Mental Indigestion

by Jim Caryl

Month: September, 2008

Appaloosa…

I went to see the film Appaloosa last night, starring Ed Harris, Viggo Mortenssen, Jeremy Irons, Tim Spall and Renée Zellweger; directed by Ed Harris.

Whilst many will dismiss it as yet another Western, I will add it to one of the many recent Westerns (including 3-10 to Yuma and Cold Mountain) that demonstrate how the genre is benefiting from improved photography, timing and attention to detail in both language and physical accoutrements. Appaloosa makes fantastic use of photography, costume and lighting. The pace of the story was excellent, permitting time for good character development, particularly in the form of the friendship between Harris’s and Mortensen’s eminently likeable characters as gunmen and law men.

Harris and Mortensen have great on screen chemistry, and Jeremy Irons plays the suitably self-righteous “baddy” very well; I was however less impressed by Zelleger’s acting role in the film. Zellweger has demonstrated her ability to perform in the genre (c.f. Cold Mountain), yet I’m beginning to wonder if she can deploy any speech patterns or facial expressions that aren’t Bridgit Jones come Beatrix Potter. Perhaps she should watch herself in Cold Mountain and remind herself of the suitably sour and beguiling face she managed there in portrayal of her character, Ruby.

Appaloosa is, by all accounts, a faithfully rendition of the book by Robert B. Parker, about a town called Appaloosa (after the Nez Perce American Indian breed of horse). I’ve never read any western fiction strangely enough, favouring non-fictional accounts of the history of the American west instead, thus I haven’t read the book; I have ordered Parker’s sequel to Appaloosa, Resolution, which sees the roles of Everett Hitch (Mortenssen’s character) and Virgil Cole (Harris’s haracter) reversed in a town called Resolution; we’ll see how it goes.

Word up…

Created using Wordle, a website that generates a Word Cloud based on imputed text or website, giving size emphasis to words used more frequently; it’s quite illuminating, although there was no doubt over what words might appear most frequently in my blog!

Viruses in the genes

[ratings]

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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Phew!

Well the new student residents are moved in, over a very long, but thankfully very sunny weekend! The sheer force of humanity entering the site over the weekend was overwhelming, the different personalities of bouncy, excited people was quite a heady mix. I have a team of sub-wardens working for me and they worked tirelessly to welcome all the new students and get them set up, I was very impressed. It’s good fun though, handling 6-10 questions at the same time, running around, making on the spot decisions. It’s nothing I don’t do in the lab on a day to day basis, but it’s far more fun when it’s to help people.

The whole weekend of events went perfectly, with the final Welcome Meeting (big dinner, a bit of a welcome address by me, then a chill out tent) last night coming off with excellent attendance, giving me a very positive view of the people we have in this year; most of them seem like a good bunch.

The task now is to get them organised to form a JCR and start organising things for themselves, so my task this week is to organise the JCR forming “Jarbeque” – that’s a “jar party” come BBQ – for this Saturday.

Then I might take a rest and get back to my philosophical digressions.

Fallacies of logic

[ratings]

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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Go Matt!

Some sound views from the inimitably sensible Matt Damon:

“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

[ratings]

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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Hope

I used to attend creative writing classes, if anything to attempt to undo the damage wrought by years of technical writing. Technical writing robs you of certain freedoms: to make mistakes as you write, to use active verbs, present tense, embellishing adjectives and superlatives. Technical writing is precise, well crafted, but passive and impersonal. It is utilitarian and functional “nuts and bolts”, to the “heart and minds” of popular prose.

Exercise (warming up the mind and fingers): write anything within 5 minutes (from an old class):

Small vortices caught dust on the desert floor, swirling them into the face of the oncoming Touareg, peppering his face, mapping his sweat with a glittering foundation.

A haze of flies danced in the grains of sand, a mesmerising display of light and dark. The nomad, oblivious to this battle between light and dark, trudged his way along the fading track of his leader, hating every step, but enjoying the thought of sweet water at journey’s end.

Upon his mind, stripped bare by days of relentless heat, was the Bedouin girl he’d seen at the bazaar. Her face a mystery, only her crystal green eyes telling of heretical beauty.

Such thoughts open holes for hope to fill, but if not filled allow despair to flow in hope’s stead. Such thoughts are wasted, when the day is hot and you are robbed of your life energy.