Friday, March 28, 2008

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:
(9.6MB includes large images)

Wednesday, March 26, 2008

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?