Sunday, January 28, 2024


There has been a long gap on this blog.

I got into lots of discussions with atheists and materialists about intelligent design (ID).

One of the common objections to ID was that IDers never did any science and never did any work other than attack atheism.

I felt that this was grossly unfair but I have done the work and now am ready to do battle again.

I am also going to change my approach. Earlier posts sought to be respectably scientific and I sought to keep out of my posts and arguments anything explicitly Theistic and Christian. I am not going to restrict myself in any way like that from this point. I am a Theist. I am a Christian. I am a Creationist. I am also a scientist and I love matter and I love logic and I love reason... intensely...fiercely.. but I am convinced that the matter that actually exists points to an origin which matter cannot account for in itself!


Round 2 - let the battle recommence! 

Wednesday, December 15, 2010

What is Intelligent Design?

It is the area of science that studies the signs of intelligence.
Intelligent agents produce artifacts that other intelligent agents can recognize as the products of intelligence.
These artifacts may include:
1. Complex information


2. Multiple parts functioning together which have an irreducible core.

Sunday, October 17, 2010

Shortcuts to new protein folds.

There are some possible shortcuts.
1. The changes that are known to occur which change how specific an enzyme is for a particular reaction thus allowing it to use a slightly different chemical.
These are where a small change in the structure of an existing protein means that it can use a slightly altered substrate.
Examples of this kind of change are the oscillations in the antibiotics battle.
People discover an antibiotic --> microbes die
a microbe develops resistance by a small change in protein structure --> people die
People develop a slightly changed antibiotic --> microbes die.
In these cases there is a shortcut to other similar functions by a relatively small number of mutations.
(Usually it is this kind of change that is presented as evidence for evolution.)
Why aren’t this kind of shortcuts sufficient to reassure us that evolution can solve the problem?
Not all proteins have this kind of relationship with each other. Protein databases have 1777 classes of structural domains These are the “superfamilies” of protein structures. There may be recognisable similarities between domains within a superfamily … but the superfamilies themselves are not related.
Even if all the proteins within a superfamily can be derived from one original sequence this does not explain the origin of all the 1777 plus classes of superfamily.
2. If a relatively few changes causes a change in function and this is followed by subsequent sequence divergence in the new protein. Axe considers an example of this from PA Alexander published in PNAS….. and argues that this will not get us very far.
3. If proteins are made up of a relatively small set of “chunks” rather like a lego kit. This would simplify the problem of building a new protein superfamily. Gene fusion events can be used to build a new structure.
But Axe states that…”The binding interfaces by which elements of secondary structure combine to become units of tertiary structure are predominantly sequence dependent, and therefore not generic.”
Thus enzymes with an identical function and 50% sequence similarity do not have chunks which are interchangeable. Even when this similarity is increased to 90% equivalent chunks are not interchangeable. Graziano and his co-workers constructed and tested a huge library of 10^8 variants of gene segments and found none that formed a folded structure.

Axe concludes that all of these putative shortcuts are dead ends. The Darwinian search mechanism is not capable of finding new protein folds by random sampling and all the shortcuts to new folds are dead ends.

Sunday, September 26, 2010

The Origin of Protein folds

Just trying to simplify the arguments of Axe in his review paper...

If we take E.coli as our model then the average length of a functional protein is around 300 amino acids.

If the protein is longer or if a number of different proteins are required to act in concert then the problem is made worse.

The number of possible sequences to be sampled to find functional proteins of this moderate size is vast...

There are two ways of reducing the sparse sampling problem.

(a) The number of possible sequences with a particular function is very large. Sequence space is rich in function.

(b) The functional sequences are in some way linked- once you have one function it is easy to jump to the next.

Axe argues that experimental results indicate that (a) is not big enough to solve the sparse search problem....

I will look at what he says about (b) next week!

Tuesday, August 17, 2010

The Case Against a Darwinian Origin of Protein Folds

One of the paragraphs from the conclusion of Douglas Axe's recent article:
Clearly, if this conclusion (A dawinian search is insufficient to find new protein folds) is correct it calls for a serious rethink of how we explain protein origins, and that means a rethink of biological origins as a whole. Drawing on some of the points developed here, I presented an earlier version of this case several years ago to two prominent experts in the field. Bothered by my conclusion, both felt that it must be in error. When the three of us met for a discussion, they had their own hunches about where my reasoning might have gone wrong. Interestingly, though, after perhaps two hours of heated discussion neither agreed with the other’s hunch, and we ended up at a polite but dissatisfying impasse. I left with the distinct impression that my conclusion was being rejected not because it was unfounded but because it was unwelcome.