Preemption is the core concern that drives the Court’s “exclusionary principle”. The Supreme Court in Alice stated:
We have described the concern that drives this exclusionary principle as one of pre-emption. See, e.g., Bilski, supra, at 611-612 (upholding the patent “would pre-empt use of this approach in all fields, and would effectively grant a monopoly over an abstract idea”). Laws of nature, natural phenomena, and abstract ideas are “”the basic tools of scientific and technological work.”” Alice, at 2354.
Patents on “building blocks of human ingenuity” “would risk disproportionately tying up the use of the underlying” ideas, and are therefore ineligible for patent protection.” Id. at 2354-2355. (internal quotations and citations omitted).
Again, many of the commentators on the June 2014 Preliminary Guidance identified preemption as a primary concern that must drive the patent eligibility analysis, including parties on opposite sides of the patent eligibility debate: ACLU, AIPLA, BSA IEEE, Microsoft, Public Knowledge, Trading Tech, and six law firms and individuals. The Interim Guidance only mentioned preemption as result from the examiner identifying claim elements that “amount to significantly more than that exception,” rather than the core inquiry that drives the entire eligibility analysis.
For example, both the ACLU and Public Knowledge, supporters of narrow eligibility scope, noted the importance of preemption:
Public Knowledge: Preemption is the guide star that “undergirds our § 101 jurisprudence,” and the PTO’s guidance must reflect that strong holding.” In particular, the PTO should advise that (1) examiners should apply the Court’s preemption doctrine in evaluating patent claims involving abstract ideas.
ACLU: While preemption of substantially all practical applications would demonstrate a lack of an invention, the analysis requires looking at what is preempted in relation to the contribution of the inventor.,
Muskin & Farmer: When determining whether a claim is directed to an abstract idea, the examiner should be instructed to consider the preemptive effect of the claim.
Howard IP Law Group: We recommend that the instructions advise Examiners that the underlying basis for Part 2 of the analysis is the Supreme Court’s overriding concern of avoiding preemption of the use of the abstract idea implemented in computer technology. Conversely, if the technological recitations leave open the practice of the abstract idea using alternative technologies, then the claim is patent eligible.
Trading Technologies: The Preliminary Instructions are devoid of any discussion of the central, motivational role that preemption analysis plays in the Mayo framework or even an indication that such analysis should be given weight…. Part 1 requires (a) first identifying the abstract idea and (b) then determining if the claim, as a whole, appears to in practical effect pre‐empt (that is, forecloses or nearly forecloses) the abstract idea.
The evaluation of preemption must guide the Step 2B determination. This in turn depends on looking at scope of the claims “in practice”. The Alice Court stated:
We have described step two of this analysis as a search for an ” ‘inventive concept’ “–i.e., an element or combination of elements that is “sufficient to ensure that the patent in practice amounts to significantly more than a patent upon the [ineligible concept] itself.” (Citing Mayo, at 3). Alice, 134 S. Ct. at 2355 (emphasis added).
Thus, if a patent’s recitation of a computer amounts to a mere instruction to “implemen[t]” an abstract idea “on . . . a computer,” Mayo, supra, at ___, 132 S. Ct. 1289, 182 L. Ed. 2d 321, 337), that addition cannot impart patent eligibility. This conclusion accords with the preemption concern that undergirds our §101 jurisprudence. Alice, 134 S. Ct. at 2358 (emphasis added).
The attention to what happens “in practice” is necessary to distinguish between claims that in fact preempt fundamental building blocks and those that “pose no comparable risk of pre-emption, and therefore remain eligible for the monopoly granted under our patent laws.”
In Alice, the Court’s identification of the abstract idea of intermediated settlement and Alice’s acknowledgement at oral argument that the software implementation was not significant  provides the necessary insight into what the Court meant by “generic functions.” To the Court the claimed steps—creating shadow accounts, obtaining data from the exchange institutions, updating records and transmitting instructions—were the essential steps of intermediated settlement, and thus recited the abstract idea. Turning to Mayo step two, the Court viewed these steps as entirely co-extensive with whatever was being done by the computer implementation, which it considered to be trivial: at oral argument, Alice essentially admitted this to the Court, agreeing that it “would be fairly easy to program” and could be done in a weekend. Similarly, the system claims recited elements that appeared to the Court to be entirely generic: various “input means,” “data storage means,” and “data processing means.” To the Court, the collapsing of the claim elements with the basic computer functions and components meant that the patent claim was a “mere instruction” that implemented the idea on a computer, since it necessitated only the generic capabilities of a computer to perform steps that were “conventional” and “routine.” To the Court this meant that the claim would “in practice” preempt all others from implementing the abstract idea. Thus, Alice’s patent claim was ineligible not because it was implemented using the generic functions of storing data, transmitting data etc. Rather, it was ineligible because these generic functions were the only thing necessary to “practice” the steps of the abstract idea itself. In short: there was no daylight between the abstract idea and the claimed implementation. That is what Judge Lourie meant in his plurality opinion in CLS when he said that “the animating concern is that claims should not be coextensive with natural law, natural phenomenon, or abstract idea”. CLS Bank Int’l v. Alice Corp. Pty. Ltd., 717 F.3d 1269, 1281 (Fed. Cir. 2013) (Lourie, J.).
