Category: Science

Superorganisms…

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NO, don’t get excited, I said super organisms. Yesterday’s The Scientist led with an article on Super organisms, which reminds me of my invertebrate neural and endocrinology lectures of years past. I used to be fascinated by the idea of super organisms, which is simply an organism of many organisms.

Being a prokaryotic biologist, I tend to think of things at the scale of planktonic (free-living) single cells, and occasionally we enjoy the concept of cooperative living in biofilms or other more complex structured consortia like stromatolites. Ultimately, evolution has resulted in multicellular organisms, some of which were further refined into organisms consisting of many different tissues with disparate characteristics; most people are not unfamiliar with this.

An interesting idea in biology is the idea of a super organism, where parallels can be drawn between the essential components of a complex higher organism, such as a mammal, and individual organisms within the super organism:

It is a rather contentious idea as it runs into the semanto-scientific diction of what exactly constitutes an organism. Are we limited by our usual scale-interpretation as Humans, where an abstract idea of a super organism clashes with our own biological recognition of what constitutes an organism? The big question is of course, how can such a super organism evolve? This is one of those great challenges that evolutionary biologists love.

At what scale does natural selection, the active force of evolution, have its effect? Does it act at the level of the individual? Yes, probably; I am still with Dawkins on the idea of selection acting at the level of the gene. However, for natural selection to have an effect, it depends on individual differences within a population, and crucially, on the ability of the “fittest” individual to survive and reproduce. However, in Ant colonies the Ants are sterile drones; the reproductive entity of a such a super organism is the queen of an Ant colony.

Thus we have a situation where “unfit” worker Ants can result in the collapse of a colony, therefore selection feeds back to the Queen where reproductive success is dependant upon producing workers that are capable of fulfilling their roles in the provision of food, looking after eggs, defending the colony and building infrastructure; thus a very indirect form of selection. So is the superorganism being selected or not?

Good question,  it’ll be fun finding out.

Viruses in the genes

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THERE was a recent article in NewScientist suggesting that viruses are the unsung heroes of evolution. Whilst that is somewhat of a sensationalist position, there is a great degree of truth in it. Many anti-evolutionists seem convinced that it is mathematically impossible that genetic variation and mutation can be a sufficient substrate upon which natural selection can act.

What they forget is that whilst a mathematical proof is always the truth, it is a truth that is dependent upon whether the mathematical model accurately reflects the physical problem. Mathematics is limited to the validity of the assumptions that underpin the statement of the problem, thus in the fixing of certain variables it’s important to distinguish between getting the maths right and getting the problem right.

The variation seen in a species, upon which natural selection can act given circumstances that favour one variation over another, is encoded by alleles; this is the name given to different “versions” of the same gene, thus for eye colour, different alleles may be: brown, blue, green etc. Some alleles are dominant, some are recessive; the dominant ones win and get used, the recessive ones lose  and don’t get used. The dominant and recessive alleles are both part of your genetic make up, and this is called your genotype. The dominant alleles result in a physical attributes in the organism, such as brown eyes, and these physical attributes are known as the phenotype.

It is true to say that whilst all phenotype is derived from the genotype, not all genotype results in phenotype. Dominant traits, because they are aspects of the genotype that are reflected in the phenotype, are traits that can be acted upon by natural selection; however recessive traits are effectively hidden from natural selection unless the DNA that codes for the recessive alleles is physically linked to a piece of DNA that results in some other dominant trait that can be selected for or against. This recessivity maintains a store of genetic diversity.
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Fallacies of logic

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THE theory of evolution is an elegant theory, but to really get at the nitty-gritty details takes some discipline and a head for new concepts. There is much excellent literature out there, and plenty online; my links under the title  “Free-thinking”, to the right, are as good a starting point as any.

If you are going to learn about evolution, or science as a whole, then you should hear it from scientists, or other communicators of science, and NOT at websites such as “allaboutscience.org“. With a little reading, you may spot that the site is actually hosted by “allaboutcreation.org“, and I can assure you of three things:

  • There are many such sites on the internet.
  • They use scientific sounding language, but in fact demonstrate complete and universal ignorance of the theory of evolution and of the method of science.
  • They can all be recognised because somewhere they will mention the words “creator” or “designer”; they can’t help themselves. They may also use the word “evolutionist” to describe one who accepts evolution, this is almost uniquely a creationist terminology.
  • Their websites will be based largely around the notion that evolution cannot explain the complexity that is seen in nature, or other notions that they have little comprehension of themselves. Their aim is to raise the more complex issues that they know the average person isn’t going to know about.

