For another 'tude, consider Werner Heisenberg. While walking with Heisenberg one day, the physicist Felix Bloch, who had just read Weyl's Space, Time and Matter, felt moved to declare that space is simply the field of linear equations. Heisenberg replied, "Nonsense. Space is blue and birds fly through it." "What he meant," Bloch later wrote, "was that it was dangerous for a physicist to describe Nature in terms of idealized abstractions too far removed from the evidence of actual observation." Let us explore this dichotomy.
|Jerry playing the theramin
for the ANALOG Mafia
|TOF (left) playing bass clarinet for the
ANALOG Mafia Ragtime Band. Julia
Ecklar on trombone
But in the course of his essay, Jerry claimed authority for science to define love and joy and, well... everything. This fulsome belief in the omnicompetence of the scientific method has been called scientism by such skeptical thinkers as Friedrich Hayek, Karl Popper, Paul Feyerabend, Hilary Putnam, and Mary Midgley. The idea that empirical science is the sole authoritative worldview is akin to the man who, having a hammer -- albeit a very fine and excellent hammer -- therefore sees everything around him as a nail.
It is an extreme expression of the logical positivism that Popper so thoroughly demolished. Jerry provides an idealized description of the scientific method; but as such diverse writers as Pierre Duhem and Feyerabend have pointed out, this is not a description of how scientists actually work. Ampère, indeed, developed an electrodynamics of conducting bodies by meticulous observation of detailed experiments, forming hypotheses, testing the hypothesis, and so on. But Maxwell developed the electrodynamics of dielectric bodies from an intuition, a flash of genius. The experimentation to verify the intuition followed, even in the face of what appeared to be a decisive falsification. Namely, that the proposition that magnetism is a consequence of an electrical current was "falsified" by permanent magnets. To account for them, Hertz and Boltzmann and other Maxwellians simply made up "electrons." Hence, the difference between a lucky guess and an inspired or educated guess. They did not discover an electron and develop a theory to explain it; they developed a theory and postulated an electron to make it work. "The link between theoretical physics and experimental physics," wrote Duhem, "is felt, not concluded." This sort of thing led Feyerabend to conclude that there was no "scientific method." Rather, there are many scientific methods.
Insofar as a paen to science is deserved, there is no quarrel with the gist of the essay. But the devil is in the details, as the saying has it, and there are several points that are problematic, or where Jerry has failed to apply the scientific method by checking facts. Comments are ordered as follows:
- Are there things science cannot explain?
 See, e.g., Midgley, Science as Salvation (Routledge, 1994) Esp. Chapter 8.
 See Feyerabend, Against Method: Outline of an Anarchistic Theory of Knowledge (Verso, 1993)
First and most trivially, Jerry writes that two millennia ago, "Science was mostly 'argument from first principles.' People ... assumed that anything they could prove logically based on a true premise must also be true." Now, this is pretty much the basis of logic, reason, and mathematics, so it's hard to imagine modern physics proceeding without it. But it was not the whole story, even for the ancients.
Then he goes on to say, "that led to things like the geocentric universe theory."
Well, no, actually not. It was Greek heliocentristm that was a dogmatic deduction from premises. The sun was declared to be in the center of the world because fire was nobler than earth and the center was a nobler position.  (We would not today regard the nobility of fire or centers as self-evidently true premises.)
Geocentrism, otoh, was based firmly in empirical fact. Aristotle's maxim was that "Nothing is in the intellect unless it is first in the senses." Empirically, you can sense no motion in the earth; and you can see the sun (and everything else) going around sky in eternally repeating circles. The simplest hypothesis for this apparent motion is that the sun, moon, and stars actually do circle a stationary earth. Aristotle, Archimedes, and the Greek mainstream regarded Pythagorean heliocentrism as mystical woo-woo self-evidently falsified by the data.
2. If the earth is rotating, an object at the top of the tower would be moving east with a higher velocity than one at the base. So, an object dropped from the tower should fall slightly to the east of the plumb line. (Galileo actually proposed this experiment, but there is no record he ever carried it out. Perhaps he did, failed to find the predicted deflection, and kept his mouth shut.) 
