The difference between the two modes of inquiry is clear from the start. Dewey gives us a basic characterization:
[Commonsense problems] may be reduced to problems of use and enjoyment of the objects, activities and products, material and ideological, (or "ideal") of the world in which the individuals live. Such inquiries are, accordingly, different from those which have knowledge as their goal. The attainment of knowledge of some things is necessarily invovled in common sense inquiries, but it occurs for the sake of settlement of some issue of use and enjoyment, and not, as in scientific inquiry, for its own sake. In the latter, there is no direct involvement of human beings in the immediate environment---a fact which carries with it the ground of distinguishing the theoretical from the practical.
[Common sense inquiries] are those which continuously arise in the conduct of life and the ordering of day-by-day behavior. They are such as constantly arise in the development of the young as they learn to make their way in the physical and social environments in which they live; they occur and recur in the life-activity of every adult, whether farmer, artisan, professional man, law-maker or administrator... On their very face they need to be discriminated from inquiries that are distinctively scientific, or that aim at attaining confirmed facts, "laws" and theories. (LW 12:66-7)
Dewey sharpens the distinction a bit by suggestion that it is, fundamentally,
that between significances and meanings that are determined in reference to pretty direct existential application and those that are determined on the ground of their systematic relations of coherence and consistency with one another. (LW 12:71)
While this is clearly true, so far as it goes, it doesn't help us to understand how scientific inquiry can yet be genuine inquiry in the sense that we've discussed so far. That is, we need some explanation about the continuity of scientific and common sense inquiry such that, despite scientific inquiry not being directly involved in the immediate environment of the agent, it can nevertheless be seen as a genuine inquiry.
The problem is, in essence, a problem of the relation of the problems and subject-matters of the two kinds of inquiry:
In saying that [that the difference between common sense and science] is logical [not metaphysical or epistemological], it is affirmed that the question at issue is that of the relation to each other of different kinds of problems, since difference in the type of problem demands different emphases in inquiry. It is because of this fact that different logical forms accrue to common sense and scientific objects... the question... is that of the relation to each other of the subject-matters of practical use and concrete enjoyments and of scientific conclusions. (LW 12:71)
As a first pass at an explanation of their relationship, consider the following story:
A young auto mechanic, call him Rob, is confronted by a problematic situation involving the engine of a 1974 Volkswagen Beetle. He has proceeded from the initial indeterminate situation which confronted the owner of the car and was communicated to him when the car was brought to his shop, to the point of locating the source of the problem somewhere in the engine, though a more specific and adequate determination of the problem has not yet been reached. Luckily, Rob is something of an expert in engine repair, especially in vintage German cars. He has even spent some of his spare time studying up on the theory of combustion engines from the field of mechanical engineering, and while his amateur knowledge is far from systematic, it occasionally helps him to solve certain prickly problems.
Normally, in the course of engine repair, Rob might use various pieces of this accumulated knowledge as ideas, as theoretical resources that might help resolve the problem. Suppose things don't go quite as swimmingly in this case, however. Rob, at first convinced that he is guilty of some major confusion, dives into the relevant textbook on the theory of combustion engines, and as far as he is able to determine in his personal study, he has understood the relevant theoretical ideas, and yet they fail to function as advertised.
Now, for Rob, the theoretical materials in question themselves cause a new problematic situation. If he chooses to pursue the resolution of that problem, he must begin a new inquiry, related to but distinct from the inquiry into the concrete car engine. The inquiry is into a difficulty in the theoretical materials, as they play their role in the practice of analyzing and diagnosing problems in automobile engines. The problem at hand is no longer with the car engine, or more properly, in the practice of using car engines, but rather in the theory of combustion engines, or rather, in Rob's practice of using that theory for solving the problems that it is putatively designed to help solve. Its problematic character depends crucially on a real feeling of doubtfulness produced when they disrupt the practice in which Rob is attempting to use them.
We might imagine that Rob gets an education in mechanical engineering and goes on to do important work in the field on the topic of combustion engines. He is devoting the major portion of his efforts now in investigating the problematic situation that involves these ideas from the theory of combustion engines. And one might imagine a similar story that moves from combustion-engine engineering to thermodynamics and statistical mechanics to higher-level physics and so on, though of course such extensions strain credulity if we're talking about a single person.
