Thursday, January 26, 2006

Very surprising results from the BBC biological origins poll.

In connection with tonight’s Horizon program on BBC2 examining intelligent design the BBC conducted what is probably the first poll on British attitudes to biological origins.

The results are shown here and are very surprising indeed. There was two parts to the poll with some analysis of the answers by age.

In the first part 2000 people were asked about their personal views on biological origins.

22% indicated their belief in “creationism”
a further 17% indicated their belief in “intelligent design”
with 48% indicating their belief in “evolution.”

The remaining 13% indicated that they “did not know.”

In the second part of the survey respondents were asked about what they thought should be taught about biological origins in science lessons.

In each case respondents were asked whether they thought each subject should be taught in science lessons.

44% said creationism should be included 41% intelligent design 69% wanted evolution as part of the science curriculum.

These are really quite surprising results as presumably the 31% who responded negatively to the teaching of evolution thought that NO evolution should be taught in science lessons!

With thanks to Wires from the Bunker


Imagine I had in my briefcase two papers ready to be sent to Nature which demonstrated beyond a shadow of a doubt that there was such a thing as irreducible complexity and that it could not be explained by random mutation and natural selection.
How would this affect the intellectual climate of the 21st Century?

Friday, January 20, 2006

Is the bacterial flagellum Irreducibly Complex?

By irreducibly complex I mean that the production of a particular function (in this case selectively advantageous propulsion by a rotating propellor of some kind) requires many specific simultaneous changes in 2 or more proteins such that it is unreasonable to think of them happening by chance.

I am interested to know whether any readers of this blog have read useful articles on the web which take the argument further.

I have looked at these:
1. Evolution in (Brownian) space:a model for the origin of the bacterial flagellum by N. J. Matzke 2. Mike Genes Series on Evolving the Bacterial Flagellum Through Mutation and Cooption
3. Ken Millers - The flagellum Unspun
4. William Dembski's Still Spinning just fine

If you have any suggestions please paste your link in a comment....many thanks!

Thursday, January 19, 2006

ID Falsification - Stage 1

ID is rejected as science both because it cannot be falsified and because it has been falsified (Ken Miller) which seems rather odd to me. I tend to agree with Ken Miller... that ID is falsifiable but that the Type 3 secretory system is insufficient for a really good hit below the water line!

The suggestion of co-option as one of the means by which biological complexity is generated is used to explain apparent irreducible complexity and the Type 3 Secretory system is suggested as a clear candidate for a functional intermediate along the way to a fully functional motor.

Behe and other ID theorists respond by saying that the Type 3 system is a broken flagellum rather than a stepping stone on the way there and if if it was a stepping stone on the way there it does not allow macro-evolutionists to cross the river.

Can this impasse be resolved?

I suggest that it could. Matzke proposes 6 stages along the way to a functional flagellum.
If it could be shown that these six stages provide a selectively advantageous function and that the steps in between are "mutationally plausible" as Matzke claims then for me the argument over the flagellum is over.

If we take as an example the two putative structures from Matzke’s series either side of the acquisition of the mutation which gives a selectable motility trait:

It surely cannot be beyond the limits of modern mathematics, computer science and molecular biology to work out the probability of the necessary changes occurring independently in the relevant proteins to get a primitive flagellum can it?

Given the mutation rate and an estimate for the time and approximate number ofrelevant this a reasonable step?

I have no idea...but If it is and if the Protoflagellum works and provides a selective advantage then as far as I am concerned the argument over the flagellum is over. Those "if's" are very big however!

Show me 6 selectable intermediates and show me that the above step is indeed mutationally possible and I will stop shouting....Look at this motor .....Look at this motor!

Is that a reasonable challenge? Is it falsifiable?

Saturday, January 14, 2006

Paul Davies clarifies the origin of life:

"All it takes to get life started is a quantum replicator - a process that clones bits of information attached to quantum systems by allowing them to interact with other quantum systems in a specific way. The actual system could be anything at all - the spin of an electron, a meta-stable atomic state, or a molecule that can flip between two conformations. The uncertainty inherent in quantum mechanics provides an in-built mechanism for generating variations."

Ahhh....that clears things up then!

Friday, January 13, 2006

Which Golf Course?

As I understand it....

Darwin himself proposed the following make or break test for his theory:
"If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.”

