Friday, 10 December 2010

SOS: Save our science - Good Science or good publicity?

So this is the second part of my ramblings, and probably the most important bit. This part is all about accurately reporting on science in the media. I’m going to write about science stories that have got people talking, the ones that actually make it into the mainstream. I’m going to write about them in a pragmatic (and possibly occasionally cynical) manner that cuts to the truth of the matter without all the overblown revolutionary claims that are usually applied to these stories.

It seems appropriate to start with this one; I should say before I begin that I do strongly believe in NASA and hope they get the shuttle program back on track soon. But as far as overblowing things goes, I thought this was pretty good.

(Ed. Since this whole story is rapidly collapsing into random mud slinging I would like to point out that this post was written to highlight the way in which science can be distorted by the media, and is not meant as a personal affront to anyone directly involved).
Good science or good publicity?

Good Publicity

Big news! NASA has found aliens living in California (like we didn’t already know) and everyone is getting excited that we’re not alone in the universe. But is it really that big a deal, or has NASAs publicity department just been very clever in distracting everyone from the fact they still haven’t managed to get the shuttle off the ground?

To start with, I’m going to assume that the science underlying all of this is actually correct, and we’ll look at the actual implications and meanings of such a discovery and how it can be blow out of all proportion by the press. Later, I will briefly look at why this work seems to have very little sound scientific foundation and does not really demonstrate anything important.

Since the whole Mars meteorite incident (2005), I’ve been a little wary of NASA claiming to have found new life. Which is why when they announced that they were going to make a big announcement (a redundant move in itself), I was already more than a little suspicious.

The big deal is about a new bacterial strain (GFAJ1) which appears to be able to survive without phosphorus and which instead uses arsenic. Until now phosphorus has been accepted as one of the six elements essential to life as we know it. This is also extremely media friendly as arsenic is probably one of the most widely known poisons in the world. The bit everyone seems to be missing is that, according to the research, this bacterium can use arsenic, it doesn’t need to use it, and would in fact much prefer to use phosphorus, just like the rest of us. As such it is still part of our evolutionary tree, that is to say, that we are very, very distantly related to it in some way.

So let’s look quickly at the background to all of this. Everything is made up of atoms, each different type of atom is called an element. The smallest and simplest element is hydrogen and this is currently the first of 118 known elements. Six of these elements are key to all known life (Carbon-based life), these are Carbon, Hydrogen, Oxygen, Nitrogen, Sulphur and Phosphorus. These are the main structural atoms in DNA, proteins, fats and sugars which make up our cells. When searching for alien life we often search for these essential elements.

However, it is believed that other elements may also support life. For example Silicon is very similar to Carbon in a lot of ways, it is just a bit larger, and so may be able to act in a similar manner in a living system (Silicon-based life forms). The relationship between Phosphorus and Arsenic is comparable, although Phosphorus is generally considered to be much less important to life than Carbon. This discovery does provide some small support to the argument for alien life based on other elements, but it only proves that existing life can adapt to use alternatives when forced to do so, it does not mean that a planet with no phosphorus could actually produce life.

Relatively speaking it is very easy to replace phosphorus with arsenic, similar substitutions are made regularly throughout biology (usually of different metals). The toxicity of arsenic shows how easily it can replace phosphorus. Most biological machinery can’t tell the difference between phosphorus and arsenic and so may accidentally use arsenic. This results in toxicity because arsenic is much less stable than phosphorus. A stable chemical will exist for longer, and this is usually crucial to correct biological function. The prime example of this is DNA; phosphorus is an integral part of the structure of DNA, replace it with arsenic and pretty soon the DNA will start to fall apart and your cells will die. It is these slight differences in chemical properties that generally limit biological systems to dependence on the same six elements.
However, if you can find a way to alter your system to cope with the slight changes in stability resulting from using arsenic, you might be able survive on it. This, the paper claims, is the case with these bacteria. Arsenic is unstable because it reacts with water. These bacteria produce waxes (polyhydroxybutyrate) to exclude water and stabilise the arsenic.

Bacteria are extremely good at adapting, their comparatively simple single-cell body plan means they can be enormously flexible to whatever environment they find themselves in. They also have many mechanisms which allow them to rapidly change their genes to create whole new systems to cope with different challenges. Most interesting is the capacity for horizontal gene transfer, the process by which bacteria are able to share genes not just with other members of the same species but also with other distantly related species. It is comparable to us being able to gain the ability to fly from birds or to swim like fish, to run like a cheetah or to climb walls like an insect, simply by touching a member of that species. It is this mechanism that means bacteria are constantly being found in the harshest of environments, living in the most unusual ways. Many species of bacteria are able to produce energy without the needs for oxygen or carbon dioxide, they can use rocks, volcanic fumes, even concrete. Admittedly this is much easier than actually using different elements to build yourself, but given that arsenic is easily incorporated accidentally into cells, would it really be that big a step to actively encourage it, and to work around the disadvantages?

