Thursday, February 22, 2007

Douglas Axe - J.Mol.Biol.(2000) 301, 585-595

Thanks to "Smokey" for the paper.
Previous blog post here.
This paper examines the idea that there are many amino acid residues in an enzyme which almost act as non-specific spacer residues and the nature of their side groups is almost completely irrelevant to the enzyme function. The only requirement is that the external residues be polar and the internal ones be hydrophobic (the binary code hypothesis). The paper argues that this idea is erroneous. Axe’s arguments rely on data from two different, unrelated enzymes.

Firstly, several amino acids are exchanged with several other very similar amino acids on the surface of the molecule and away from the active site and the effects measured. When roughly 1 in 5 of these residues is changed this results in complete loss of function in both enzymes examined.

Secondly, hybrids are constructed between two different versions of B-lactamase enzymes using various combinations of their surface sections. All of these hybrids are inactive.

Axe concludes that homologues that share less than 2/3 sequence identity should be considered as distinct designs with their own set of optimising features.

These results were surprising as they followed similar experiments where the hydrophobic core or an enzyme was systematically replaced and the conclusion was that general hydrophobicity was the only requirement for these core residues.

It was expected that the surface residues distant from the active site would show an even greater degree of tolerance to change than the hydrophobic core residues.

Axe compares the two hybrid situations with two functionally equivalent linguistic messages where exchanges between the non-conserved letters is functionally disastrous.

Tuesday, February 13, 2007

Away for a few days.

I will not be around for a few days so I will look at comments when I get back.

Thursday, February 08, 2007

Inside the Cell.

David Goodsell is a biochemist who is also an excellent artist. He has combined these skills in the production of beautiful paintings which seek to portray an idea of the molecular biology of the cell. More of his illustrations are here. He kindly gave me permission to use these pictures here:

This picture shows part of a bacterium.

(Can you spot the motor? :-) )

This one shows a section across a red blood cell with the blood serum outside the cell.

This is an enlargement of a small part of the same picture.

This picture shows an HIV virus particle under attack from the immune system.

(Thanks to Tony Jackson for the original link.)

"Strong indications of design."

Nick Jackson of the Independent interviews Stuart Burgess who argues that there are "strong indications of design" in the four bar linkage of the knee joint. The report is here.

Monday, February 05, 2007

The making of "The Root of All Evil."

In response to this question:
Why have you not engaged in public debate with Alister McGrath, Mary Midgley, Michael Ruse, Keith Ward, or indeed anyone else who would present you with a serious challenge? JAMES RADFORD, By e-mail
Richard Dawkins replied:
The producers of my Channel 4 documentary [Root of All Evil?] invited the Archbishop of Canterbury, the Cardinal Archbishop of Westminster and the Chief Rabbi to be interviewed by me. All declined, doubtless for good reasons. I don't enjoy the debate format, but I once had a public debate with the then Archbishop of York, and The Observer quoted the verdict of one disconsolate clergyman as he left the hall: "That was easy to sum up - Lions 10, Christians nil."
(from here)

Alistair McGrath gives a somewhat different slant...
Dawkins and I both love the sciences; we both believe in evidence-based reasoning. So how do we make sense of our different ways of looking at the world? That is one of the issues about which I have often wished we might have a proper discussion. Our paths do cross on the television networks and we even managed to spar briefly across a BBC sofa a few months back. We were also filmed having a debate for Dawkins's recent Channel 4 programme, The Root Of All Evil? Dawkins outlined his main criticisms of God, and I offered answers to what were clearly exaggerations and misunderstandings. It was hardly rocket science.
For instance, Dawkins often compares belief in God to an infantile belief in Santa Claus or the Tooth Fairy, saying it is something we should all outgrow. But the analogy is flawed. How many people do you know who started to believe in Santa Claus in adulthood?
Many people discover God decades after they have ceased believing in the Tooth Fairy. Dawkins, of course, would just respond that people such as this are senile or mad, but that is not logical argument. Dawkins can no more 'prove' the non-existence of God than anyone else can prove He does exist.
Most of us are aware that we hold many beliefs we cannot prove to be true. It reminds us that we need to treat those who disagree with us with intellectual respect, rather than dismissing them - as Dawkins does - as liars, knaves and charlatans. But when I debated these points with him, Dawkins seemed uncomfortable. I was not surprised to be told that my contribution was to be cut. The Root Of All Evil? was subsequently panned for its blatant unfairness. Where, the critics asked, was a responsible, informed Christian response to Dawkins? The answer: on the cutting-room floor.

(from here)

Saturday, February 03, 2007


The comments section at IDintheUK has been entirely uncensored up till now (apart from really foul comments and obvious advertising.) I would like it to remain like this. I have learned a lot from the very high quality of comments from people on both sides of this argument. This seems to me a great benefit of this kind of site.

In order for this to continue it does require some self discipline on the part of the commenters.

Generally you have responded well to previous pleas.

I would like people to feel free to comment under whatever name they like and to be able to comment annonymously if they so choose. I think that part of good blog behaviour is to respect that choice. Attacks on another commenter because of their background and percieved or actual bias are to be avoided- it is the arguments about the data and its interpretation that we should focus on.

Please try to avoid overly emotive language- I know that many commenters feel very very strongly about this area - It is good to feel strongly about truth and to expose what is not true ruthlessly and energetically. However resorting to the red card "LIAR" is rarely helpful in my experience. Even if you are convinced that someone is deliberately and knowingly lying it is better to suggest that they may be mistaken first and point to the evidence. If you must make an allegation of deliberate, knowing deception please make sure you have a cast iron case and please try to do it as little as you possibly can.

Friday, February 02, 2007

The Dawkins Delusion.

I have noticed several pieces about this odd phenomenon. Bill Dembski seems to have got hold of a very strange interview with Dr Terry Tommyrot, available here. Another interesting report of a discussion on the same subject is here.