Now having resolved the problem in physics, Rob might never actually return to the "lower-level" problems from which this one grew. Nevertheless, Rob has solved an important problem, one that originated way back in the activity of car repair, and it is not diminished in any degree if he chooses to stop there. In any case, the original customer who brought her old Beetle to him is probably not counting on his return. Rob's story serves to make vivid how a highly abstract and theoretical pursuit, such as the working out of certain improvements in the general theories of thermodynamics and statistical mechanics, might be connected to and continuous with those commonsense, narrowly practical inquiries which more obviously fit the pattern and tests of genuine pragmatic inquiry. It also shows us that such high-level inquiries nonetheless fit the basic patten: they begin in a qualitatively felt problematic situation, they require the determination of a specific problem, the problem is pragmatic in the sense that it arises from the disruption of a kind of practice, etc.
Now, this just-so story is no literal description of how we get from commonsense to scientific inquiry. Nevertheless, it makes it clear how current scientific practices might be continuous with commonsense inquiry, and it shows how they might be counted as genuine examples of inquiry. In order to make the example more realistic, one might consider how the story could be extended from a story about a single agent, to a story about a community.
Dewey describes the fundamental continuity between the subject-matters of science and common sense in this way:
In the first place, science takes its departure of necessity from the qualitative objects, processes, and instruments of the common sense world of use and concrete enjoyments and sufferings. The scientific theory of colors and light is extremely abstract and technical. But it is about the colors and light involved in everyday affairs. (LW 12:76)
Which is to say, the theory of combustion engines is about the combustion engines that are actually used in car engines, and which car mechanics must repair, despite the fact that it is abstract and technical. And the theory of thermodynamics is itself about the quality of heat that plays a role in everyday affairs, despite the fact that it treats heat in a highly abstract, technical, and quantitative way. Despite the fact that thermodynamics may well abstract away from qualitative features of heat that are absolutely crucial to the meaning that heat has for common sense affairs of use-enjoyment (just as optical theory abstracts away from the place that light and color play in social and fine arts, the daily routine of waking, business, going about one's business, and sleeping, and the practices of dyeing, rug-making, and so on), it nevertheless should provide help in those pursuits.
As to how the current scientific disciplines came into existence, that is a historical question that probably contains as many contingent, arbitrary factors as ones that might be explicitly justified. On the other hand, the reason that they continue to exist has much to do with their ability to provide systematic ideas, liberated in a sense from their particular circumstances, which can replace the highly parochial and unreliable ideas that had previously played a role in common inquiry. As Dewey says,
Gradually and by processes that are more or less tortuous and originally unplanned, definite technical processes and instrumentalities are formed and transmitted. Information about things, their properties and behaviors, is amassed, independently of any particular immediate application. It becomes increasingly remote from the situations of use and enjoyment in which it originated. There is then a background of materials and operations available for the development of what we term science, although there is still no sharp dividing line between common sense and science. (LW 12:77)
In the story about Rob, the relevant scientific disciplines may already be in place. But consider a similar scenario outlined by Dewey:
For purposes of illustration, it may be supposed that primitive astronomy and primitive methods of keeping track of time (closely connected with astronomical observations) grew out of the practical necessities of groups with herds in care of animals with respect to mating and reproduction, and of agricultural groups with reference to sowing, tilling and reaping. Observation of the change of position of constellations and stars, of the relation of the length of daylight to the sun's place in relation to the constellations along the line of the equinox provided the required information. Instrumental devices were developed in order that the observations might be made; definite techniques for using the instruments followed.
Measurement of angles of inclunation was a partical part of meeting a practical need... something of this general kind certainly effected the transition from what we call common sense to what we call science. (LW 12:77)
And so we move from the common sense purposes of husbandry and agriculture to scientific astronomy and horology. Dewey suggests we might tell a similar story moving from medicine and the practical needs of healing to the development of physiology and anatomy.
We might consider the mark of science to be its systematicity, then, and its major aim as achieving coherence and consistency in providing resources for the resolution of problems of more specific, concrete situations.
