Self Organisation is the Answer

From an interesting Telegraph article here.

"Evolution on its own doesn't look like it can make the creative leaps that have occurred in the history of life," says Dr Seth Bullock, another of the conference's organisers. "It's a great process for refining, tinkering, and so on. But self-organisation is the process that is needed alongside natural selection before you get the kind of creative power that we see around us.

Is Science atheistic?

“Some say God is living there. I was looking around very attentively, but I did not see anyone there. I did not detect either angels or gods…. I don’t believe in God. I believe in man—his strength, his possibilities, his reason.” (Titov USSR)

The question that interests me is whether atheistic scientists are willing to acknowledge that a clear line can be drawn between science and atheism. Can one be just as committed to science and yet believe in the reality of God, spirits, miracles and special revelation or is an atheistic, materialistic world view the only real position that a true scientist can take.

1. Is science intrinsically atheistic? Atheistic science is the true un-encrusted form whereas theistic science is a primitive medieval form of science prior to its emancipation to full grown materialism.

2. Can the tools of science be seen as a valuable toolbox which can be used usefully within a variety of philosophical contexts and presuppositions but has limited value in actually testing those contexts and presuppositions.

3. Can the results and evidence produced by the toolbox of science be seen in different ways according to the presuppositions and philosophical contexts of the individual scientist? Do the presuppositions and philosophical context of the scientist affect the way in which the data is interpreted and put together? Do the presuppositions and philosophical context predispose individual scientists to particular interpretations of the evidence?

Institutionalised Idolatry

One of the key blindspots of atheistic scientists it seems to me is their inability to distinguish between beliefs based on evidence and beliefs based on presupposition. There seems to be the assumption that any "religious" position is antagonistic to some kind of "normal" view of any civilised democracy. The "normal" view of any civilised democracy is of course secular humanism - atheism- the worship of man as the highest authority. What they seem to have missed and be apparently completely blind to is that this secular humanism is just as much a "religious" position and faith as any other "religious" position. Its assumed "normal" and superior status is just another kind of religious orthodoxy seeking to impose its dogmas upon a society. Many people including top scientists seem to be entirely blind to this.

I thought Geoffrey Lean's article very perceptive.

Tail on the Donkey

I was thinking about Intelligent Design and I thought of the old children’s game that we used to play – Pin a tail on the donkey. The children competing would be blindfolded and each would be given a tail with a pin in it. They would have to guess the correct position of the donkey and pin the tail where it was supposed to go. Get the tail in the right place and you are a winner.

This is a bit like finding a protein that works by random mutation. The protein that works is the donkey with the tail in the right place.

The key variables are the size of the available space for your pin and the number of people trying to stick the pin in the right place.

Of course there is not just one right sequence that works and gives a selective advantage and there are of course many more players in protein building than children at a party. However the key question is - how realistic is it to think that random mutation and natural selection are sufficient tools to build all the proteins and protein combinations that are required to explain biology as we know it?

If we made our illustration realistic….

• How big would the board space be for sticking the pins in?
• How big would the area be that give a selective advantage?
• How many tails need to be stuck on how many donkeys at once?
• How many children do we need on the board to make life as we know it a realistic achievement for chance mutation and natural selection?

These are the big questions for ID research. One would have thought that biologists would agree that these are really exciting questions to be asking. This is the area where there is a real possibility for the main mechanism proposed for evolution to be falsified and shown to be unrealistic. That surely makes this research great science and exciting science.

That is the sort of research that Doug Axe is trying to do…. But it isn’t being funded by the usual biology funding pathways. He has developed a good method. He has published good work in the field. When you mention that he works in the Biologic Institute to the Darwin faithful at best you get a sneer at worst a snarl and curses!

You could put his decisions down to one big weird publicity stunt or say that the fellow has lost his marbles or you could say that there is more going on in modern molecular biology than a disinterested pursuit of the truth…wherever it leads.

I have a hunch that it isn’t just a publicity stunt and that his marbles are pretty much all present and correct and that he might be right and he might be able to demonstrate that he is right. I hope so and wish him well!