3. The distance to the stars can be calculated from their apparent brightness and diameters. That puts them at an unimaginable seventy million-mile distance. If the earth revolves around the sun, stellar parallax should be clearly visible; but is not.
Now, this is not to say that the geocentric model was true -- believe it or not, there are people even today who claim this -- but that it was a model based on empirical observation and confirmed by experience. That model withstood challenges for about 2000 years. It was "settled science," the "scientific consensus," despite the occasional heliocentric "denialist."
|A page from a text of Oresme in which he
comes to the verge of analytical geo
"Geocentrists kept patching their argument to account for new observations. .... That's not science. That's dogma."
The Ptolemaic model worked well enough right up to the point where it was discarded for the Tychonic model in the 17th century. That it had to be "patched" now and then to account for new data is a myth. When was it patched? What new data? There were improved methods of computation introduced from time to time, such as the Tusi couple, invented by Nasir al-Din al-Tusi to replace the equant. But this did not alter the basic model.
Besides, scientific theories are constantly patched in this sense. That's how the Big Bang became the Hot Big Bang, then the Hot Big Bang with Inflation, and how evolutionary theory evolved, adding sexual selection, genetics, epigenetics, and so on. Examples of dogma might be Galileo insisting that the Copernican model (with its 20 epicycles) was physically true even though he had no empirical evidence for it; or Einstein adding a cosmological constant because he believed the universe to be eternal and unchanging and his equations kept insisting it was not. 
Tables based on Copernicus' De revolutionibus proved to be no better than those based on Ptolemy's Syntaxis Mathematiké. This was largely because Copernicus had made almost no original observations and depended on the same old star tables, tables which had become corrupted over the centuries by copyist errors.
|Copernican model on left; Ptolemaic model on right.
Yes, Copernicus used epicycles.
"Geocentrism gave way to heliocentrism when the advent of the telescope brought new observational data..."
No, it took about 120 years to overturn the paradigm. The only relevant telescopic observation in the era of gosh-wow-look astronomy was the discovery of the phases of Venus. These were impossible in the Ptolemaic model, but were predicted by both the Copernican and Tychonic models. So, astronomers immediately abandoned the Ptolemaic system... for the Tychonic or Ursine systems.
|Tychonic system: it all goes around the sun
but the sun and moon go around the earth.
Ursine variant: the earth rotates.
To late moderns, accustomed to Newton's universal gravitation, the Tychonic system looks like a kludge. But the proper way to look at history is not from the hindsight of the future but from the past itself. Tycho had excellent scientific reasons for proposing what he did! See this essay at The Renaissance Mathematicus.
Summary. Geocentrism was not the result of a priori deduction from first principles, but rather the result of empirical observation and experience. It was the best hypothesis, given the data possible at the time. It was not until Kepler that a heliocentric model was developed that worked better; and not until Newton was there a reason to believe that it ought to be physically true. Don't forget that the real telescopic revolution was the revelation of the heavens as a place where physical discoveries could be made. The switched astronomy from the math department to the physics department, and people began to wonder if these purely mathematical models might be physically true. Ptolemaic astronomers had never claimed physical reality for their epicycles.
 Many Pythagoreans believed that there was an invisible central fire and the sun was a bronze mirror that reflected it. Greek "heliocentrism" might be called many things, but "empirical" was not one of them.
 This led many civilizations down the primrose path of eternally repeating cyclic universes, a mental milieu in which natural science failed to develop even though mathematics and astronomy flourished.
 Yes, we know. The atmosphere and everything on the earth is also carried along. Nicholas Oresme proposed this answer in the 14th century and Copernicus repeated it in the 16th. But the physics to support it didn’t exist until the late 17th. With no concept of force or mass, no correct definition of inertia or even of gravity, how was this atmospheric envelope supposed to work?
 The rotation of the earth was not demonstrated empirically until the 1790s, when Guglielmini dropped balls down the inside of the Bologna tower and noted the eastward deflection predicted by inertial motion. It was later demonstrated by Foucault and his pendulum.
