Asimov rules!

So, today's candidate for Great Man of the Day is Isaac Asimov (2(?) January 1920 - 6 April 1992): scientist, science fiction writer, humanist and humorist? I like the fact that he called himself "humanist" because he "atheist" defined what he didn't believe in, rather than what he did.

I was already a fan of the Robot, Foundation and 2001 series but he did loads of other cool stuff that I had no idea about. I never realised he was president of the American Humanist Association, or wrote books of jokes! The thing that really caught my eye, given my original motivation for quest, was that he suggested his own calendar reform “called the World Season Calendar. It divides the year into four seasons (named A–D) of 13 weeks (91 days) each. This allows days to be named, e.g., “D-73” instead of December 1. An extra Year Day is added for a total of 365 days.” [Quoted from Wikipedia.]

I quite like this idea - must look into it some more. (And track down some of his religious jokes!

Happy Erlang Day

2011 is upon us and I feel renewed enthusiasm to embark on an exercise of folly. One such folly is the development of an atheist/rationalist calendar.

I did think such a calendar should really start on December 22/23, following the Winter Solstice. At this time, the tilt of the Earth is such that the days once again begin to get longer. This, of course, is a very Northern-hemisphere-biased view of the world, so maybe it is not so appropriate after all. I am fairly convinced that the calendar should be divided into four quarters, divided at each Solstice and Equinox. (Perhaps an Equinox would be a more neutral start for the year?) But how best to divide the rest of the time is more tricky.

Then we have the problem of what the year should be? It obviously cannot relate to the alleged year of Jesus' birth but what event, which must by definition occur in recorded history, is defining enough to take this place as defining Year 1.

One thing that can be modified quite easily though, is the association of days with Saints. I have therefore decided to look each day for an important non-religious scientific figure. Not sure how long this will last.

Today is the turn of Dane Agner Krarup Erlang (January 1, 1878 – February 3, 1929) who was a big man in the field of communications and is credited with the invention of Queueing Theory (used in everything from telecommunications to hospitals to computer programming) and Traffic Engineering, which is heavily used in communication network designs, including the design of this here internet. He even got a Unit of Measurement named after him - the Erlang - although my brain is not sufficiently awake to make sense of what this is. It has something to do with communication. He also has his own statistical probability distribution and a programming language named after him. That beats three miracles in my book. Well done A. K. Erlang.

Erlang shares this day with St Basil "the Great" of Caesarea who, from his Wikipedia entry, seemed to be quite a nice chap. Basil does also seem to be partially responsible for the Christianity fixing the decision that Christ was divine, which appears to have been a matter of some debate for the preceding three centuries. One cannot help but speculate what subsequent conflicts might have been resolved, and how much easier religious harmony might be, had this decision gone the other way. Oh well. I have a soft spot for people who help poor and underprivileged.

Yak Yeti Yak

Next time you're in Bath and looking for a great place to eat, I recommend "Yak Yeti Yak". This is a great little family run Nepalese restaurant.

I've had Nepalese once before, in Southampton, and didn't find it significantly different from Indian food, though the preceeding wine reception may have dulled my powers of culinary discernment a tad. Yak Yeti Yak was much more distinctive. We were a group of six and so we ordered a bunch of dishes, with rice and daal; sadly, I cannot remember any of the names of the dishes but it was all good. At just over £20 a head, including drinks and starters, it was good value too. Another Google/iPhone success and well worth a visit.

No Intelligence Allowed

A review of the Ben Stein DVD - "Expelled: No intelligence allowed"

I watched this film with a "theistic evolutionsist" friend of mine (i.e. a committed Christian who agrees with the scientific fact of evolution) and we were both thoroughly disappointed with the total lack of content. To save you the bother of wasting money and an hour or so of your valuable lives, I will now summarise the DVD for you. It can be broadly divided into three sections: (1) An "expose" on the scientific gagging of ID supporters; (2) A demonstration of the extent and all round good-eggness of the ID community, and (3) The evil of evolution.

~ The Expose ~
The cleverest thing of the whole film is are the propaganda techniques the editor uses to equate the scientific establishment with Communist East Berlin (building a wall to keep dangerous democratic ideas out) and, worse, equating support of evolution with support for Hitler's genocide of the jews. (More on that later.)

