Some beliefs that are usually incorporated to support evolution are:

-The world is purely physical/material in nature

-There is no such thing as real agency (free will)

There is no real purpose/meaning in the universe

I'd be curious where you can point to these being used as evidence for evolution. You won't see them in any major biology textbook. Note that even if they are used that way that doesn't become a problem with evolution by itself.

. If for example a person does not accept that all of existence is physical in nature, then he is more likely to question the 'evidence' of evolution.

This statement is probably true. But why is it true? It doesn't have anything to do with evolution as an issue and primarily has to do with the fact that most classical religions have creation stories and other aspects which make evolution uncomfortable for them, and people who are religious form a substantial overlap with people who make claims about non-physical or non-material existence. Similar remarks apply to your other bits. These are people who are unhappy with evolution not because of evidence but because it goes against their theological predilections.

Evolution is seen by many people through the lens of materialism/atheism. That means that while studying evolution these people ASSUME the world has no creator and and is purely physical and closed system, free from anything super-natural....and so on.

In that way, any discovery in biology is treated in this interpretation and millions of dollars of research money is used to search for evidence in that way.

If we found in every single mammal a long conserved sequence in its genome which had its own extra code to help conserve it and it spelled out in easy substitution code the entire text of some religious text, you can be very sure that every biologist would stand up and take notice. Moreover, your claim doesn't really follow since there are many religious biologists (like Ken Miller, a very religious Catholic) who are perfectly ok with evolution and the entire standard understanding of biological history.

At this point, your argument really doesn't amount to anything other than apologetics. In this context, we've looked at every single thing that we know for sure is designed, and we can see simple common patterns (which moreover are patterns that make sense for designers to use). It is possible that you are missing part of the point so lets make it clear: most of what I've talked about above has nothing to do with "good" or "bad" design. Products that really suck (e.g. Windows ME) show the same basic patterns. The only one of the above that hits on the quality of the design is efficiency. Things like reuse are simply habits of design.

At this point, you are claiming that something is a philosophical presupposition, but even without that class of presupposition, we get the same result by simply looking at the designed objects around us. To then claim that no matter what we see it may or may not be designed makes the claim unfalsifiable.

To focus in on those sporadic examples of design that we do not understand and to leave everything else that seems so complicated and fine tuned for life is the ultimate example of how a philosophy is driving your view of science and the world around you.

They aren't sporadic examples, they are the entire tree of life. To use just one example from my list- we see essentially no examples of reuse of the same designs or parts of designs. And this is true not just for examples in specific body parts (such as the panda's thumb, or the mammalian eye) but for whole species. In isolated areas like Australia and Madagascar, species have filled nearly identical niches to the niches filled in much of the rest of the world, exactly as you'd expect from evolution, and not what we see human desigers do.

At that point, you have a deity who is not only making things not as a designer would be likely to make them, but you have a deity that is making things in a way that is actively deceptive. The deity has made life which down to the last detail looks old and evolved.

It may help to ask yourself what it would take for you to accept evolution. Is there any evidence that would do so? If not, the problems of philosophical presuppositions would seem to be if anything an issue of projection.

FWIW, I have heard a more generalized version of Ghazzali's argument, which goes something like this:

The way a person sees the world is colored by his preferences and biases. We all have them. You personally place a very high value on empirically reproducible results; this is what you call "truth", and you are strongly biased in favor of it; your insistence on proper logic and evidence stems from this core belief. There's nothing wrong with that, but I personally don't value this specific notion of "truth" as much as you do. Instead, I place a higher value on personal happiness/simplicity/social approval/niceness/whatever. Thus, I choose to believe in an unseen designer/universal consciousness/karma/etc., and it doesn't matter to me whether there's any evidence for it or not. Evidence is your thing, not mine.

I'm not endorsing this worldview (and I'm probably not even rendering it properly here), but I do believe it to be pretty much argument-proof. You can't have a rational discussion with someone who denies the value of rational discussions.

First of all, what are you defining as a "world view" and why is that a useful definition to have? It seems like you're trying to say "You believe things, beliefs are dogmas, you're being dogmatic". That is whole manners of cheating.

Secondly, you're right. It is possible that the universe was intelligently designed. But the Kolmogorov complexity formulation of Occam's Razor necessarily requires I assign that a very small probability prior. In order to simulate a universe designed by God, a computer must first simulate God, including why ey would create the universe the way that it is, then simulate that universe, as opposed to just simulating the universe.

So there's some seed of a potentially valid point here. Phrased in a Bayesian fashion, if one assigns low enough priors to certain hypotheses, one isn't going to practically consider those hypotheses unless one has ridiculous levels of evidence. So is something like that happening here?