 There is parallax, but too small to be seen with the eye. The stars are much farther away than measurements of their apparent brightness and diameter indicated. But in all these cases, you cannot demonstrate one unproven hypothesis by throwing in a second unproven hypothesis. Callendrelli detected parallax in a-Lyrae in 1803; Bessel made a clearer measurement in 1831 of 61 Cygni. At that point the revolution of the earth was empirically proven.
 and when he developed relativity, the "universe" consisted of the Milky Way. Other galaxies were not yet recognized as such and were called "extra-galactic nebulae."
 It took about as long for relativity and quantum mechanics to become the establishment, too.
 And a good thing, too. Kepler would never have discovered ellipses in the old crappy tables.
+ + +
Aside from the confusion of "pleasure" with "love," there is no suspicion that it might be the pleasure that regulates the chemicals. After all, it is not the footsteps that cause the walk, but the walk that causes the footsteps. Iambic pentameter was not the cause of Shakespeare's plays.
A statistician soon learns that on any problem on which he is consulted there are statistical aspects and subject-matter aspects, and the statistical aspects are not the entirety of the matter. The same is true of the domain of science. Natural science is the study of the abstracted metrical properties of material bodies. As such, it has limitless scope, "from quarks to quasars." But also as such, it has limited scope: it is limited to material bodies and to metrical properties. Consequently, in the spirit of see-a-nail-everywhere, the natural scientist -- and more particularly the fan of natural science -- tends to see only the metrical and material aspects of a thing. Hence, color is re-imagined as reflected light frequencies; and so on. If the only legitimate methodology you allow yourself is a metal detector, you will never discover wood. It is operationally invisible to the method. But that doesn't mean it doesn't exist! So if only the metrical and material aspects are "visible" to the scientific method, an examination of "love" will only see brain chemicals. To suppose that these comprise a description of love (let alone an explanation) is like supposing that the physics of vibrating strings accounts for the Waldstein Sonata. 
There is a famous thought experiment: Mary in the Black-and-White Room, also known as the Knowledge Argument against Physical Closure. Mary has lived all her life in a room entirely black-and-white. But Mary is a genius neuroscientist of the Future™ and knows everything there is to know about the physics and physiology of color perception: light wavelengths, surface reflectance, the retina, optic nerve -- everything there is to know about what goes on in someone’s brain when he sees a red object. Then one day the door to the room is opened and she steps outside and sees a bright red rose. Does she learn something new? Of course. She learns what it’s like to see red. But then the essence of redness is not exhausted by wavelengths and retinas and optic centers in the brain. There is more to redness than its metrical properties and efficient causes. Mary knew all the physical facts about human perceptual experience before she left the room but, since she learned something when she left the room, she didn’t know all the facts.
In short, qualia exist and are not physical. Forget about love. Natural science cannot tell us everything about "red."
The "problem" of the qualia was anticipated by Thomas Nagel  and discussed in detail by Howard Robinson in "Why Frank Should Not Have Jilted Mary" 
"'Why do we love?' Ah, now we're talking about evolutionary advantage. We love because it increases our reproductive success"
That's a tautological answer, since the same answer could be given if, like amoebas, cockroaches, cod, and pine trees, we did not love. Or if like many other species, we simply responded to chemical cues when our females went into heat. Any extant species has been by definition reproductively successful. Otherwise, it would not be an extant species. It is only necessary to append the sentence, "We [have trait X] because it increases our reproductive success."
nearly all traits are "spandrels." 
Besides, "reproductive success" does not explain "why" we love. At best, it may describe "how" we have come to love. Besides, I love both Mozart's music and asparagus. I don't see how that increases my reproductive success. The invocation of "evolutionary advantage" is really nothing more than a kerygma of faith. Like physical closure, it is assumed, not demonstrated.
"A scientist looks at the question "What is the meaning of life?" and realizes it's meaningless."
By this Jerry appears to mean both that the question is meaningless and also that science tells us that life is meaningless. But if the question is meaningless, the answer could not be "there is no meaning to life," since there can be no answer to a meaningless question. Our Perceptive Reader will by now realize that by "meaningless," Jerry evidently means that the question does not deal with the metrical properties of material bodies. IOW, "meaningless" is precisely his term for "questions science cannot deal with." And therefore Question 2 is answered in the affirmative.