The Biologic Institute.

I have been following Douglas Axe's work with interest (see here and here) so I was very keen to look at the website of the Biologic Institute. This is the research institute that is funded by the Centre for Science and Culture which Douglas Axe is in charge of.

On the research page there are reports of what they have been working on and descriptions of the research which has been or is shortly to be submitted for peer review. "The difficulty of interconverting the functions of structurally similar enzymes" is one of the areas in which I will be interested.

The sad part of the story is why such an institute is needed at all. The work that Douglas Axe has done and the systems that he has set up should be supported in the usual way without the need to set up a separately funded institute.

How do Scientists use the word “Theory”?

I have heard many people who believe in Creation say “But evolution is only a theory.”
What they mean is that in denying the evolutionary view of life they are not denying proven facts.

The difficulty is that the statement includes two words which are used in very different ways and the statement is therefore open to serious misunderstanding.

I explained why I believe that distinguishing between micro and macro evolution here.


I want to set out a few thoughts about the word “theory” here.

It is a word with multiple senses from relatively loose to very tight and is therefore a source of confusion.

In ordinary speech it is used in the following ways:
Speculative suggestion which provides an explanation for one or more observations. The Shorter Oxford dictionary has this description: “An unsubstantiated hypothesis; a speculative (esp. fanciful) view.
Theory vs Practice – In theory how something should be done – Abstract knowledge and speculative thought. A scheme of how to do something including all the rules and principles to be followed- eg a theory about bringing up children.
A hypothesis that has been confirmed or established by experiments or observations and is accepted as accounting for known facts.
In science the word has a set of more specialised meanings.
There seem to be two dimensions of use of the word “Theory” in Science.

Its reach – how high in the hierarchy of scientific knowledge is it?
“a comprehensive explanation”
The oxidative stress theory of Ageing is of a much lower order in Biological Theories than the theory of evolution.

Its validity – how certain are we that it is correct?

There are five ways the word is used in science:

1. The NAS definition of scientific theory indicates that the use of the word theory should be reserved for the very highest level of validity:

“supported by many facts gathered over time” “so well established that no new evidence is likely to alter them”
Tests – Logical consistency, How throroughly it explains data and how broadly it can be applied.
The Panspermia theory of the origin of life on earth is of much lower validity than Theory of DNA being the coding molecule for the production of proteins in the cell.


The NAS has attempted to define the word theory as having a very wide reach and the highest possible standard of validity.

“In science, the word theory refers to a comprehensive explanation of an important feature of nature that is supported by many facts gathered over time.”
“Some scientific explanations are so well established that no new evidence is likely to alter them. The explanation becomes a scientific theory.”

However though the NAS clearly uses the word like this in some of its publications this is not a comprehensive definition covering all uses of the word in the current professional scientific literature. On its own this is actually a misleading definition and is therefore unhelpful. It does not relect the real usage of the word in science.



2. It is used for a confirmed hypothesis.
e.g. New theory confirms that genetic kin recognition is inherently unstable, explaining its rarity.
3. It is used for an unconfirmed hypothesis or for one of several competing hypotheses.
e.g. here
4. It is used for explanations which have been shown to be incomplete or even wrong.
e.g The Ether Theory for the propagation of light.
Newtons theory of motion ie it is not a complete theory and does not work well near the speed of light.
5. Theoretical speculation currently unverifiable- String Theory or Theories of Everything.

Now in what way is ID a scientific theory and in what way is it not?

I would answer
1. No
2. No
3. Yes
ID is one of several competing hypotheses for the origin of biological complexity.
4. No
5. No

Other references:
http://en.wikipedia.org/wiki/Theory

http://www2.ncseweb.org/kvd/experts/behe.pdf
(9.6MB includes large images)

Realistic Cooption.

It seems clear to me that, at the very least, Behe’s book “Darwin’s black box” stimulated interest in, thinking about and probably research into - the origin of complex integrated biological systems.

As I understand it the current Miller/Matzke etal explanation for the origin of the rotary motor propulsion systems in bacteria is a series of cooption events.