Understood in this way, examiners can more readily evaluate whether particular claims are a “mere instruction” to implement an abstract idea on a computer. Instead of focusing on whether a generic computer is disclosed as the underlying structure for a computer implemented invention—which is surely the case in the vast majority of software patent applications—examiners should focus on whether a patent claim recites elements that differentiate it from other ways of practicing of the same abstract idea. Specifically, if the claims at issue recite an implementation of an abstract idea that includes elements that are meaningfully different from other implementations, then those elements are “sufficient to ensure that the patent in practice amounts to significantly more than a patent upon the [ineligible concept] itself.” As a result, such a claim is not coextensive with, and does not preempt the all practical applications of an abstract idea.
The Use of a Generic Computer
The nature of a “generic computer” is entirely overlooked by both the courts and the Office. This is a non-trivial question. The vast majority of the software industry develops software applications—and thus inventions—for execution what could be characterized as “generic computers. That is not a damning admission: it is a direct result of the very nature of the stored program computer architecture, the architecture designed by Alan Turing, John von Neumann and others that revolutionized the computer industry. The stored program architecture makes it possible to embed innovative functionality in the software, instead of the hardware of the machine. To turn this fundamental and valuable property of modern computer design against the patent eligibility of software is to turn the entire enterprise of software innovation upside down.
The Supreme Court and the current Federal Circuit have failed to recognize this fact. Rather, the original Federal Circuit under the lead of Judge Giles Rich, did indeed recognize this reality, in In re Alappat, 33 F.3d 1526, 1545 (Fed. Cir. 1994) (en banc). The court there stated that “Alappat admits that claim 15 would read on a general purpose computer programmed to carry out the claimed invention, but argues that this alone also does not justify holding claim 15 unpatentable as directed to nonstatutory subject matter. We agree. We have held that such programming creates a new machine, because a general purpose computer in effect becomes a special purpose computer once it is programmed to perform particular functions pursuant to instructions from program software.” Since the Supreme Court has not overruled Alappat, the Office should adopted this precedential holding as good law and instruct examiners accordingly.
A final clarification on this point is called for in view of the current practice of many examiners in making § 101 rejections. The Alice Court did not hold that implementing a process on a generic computer makes it abstract. Rather, the question of whether the claim calls for merely a generic computer is address only after it has been determined that the claim is directed to an abstract idea–not as part of that determination. Concluding that a claim is abstract because it is implemented on a generic computer is a logical fallacy. However, this is precisely the argument that many examiners use in their § 101 rejections. The Office must make absolutely clear to examiners that this is not a proper basis for rejection, that implementing a process on a generic computer does not make the underlying idea “abstract.”
 Interim Guidance, p.24.
 Public Knowledge, p. 6.
 ACLU, p. 3.
 To be fair, the ACLU and Public Knowledge take a very different approach from the broad eligibility supporters as to how to evaluate preemption; they would ignore for example, the availability of alternative implementations as evidence of non-preemption. See ACLU, p. 3-4, Public Knowledge, p. 6. My point here is narrower: merely to show that preemption was identified as a key issue that was overlooked by the Interim Guidance.
 Muskin & Farmer, p. 5.
 Howard IP Law Group, p. 3.
 Trading Technologies, p. 3 (emphasis in original).
 At the oral argument for Alice, Justice Kennedy asserted that a second-year college class in engineering could program Alice’s invention over a weekend, “that would be fairly easy to program,” to which Alice’s counsel Carter Phillips replied “I don’t disagree with it,” Transcript of Oral Argument at 5, Alice Corp. Pty. Ltd. v. CLS Bank Int’l, 573 U.S. ___ (2014) (No. 13-298) and then later “Well, that’s absolutely, I’m certain that’s true.” Id. at 12.
 To be clear, the suggestions made in this paragraph are opposed by ACLU, Public Knowledge and other supporters of narrower scope of eligibility.