New Research blog

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I have started up a new blog over at Wordpress. I wanted to start writing about my research and things related to it. I will most likely post the odd thing here still. So head on over and check out The Hip Ecologist and read about plants and CO2.

Cutlery birds

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Several months ago I was out riding my bike past some tidal mudflats when I saw a couple with a giant camera lens looking out at the exposed shore. I had no idea what the couple were looking at but I was intrigued, and had my suspicions so I stopped to see. Lo and behold they were twitchers (I should really have guessed given the enormity of their camera lenses). And what were they looking at? The beautiful Royal Spoonbill (Platalea regia). The Royal Spoonbill (kōtuku ngutupapa) breeds across most of Australia and in several places in New Zealand. They are also found as stragglers in Indonesia, New Guinea and several Pacific islands. Apparently, these birds a relatively new arrival to New Zealand (1950s) but have established several breeding colonies since that time.

Royal Spoonbill (from http://www.forestandbird.org.nz/, photo credit Craig McKenzie)
I had intended writing more about this bird but in my search for info I was reminded of a new resource for New Zealand birds - New Zealand Birds Online. All I can say is Wow! It is an amazing resource for anyone including; hardcore twitchers, scientists and those who are just interested in "that bird they saw".

The science (and scandal) of doping in cycling

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I began commuting by bicycle about two years ago and I am now hooked on cycling. For about 18 months I rode around on my hip(ster) single-speed, Charge Plug (mine is dark blue). But, I began to steadily increase the distances I was riding on weekends and having one gear became limiting, particularly for going up hills. So after my mate Paul got a road bike I decided I should too. It took about two rides to get used to the bike and within a couple of months I was riding at least eight hours a week, including a long three/four hour ride (100km) on Saturday or Sunday. I am obsessed with cycling now and can't get enough of it. So much so that for the first time since I was about 10 or 11 I watch sport intently.

Because of my obsession with cycling it often comes up in conversation with people. In these conversations, doping is often brought up by the other party, and usually quite early on in the piece. Obviously I can understand why this occurs: cycling has a long history of doping scandals. In recent history there have been some particularly prominent incidences including the Festina AffairOperación Puerto and of course the latest Lance Pharmstrong saga with the 1000 page reasoned decision from the United States Anti Doping Agency (USADA)

So the obvious question that arises is why is cycling so bad for doping? There are several potential reasons but first I think it is worth going into some of the specifics of what doping is in a general sense, understanding it in a basic biochemistry framework and how this relates to cycling. I will attempt to keep the discussion grounded in science and relatively simple but may stray into subjective opinion from time to time.

 So what is doping? Most people have a general understanding that doping makes athletes better at sport. But it is important to understand how doping does this. It is in understanding what or how doping works that will point to one of the reasons that doping has been so pervasive in cycling. Doping in endurance sports is typically related to improving aerobic capacity allowing athletes to go faster for longer. The pathway through which this is achieved is by using 'something' to elevate haemoglobin or red blood cell levels (haematocrit levels): haemoglobin is the component of blood that carries oxygen so by having more haemoglobin the oxygen carrying capacity of blood is increased. Typically males have a haematocrit level of around 45 percent and females around 40 percent. So quite simply, the most common form of doping in cycling (and other endurance sports) is to increase the proportion of red blood cells in your blood.
So how does more oxygen help you go faster for longer? I mentioned aerobic capacity previously but it is useful to look at what this means. Our bodies need energy to do all metabolic tasks and to power the muscles. I used the two images in a lecture on cellular respiration for my foundation biology class this semester to illustrate that both Philippe Gilbert winning the world champs and sleeping polar bears need energy, but that some activities require more energy than others. Energy in mammals is stored in the form of a polysaccharide called glycogen (glycogen is basically a long chain of glucose-sugar-molecules). The body then uses a process, cellular respiration, to 'release' usable energy in the form of the molecule ATP: ATP is often referred to as the 'currency of energy' and is the molecule that powers metabolic processes in cells and the biochemical energy to power muscles.
Inkedoutloud.wordpress.com
BMC racing team
The final stage of cellular respiration is called oxidative phosphorylation and it is this process oxygen plays a crucial role. The process is relatively complex and so won't go into too much detail. What is important to know is that oxidative phosphorylation produces the ATP energy molecules with the help of oxygen. During intensive exercise the demand for ATP can outstrip the supply if there is not enough oxygen available for the ATP-producing reactions. It is at this stage when demand outstrips supply that you feel the burn in your muscles. This is commonly thought to be because of lactic acid build-up. This, however, is not the case. Larry Moran has an excellent post that debunks the idea of acidosis (the burn). Nonetheless, regardless of what the specifics of the burn are we know it is the result of energy use exceeding energy production in which oxygen is a key ingredient.     