The film starts with Ben Stein addressing an audience in a very "Inconvenient Truth" fashion but, unlike Al Gore, he presents no data to support his arguments. Instead, we are treated to a small number of anecdotes of academics who failed to secure tenure in American Universities (in itself not uncommon) and their belief that this was because they had entertained the notion of Intelligent Design (ID) as science. The institutions themselves deny these reasons and no actual evidence (or successful legal action) other than speculation was provided in support. If any of these did turn out to be true then it is very sad - and wrong - but is certainly not indicative of some major conspiracy. The fact remains that ID is simply not science and explains nothing, which bring us to...

~ The ID position ~
The most disappointing (but not upsetting) aspect of the whole film is the total lack of information of what the ID argument actually is. Basically, the argument Ben Stein makes is... "Look, here is an intelligent person. They think ID is right. Therefore it should be taken seriously." Wrong. Lots of intelligent people believe nonsense. Worse, lots of intelligent people take advantage of other people beliefs in proven nonsense to make money out of them. (E.g. Homeopathy.) Is ID an "intelligent" endeavour? Well, on commercial grounds, yes! There are lots of people who would like to be true and can be convinced to part with their money on books and DVDs, like this one. Is ID a "scientific" endeavour? No. At least, not as presented in this DVD, which presents no arguments against evolution (except the sickening one below) nor arguments for ID.

The closest there was to an argument for ID was a statement that (a) biological information has increased with time, and (b) evolution cannot add information, therefore there must have been an intelligent designer to add this information. This is just plain wrong. While *random* evolution cannot add information (which, in this context (information theory) basically means a deviation from random (similar to entropy)), the process of *natural selection* can. In fact, it is this very observation (in different words) that made Darwin so famous. In other word, ID is trying to argue that Darwin was wrong using an argument that Darwin himself revealed to be rubbish.

I should point out at this point that I am an evolutionary biologist, so I know something about evolutionary theory and encounter supporting evidence on a daily basis. I also know that, far from blindly accepting evolution without argument, any scientist worth his salt would *love* to disprove something as big as evolution. Look at Darwin's legacy. Does Ben Stein really think that there are no scientists with egos who would love to replace Darwin as the number one biologist of all time? Now who's being naive? Let's be clear about this - there is no cover-up and no controversy because there is no scientific evidence for ID. I was hoping this DVD might present some - it would have given me some interesting things to research - but it did not. As the opening sequence makes clear, this DVD is pure propaganda. Which brings us to...

~ The evil of evolution ~
The icing on the cake - and the true revelation of the weakness of the ID position - was the last third or so of the DVD. Rather than presenting a cogent scientific argument for ID, Ben Stein instead focuses on the fact that Hitler was essentially a Darwinist and used ideas of "Survival of the fittest" as an excuse for some of his horrendous activities during the Nazi rule of Germany, including the holocaust. Apart from being deeply insulting to me as an atheist, this argument is totally irrelevant to the issue of whether evolution is scientifically supported. It's a bit like saying that we shouldn't believe Atomic Physics because people have abused it and made nuclear weapons. Whilst it is true that some people use evolutionary theory to support their own radical agendas, that argument is equally true of religious ideas; it is a matter for society to deal with, not science. You could argue equally strongly that an atheist who does not believe in life after death is going to cherish life on this planet more than a theist, and concentrate on making *this* world a better place (rather than the next one) because this is all we have. Still doesn't make evolution more or less true.

In short, there is only one reason to buy this DVD - because you want to support the *political* ID/creationism machine. But in this case you might as well just send them some money directly and spend the hour or two you would have wasted doing something more useful to humanity, like sitting in a dark room with the TV firmly off. (It would also make Al Gore happy.) Or, better still, visit a website that contains some actual factual content (e.g. http://www.oeaw.ac.at/klivv/evolution/) and make up your own mind rather than letting some ignoramus spout lies and hate at you.

Dawkins & Darwin - a missed opportunity

I've just watched the first part of Channel 4's "The Genius of Charles Darwin", presented by Richard Dawkins, with decidedly mixed feelings. It had a lot going for it but I can't help thinking that it was a missed opportunity.