They are however flawed because they try to interpret scientific evidence using their own parochial world view, i.e. that we’ve only been here 6,000 years, and we all arrived here in more or less the same form as we are now. Thus they can never hope to understand the time-scales and gradual change through intermediate forms upon which evolution is based.

Here’s an example from the website I cited, on their section about evolution:

Evolution – The Evidence of Why Scientists Believe in Evolution
Evolution, in this context, can be defined as: the belief that all living things, including man, resulted by natural changes from lifeless matter, with no supernatural intervention involved. If life on earth really came to be in this manner, by chance and from lifeless matter, then why are there so many intelligent people — even PhD scientists — who reject the theory?

Well, seeing as this is the first paragraph of the page, one wonders what “context” exactly they’re talking about? Secondly, their definition of evolution is completely wrong; evolution has nothing to say about the origin of life from lifeless matter, this discipline is called Abiogenesis. The theory of evolution, as I’ve described before, explains the origin of species, how natural variation in a species can be acted upon by natural selection over time, resulting in a diversity of different species. By mis-defining evolution, they are attempting to set up a classic fallacy in logic known as a “Straw Man”; by distorting the original definition into something that it clearly doesn’t state, making it easier to defeat, e.g.:

  • Person A has position X.
  • Person B presents position Y (which is a distorted version of X).
  • Person B attacks position Y.
  • Therefore X is false/incorrect/flawed.

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“Two plus two makes five” – Winston Smith, 1984.

IF enough people believe it, or if it is illegal not to believe it, will it be true?

I spend a lot of my time, probably too much, waging a battle of wits and reason with the truly and irredeemably unreasonable. The usual subject is the scientific theory of evolution. I preface the noun “theory” with scientific so as there is no mistaking exactly what we mean by theory.

Whenever I hear the words “Just a theory….” levied at a scientific theory, it sends a shudder down my spine. As I’ve mentioned before, and I will undoubtedly continue to do so, a scientific theory is not speculation or opinion, it is a comprehensive, logical and above all testable model that represents the best means of explaining the evidence. Furthermore it facilitates predictions that can be tested experimentally to continue to verify the reliability of the theory. The theory of evolution is just such a theory:

The theory of evolution explains that variation exists between individuals within a species, it explains how natural selection can act to drive this variation and it shows how, and describes why, some organisms display characteristics that make them better suited, i.e. fitter, for life in the environment in which they live. It explains how these “fitter” organisms are the ones more likely to survive and pass on their characteristics to offspring. It explains how, over time, these characteristics become a trait in all members of a species, and how less favourable characteristics can be lost. Ultimately, the theory of evolution explains how a species, over this long period of time and subject to much genetic change steered by natural selection, can be very different from its ancestors.

Now, the above paragraph is qualitative, and largely non-technical. However, bound up within the above is some impressively complex science. The debates that rage amongst scientists is not about the validity of the above, it’s about the specifics of how they’re achieved. Part of what I aim to do with this blog is not re-write any of the perfectly excellent books on evolution that are available, but to tackle those areas that are taken advantage of by religious fundamentalists. Science is a dynamic subject; by the time it is written up in a book, it is already out of date. As I mentioned before, there is a battle of wits going on out there, between scientists or other such rational free-thinkers, and religious fundamentalists (which for want of a better term, I call “Fundies”).
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On science in society

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AT this time, as the Large Hadron collider (LHC) comes online, and we hear tales of the doomsayers (and here) who would stifle curiosity, free enquiry and discovery, I think to my own area of science and the great efforts we have to go to defend the science that gives, and has given, so much to society. The LHC beam line has thus far met all expectations, and when it starts the actual collisions in the next few months there is absolutely nothing to suggest that it will cause the end of the world. Science is under attack like never before; media sensationalisation, poor science education, the barrier between those “in the know” and those not, and the rise of religious fundamentalism are largely to blame.