Knowing the basics of how cellular respiration works and how doping increasing the oxygen carrying capacity of the blood allows us to see the benefits for cycling over some other sports. Most competitive sports require a high level of fitness, but for many sports there is a an additional set of skills required. Consider rugby or football for example. Both require a high level of fitness but ball handling skills etc. are also extremely important. Compared to cycling the period of time over which intense activity needs to be maintained in rugby and football is relatively low. Rugby and football games last 80 and 90 minutes respectively. Professional road cycling races on the other hand are significantly longer. One-day races may last four hours for a short race to and over six for long ones. Then there are the multi-day stage races - the most famous is of course the Tour de France which lasts three weeks with the riders averaging over 180km per day in next year’s edition (excluding the two rest days and three time-trials). When you look at the differences in activity periods it makes sense that over such long distances even small differences in fitness/aerobic capacity makes a huge difference in cycling. So it makes sense that doping is 'useful' in cycling because it can result in significant gains in aerobic fitness. And compared to many other non-endurance sports aerobic fitness is the single most important factor contributing to success in cycling. Therefore, if there were a way to increase aerobic fitness quickly you can see how it might be tempting for some.  (At this stage it is important to note that doping can be used either in or outside of competition. In competition the benefits are obvious. Outside of competition doping can allow you to train more and harder which is beneficial for muscle conditioning, blood vessel development and increasing mitochondria levels in cells. Mitochondria are the power stations of the cell in which cellular respiration takes place. The more mitochondria you have the more efficiently you can produce usable energy (ATP).)

How do you boost haematocrit levels? There are two way to do this. One is using a substance to stimulate red blood-cell production, and the other is blood doping. The most commonly used substance by cyclists to boost haematocrit is erythropoietin (EPO). EPO is a hormone that occurs naturally in humans (and other animals) that regulates red blood cell production. However, EPO is now synthesised as a drug to treat patients suffering from anaemia - a disease related to low red blood cell levels.  It is this synthesised EPO that sports people use to do the cheating. Until recently (2001) there was no test for EPO and even today it can be difficult to detect if taken 'correctly'. Thus, combining the potential gain from EPO and difficulty in detecting it why the hell not use it? Of course you could say that is was ethically or morally wrong, a point with which I agree. But, as some have argued, if other people are doing it and they are winning, I am not going to win if I don't do it too. Anyways I have strayed into subjective territory which I wanted to avoid. 

With the advent of the EPO test riders began to seek alternatives. Blood doping became the cheating of choice. Blood doping is quite straight forward if not a little creepy if you ask me. Riders will have blood extracted and stored. Then, during a stage race after haematocrit levels have dropped (this happens due to the high physiological stress), the blood is re-infused to top-up red blood cell counts. There is no direct test available for blood doping but it is possible to find evidence that indicates that it has taken place using a rider's biological passport. The biological passport is essentially a way comparing a rider’s normal blood to their blood taken during random testing controls. If there are significant variations from normal it suggests doping.

Now that we know how doping works and how it benefits cycling we can understand begin to reason why is so prevalent in the sport.  But, is it really more prevalent than other sports? Another sport where doping is known to be common is cross-country skiing. Cross-country skiing is an extremely demanding endurance sport and so it makes sense that doping can result in significant gains. However, we hear very little about it because compared to cycling it has relatively small coverage outside of the countries that participate in the sport. For me one of the most important things is testing. This again  relates back to the potential gains  available from doping in cycling. Cycling has one of the (the) most rigorous testing regimes in any sport. After every race, or stage in a stage race, you see riders going into little booths to give doping control samples. But, in addition to in-competition testing cycling also has rigorous, bordering on invasive, out-of-competition testing. Basically testers can show up at your door any time and test you. Furthermore, if you aren't at home you need to be able to account for exactly where you were and what you were doing. I know of no other sport that does this. I read a quote from a pro cyclist who claimed he gets tested more in a year than a professional footballer does in their whole career. Whether that is entirely true or not it still demonstrates the point. Thus, it seems more difficult to get away with doping in cycling than other sports*. That means dopers get caught more often than they might be in other sports.

