Tuesday, 5 August 2008

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.

Wednesday, 25 June 2008

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.

Sunday, 8 June 2008

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.

Thursday, 5 June 2008

SOLD! (Subject to contract)

This is our new house! (Hopefully.) Today I went by and took this photo. I'm not sure how clear it is but that's a "SOLD" sign outside now, rather than "For Sale". Yay! I know it doesn't really mean anything until the contract is signed but still, it's a step in the right direction.

We also had to get identification forms signed for the solicitors today. The world is such a distrustful place now. Before, I am sure you could just get a copy of an important document signed by a responsible member of the community, such as a policeman or teacher. (My old lab head signed my passport photo.) Now, you have to take a form along to the Post Office, where they charge you a fiver for the privilege! Oh well.

The one thing (so far) I think I would do differently if/when going through the house-buying thing again is to get a solicitor sorted out before putting in an offer. The first thing they wanted was our solicitor's address (before we had one sorted!) to get things moving. And while I am hoping it won't make much difference from now on, if we had got someone local at least we could have popped in and identified ourselves in person.

Thank you and wish me good luck

From time to time I am randomly contacted by people looking for a placement in my lab. Generally, it is very obvious that they have just sent round a blanket e-mail without bothering to find out what I actually do. (At least I am now a lab leader - when I was a postdoc I got contacted by people who obviously did not even know what I was, let alone what I did.)

Yesterday, I got a particularly entertaining one. Unlike most, he was applying with his own funding, which therefore made him of potential interest, but he was clearly just spamming labs in hope of a response. This seemed a bit odd to me, as if he had funding he should have been able to be quite selective of where he went.

I directed him to findaphd.com, which has many self-funded PhD placements advertised, and pointed out that I was a computational (not "wet") biologist. As expected, he replied to say that he was not interested in bioinformatics. The best bit, though, was his parting comment: "Thank you and wish me good luck." :o)

Saturday, 31 May 2008

Growing Up

Well, I suppose it had to happen some time...! This week has a been a big week for me, having:
  1. Passed my driving test. (Now I just need to buy a car.)
  2. Bought a house (subject to contract etc.)
  3. Got my first grant for a minion (a.k.a. PhD student).
  4. Got allocated my first teaching duties for next year.
  5. Signed up for health insurance.
Not bad, eh? Time to become a responsible member of the community. Of course, I also played a good few hours of GTA IV. After all, as a friend told me this week: "growing old is inevitable growing up is optional!"

Monday, 7 April 2008

The Fall of Man

My inability to find a supermarket open after 4pm on Sunday has led me to dwell instead on religious matters. As someone who used to be a fervent believer in the Bible, it never ceases to amaze me how easily I once overlooked certain obvious nonsenses in the whole thing. I mean, for example, take the original "Fall", i.e. the famous Adam and Eve thing.

"And the LORD God planted a garden eastward in Eden; and there he put the man whom he had formed. And out of the ground made the LORD God to grow every tree that is pleasant to the sight, and good for food; the tree of life also in the midst of the garden, and the tree of knowledge of good and evil. ... And the LORD God commanded the man, saying, Of every tree of the garden thou mayest freely eat: But of the tree of the knowledge of good and evil, thou shalt not eat of it: for in the day that thou eatest thereof thou shalt surely die." - Genesis 2:8-9,16-17.

1. If God didn't want Adam to have the knowledge of good and evil, why plant the tree in the garden?

2. If Adam doesn't have knowledge of good and evil, how's he supposed to know that disobeying God is wrong?

3. If Adam "in the day that thou eatest thereof thou shalt surely die", why did he not die for another nine hundred and thirty years (minus the length of time (no more than 130 years) spent in the garden before eating the fruit)?

Now, we all know what happened next:

"Now the serpent was more subtil than any beast of the field which the LORD God had made. And he said unto the woman, Yea, hath God said, Ye shall not eat of every tree of the garden? And the woman said unto the serpent, We may eat of the fruit of the trees of the garden: But of the fruit of the tree which [is] in the midst of the garden, God hath said, Ye shall not eat of it, neither shall ye touch it, lest ye die. And the serpent said unto the woman, Ye shall not surely die: For God doth know that in the day ye eat thereof, then your eyes shall be opened, and ye shall be as gods, knowing good and evil. And when the woman saw that the tree [was] good for food, and that it [was] pleasant to the eyes, and a tree to be desired to make [one] wise, she took of the fruit thereof, and did eat, and gave also unto her husband with her; and he did eat. And the eyes of them both were opened, and they knew that they [were] naked; and they sewed fig leaves together, and made themselves aprons." - Genesis 3:1-7

4. The implication in verse 1 is that God did not make the serpent. If not, who did? And if he did, why did he make such a sneaky creature and why did he not warn Adam and Eve not to listen to it? (Omniscient God, surely could have seen that one coming?!)