While something like the story of Rob may be helpful in justifying the practices of higher-level science, it should not be the only story about how scientific problems can be counted as genuine. Once we recognize that science is an relatively autonomous practice, we can see that a wide variety of problems might arise in the course of its pursuit. A working physicist may encounter a variety of perplexities that are not tied to specific problems of application, such as the ones that Rob dealt with, and yet they might be quite genuine. For example, a practitioner may disturbed by the lack of consistency between two fundamental theories in physics, or the lack of a comprehensive theory of measurement in quantum physics, or the inchoate and inconsistent uses of the concept "species" in biology, and this may lead them to investigate these problems, though nothing is immediately at stake in terms of everyday practices of use. This is, in part, because for applicability to be both wide and consistent, the theory must be both internally coherent and consistent and clear in its application.
There is some reason to think that the bottom-up story I've told, from "application" (i.e., use) up to theory and back down again, has some plausibility. Frequently, technology has progressed independently of any science that might explain how or justify that it works, for example, prior to the existence of systematic and applicable theory in the area, and it would seem that even in areas where the science is quite mature, related technology might progress largely independent of specific reference to the theory, especially the cutting edge.
For example, consider Steven Gulie's account of how he was treated for Parkinson's using implanted electrodes ("A Shock to the System," WIRED Magazine vol 15.03, March 2007). The surgery implants two sets of electrodes near the subthalamic nucleus, an small cluster of neurons near the center of the brain. The electrodes are hooked up to a kind of pacemaker-like computer than is implanted under the collarbone, and delivers a constant flow of electricity to the electrodes. A variety of options on voltage and number of contact points activated can control the exact area stimulated. This stimulation counteracts the disease, which is caused by the death of cells in substantia nigra, where the neurotransmitter dopamine is produced.
The FDA approved this procedure for treatment of Parkinson's in 2002, which meant that it met the government standards for being an effective treatment, though long-term side-effects are unknown. What is certain is that it is far more effective, with fewer side effeccts, than the older chemical treatment, which is taking high doses of a L-dopa, a building block of dopamine, in attempts to spur dopamine production. On the effectiveness of his own implant, Gulie writes,
[M]y body is almost free of symptoms. With the stimulator turned off, a Parkinson's test shows 20 significant impairments. With the stimulator on, it drops to two. Add just a touch of L-dopa and it drops to zero.
... It's been five months since the surgery, but it has finally all come together: It works. I forget that I even have Parkinson's most of the time. And last November, I went back to work full time. It's a miracle. A second chance at life.
And while Parkinson's is a degenerative disease (the dopamine-producing cells keep dying), patients four years after the surgery still required an average of fifty percept less L-dopa than they did prior to it.
And yet, in terms of the science behind the treatment, there are more questions than answers. Anyone familiar with the neuroscience knows that our knowledge is largely incomplete. Even those philosophers who tell us to look to neuroscience when worrying about philosophical problems do so with a bevy of warnings about the tentativeness and incompleteness of the science, and a litany of promissory notes about future developments. What systematic treatments we have are highly idealized and largely unrelated to specific application and fine-grained detail, and what we do know at a more fine-grained level is very narrow to specific neuronal and sub-neuronal structures and low-level systems.
In terms of his procedure, Guiles writes,
No one really knows precisely why deep brain stimulation works. Some things about deep brain structures, like the thalamus, are understood well enough for stimulators to be routinely successful. But the high-level brain structures in the neocortex, where all the evolutionary action has ben for the past 100,000 years or so, are still largely a mystery. How does shocking the thalamus in the deep brain help the cortex in the upper-level brain control fine motor movement? Is this suppressing electrical activity or enhancing it?
In terms of programming the stimulator to effectively control the symptoms, Guiles at first speaks charitably: "Getting the settings right is midway between an art and a science." But his further descriptions show a mounting frustration, "Ultimately, getting the system to work comes down to trial and error," and "Finally, after three months of tinkering..." Guiles goes back and forth between neurologists, goes through months of trial and error, and has many frustrations along the way. Clearly, no sorts of systematic knowledge yet guide this part of the process. There are, according to Guiles, 1,200 permutations of the settings of the device, and the hope is that one of them will work out. And yet, in the end, for Guiles, and for many other patients, it does!