*Of course the Pharmstrong saga suggests otherwise but there is much more to that situation than passing tests and should be viewed in a somewhat different light.





















Times are a changing: about time

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For those who don't know, New Zealand's Parliament has just voted on a bill called the Marriage Equality Bill (MEB). What the bill essentially proposes is that same-sex couples can be afforded the same marital rights as heterosexual couples. The vote was pretty convincing with 80 ayes and 40 nayes. This doesn't mean the bill has passed into law but it does mean the process has begun. The bill first needs to go to select committee and voted on twice more. However, it seems very likely that the bill will pass and become an Act (i.e. the law). This will be a momentous occasion and should be celebrated by all New Zealanders.

Sadly there are a minority who think that their outdated and bigoted views should determine the rights of other humans. This minority typically consists of religious conservatives (are you surprised?). The prominent organised groups that I have encountered are The Conservative Party of New Zealand and Protect Marriage NZ. Their arguments against the bill surround the definition of marriage, or at least what they think the definition should be. They claim that marriage is only between a man and woman, an argument that is religiously charged. I see no problem redefining marriage in the legal sense if it means equal rights for fellow humans. In a less clinical sense marriage is an open commitment and expression of love for another person. That is how I view my marriage and that is how I view any other marriage. Another common strategy employed is the allusion to a 'slippery slope': if gays can marry what next? Legalising incest and bestiality? It is remarkable that somehow homosexuality is equated with incest and bestiality.

Colin Craig is also one of those bigots that thinks homosexuality is a choice and it is not normal or is unnatural. Of course anyone without a preconceived agenda knows that is bullshit and it is hardly worth getting into. I have written about the spectrum of sexuality in the past which demonstrates that 'normal' is an obtuse word with regard to sexuality. The 'unnatural' argument is a nonstarter. There is truckloads of evidence that homo- or bisexual behavior occurs in over 1000 animal species. Specifically, bonobos (our closest living relatives along with chimpanzees) are apparently fully bisexual suggesting that homo- and bisexuality is anything but unnatural.

Recently, Colin Craig (leader of The Conservative Party of NZ) has been calling for a referendum on the issue. He wants to put the fundamental rights of a minority in the hands of the majority, a strategy that is morally objectionable. Nonetheless, the issue is contentious and people have their opinions. Guess what the opinion was? Two to one 2:1 in favour of the bill according to polls. Interestingly the bill passed its first vote in Parliament two to one, exactly in line with the opinion polls. Seems pretty democratic and consistent with what the people of NZ want. Despite this Colin Craig thinks that it is undemocratic to exclude the public from deciding the issue and that MPs should not be the deciders on the bill. Craig then goes on to say that MPs voted against the desires of their constituents but provides not evidence for his claim. It would have taken a huge number of MPs to vote contrary to their constituents desires making his claim exceptionally unlikely, particularly when we look at the synergy between opinion polls and MPs' votes.

In regard to this whole thing I have had a 'personal experience' with Colin Craig. I, and many others, were directed through social media to his facebook page where he shared his press release of the above situation. Several people commented pointing out the flaws in his logic (i.e. democracy had not failed but succeeded). He proceeded to delete the comments that went against his views. I decided to comment too: he gave me the same treatment and barred me from future comments. In the end Craig got so many comments that were wrong and undemocratic (i.e. not in line with his views) he deleted the whole post. He is an astoundingly silly man who couldn't see the irony in what he was doing. Fortunately I took some screen shots of my comments before and after (see below and see here for a much larger set of before and after deletion).  Subsequently I went to the Conservative Party's facebook page and made some comments for which I got the same treatment. They haven't taken that post down so why not head over and have your say too. I also got accused of trolling despite my comments being civil and directly relevant to the post and comments from others. I wonder what Jesus would have done?