ID reads “complex multi-protein genetically defined structure with a novel function” for “complex organ” and proposes that the bacterial flagellum motor function is one such case. Not that it could not occur by numerous successive slight modifications BUT that the pathway to the final working structure is too improbable to allow us to accept chance mutation and natural selection as reasonable causes of the structure.

ID suggests that the pathway to a useful motor function does not have sufficient selectively advantageous “stopping places” along the way to allow an unintelligent process to reach it in the amount of time available.

Thus Darwin proposes that the “golf course” where the “hole” is the working motor performing a useful function is more like a cone with the hole at the tip….gradually the “golf ball” will move under the weight of selective advantage to the “hole” of molecular motor function.

ID proposes that the “golf course” is more like a real golfcourse where blind and deaf golfers are at a distinct disadvantage!

If ID is true then one would hope to find:
(a) there would be very few functional selectively advantageous structures as intermediate stopping places along the way to the motor function. (the golf course is not designed to make a 'hole in one' likely for any rolling golf ball)
(b) The number of possible structures with a motor function will be relatively few (the hole is small)

If Darwin’s theory were the true explanation of the origin of the motor function of the bacterial flagellum then one would hope to find:

(a) there would be many functional selectively advantageous structures as intermediate “stopping places” along the way to motor function. (the golf course slopes down to the hole)
(b) The number of possible structures with a selectively advantageous motor function will be relatively large (the hole is large.)

...have I grasped the issue?

Tuesday, January 10, 2006

Richard Dawkins....Fraudster?

Richard Dawkins is the Microsoft supported - Charles Simonyi Professor of the Public Understanding of Science at Oxford University and is perhaps the world's best known atheist.

Is he trustworthy in his presentation of the evidence that evolution can explain a complex structure like an eye?

In his book 1995 Book "River out of Eden" he says the following about a scientific paper written by Dan Nilsson and Susan Pelger:

[Their] task was to set up computer models ofevolving eyes to answer two questions ... [:] isthere a smooth gradient of change, from flat skin to full camera eye, such that every intermediate is an improvement? ... [and] how long would the necessary quantity of evolutionary change take?In their computer models, Nilsson and Pelger made no attempt to simulate the internal workings of cells.... Nilsson and Pelger began with a flat retina atop a flat pigment layer and surmounted by a flat, protective transparent layer. The transparent layer was allowed to undergo localized random mutations of its refractive index.They then let the model transform itself at random,constrained only by the requirement thatany change must be small and must be an improvement on what went before. The results were swift and decisive. A trajectoryof steadily mounting acuity led unhesitatingly from the flat beginning through a shallow indentation to a steadily deepening cup, as the shape of the model eye deformed itself on the computer screen... And then, almost like a conjuring trick, a portion of this transparent filling condensed into a local, spherical region of higher refractive index.... This ratio is called Mattiessen's ratio.Nilsson and Pelger's computer-simulation model homed in unerringly on Mattiessen's ratio.
As far as I know Dr Dawkins has made no attempt to retract or modify these sentences. They are seriously misleading. Dan Nilsson has stated in a letter sent to David Berlinski that there was no computer simulation in the research that led to the paper despite the fact that this simulation is brandished around the world as one of the most startling testimonies to the ability of random mutation and natural selection to produce complex structures like an eye!

This controversy blew up in the "Commentary" as "A Scientific Scandal" (available on the Discovery site abbreviated here)and David Berlinski has made available the letters and his response here.

If David Berlinski is to be believed the paper actually makes some fairly basic mathematical blunders.

Two things irritate me:
1. This serious case of misinformation has gone uncorrected for so long and is treated as a "minor error."
2. This kind of study fails to deal with the real issue which is in the area of a particular genetic program controlling the development of the eye and yet is presented as if the huge problems with making an eye have effectively been solved.

ID - Untestable? Unfalsifiable?

The opponents of ID cannot have it both ways...or as the saying goes they cannot have their cake and eat it.

If ID is not testable or falsifiable then it can never be argued that examples of so called "bad design" show that ID is wrong. If ID is not testable or falsifiable then the critics who claim this should attack Ken Miller for presenting the Type3 Secretory system as evidence that ID is wrong.

An untestable and unfalsifiable hypothesis is "not even wrong." As far as hypotheses go that was the ultimate insult....but a hypothesis that is "not even wrong" cannot be shown to be wrong.