There comes a point when you really must accept the advice of experts, because you can’t expect to be an expert on everything about which you hold an opinion, this would be an unreasonable and untenable position. You trust that a cardiac surgeon knows how to perform your quadruple by-pass surgery; you trust that aeronautic engineers have really created an aeroplane that will fly; and you trust that if you buy a phone, you are in fact going to be able to call someone with it. So if the LHC scientists say that the comparatively low energy bombardments (yes, large for human experiments, but nothing compared to what the Earth experiences from the Sun) are not going to cause cataclysmic damage to the Earth, then you have to trust that they are sensible, rational, careful and intelligent people who know what they’re about, and believe that what they are doing is good for our society.

Many people go through life imagining worldly attributes into a world that is inherently, and obviously, physical in nature. A world that does not in fact conform to any such imaginings, except in the heads and societies of those who enjoy protection from the crueller and more selective attributes of the physical world; a protection afforded to them by scientists, technologists and engineers, people whom they presume to lecture, deride and slander in the errors of our ways. This is largely because the pursuit of knowledge in the physical world has resulted in knowledge that contradicts the inherited fantasy of some social groups. All I would say is that it is not sensible to hold an opinion in the face of overwhelming evidence to the contrary; wisdom comes from noticing when ones opinions are disproved by evidence.
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Intellectual vandalism….

There is a new fictional film, masquerading as a documentary, currently being aired in the US.  Several of my US friends went to see it (admittedly mourning their monetary contribution to the creationist cause) and have let me know not to waste my life, or money, going to see it. In turn, I encourage similar of anyone reading this. The fiction-doc is called “Expelled: No Intelligence Allowed” and it is yet more anti-science propaganda in favour of Intelligent Design, spewing outlandish, intellectually dishonest rhetoric. In their polemic pursuit of self-righteousness they also managed to demean a host very respected scientists, including Richard Dawkins and PZ Myers.

I’m not fond of commenting on things I haven’t actually seen, but I am of like-mind with my friends, and to be honest, I’m painfully well aware of the nature of such attacks on science; the very discipline that has permitted them the technology of producing a film in the first place. The National Centre for Science Education has produced a website to address the intellectual vandalism the film may do to those lay audience members who may inadvertently take the producer at his word.

The producer, amongst other things, contends that the theory of evolution contributed to the holocaust committed by the Nazis, communism and the rise of atheism. This is of course nothing new, creationists have been peddling this tripe for a long time; it is all part of their belief that atheists are inherently immoral, as if atheism is itself a religion that preaches immorality. Alas, like little children, they cannot believe that anyone can know something that they don’t.

To address one point however, one might suspect that such an arrogant and self-righteous man as Hitler would happily go into depth about how he employed evolutionary theory in his final solution, yet never once does mention evolutionary theory in the whole sorry tirade of Mein Kampf, I know, I’ve read it. Furthermore, he was on a crusade to create an Aryan race, whom he believed to be the created in the highest image of the lord; hardly the comment of a proud atheist or evolutionist.

Religions deal in the manner in which they believe people should live their lives, unfortunately, to those arguing from a platform of ignorance about science, there is a general misunderstanding that science similarly prescribes a way of living. This is not correct. Even if Hitler had been employing the theory of evolution in his reasoning, this does not mean that the theory is any way morally awry. Evolution is a scientific theory, it is neither good, nor evil; science makes no prescriptions on how to live your life. It is not to be confused with Social Darwinism, which is a philosophical construct based upon “survival of the fittest”.

Richard Dawkin’s premise is that by understanding natural selection we can selectively abrogate the rather emotionless and indifferent edge of this process, not become slaves to it.

Communal peeing

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I happened upon a paper that made me smile this morning.

Apparently there are these Ants, Cataulacus muticus, which happen to be obligate bamboo-nesting Ants. They live inside giant bamboo, which as any survival expert knows is prone to a bit of flooding in the hollow internodes. This of course riles the Ants a little, so their response is apparently two-fold. During the heavy rains, the workers form a living umbrella over their nest entrance using their packed heads.

Of course, rainwater may still seep in. So not being ones to shirk responsibility, the Ants respond by drinking the water, exiting the nest and excreting the water droplets down the outer stem surface – basically, they hang their arses out of the window. This, in the wit of the authors, has been termed communal, or cooperative, “peeing”. Fantastic.