Before deletion

After deletion



Ultimately I have learned a couple of things: (1) Colin Craig and his associates are bigoted hypocrites and (2) New Zealand's gay couples will have the same rights as their fellow humans. Boo for the former and hurray for the latter. 

Another rare bird sighting

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On Thursday last week I was fortunate enough to spot a particularly rare bird, the Australsian Bittern or matuku (Botaurus poiciloptilus). Along with the matuku I also had a brief sighing of a Fernbird, the topic of a previous post.

The matuku is a large wetland bird (it was much larger than I expected it to be) native to Australia and New Zealand. It is, like so much of New Zealand's wetland biota, in decline because of clearing and draining of wetlands for farming. According to the IUCN Red List the matutku numbers fewer than 1,000 individuals in Australia, and an estimated 580-725 individuals in New Zealand according to a report from 1980. That means that there are less than 2,000 individuals left placing it on the IUCN 'Endangered' list. Interestingly, however, the 1980 New Zealand estimate is possibly an underestimate because much of the habitat suitable for the matuku is on private land. That means that population counts have excluded these areas which may harbour many small populations. This possibility provides some hope but unfortunately the discontinuous, fragmented nature of wetland habitats in New Zealand is problematic.

The issue of habitat fragmentation has long been known be a significant threat to biodiversity. In a effort to remedy fragmentation, many people advocate the use of wildlife corridors or green belts. Interestingly, despite the pragmatic assumption that corridors are 'good' there is apparently little evidence that large corridors (over one mile) are, and if they are, what is 'good' about them. A couple of conservation biologists are hoping to answer this using a global dataset of large, long-term corridors. If you know of any potential useful sites (see the link for criteria) you could win cash for suggesting it as a study site.




Insulting intelligence or just not having any

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The 'natural' medicine industry is a huge market. For some reason or another, more and more people are seeking alternative or complementary treatments. The most common reasons seem to stem from a distrust of conventional medicine (said medicine, see video below). Unfortunately this distrust is most likely a result of a lack of understanding of the scientific method and how it is applied to clinical science. It is not unusual to hear people accuse pharmaceutical companies of only wanting to line their pockets. Of course one would have to be ignorant to assume that pharmaceutical companies are angels, but one would have to be equally ignorant to assume they are only focused on profit. Any logical person can make the simple observation that products produced by pharmaceutical companies save lives. It is really that simple. Furthermore, if we consider the implications of producing products that don't work, or worse yet, cause harm, the companies that produce them would held accountable. That is the bottom line.

Yet despite the clear evidence, both that which everyone can observe on their own, as well as the scientific evidence required before a product can be sold as medicine, people still want alternatives. A pet peeve of mine is the 'natural' vs 'synthetic' argument wheeled out by skeptics (said denialists just like the climate change ones). The fact that a huge proportion of medicine (the stuff that works) is either directly derived from natural sources or synthesised from naturally occurring compounds makes that argument redundant. I personally think that it is ironic that advocates of 'natural' treatments and supplements accuse pharmaceutical companies of dubious practices rarely have any evidence that the 'natural' products do what they claim to.

Here is a perfect example of how 'natural' advocates tend to shy away from evidence. I recently found pamphlet from safe, a 'natural' products company in Australia. The front page of the pamphlet has a brief section entitled Essentials of Informed Choices. It goes on about how we are in charge of our own health which can involve the use of supplements. Supplements are a tricky subject and depend entirely on what the supplement is and what health benefits they are supposed to have, and of course if it has actually be shown to do what it says it does. However, in the "[seven] factors to consider when looking for a quality health supplement" provided, not one of them suggests that you should actually find out if it is indeed effective at improving health. See the advice below.

  • Is it organically grown?
  • What temperature is used during manufacture?
  • Does it contain any sugars, artificial sweeteners, colours or additives?
  • Is it manufactured in Australia or overseas?
  • Does the label offer comprehensive contact details?
  • Is the company sustainably focused?
  • Is it manufactured/packaged in registered premises?

