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I am Catholic, so I find it interesting that the Catholic teachings in your source ends with Pius XII when John Paul II said this:
"In his encyclical Humani Generis (1950), my predecessor Pius XII has already affirmed that there is no conflict between evolution and the doctrine of the faith regarding man and his vocation.... Today, more than a half-century after the appearance of that encyclical, some new findings lead us toward the recognition of evolution as more than an hypothesis. In fact it is remarkable that this theory has had progressively greater influence on the spirit of researchers, following a series of discoveries in different scholarly disciplines. The convergence in the results of these independent studies -- which was neither planned nor sought -- constitutes in itself a significant argument in favor of the theory.”

Your source ignores some very relevant, recent information in regards to faith. It also ignores recent relevant science, so allow me to clear up a few things, bullet by bullet:

- Chemicals certainly don’t react randomly; there is a whole branch of science based on the assumption and observation that chemical reactions are predictable and repeatable. I suppose what you are attempting to say is that amino acids do not form from simple molecules under conditions found in nature. If this does not happen, where does your body get its amino acids from? It has to synthesize them from smaller molecules.
I guess what you mean, then, is that the first amino acids could not arise from simpler molecules. I’ll direct you to the Miller-Urey experiment, in which a prebiotic mixture of atmospheric gases (water, methane, ammonia, and hydrogen) was activated with heat and electricity. All these components are found quite commonly on Earth. The result of the experiment was amino acids – 13 of the 20 found in life on this planet, just from that simple mixture. Follow up experiments used different atmosphere mixtures and different energy sources - all of which are already found on Earth – and they also produced amino acids.
Of course, these experiments make educated hypotheses about what Earth might have been like before life, and might be wrong. However, we don’t even need to set up an experiment to know that amino acids can form though “natural processes.” A meteorite found in Australia contained over 90 types of amino acids, which is almost five times the number used in life forms on Earth.
There is plenty of evidence to show that amino acids – and other complex organic molecules, for that matter – can form in nature from simpler molecules without any extraordinary treatment.

- Cells are far more than just amino acids, so amino acids alone wouldn’t form cells. But, as I also addressed above, the chemicals needed to set the stage for primitive life would not interact “randomly.” The molecules behave in a specific, predictable way under specific conditions. One of these specific conditions - like around hydrothermal vents, or in the primordial soup, or a few other proposed settings - could have allowed the molecules to form a unit that would self-replicate. Self-replication sets the stage for cells to appear.

- This is a misunderstanding of abiogenesis. Until Pasteur’s experiments using sterile techniques, people believed that complex life could arise fully formed from nothing, based on observations such as food being spoiled by maggots and mold, when the organisms apparently had no source. Pasteur’s experimental setups prevented the decomposing organisms from reaching the food from outside its container, and observed that no life appeared inside. If complex life forms did spontaneously arise in the container, it would be abiogensis. That is a form of creationism. The law of biogenesis has nothing to say about life arising from increasingly complex molecules, because it is addressing a different issue and is not relevant to current discussions on the origins of life.

- You are essentially dismissing all of evolutionary biology here, which is backed by an Everest of data. These are the core principles: variations in the species genome occur, which are then selected against to cause the species to further diverge from its closest relatives. Until you can give an example or definition of specific complexity, however, all I can do is provide the several different ways we have indeed observed an increase in genetic information:
An increase in genetic variety in a population, gene duplication, completely new genes, and new abilities regulated by existing genes. One of those must fit your definition of specific complexity, and whichever one it is, it has been observed.
Also, there is a natural process by which new species arise from old ones. We call it evolution, using the mechanism of natural selection. It's a very well-developed and supported theory. There is no higher level of scientific certainly.

- There is no gradualism in the fossil record, no intermediate types? No? Allow me to name a few intermediate types that science recognizes as part of a record of gradual evolution: Eoraptor, Herrerasaurus, Ceratosaurus, Allosaurus, Compsognathus, Sinosauropteryx, Protarchaeopteryx, Caudipteryx, Velociraptor, Sinovenator, Beipiaosaurus, Sinornithosaurus, Microraptor, Archaeopteryx, Rahonavis, Confuciusornis, Sinornis, Patagopteryx, Hesperornis, Apsaravis, Ichthyornis, and Columba - and these are just the fossils that document the transition from dinosaur to bird. These fossils either have characteristics that lie in between dinosaur-like and bird-like, or their bodies have both bird- and dino-like features present simultaneously. You cannot easily assign the fossil to either group. This pattern of intermediate forms shows up again and again, across all the phyla that left fossilized parts behind, if you only cared to look for it.

There is no controversy in science about evolution. Data from biochemistry, genetics, phylogeny, developmental biology, paleontology, and behavioral biology all support it. You will not convince anybody otherwise by presenting a few misinterpreted, misinformed, or fabricated statements. If religion and theology have problems with the implications of evolution that's okay, but they should not try to use science against itself when they are clearly unfamiliar with the territory.

This article only "preaches to the choir." I suggest at least reading another article to grasp more knowledge on Ida

http://opinionator.blogs.nytimes.com/2009/05/20/lets-not-go-ape-over-ida/