5. The serpent is always made out to be the deceiver, so how come he's the one that tells the truth?! As the serpent told them, "your eyes shall be opened, and ye shall be as gods, knowing good and evil." ... "And the eyes of them both were opened". God himself confirms what the serpent told them:

"And the LORD God said, Behold, the man is become as one of us, to know good and evil: and now, lest he put forth his hand, and take also of the tree of life, and eat, and live for ever: Therefore the LORD God sent him forth from the garden of Eden, to till the ground from whence he was taken. So he drove out the man; and he placed at the east of the garden of Eden Cherubims, and a flaming sword which turned every way, to keep the way of the tree of life." - Genesis 3:22-24.

6. If Adam was to die the day he ate the fruit, why the need to keep him away from the tree of life?

7. If Adam only "[became] as one of [God and ???]" after eating in the fruit, in what capacity was he created "in the image/likeness of God" (Genesis 1:27/5:1)?

8. Given the presumed perfection of Adam and Eve, made by God himself, the fact that they now knew about nakedness, their obvious inability to resist any form of temptation, and the lack of contraception... how did it take 130 years for them to make a baby?!

Answers on a postcard please...

I can't help but feel that far from the eating of the mythical fruit, the real "Fall of Man" was when widespread brainwashing with this nonsense became the norm in Western civilisation.

Wednesday, 30 January 2008

The Dragon Palace, Chinese Restaurant

Yesterday we went out for dinner to celebrate Caitriona getting a job. (Yay!) We went to a Chinese restaurant in Southampton, called The Dragon Palace.

It looks a bit cheap on the way in as you have to go up two flights of fairly basic stairs that look like a fire escape. Once you get to the top, though, the restaurant itself is fairly well decked out. Most of the customers were Chinese, which is always a good sign.

The best thing about it, I think, was that it felt like it was a social hub for the Chinese community in Southampton, with a fair amount of coming and going and happy chatter. There was some kind of party going on in a small room off the main restaurant, near where we were sat. This was fun except for the occasional wail of karaoke that made it as far as our table!

The Dragon Palace does an evening eat-as-much-as-you-like buffet. We intended to order from the menu, as buffets aren't always that great, but it turned out to be a really good deal; it wasn't a buffet in the all-laid-out-and-help-yourself way. Instead, you simply ordered whatever you liked (basically a choice of the entire menu) and paid for anything you didn't eat. You could keep ordering little and often, if you liked. We just had starters and a main.

We had one of my favourite foods of all time: crispy aromatic duck pancakes with hoisin sauce. Mmmmm... And one of my other Chinese favourites, crispy seaweed. Not sure exactly what they do to the seaweed (fry it sugar?) but it's very tasty! The hot and sour soup was also very good. All-in-all, well worth a visit if you're ever in Southampton looking for Chinese food. Another time, we'll have to go for dim sum!

Sunday, 27 January 2008


Today we had a little day trip to Winchester (on the bus). Winchester is lovely - a good mix of fairly narrow streets and old buildings, with great shops and nice places to eat. We'd been once before, to the Christmas Fair in the Cathedral grounds, but it was raining that day, so not quite so good for wandering around. Today was lovely a sunny, so much better for aimless meandering.

We had lunch in the Pitcher & Piano - part of pub chain that I last encountered when I lived in Nottingham. The Winchester Pitcher & Piano was not quite as grand as the Nottingham one, which is in an old church, but the food was very tasty. I had a lamb burger. Yum. Good chips too - you could tell they were once potatoes.

Instead of dessert, we got some lovely chocolates from Montezuma's. This shop is great and sells really tasty chocolate. I can particularly recommend Montezuma's Revenge (Dark chocolate, lime & chilli) and Tiger Tiger (Dark chocolate & vanilla).

Wednesday, 23 January 2008


Sue is a Tyrannosaurus in The Field Museum - the largest specimen found to date, I believe. (Obviously, there are more Sues than this, but it is the Tyrannosaurus Sue to which I refer.) She is pretty big as you might imagine. (At 12.8m long, I doubt that any of the other Sues are bigger than her.) Sue's head has a display case all to itself in the museum (shown) and the one on the rest of the skeleton is a reconstruction (as are many of the other bones).

Right now, I am drinking from a Sue mug, bought in the afore-mentioned Field Museum. Like Sue herself, this is rather giant. Nice.

Just do it!

I'm one of life's procrastinators. I'm especially good at "activity displacement" - the performing of any task except the one that needs to be done in order to avoid doing something I don't want to do. Unfortunately, while stuff does get done, this means that I build up an accumulation of things that I don't want to do. Invariably, these are far worse in my head than in reality, and the days of thinking about how I don't want to do them sum up to more discomfort than just doing them in the first place.

Today, I just said "stuff it" and did a bunch of things I'd been putting off for ages. Now they are done and I can forget about them! Hoorah! It's much better to be a doer than a procrastinator. I suspect that this new attitude will only until bedtime but nevermind, eh?