This is one isolated example of our own evolutionary tree adapting to an unusual environment. I feel it says more about the immense capacity of evolution to adapt organisms to extremes, which has already been demonstrated through the immense group of bacteria known as extremophiles (beings which like extreme environments). It serves to expand our understanding of what is possible with the right genes, but it is still just a diversification of our own lives, clinging to many of the same core principles; It still uses the other 5 elements, it has cells, DNA, uses the same mechanisms to move, grow, feed and reproduce etc. There is certainly no need to “rewrite the biology textbooks” unless to add this as a minor footnote somewhere near the back.

Good Science

Whilst I was researching this story I read the original paper (soon to appear in the major journal Science) and found several cases of enraged academics denouncing this work online (most famously and also. It seems that the original science underlying all of these grand claims is of incredibly poor quality and does not really demonstrate anything.

The paper uses a lot of overly complex methods to general indirect data, which require several assumptions and estimations to give any kind of conclusion. By the time the paper does draw conclusions the original data has been so mangled it is practically useless. What is most annoying about this is that there are easier ways to achieve many of their goals, which give much more reliable results and which have been completely ignored or intentionally left out by the authors. In many experiments the controls (versions of the experiment which will have a known result) are extremely poor, and render the actual results irrelevant. There are also several cases of blatant data manipulation to make the data seem more plausible.

In the paper they admit that the cells grown in arsenic also had access to 3 ┬ÁM phosphorus. The authors claim that this is an insignificantly small amount and compare this to their observations of phosphorus use by a cell with easy access to plenty of phosphorus. However, a cell starved of phosphorus will adapt to use less of it, so will have lower demands. Through a few simple calculations it becomes clear that this amount of phosphate can easily support the number of cells reported in the paper. A region of the Atlantic Ocean has 300 times less phosphate than this (1 nM) and is still easily able to support a wide variety of bacterial life; all of which use phosphorus normally. The concentration of phosphorus in Mono lake is 100 000 times higher than the Sargasso Sea and so there is no need for these bacteria to be using arsenic instead.

Besides the chemical instability, arsenic DNA would also introduce a myriad of other difficulties in normal life processes. The suggestion that instability could be compensated for by excluding water is highly unlikely. The waxes that are mentioned in the paper, are produced by many bacteria as a way to store carbon and energy when they don’t have enough phosphorus (or other key elements) and are not a unique adaptation to arsenic use.

To show where the arsenic was found in cells, the researchers used a variety of standard chemical methods to separate the different parts of the cells, identifying that supposedly 10% was found with the DNA. However this process does not completely purify DNA or proteins, so there is still a lot of contamination. As it turns out this experiment may have accidentally provided the one useful piece of data in the whole paper. In this process, DNA is dissolved in water for several hours, if the DNA was really using arsenic it should have fallen apart very quickly and would not have been identifiable at the end, since it stayed together this must be normal phosphorus DNA and so conclusively disproves their own argument.

It seems pretty obvious, with just a bit of research, that this is most definitely a case of very good publicity, but of truly terrible science, both of which work very hard to produce something exciting but most likely completely false.

A final comment: Why are we doing this?

The true goal of studying unusual environment such as Mono Lake is to find examples of life evolving in a different setting to our own. It is believed by many that life on Earth evolved to use the elements most readily available to it and that on a different planet (or even on a different part of our own world) life may have evolved differently. This is generally used as an explanation for why certain metals are used within our bodies (iron in blood, calcium in teeth and bones, sodium and potassium in nerve signalling) and it is possible to apply this same thinking to the non-metal components of life.

The difficulty in searching for these alternative life forms is knowing what to look for, our idea of biology is based on observation of our own evolutionary tree. Life using other elements may work very differently and to us may not initially appear as life. For example, whilst silicon is very similar to carbon many of the structures it forms are much more rigid and crystalline than those based on carbon. Thus silicon-based life is likely to be much less mobile and have a very different body shape, as well as being very different chemically, and having very different requirements to our own. How do you begin searching for life forms that might be made of crystals, may breathe sulphur, eat rocks and drink acids and what planets might this life live on?

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