Many scientists have convinced themselves that nothing exists except the material world. Reality is limited to that which can be objectified, quantified, and verified. For them, if the soul cannot be weighed, it must not exist. Unless God can be measured, he must be fanciful. Unless morality can be quantified, it must be illusion. There is no such thing as metaphysics...all reality is material. Period.
Of course, the assertion that reality is only material is, itself, a metaphysical claim—one that modern scientists are simply not qualified to make. Though they are skilled at measuring the material world, scientists do not have the expertise or authority to declare that there is nothing but a material world. The limits of scientific detection do not circumscribe the boundaries of our existence. There once was a time when we could not detect other planets, but that does not mean they did not exist. Likewise, there are metaphysical truths—some known by reason, some by revelation—but just because they are non-material, does not mean they do not exist.
J. B. S. Haldane showed how the limits of materialism make human reason incomprehensible: "If my mental processes are determined wholly by the motions of atoms in my brain, I have no reason to suppose that my beliefs are true...and hence I have no reason for supposing my brain to be composed of atoms." If we are solely material beings as the New York Times is keen to argue, then there is no basis for truly rational thought. There is, therefore, no basis for believing that the article declaring the non existence of the soul is true.
Reasonable people, however, should not ignore the implications of the notions articulated in the Times article. Ideas have consequences, whether we acknowledge the existence of ideas to be true or not. If the breezily asserted claim that morals are nothing but feelings produced by the brain is true, then clearly, we would no longer be bound by morals. The powerful could impose whatever "morality" they want on the weak. And what if it is true that we are purely material beings and, therefore, lack free will? Who would be responsible for their actions? And what if human beings are not fundamentally different from animals, as the article also asserts? Does that mean the local butcher is a murderer, or does it mean murderers are no less immoral than the butcher?
We may not all have Ph.D.'s in neuroscience or evolutionary biology, but that doesn't mean that we are stupid. Notwithstanding what some members of the scientific community may think, scientists are not all knowing and the field of science is not competent to unravel all of the mysteries of human existence. On that, you can bet your immortal soul.