 For the benefit of the overly literal we hasten to add that "the physics of vibrating strings" is shorthand for all the acoustic factors: keys, hammers, soundbox, etc.
 Thomas Nagel, "What is it Like to be a Bat?" The Philosophical Review LXXXIII, 4 (October 1974):435-50
 in The Case for Qualia, Edmond Leo Wright (ed.) (MIT Press, 2008)
 Jerry Fodor, "Why Pigs Don’t Have Wings," London Review of Books, Vol. 29 No. 20 (18 October 2007), pp 19-22
To which one can only say, well of course not. Science deals with the metrical properties of material bodies; and (except in some eccentric modern sects) God is not the latter and has not the former. A scientist playing the trumpet is being a musician, not a scientist. A scientist cheering on his home team is being a sports fan, not a scientist. So what?
"Belief in God doesn't hold up to scrutiny. It's not testable."
Heck, neither is string theory. (Rim shot!) Presumably, "scrutiny" is narrowly construed here as some sort of scientificalistic test. But that's like a scientificalistic test for the irrationality of pi. No matter how many empirical circles you measure, the ratio of the actual measured circumference to the actual measured diameter will be a rational number. The irrationality of pi can be demonstrated only by mathematical proof, not by scientific experiment. So we know of at least one domain -- mathematics -- not subject to scientific proof, one which leads to more certain conclusions. Surely there can be others.  Like the existence of objective reality, belief in God may not be testable, but that does not mean it cannot be reasonable.
The existence of God is a proposition in metaphysics, not in the physics. It cannot be demonstrated in physics, even in principle. One of the deductions from the existence of God is that He is Existence Itself . But physical science must take existence as one of its assumptions -- you cannot demand empirical evidence without assuming an empirical universe -- and no science can demonstrate its own assumptions or axioms. That would be circular reasoning (a.k.a. "begging the question"). Therefore, physical science cannot demonstrate either Existence or God.
Metaphysical demonstrations are more akin to mathematical demonstrations than to physical ones. However, in the interests of having fun, we will essay a "scientifical demonstration" using the criteria Jerry gave for scientific method; viz., that a "theory" should make "predictions" and these predictions should be empirically verifiable. Now, in Christian theology some of the consequences of the Christian concept of God are:
- Existence exists.
- There is an objective universe.
- That universe is rationally ordered. (There are natural laws.)
- The order of the universe is consistent.
- That order is knowable to human reasoning.
- It is knowable "by number, weight, and measure."
- Material bodies have natures that have the power of acting directly upon one another (secondary causation) and therefore natural phenomena have natural causes.
- The universe had a beginning in time.
- All human beings share a common descent.
- Human beings have a "selfish gene" that makes them prone to pride and selfishness.
- New species of animals, if any such appear, would be produced by natural powers "which the stars and elements received at the beginning." (Summa theologica, Part I Q73 A1 reply3)
"every time a religious explanation for how the universe works bumps up against a scientific one, the scientific one prevails. We're left with a 'god of the gaps,'... but those gaps continue to close."
The atheist Terry Eagleton once commented that “believing that religion is a botched attempt to explain the world . . . is like seeing ballet as a botched attempt to run for a bus.” It simply misses the whole point. But such a belief is to be expected if one sees science as omnicompetent and omnipresent. Of course, religion is trying to explain the physical universe. What else would they be trying to do? What else is there to do? But as Augustine of Hippo wrote (Contra Faustum manichaeum):
"In the Gospel we do not read that the Lord said: ‘I send you the Holy Spirit so that He might teach you all about the course of the sun and the moon.’ The Lord wanted to make Christians, not astronomers. You learn at school all the useful things you need to know about nature.”This actually seems quite reasonable. These beliefs are common to the Catholic and Orthodox Churches, which between them account for about two-thirds of all self-identified Christians. Bill and Ted's Excellent Bible Shack is another matter.