The first point is fine but there is no evaluation of what is good about being organic. What if it is a mineral?
Second point is again vague and you are given no indication of the importance of temperature. I know that temperature can affect certain compounds such as, proteins. But, how in a general sense does it matter?
I love anti-sugar 'naturalists'. Sugar (and other carbohydrates) are an essential source of energy for our bodies to perform metabolic tasks. Sure, an excess of sugar is not great if we don't use up the energy it provides, but sugar is not the evil substance as made out by so many. Like all things, it is best in moderation. Artificial sweeteners are again not as evil as some make them out to be. Claims about cancer have generally been shown to be false. Moreover, it is very unlikely, in the developed world at least, that you will get fed toxic doses of anything because of strict food control agencies. Ironically, the 'natural medicine' industry is often exempt from these controls. I see this as problematic and contradictory to claims about 'western' medicines which are subjected to scrutiny.
The fourth point is odd and again there is no advice given on how to make a judgement based on where the product is made. Presumably they mean that Australian products are the best ones. I suspect that that is untrue.
The fifth point is probably the most useful in terms of finding out the efficacy of the product because if contact details were provided you could ask the manufacturer. Although I imagine that they would spin some woo webs.
Sustainability is important, but again not useful in terms of my personal and immediate health benefits that may or may not be gained from the product.
Finally, a registered premises is important, but rather than giving confidence in the products efficacy you can be confident that it won't harm you. That's good.

So all in pretty useless advice if you want to know if something actually works or not.

Note: I have place the term 'natural' in scare quote throughout. See here for an explanation. 

This is not peer-review

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Whoa, they are coming thick and fast this week.

A screen shot from the film Super of God touching Frank's brain
 This is inspired by my previous post that talked a little about peer-review. Actually it is the other way around. I got side tracked before I got started but was reminded about my initial idea after seeing this post over at Pharyngula about a terrible piece of Intelligent Design (ID) masquerading as science published. My idea initially came from a the list of peer-reviewed article by Discovery Institute (DI) members proudly displayed on their website. I scanned the list and noticed the journal called BIO-complexity popping up often. The name immediately set alarm bells off. It sounds very ID like: they love complexity as if it were some massive hurdle for evolution to overcome.

I googled BIO-complexity and guess what? It is just as I suspected. The opening line of their purpose statement is classic: "BIO-Complexity is a peer-reviewed scientific journal with a unique goal" (my emphasis). Unique indeed, peer-reviewed in the fairest sense, probably not. Although given that the journal has been around for two years and only has seven published articles could mean that they have such high standards very few manuscripts make it to publication. Again, probably not. Looking at the authors of the papers is no surprise, it is all the usual suspects, Gauger, Dempski, Axe et al. Moreover, in 2011 Axe was an author on two of the three articles in 2011 and two of the four in 2010. He is also the managing editor of the journal. A look at the editorial board shows that most of the authors are on the editorial board. Seems like bullshit to me. One the editors is the author of the paper criticised by PZ in the post linked above.

So is it appropriate for the DI to make claims about their members publishing in peer-reviewed journals if they are all just reviewing each others work? Well this is not unlike 'mainstream' science. In fact the word peer by definition means that is exactly what happens. But, the case of Lynn Margulis pulling a shifty to get Donald I. Williamson's paper published shows that there can be flaws in the peer-review process among mainstream journals. However, the science literature has a final line of defence in the form of commentary. If a published paper is found by another scientist in the field to be faulty, they can submit a comment to the journal arguing the case. This is exactly what happened with the above paper as with other famous cases like 'arsenic life'.

Not to worry though because according to BIO-Complexity they accept comments or Critiques as they call them. They also say that they "[all research articles] will followed by a brief published Critique when this becomes available." To date there have been no critiques published on any of their five research articles or critical reviews. In science, all comments are peer-reviewed as you would expect. Is it the same for BIO-Complextiy? Apparently not. Commentary is not peer-reviewed. Instead comments are published " at the sole discretion of the editor of the original article". So if I submit a comment challenging any of the papers published the editor is not likely to publish it because they look bad for publishing the original article. Basically because all the crap they publish is supportive of the underlying goals of the journal, all the authors who publish in the journal, and the most likely the ID community at large no comments will ever be published. How dishonest.