Function 1 (1 or more proteins)

↓

← Function 2 (1 or more proteins)
↓

Function 3 (2 or more proteins)

There is an assumption that all the proteins which form the motor have all been collected and modified from other purposes in the bacterial cell. In the words of the New Scientist article- it was “cobbled together.” Some of the proteins in the motor have not been found to have any homologues elsewhere but let us assume that homologies for all the proteins will be found at some point.

My big question is whether this explanation is realistic. Obviously we can imagine it happening providing if we try hard enough. The big question that remains to me is whether this is just wishful thinking. Is it realistic to imagine this happening? How can we know when a series of imagined cooption events is realistic or not.

Obviously if we find compelling examples of intermediate stages this helps but is there a way in which we can test whether our evolutionary imaginations are being kept within realistic limits?

Outboard motors made without design.

The New Scientist has a piece announcing the death of the flagellum as the great champion of the demonstrations of design in biology.

It is a well written piece and gives a useful summary of the response of Darwinists to Michael Behe's argument of Darwin's Black box.


The arguments can be summarised:

1. There are lots of different flagellum like systems. If there was a designer he would not design this more than once

[This makes the assumption that people who believe in design do not believe in any evolution at all. It is a theological argument which claims to be able to see into the mind of God and say what he would or would not do.]

2. There are strong homologies of the flagellum proteins with the proteins of the Type 3 secretory system(T3SS). (Workers acknowledge that the T3SS probably came from the flagellum rather than the other way around.)

3. There are homologies with many of the other proteins suggesting that many of the flagellum proteins may have been co-opted from other functioning structures.

The conclusion is...
"this abundance of homology provides incontrovertible evidence that bacterial flagella are cobbled together from recycled components of other systems - and vice versa - through gene duplication and diversification. In other words, they evolved."

To my mind that is just rubbish.
Most of the proteins showing some homology to other proteins does not prove that it is reasonable to think that the blind watchmaker made it without any help.

"Evolutionary biologists have put their house in order. It's time for their opponents to do the same." Doolittle

This is about as close as Darwinists go to saying that Behe made an important point in his book!

I am afraid that I still think that it is reasonable to conclude that the bacterial flagellum could not be assembled in the way that these champions of the fight against "unreason" maintain. [Unreason = any vestige of a conviction that intelligence is required for the origin or diversity of life]

It is a pretty cheap response to Behe's argument to present the whole problem as essentially concluded in favour of a blind watchmaker simply by showing that many of the proteins in the flagellum have sequence similarity to other bacterial proteins.

The big questions that still remain in my mind are these:

1. Is it reasonable to think that there is a pathway from these proteins doing something else to their specific function in the flagellum that we see today.

2. Is it reasonable to think that the proteins that are required but which have no known homologies could also arrive to allow the flagellum to function.
3. Is it possible to get to a clear answer for the above two questions. Is it possible to test whether Darwinists are simply excercising too much faith in the power of the blind watchmaker or not.


I am aware that Darwinists are good at imagining long pathways of functioning machines with gradually increasing complexity...but how do we know if they are reasonable or not? Should I believe them until someone demonstrates it is impossible or should I disbelieve them until someone demonstrates it is possible?

Maybe a simple thought experiment will clarify what I mean...

Let us imagine a machine which does something useful (but is not a motor)which contains all but 4 of the proteins needed to make a motor.

Let us imagine that those four proteins are busy doing something else in the boring but busy immobile bacterium.

Let us imagine that those four proteins have all duplicated and the duplicate of each is busy accumulating point mutations etc such that they can no longer perform the function the blind watchmaker made them for.

Let us imagine that the times are good- all the economic indicators for bacteria are favourable - it is a real baby boom and the population is rocketing!

My question is - How big are the targets that these four proteins are aiming for? (please excuse the teleological nature of the sentence!)

Is it reasonable to think of all four hitting the target at the same time?

Is that a reasonable scenario or do Darwinists imagine the co-option of one protein at once? With each addition providing selective advantage??

Who adjudicates fairly what is reasonable here? The champions of reason of course.