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.

Freak spaghetti arrangement?

Synthetic Life.

Spontaneous living cells in a test tube from simple ingredients?
Well no …..not quite…. we supply the carefully made membranes….oh and the 36 enzymes…. Oh and also the ribosomes…..oh and also the genetic information! But we are nearly there!

At least this is the illusion that some origin of life researchers seek to indicate.

Dr. Giovanni Murtas from the Synthetic Biology and Supramolecular Chemistry group at RomaTre University says:

"We can prove at this point that we can have protein synthesis with a minimum set of enzymes - 36 at the moment."

The fluescent green colouring indicates that these "primitive cells" can synthesize a protein from the supplied genetic information.

According to the guardian account this result “will teach us about the earliest stirrings of life in Earth’s primeval slime some 3.5bn years ago.”

Yerrr sure!

I would have thought that to any unbiased observer this result simply reminds us all that there is no hope that the primeval slime…no matter how exotic and how many billion years you give it will ever produce a living organism with minimal information and functioning protein machinery.

The information to specify such elegant structures as these does not hang around in primeval slime waiting for 36 enzymes and a few ribosomes to arrive.


I am not against this kind of work at all... I applaud it! What I am against is giving the impression that the solution to the problem of the origin of life is nearly solved and it is just a matter of time before we crack it.