Although he doesn't spend much time saying how religion is no longer necessary, Dawkins still wastes a few minutes that would be much better spent, in my view, demonstrating the evidence for evolution. As an evolutionary biologist, I am well aware of the overwhelming evidence for evolution - I deal with it every day at work - and Dawkins mentions it several times but I feel that he dumbs it down too much and refers to it in general terms rather than really giving good examples, of which there are many. I wish he had removed a few interviews with people - trying to get school children to think for themselves, for example, - and shown a few more examples of anatomical, developmental and genetic similarities between organisms and evolutionary transitions.

There is nothing in biology that we have yet discovered that makes more sense in the light of some "design" theory than in the light of evolutionary theory, and there are plenty of things that we have discovered for which the "design" theories flounder while evolution makes perfect sense, but this does not really come across in the program. He talks about DNA but does not show any actual alignments of sequences and explain how they fit the family-tree structure
predicted by evolution but not the independent-origin structure predicted by independent creation - the competing hypothesis of the time. He talks about fossils but doesn't actually show any of the classic examples of form changing through time. He shows animal limbs and a few embryos in a few seconds but could have gone so much further with far more examples of anatomical similarities that simply make no sense without evolution. Ditto developmental genes. And the genetic code. And biochemical pathways. Etc. etc.

Oh well. Maybe the next episode will hit the mark.

Mutation can be a good thing

Creationists often make statements about mutation always being bad and necessarily messing things up. (Usually followed by an inappropriate analogy.) Of course, in reality, many "good" examples of mutations have been discovered or even deliberately engineered.

One particularly nice example can be found in an article from Nature earlier this year (Isalan, M. et al. Evolvability and hierarchy in rewired bacterial gene networks. Nature 452, 840–845 (2008)). In this experiment, Isalan and co. simulated a bunch of random mutations by adding copies of genes to E. coli that were attached to different promoters and thus expressed under totally different control mechanisms than normal.

By creationist logic, each of these should be pretty detrimental to the organism. I mean, if the bacterium was perfectly designed, then this kind of approach (akin in their (misleading) analogies to adding an extra set of indicator lights to a car, controlled by the brake pedal (along with the brake),) should stuff things up. Indeed, even most biologists would assume that most of the constructs would be bad news.

Interestingly, however, this turned out not to be the case. The majority of constructs were tolerated by the bacteria in question. Furthermore, some of them actually conferred a selective advantage in certain conditions, demonstrating that not only can such mutations be tolerated, in certain scenarios they may be retained by the organism. i.e. evolution. (See more in Allison Doerr's article at "The Signaling Gateway".)

Although generally not as striking as this, articles demonstrating the potential power of mutation and selection are published every week. While they do not prove evolution in the unscientific way that Creationists seem to crave, they are certainly and indisputably entirely consistent with it. Despite nearly 150 years since the publication of "Darwin's Origin of Species", no evidence that has been unearthed that clearly contradicts evolution, despite the fact that every fossil dig or sequenced genome has that potential. Evolution is falsifiable - don't believe otherwise. Just because no evidence has been found that shows evolution to be false, it doesn't mean that such evidence couldn't exist, it just means that it's unlikely to be false.

All aboard the schouler ship

I know it's bad form to make fun of people with bad English but sometimes circumstances indicate that they deserve it. Following on from my "thank you and wish me luck" experience, I got another e-mail over the weekend from another Egyptian, this time with the subject "schouler ship". (Scholarship, I presume?) Now, while the first guy obviously had no idea I was a computational biologist, this guy hasn't even bothered to find out which country I am in!

"Dear prof.Dr. Richard J. Edwards
best wishes from the sky of Egypt
i would like to introduce myself to you
my name is:#### ####
underdraduate student at El-Azhar University Faculty of Science (Biology Department) have a geart interest for continuing my undergraduate study in biology at USA (i`m a student at the final course of the first year (biology department)
please you can direct me about what is the document papers or certificates i must sended it you for continuing my study at USA and what about the avilability for gaining a schoulership for continuning my study.
my interest in Genetics
thanks for your helping
#### ####"

Come on, people! Who do you think you are going to impress with such an error-riddled mis-directed e-mail?! I liked the "best wishes from the sky of Egypt" bit, though. I like to think he beamed the e-mail from a hot air balloon using a satellite uplink or something.