I think the conclusion is "no". There are many religious individuals who have no objection to evolution. The objections stand essentially from religions which have creation stories which are important to the theology. For example, in Christianity, the Fall is very important, and you get a lot of Christians who object to evolution. Islam and Judaism have as important theological points that there deity is the creator, but the method of creation isn't as important, and one sees less objection to evolution in those religions. Among some religions which don't have any issues of this sort, or have very weak or very seldomly directly intervening deities (such as some forms of New Age religions) one sees close to no objections to evolution (although there are some prominent exceptions such as Deepak Chopra). But in all these cases, there are people who adopt an essentially similar theological standpoint and yet accept evolution, and this includes full-out major denominations such as Roman Catholicism. Now, it is possible that they simply haven't really adapted a consistent world-view (consistency isn't a human strongpoint), but that's an argument that would need to be made in detail.

In this case you see the amazing complexity of life as a product of chance/random events and not because of some genius unseen designer. The beautiful world you are describing could be interpreted as being the product of either, and the science itself would not change.

So this actually isn't the case. Evolved life doesn't look like what you might expect from a designer. When we looked at designed objects we see all sorts of commonalities that make sense from a design standpoint: we see efficiency, modularity, and reuse of parts between designs. We don't see any of those in evolved life.

Large amounts of life-designs are highly inefficient, almost as if they were added haphazardly by evolution. The giraffe's nerves which loop all the way from the head down through the neck and then back up again to the head are a good example.

We don't see modularity- pieces don't develop and integrate separately except at a very weak level. Thus birth defects that cause one organ to not grow frequently cause problems throughout the body or at very minimum in neighboring organs.

And we don't reuse of design pieces except for the very basic aspects that form a perfect nested hierarchy. This is in contrast to for example computers. This would be akin to having only mice on one type of computer, and only joysticks on another, and the only computers with USB drives were a subset of the computers with mice that didn't overlap at all with some subset of computers with mice with CD drives. But we don't see that with computers, or cars, or any other designed object that has many different designed versions. They reuse the same ideas and technologies. This is something designers do for obvious reasons: you don't need to reinvent the wheel. But evolution (aside from some very tiny examples of horizontal evolution where a single gene or small number of genes has been copied over due to viruses and a few neato parasites like my favorite parasite, Wolbachia) doesn't have that option. Pandas would have a much easier time if they had a real thumb instead of an inefficient bone spur. A direct design would have copied over the great ape thumb over or use a very similar design.

So this really is an example where one can look at what one would expect from design and from evolution and conclude that evolution makes more sense in context. This doesn't rule out less direct intervention, say a deity setting up life on the planet, letting it evolve and then showing a few thousand years ago to talk to a desert tribe and tell them not to eat shellfish. But that's a distinct issue from evolution except in so far as that if the same text that claims this deity did intervene also claims that the deity did design everything from scratch, then that's a reason to maybe doubt the text. But this has nothing to do with belief structures or as the Bayesian would say, extreme priors. This is about evidence.

For what it's worth, I used to draw a distinction between macro and micro evolution. I always argued that it made little to no sense for species to evolve sexual reproduction - and how would that work anyway?

But I remember exactly when I changed my mind. I was in a genetics class, and we were learning about sex pili - they're basically channels that bacteria can form to pass DNA between themselves. I realized that life (and evolution) are a whole hell of a lot more complicated than I gave them credit for, and that perhaps evolution is the tiniest bit more creative than I am.

Can you explain how the view that there is purpose, meaning, agency or design in the universe helps us address any anomalies better? With examples?

That depends on how you define 'system'. Is 'system' the entire biological existence of earth? In that case, yes evolution would be a mathematical certainty eventually. But is system a specific species? In that case evolution would only occurr within those species.

He goes on to tell you exactly what systems: any with random heritable changes that can selectively help or hinder reproduction. This would mean both all life on earth that fits within that definition, and any particular species also under that umbrella.

It seems to me like you're trying to make a distinction between "microevolution" and "macroevolution" here, but I may be misreading you. If you are, however, notice that thomblake's process makes no distinction between them; to suppose one but not the other could occur, you'd need a specific mechanism or reason.

Also, time is another factor. Your explanation logically does not necessitate that evolution has already happened, only that it will eventually happen.

No, it necessitates that it is happening and has happened in any such system. The process, that is. You're correct if you're just saying that the process may not have resulted in any differentiation at any given time.

I addressed this here, but I missed a few things. For one, I address the extremity of the hypotheticals in the linked post, but I didn't point out, also, that these things seem extreme because we're used to seeing things work out as if evolution were true. These things wouldn't seem extreme if we had been seeing them all along; it's precisely because evolution fits what we do find so well that evolution-falsifying examples seem so extreme. Fossil rabbits in the Precambrian would probably not seem so extreme to a creationist; it's what they'd expect to find (since all species supposedly lived alongside one another, AFAIK).

For two:

We are limited to these two conclusions and nothing else. Therefore any hit on a theory that advocates one, is a support for the other.

I don't think that follows. A hit on a chance-favoring theory could be a "hit" in such a way as to support a different chance-favoring theory, rather than any favoring design.

I think this pushes scientists (even sub-consciously) to view evolution almost as a belief system rather than a science.

Can you point out some ways that scientists view evolution as a belief system rather than science?