Comments on errors in the article follow. Mostly, I will concentrate on the physics errors, but I will also mention a few other mistakes. There are too many in the article to make it necessary to cover the whole thing.
<i>The first blow to atheism from science in the 20th century was in the field of cosmology. The idea that the universe had existed forever was discounted and it was discovered that it had a beginning; in other words, it was scientifically proved that it was created from nothing.</i>
This has not been proved. The big bang theory says nothing about what existed prior to a certain time. For that, we will at least need a quantum theory of gravity.
<i>[T]o accept that the universe had a beginning would mean that God created it and the only way to counter this idea was to claim that the universe was eternal, even though this claim had no basis on science.</i>
This is not true. Showing that the universe has a beginning in no way mandates the existence of god. The universe could be self-caused - perhaps a fluctuation in the quantum vacuum.
<i>the fact arrived at finally by modern astronomy is this: time and matter were brought into being by an eternally powerful Creator independent of both of them.</i>
This is simply not true. Is this an example of the lack of bias you are talking about, Flores?
<i>With the advance of research, it has been discovered that the physical, chemical and biological laws of the universe, basic forces such as gravity and electro-magnetism, the structure of atoms and elements are all ordered exactly as they have to be for human life. Western scientists have called this extraordinary design the “anthropic principle”.</i>
There's nothing remarkable about this. Any universe in which humans exist must have physical laws which permit that existence. The use of the term "design" is misleading, since there is no necessary implication of a designer.
<i>The wellknown astronomer, Paul Davies, writes in the last paragraph of his book The Cosmic Blueprint, "The impression of Design is overwhelming."</i>
...and, as we all know, looks can be deceiving.
<i>In short, the idea of a random universe, perhaps atheism’s most basic pillar, has been proved invalid.</i>
Atheism is a disbelief in the existence of gods. It has no extra baggage of the kind indicated in the article. Here we see one example. Atheism does not require any belief in a random universe.
<i>The quarks, those energy packets, act in such a way that they maybe described as "conscious."</i>
This statement is false. It is immediately followed in the article by a quote from physicist Freeman Dyson. Note that Dyson does not refer to consciousness at all. The juxtaposition of his statement and the previous statement aims to create a false impression of what Dyson is saying.
<i>The discoveries by various branches of science such as paleontology, biochemistry, anatomy and genetics have shattered the theory of evolution from various aspects.</i>
On the contrary, evolution is accepted by paleontologists, biologists, anatomists and geneticists today as the only viable scientific explanation for the diversity of life on Earth.
<i>The fossil of even a single undoubted intermediate species that would substantiate the belief in the gradual evolution of species has not been found.</i>
This statement is a common creationist lie. Many such fossils have been found.
<i>On the other hand, observations and experiments have shown that mutations defined by Neo- Darwinism as an evolutionary mechanism add no new genetic information to living creatures.</i>
This is another false claim, which has been eloquently refuted by Richard Dawkins (among others).
<i>All observations and experiments showed that it was, in a word, impossible for a living cell to arise within inanimate matter by random chemical reactions. </i>
No experiment, nor anything else, has shown this to be impossible.
<i>Intricate examples of design, including our eyes that are too superior to be compared to any camera, the wings of birds that have inspired flight technology, the complexly integrated system of the cells of living things and the remarkable information stored in DNA, have vitiated the theory of evolution which regards living things as the product of blind chance.</i>
Our eyes are actually far inferior to even the most basic camera. They are very badly designed, from an optical point of view. There are a number of very clear explanations of how eyes have evolved independently many times over the lifetime of the Earth. None of these require a god.
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In general, the article is quite clever in the ways it attempts to mislead. Practically all of the things it mentions in terms of medicine, psychology, politics and so on are unconnected in any way with atheism. The examples given are twisted so that they seem to support the overall argument of the piece.
I encourage anybody who is interested to read other sources if you want to find out more about the things discussed. Just a little research will quickly show you that this article is hopelessly biased.