This modern example is complemented by a variety of examples employed by Feyerabend to call into question the view that development of science is univocally beneficial and progressive. On the one hand, Feyerabend points to the variety of specific knowledge of materials, how to manipulate them and use them, that was possessed by common people and alchemists prior to the rise of Chemistry, which was originally quite impoverished in terms of specific knowledge about how to manipulate various materials, relative to those traditions it purported to overthrow. Likewise, folk or traditional medicine in various parts of the world was able to do much that scientific medicine could not do, and some things that it still has yet to reproduce.
One might likewise point to the relative success of local, subsistence agriculture in poorer cultures, in terms of meeting basic needs of the populace, as compared to what happens when entities like the World Bank come in to attempt to develop these countries. Charlie, environmental advisor to the President in Kim Stanley Robinson's novel, Sixty Days and Counting, says, in an angry diatribe at a meeting between the World Bank and the UN's Intergovernmental Panel on Climate Change,
You go into poor countries and force them to sell their assets to foreign investors and to switch from subsistence agriculture to cash crops, then when the prices of those crops collapse you call this nicely competitive on the world market. The local populations starve and you then insist on austerity measures even though your actions have shattered their economy. (p. 204)
In all these cases---cutting edge neurosurgery, the knowledge of materials and medicine in traditional culture, and subsistence agriculture---able use is made prior to, or independent of, systematic knowledge in the relevant science, whether that be as-yet-unrealized neuroscience, early chemistry, scientific medicine, or modern agricultural science and capitalist/neoclassical economic theory.
Compare discussions in philosophy of science of applications or use. The traditional answer is Euclidean: applications are deduced from a combination of general principles and specific conditions of the situation. To launch a rocket to the moon, one plugs the weight of the payload and the various properties of the Earth, Moon, and other relevant planetary bodies into Newton's laws, to determine the force necessary to launch the rocket (and further such derivations are necessary when seeking a source of the force, such as chemistry for burning fuel, and so on).
Or consider what happens in "science lab" classes in college, where one follows directions from a manual or instructor to set up an "experiment,"[Though it should be clear from the discussion of the necessity of experiments, that such demonstrations lack the force and function of real experiments.] then derives an expected result from the relevant theory. Finally, one checks the results against the expectations, and does it over again if one doesn't get the "right" answer!
The traditional answer presumes that the lab demonstration generalizes to all of science application. We know that this is problematic for a number of reasons. First, for purely logical reasons, the straighforward deductive schema for confirmation/falsification has given way to confirmation holism, so that even those who would give something like the traditional answer must admit that a variety of auxiliary assumptions play a role in such deductions. In the context of justification, this means that no evidence by itself can clearly confirm or refute a general principle, and in the context of use, it means that there is a certain slippage already between principle and application.
But more recent developments have caused further reasons to doubt the standard story. For one, there are many reasons to doubt the picture of scientific theory as a system of statements from which consequences can be deductively derived. This has led to an explosion of alternatives, from models and modeling (Suppes, Giere, van Frassen), to a mangle of practices (Pickering), to cognitive maps (Churchland). Given the complexity of the current field as compared with the traditional picture, it is not at all clear that the present thesis, which involves a significant independence of specific use from general theory, given that they occur in different kinds of inquiries, is so implausible.
A very contemporary discussion which the present picture might be revealingly contrasted with has been spear-headed by Nancy Cartwright. Cartwright asks us to look beyond the traditional questions of how is a general claim in science justified or confirmed by evidence, and how do we have evidence for a particular use of that claim. The question takes on board certain developments from recent work, and so assumes a slippage between theory and application. But it also assumes a certain temporal development that I'm trying to deny: first, a theory is justified by evidence, then we try to apply it in the various fields.
On the view discussed here, no such simple story is available. There are many options available. There could be a history of more or less unsystematic inquiries into matters of use, which eventually lead to a systematization of theory, which then helps guide further inquiries of application. Or, in the process of inquiring into general questions, we may discover a range of potential applications which we mark as future tests of the theory. What is clear is that, in an inquiry into some potential matter of use, a theory can never wear its usability on its sleeve; it is a matter to be decided by inquiry, not one decided ahead of time. If it is decided ahead of time, then there is no inquiry; but there is also no question about whether there is evidence for its usability. It is simply used unreflectively.