Now, the explanation for how the world works in the traditional churches (Latin and Greek) is that God created nature with the ability to act directly.
“But the natures with which [God] endowed His creatures accomplish a whole scheme of operations, and these too turn to His glory since it is He who created these very natures.” (William of Conches)Augustine expressed it thusly:
"It is therefore, causally that Scripture has said that earth brought forth the crops and trees, in the sense that it received the power of bringing them forth. In the earth from the beginning, in what I might call the roots of time, God created what was to be in times to come." (On the literal meanings of Genesis, Book V Ch. 4:11)
And Aquinas: 
"Nature is nothing but the plan of some art, namely a divine one, put into things themselves, by which those things move towards a concrete end: as if the man who builds up a ship could give to the pieces of wood that they could move by themselves to produce the form of the ship." (Commentary on Physics II.8, lecture 14, no. 268)
William of Conches expressed impatience with a theokinetic approach.
"[They say] 'We do not know how this is, but we know that God can do it.' You poor fools! God can make a cow out of a tree, but has He ever done so? Therefore show some reason why a thing is so, or cease to hold that it is so." (Dragmatikon)This was the mainstream doctrine of the Church during the Age of Faith. The study of the nartural world was seen as a way of appreciating God, and was thus a worthy occupations for grown-ups.
"For even creation reveals Him who formed it, and the very work made suggests Him who made it, and the world manifests Him who ordered it. The Universal Church, moreover, through the whole world, has received this tradition from the apostles."And it was further believed that these operations follow a "common course of nature," by which causes entailed the same effects "always or for the most part". That is, there are laws of nature. In fact, Aquinas famously used the lawfulness of nature as the starting point for his "Fifth Proof" of God's existence. That is, it is not supposed exceptions to natural law that signify God; but the natural laws themselves. In this doctrine, there are no "gaps" for a "god of the gaps." There are only progressive discoveries of the laws with which God "disposed everything by measure, number, and weight." (Wis. 11:21)  For that matter consider this paean to natural science, sung in the voice of Solomon:
Irenaeus, Adversus haereses bk 2 ch 9
For [God] gave me sound knowledge of what exists,
that I might know:
the structure of the universe -- and the force of its elements,
The beginning and the end -- and the midpoint of times,
the changes in the sun’s course -- and the variations of the seasons,
Cycles of years, -- positions of stars,
natures of living things, -- tempers of beasts,
Powers of the winds -- and thoughts of human beings,
uses of plants -- and virtues of roots...
Whatever is hidden or plain I learned,for Wisdom, the artisan of all, taught me.
(Wis. 7: 17-22)
For reasons like these, natural science as we know it today originated in the Latin West and nowhere else. It is diffucult to see how modern science could be encroaching on this Christian notion of the lawfulness of nature or the idea that material bodies act from their own natures. It would be encroaching on science itself if it did so, like the worm Ourobourus eating its own tail.
This is not to say that there are no sects that are hostile to or distrustful of "science." Although we often find it more due to socio-political factions using science as a sort of sock puppet. But, for example, "creation science" wants nothing more fervently than that their religious beliefs be elevated to the status of a Science™! Hence, they confuse creation with evolution, look for "gaps" and divine fingerprints, and try fervently to produce scientific proofs of their beliefs, because they too buy into the scientism that holds science as the only valid way of knowing anything.
 Aristotelians distinguished three kinds of knowledge: physics, mathematics, and metaphysics. a) Physics proceeds by induction from empirical facts to a theory that is true-to-fact. b) Mathematics proceeds by deduction from first principles to a theorem that is true-to-the-axiom system. c) Metaphysics proceeds by deduction from empirical facts to a conclusion about being as such. Metaphysical demonstrations are therefore like mathematics in being deductive and like physics in starting from empirical experience.
 cf. Thomas Aquinas, Summa theologica, Part I. Q3. Art.4 Thomas also made a distinction between a form and its quantitative extension; thus, between (e.g.) heat and temperature. This proved useful in the later development of science.
 The most frequent Biblical verse quoted in the Middle Ages.
 It might have done so in the Greek East, had Byzantium survived. It almost did in The House of Submission.