For those with access: Maschwitz & Moog (2000) Communal Peeing: a new mode of flood control in ants. Naturwissenschaften 87: 563-565.

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Supernatural dilemma

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SCIENCE is about falsifiability, an attempt to understand the world around us, and our place in it, to the point where the best sense prevails.

Usually, it is a case of the often-quoted Occam’s Razor, where, all things being equal, it is often the simplest explanation that is true. The point is to arrive at a reasoned explanation of the phenomenon, such as a ghost sighting, without resorting to fiction. It seems ludicrous to me that some people would rather accept an immeasurable “force” or “entity”, for which there is no shred of physical evidence, or requirement, when we are possessed of a human brain, the most sophisticated biochemical computer on the planet, which is more than capable of rendering highly vivid imagery, smells and sounds, none of which need actually exist in he external environment.

As much as possible, science aims to be rational, consistent, and predictive. The supernatural can be none of these things. Knowledge of them does not enable prediction of their occurrence, i.e. beyond coincidence; the observations are inconsistent, being highly biased upon the subjection of the observer; and they are by definition irrational. I also hasten to add that they are, by and large, immensely uninventive, almost uniquely anthropomorphic and require a degree of self-stupefaction that would never be entertained in other areas of people’s lives.

Believer’s belief supersedes any form of evidential support or logical rationalisation; such evidence is simply irrelevant. What I find objectionable is when believers hold they have rational grounds for their belief; the best thing we can do is to inform them that they are wrong in this. This does not mean to say that they are wrong, per se, faith is faith after all, but to attempt to legitimise their belief by logic and methodology is to pit their belief directly against rational and secular thinking, with which it cannot compete.
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Hogwash in science writing

I hate political correctness in scientific papers. It’s especially insulting given the readership of such articles. I especially hate the use of the term “sacrificed” or the one in the current paper I’m reading “euthanised” to describe the killing of test animals as part of an experiment. In the latter it was the killing of test chickens to look at the results of antibiotic trials on their gut flora. However, perhaps “killing” has it’s own connotations, but it’s semantically different from “murdered”. Perhaps “rendered dead” is the way to go?

I’m reminded of an excellent, if wax-lyrical, 1955 Nature article by John Baker entitled English Style in Scientific Papers. It was popularly received as it was one of those moments where someone sticks their head up and pull no punches when telling everyone that they’re behaving doltishly. His subject was the grandiloquence and foibles that “are the enemies of good English” and hinder the effective communication of science. [Those with subscriptions can see an online copy via an Editorial and recent reprint in the Journal of Biological Chemistry Classics series:l article via link].
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Virophage

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IN today’s issue of Nature is an account of a virus that infects a virus, a virophage. We are all familiar with the ubiquitous plant and animal viruses. Many of us are familiar with the bacteriophage, viruses that specifically attack bacterial cells and are the most abundant organism on the planet; somewhere around 10 million virus particles in a drop of sea water.

Now we hear of a small virus, called Sputnik, which infects an enormous virus, called Mamavirus. This is a larger member of a class of giant viruses, originally discovered in 2003 in a cooling tower in Bradford. The original Bradford virus of that 2003 discovery, Mimivirus, was initially mistaken for a small bacterial cell such is its size. Viruses are parasites, incapable of replicating themselves without a host cell; a virus infects and subsequently usurps the cellular machinery of the host cell to make a virus factory, spewing out replica virus particles. The small Sputnik “virophage” is able to parasitise the large virus’s factory for its own ends.

Having realised that such parasitism exists, and adjusted their views to the sizes of particles involved, researchers believe that this phenomenon may be common in nature, and particularly important in oceanic plankton blooms; the knock on effects of which have implications in ocean nutrient cycles and climate, plankton being one of the major carbon sinks on the planet.

It is a fantastically interesting discovery by Didier Raoult and colleagues, from the University of the Mediterranean, and certainly raises some questions as to the nature of whether viruses are alive or not. If the large Mimivirus is capable of being mistaken for a bacterial cell, and being parasitised by a smaller virus, at what point to we conclude that viruses are a distinct living entities, all be it obligatorily parasitic ones?