The question is as follows:
How does science get from:
"Let's see how far we can go using just reason applied to observations, while excluding any reference to God or divine purposes and revelations."
"We have disproved the existence of God, divine purpose and revelations."
And, to take a specific example - how does the biology of natural selection get from:
"Let's assume that all the variations upon which selection operates are un-directed."
(By 'un-directed' I mean that, for example, genetic mutations are not directed towards any function - but that the functionality of a beneficial mutation is a product of selection among rival genetic variants.)
"Un-directed variation is the only possible type of variation."
In other words, how is it that we get from a chosen exclusion, an imposed constraint, to the belief that the exclusion does not exist, and that the constraint is intrinsic to the universe.
I think the answer is psychological - it is something that is not a consequence of the abstract nature of science, or natural selection - but a product of the minds of scientists and biologists.
And I think the psychological mechanism is a fundamental aspect of the way that humans reason, which an astute author (name of Bruce G Charlton) described in some work on what he termed 'theory of mind delusions':
What happens to the psychology of the scientist/ biologist is something along the following lines:
As the scientist becomes adept at reasoning within his subject, the exclusion or constraint is 'marked' with a negative emotional evaluation, so that whenever it comes to mind it will tend to be avoided.
If/ when the scientist finds himself 'tempted' to reach for a divine explanation, if a biologist finds himself tempted to ascribe teleology (purpose) to genetic mutations, then a kind of 'metal alarm' goes off and makes the scientist feel bad in some way (ashamed, afraid, disgusted etc).
I mean it literally makes him feel bad - using the taboo concept in reasoning triggers nerves and hormones and alters the body state to feel bad.
And this is a property of the expert scientist, it is a product of proper training.
Over time the scientist learns (becomes conditioned to avoid) these subjects - and becomes able to reason fluently within the zone of constraint and exclusion.
However, if anybody else mentions the taboo subjects, then the negative emotional alarm goes off, and there is an attempt again to steer clear of the subject - to avoid or suppress it. It is a sign of professional incompetence to raise the taboo, excluded subject - annoying or embarrassing.
In general terms, assumptions frame investigations, so that investigations can only confirm assumptions (or be irrelevant to them) - and as a rule experience cannot contradict or refute fundamental assumptions.
This applies within science just as much as in other areas of life.
But this is not a specific problem for specific groups of people with specific beliefs - it is the nature of human discourse, and we all operate within analogous psychological mechanisms.
No amount of anomalous experience can ever cause challenge of fundamental assumptions, because it is the fundamental assumptions which make specific discourses possible, and to reject the assumptions is merely to be incompetent at that specific discourse.
No amount of failed predictions, no lack of precision, no amount of incoherence can ever, therefore, lead to the compelling inference that an exclusion was invalid, nor can it force the adjustment of a constraint.
From within a field of discourse (within philosophy, science, within biology) any acknowledged problems in the accuracy and coherence - and there always are such problems - is merely grist to the mill: they are what provides the discourse with an endless number of 'things to do'.
All problems do is imply the need for further development and elaboration of the existing theory - problems can never of themselves imply the need for a new theory.
So, once a discourse has - like science - succeeded in establishing itself as necessary; then the endless problems it encounters serve to justify endless expansion of the activity, in the case of science endless expansion of funding.
So - if not from encountering problems - why might the status of science, of natural selection, ever possibly, potentially change?
Because (for whatever reason) it becomes desired to include the exclusions, relax the constraints.
This entails the scrapping of the whole previous system (based on those constraints and exclusions), and the re-building of a new system (having different exclusions and constraints).
Qua philosopher, philosophy potentially explains everything; qua scientist science explains everything: biologist biology - and it goes further: qua lawyer law; qua journalist journalism etc.
The exclusions and biases which structure the system are invisible to the system which functions within them.
But... nobody is entirely located within their specialist discourse; and therefore nobody is wholly convinced by the hegemony of their expertise. And in society most people are outwith any particular discourse, which impinges upon them in alien ways.
So the larger and more dominating any discourse, the greater pressure is built against it. The discipline itself cannot internally perceive the force of objections to its own constraints and exclusions, but everyone outside that system, and other systems, have a growing interest in attacking those exclusions and constraints.
If and when the system ceases to provide what people want from it, or provide it at too high a cost, or if those outside the system cease to value what the system provides - and if the system is unable coercively to confiscate the resources it needs against the will of those of who provide the resources - then the system will collapse.