If ID made no specific hypotheses that could in principle be shown to be untrue then why are anti-ID people so keen on the Type 3 Secretory system....

By presenting the Type 3 secretory system they are proclaiming that ID is a testable and falsifiable hypothesis and that we have tested it and found it is wrong.

You cannot say the ID is untestable and unfalsifiable.....and then say.... we have proved that it is wrong.

Which way it is to can't have it both ways.

Monday, January 09, 2006

ID untestable? Nonsense!

Jay Richards and Jonathan Witt have put up a piece here about whether ID claims are empirically testable or not. I am interested to know what those who have claimed in comments on this blog -that ID is not science - think of this piece.

(Also, I am interested in what they think of Behe and Snokes paper in Protein Science - "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues" )

William Dembski....can he add up etc.

I brought this up before but I noticed someone who left a comment to the effect that Dembski's mathematical abilities are under question. I have heard contradictory views about this and I am personally not in a position to give his mathematical work a careful scrutiny... I am however very interested. I have heard it suggested that the inventor of the "No free lunch theorems" thinks that he abused them and I have heard that Dembski and Shallit are not on speaking terms for one reason or another. I have also heard that his maths is fine from other people is just he muddles up the conclusions!

It surely shouldn't be difficult for someone who is well qualified to work out whether he is competent and whether his work is leading to valid conclusions or not.

Who am I supposed to believe on this and why?
Can someone qualified and respected give me a truly objective report on Dembski's mathematical ability? Did CUP make a big error or not?

Friday, January 06, 2006

The Ideal Atheist State

I know it is off topic ...but I am interested.

How does an atheist like Dawkins or Dennet or Myers suggest a legal system should be contructed from first principles?

In other words upon what basis precisely does a leader have the authority to command obedience to any rules... and how is the leader supposed to get a satisfactory set of rules in a state.

In my little experiment....imagine that the Pilgrim Fathers were all persecuted atheists who wanted to set up an ideal atheistic state.... or if you like ... put Dawkins, Dennet and Myers on a boat and send them off to build the nation of their dreams...what would it look like? Any suggestions? I am especially interested in how they would go about building a new legal system from scratch.

Thursday, January 05, 2006

Failing to solve the origin of our grandchildren.

I thought these quotes over at post-darwinist were more honest and realistic than usual from Origin of Life researchers.

Tuesday, January 03, 2006

Evolve, Evolving, Evolved, Evolution, Evolutionary

The word Evolution is too elastic and its use in different ways is causing serious confusion.

The word evolution can be used to describe a range of phenomena ranging from

(a) An exclusively materialistic account of the whole subject of biology including the origin of the first “organism” and the human race.


(b) Small changes in a population of a particular gene (e.g. Industrial melanism, and bacterial antibiotic resistance)

All the creationists and pro-ID people that I have come across distinguish between the evolution that we know occurs and is real from the evolution that is more speculative and is poorly understood. A pair of terms: micro-evolution and macro-evolution has been proposed to allow this confusion to be overcome.

Interestingly anti-ID people reject the distinction between macro and micro evolution and insist that only the word evolution be used. This means that in popular level coverage pro-ID people and creationists especially of the YEC variety can be presented as those who deny obvious facts of reality. If you are pro-ID you reject evolution and therefore you reject obvious scientific facts.

It is the interesting area of macro-evolution that ID is concerned with. How we explain the origin of complex circuits with control elements as integral, motors, integrated transport systems, integrated building programs etc.

Is the proposal to seek to clarify the terminology of the debate reasonable?

Macro-evolution – Origin of Life, Origin of significantly different body plans, origin of integrated body systems – Essentially multi-protein systems and structures requiring integrated, concerted action.

Micro-evolution- Gene frequency changes, protein homology studies, gene duplication and mutation.

I am convinced that clarity in terms of what the word means is essential if any meaningful debate is to be had and especially so that a wrong impression is not created which can inflame the situation needlessly.

So my question is … why are people who are convinced that macro-evolution is an exclusively materialistic process against clarification of the terminology. I reckon it is a useful distinction even if materialistic macro-evolution turns out to be true.

P.S. I remember a paper being mentioned that dealt with this area as suggestions for biology teachers...if anyone has a reference to this paper I would be most grateful.