition (with one of the worst quality bindings in modern history), translated by Swanson and Swanson (who have done a good job).

There is a Foreword by Larry W. Swanson with a short biography of Dr. Cajal and some suggested readings from his quite large production. Then there are three prefaces, for each of the second, third and fourth editions.

There are nine chapters, each addressing a different potential difficulty.

1. Introduction
The introduction concerns itself with which theory of science a scientist should build his understanding of nature upon. The answer is determinism. Cajal is very clear that a scientist should not spend his time delving too deeply into the various theories of knowledge and science. He writes:
" abandoning the ethereal realm of philosophical principles and abstract methods we can descend to the solid ground of experimental science..."
In this he comes quite close to my own thoughts on the matter (which may be why I like the book in the first place). Today, pure determinism is still usefully utilized in Chaos Theory, or the study of non-linear dynamics, but in general the focus today should be on statistical determinism. That is, the fact that we cannot know the full state of any system (at least any interesting system) induces variation and that this punches a quite large hole in classical determinism, but can be compensated for by studying larger populations and using statistics. Actually Cajal does not mention statistics at all, probably because it was just starting out as a field at the time.

2. Beginner's Traps
In the second chapter Cajal goes through some things that might unduly discourage the beginning scientist from his chosen path. Basically that well known feeling that those who went before were smarter, saw farther and thought deeper than you ever could. He makes the case that it only seems so after the fact, and that with hard work and time a scientist starting out today will appear equally daunting to those starting out in the future.

3. Intellectual Qualities
Cajal's main point about the mind of the investigator is that it does not have to be exceedingly brilliant as long as it is tenacious and a bit vain. He does mention originality, but his focus really is on hard work and the striving for glory. These are qualities he dejectedly notes are none too present in his contemporary Spaniards, while he holds the Germans in high regard. He writes:
"In Spain, where laziness is a religion rather than a vice, there is little appreciation for how the ... work of German [scientists] is accomplished - espeially when it would appear that the time required ... might involve decades!"
Rather poignantly, the endnotes have been expanded with the editions. In relation to a section written in the original 1893 edition Cajal later notes:
"This frank optimism is now greatly undermined by the hideous international war that began in 1914... It is sad to admit, but all nations become ferociously imperialistic as soon as possible... So much for the weak and unpatriotic!"
4. What Newcomers to Biological Research Should Know
In this chapter Cajal handles the opposing needs for the investigator to know a lot about disparate fields, especially the basic sciences, and at the same time specialize as much as possible to be able to produce original work.

Perhaps his most important point is the short section on "Mastery of Technique", as he writes:
"...the most important scientific conquests have been won by only a dozen men who have become known for their invention of improvement of a research method..."
5. Diseases of the Will
This is clearly the most entertaining section. The six most dangerous personalities - "who never produce any original work and almost never write anything." - are described in detail. I will only quote the his classification, the rest you should read in his original, quite wonderful prose.
"These illustrious failures may be classified in the following way: the dilettantes of contemplators; the erudite or bibliophiles; the instrument addicts; the megalomaniacs; the misfits; and the theory builders."
While these are quite fun, and you can always find some colleague that fits each personality, the more important lesson is that everyone gets trapped in these mires of the mind from time to time. The important thing is to realise that you are stuck in an unproductive mindset and be able to move on.

6. Social Factors Beneficial to Scientific Work
These are the ever current problems of funding, combining a profession with science and combining work and family. His basic stance is that you can always do science, but you should be ready to sacrifice having a life. Good advice.

7. Stages of Scientific Research
Here Cajal goes over the practicalities of the experimental method. Observation - Experimentation - Working hypotheses - and Proof. It is material gone over many times in other books, although Cajal has the benefit of being brief.

8. On Writing Scientific Papers
To start with Cajal references a Mr. Billings and states four rules: Have something to say; Say it; and Stop once it is said. The fourth rule wasn't as catchy so I'll just drop it. Then he writes a bit about credit and curtesy.

9. The Investigator as Teacher
The final chapter expounds on the importance of fostering future researchers to continue the work once you have gone. He concedes that it might be restful and rewarding to work in solitude but that "Posterity has always been generous with the founders of schools." He then goes on to describe the pains and pleasures of trying to combine research and teaching. First, how to find a suitable potential investigator; then how to guide him; and finally how to see him become a successful scientist leave science for profit and glory.

In conclusion, it is one of the few books that actually describes what it means to be a scientist, specifically a physiologist. It is certainly one of the very, very few that does so while being well written. I heartily recommend it to all my colleagues, and to any one else who might be interested in what science really is.