OK, well that was kind of excruciating to read, but I read it all the way through nevertheless.
It seems like Fred Reed's biggest problem is really just that some scientists studying are perhaps speaking a little too authoritatively in detailed areas where there is still significant uncertainty, and that they are protective of their work (probably because they care and like to keep funding to continue their striving for knowledge).
Let me explain why I think Fred's position is unreasonable.
Firstly, it seems to exhibit a dreadful misunderstanding of the philosophy of science - how science works, and what it's for.
Science, explanations and predictability
Science is NOT about proving things. If you want proofs, go do maths instead.
That may seem like an odd assertion, but it is correct.
Science is about EXPLANATIONS, and continuous efforts to DISPROVE them.
Potential explanations may be put forth (hypothesis) and then we try to shoot them down with evidence.
In straightforward physical sciences where we can observe and measure things fairly directly, like the F=M*A sort of case, we can simply measure things a lot of times, controlling for outside influences, and thereby improve our confidence that force really is the product of mass and acceleration. If course, one day we discover that at high velocities, from some frames of reference, it doesn't get the expected results and we have to go back for a more sophisticated explanation (relativity) and things get more complicated.
Science in a messy complicated arena
In a convenient philosophical convergence, the value of good explanations as well as the efforts to shoot them down, both require that the explanations have the characteristic of making predictions.
i.e. if A is correct, then B must also be true.
This rather marvellously allows us to extend our confidence in relation to explanations that we can only evaluate indirectly. If you like maths, then Bayes Theorum succinctly explains this premise.
In English: the probability of A given B, is equal to the probability of B given A times the probability of A divided by the probability of B.
In application, you can start off with your best guess at how likely your explanation is .. P(A) .. consider your prediction of how true B must be given your explanation A ... P(B|A) (or probability of B given A), and then go measure how often B turns out to be true ... P(B). The result ... P(A|B) is how likely you should now consider your explanation A really is given its prediction of B and your measurements of B in the real world.
Yuk, that sounds complicated, but more succinctly in English, you can start off with an arbitrary level of belief in your existing explanation (A) even when you can't measure it directly, but if it is predictive (as all good explanations are), then you can go measure its predictions instead. When you do that, Bayes Theorem explains how to continually adjust your belief in A, in the face of new evidence about B.
In practice, you'll never get to 100% probability, but you will converge towards 100% for correct explanations and towards 0% for incorrect explanations. If it survives all tests of all predictions for a long time, confidence builds.
This capability is particularly important when striving for knowledge of big messy complicated things like life and evolution where we don't get the opportunity to just pop back in time a few billion years to go hunt down the special moment where the first self replicating proto-lifeform emerged. It should be no surprise at all that we're trying out a lot of educated guesses (explanations) around the origins of life.
Trying out a lot of explanations IS the process. Here's a nice summary of the efforts on that front:
Although Fred Reed claims not to be a creationist, he offers no other explanation.
He just alludes to something without every saying what it is.
BTW, his aside into giraffe necks was just weird. They definitely have longer rather than more vertebrae. Just go look at a skeleton. They have seven, just like humans and most other mammals, but theirs are longer.
For a really brilliant example of something that was clearly not designed or orderly, take a look at this dissection of a giraffe, showing its laryngeal nerve running from its brain, all the way down its neck, around an artery of the heart, and then all the way back up again, to control the larynges up near the head where it started.
and all that leads to the real problem with Creationism.
Scientists are anti-creationism, because ...
It's not an explanation at all. It's a lack of explanation.
It makes no predictions, so it's not testable.
As a consequence, it requires faith, zealotry and closed minds to maintain.
The god of the gaps
The lack of explanation for every specific thing throughout the history of life on earth, does not represent an argument against evolution. It represents an incomplete and ongoing study. Pointing to every gap doesn't make evolution wrong
Evolution as an explanation is widely supported because it makes so many predictions that have been tested and found to be true.