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Too hot to handle: Update on the PLoS ONE paper

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The retraction of a PLoS ONE paper on the hand that made repeated reference to a Creator shows that biologists are “very hostile to those who invoke the supernatural in their science,” writes Professor Jerry Coyne. But it turns out that the paper’s authors weren’t referring to God, but Nature. One of the paper’s authors, Ming-Jin Liu, explains:

We are sorry for drawing the debates about creationism. Our study has no relationship with creationism. English is not our native language. Our understanding of the word “Creator” was not actually as a native English speaker expected. Now we realized that we had misunderstood the word “Creator.” What we would like to express is that the biomechanical characteristic of tendi[n]ous connective architecture between muscles and articulations is a proper “design” by the Nature (result of evolution) to perform a multitude of daily grasping tasks. We will change the “Creator” to “nature” in the revised manuscript. We apologize for any troubles may have caused by this misunderstanding.
(Spelling of “tendinous” corrected by me. – VJT.)

Another commenter writes:

The phrase ‘the creator’ has nothing to do with a designer god from the two-party-state, the Afro-Eurasian sky deity, or Mr Paley’s writings, but is a well-known ancient Chinese way of saying something alike “nature” or “evolution”, by way of zaohua zhe 造化者 ‘the Creator, creation’ (or, more literally, “the one who forms and transforms”, or “what forms and transforms”).

The commenter then proceeds to quote from The Encyclopedia of Taoism A-Z (edited by Fabrizio Pregadio, 2008, Routledge; article “creation” by Isabelle Robinet, vol. II, p. 1214):

The term zaohua, which means ” to inform (zao) and transform (hua),” derives from the *Zhuangzi and is generally used as a synonym for the cosmos. Zaohua zhe 造化者, lit., “what informs and transforms [the world],” is the Dao itself or its *qi (pneuma), the energy of life that does not create anything, but, like a potter, gives a determinate and transient form to the indeterminate. The analogy ends here, because the zaohua zhe is neither a person nor an entity, and does everything naturally and spontaneously without working. In this sense, zaohua is a synonym of *ziran (natural or spontaneous).

Zao is the coming of something out of nothing (*wu), and hua is the return to emptiness. Zao is movement, and hua is quiescence (see *dong and jing).
(Emphasis mine – VJT.)

The commenter buttresses his case by quoting a passage from the writings of the Greek physician Galen of Pergamon (129-200 or 216), who expresses sentiments similar to those of the paper’s authors:

It was, then, for the sake of these activities [ἕνεκα μὲν δὴ τούτων] that the
convexities at the ends of the ulna and radius came to be; but nature also makes use of
them to secure another advantage [χρῆται δ’ αὐταῖς καὶ πρὸς ἄλλο τι χρηστόν],
just as she is accustomed frequently to make something that has come to be on account
of one thing serve other uses as well [τῷ δι’ ἕτερόν τι γεγονότι συγχρῆσθαι καὶ
πρὸς ἄλλα]. For she located the heads of the tendons moving the fingers in the
concavity between these eminences, thus establishing as if with a wall or tower a safe
refuge for the tendons. (UP 2.11, 1.97.19-98.2 H, 3.133 K)
(Schiefsky, Mark J. 2007. Galen’s teleology and functional explanation. In Oxford Studies in Ancient Philosophy 33, ed. D. Sedley, 369-400. Oxford: Oxford University Press.)

In his paper, Schiefsky acknowledges that Galen “describes the construction of the human body as the result of the effort of a supremely intelligent and powerful divine Craftsman or Demiurge,” but he goes on to argue that this reflects “a highly sophisticated, functional analysis of the organism,” and he suggests that in the foregoing passage, we can think of Galen as referring to “nature’s craftsmanship.”

Skeptical readers might object that in another passage, the authors of the offending article in PLoS ONE also wrote that “Hand coordination should indicate the mystery of the Creator’s invention,” which suggests a theistic interpretation. But a 2005 article in MIT Technology Review refers to “Nature’s inventions,” and similar phrases can be found in textbooks on evolution.

Retraction Watch has set up a poll inviting readers to weigh in on the issue: Should “the Creator” paper have been retracted? The results are as follows:

Correct it 42.4% (254 votes)
Retract it 26.54% (159 votes)
Issue an expression of concern while it investigates 22.2% (133 votes)
Nothing 8.85% (53 votes)

However, the main issue in this ongoing saga is not whether the authors actually intended to allude to a “Creator,” or but the clear evidence (manifested in readers’ comments) of a bias against publishing ID-friendly views in the mainstream literature. One commenter writes:

Regretfully I have to withdraw my support for the journal as a reviewer. Also to bring this shameful incident to the attention of my academic colleagues and students who might consider submitting their work for publication at PLOS ONE.

Another scientist who is also a PLoS ONE academic editor writes:

As a scientist, as well as a PLoS ONE academic editor and author I feel outraged by the publication of a ms making explicit reference to creationism. This is an extremely serious issue for which the academic editor who handled the paper as well as the journal, besides the authors themselves, should be blamed.

I feel my scientific reputation to be put at risk by this incredible mistake, so should this paper not be retracted as soon as possible I will be compelled to resign from my position of PLoS ONE academic editor. Moreover, I am determined to avoid taking on any further assignment until this issue is fully solved.

That is the kind of mindset we are up against, folks.

For readers who may be interested, here’s a short article by creationist Brian Thomas M.S., titled, Human Hand Capabilities Impossible to Duplicate. And here’s a copy of The Fourth Bridgewater Treatise on the Power, Wisdom, and Goodness of God as Manifested in the Creation: The Hand; Its Mechanism and Vital Endowments as Evincing Design (1833), by Sir Charles Bell (1770-1842), K.H., F.R.S., F.R.S.E., F.R.C.S.E., M.W.S. This was science as it used to be done.

Comments are welcome.

Comments
Yes, inevitably the non-naturalist makes assumptions about naturalism based on his own belief about what naturalism lacks because it's not theistic: all seems a bit circular to me. "Logical consequences" are only as good as their premises, and if the premises in fact reject major parts of a naturalists own viewpoint, then the "logical consequences" are going to be faulty.Aleta
March 14, 2016
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What interests me is what the ideal naturalist — who acts in perfect accord with the logical consequences of naturalism — does.
Ah, the "logical consequences of naturalism" shibboleth. Please show the logic.Daniel King
March 14, 2016
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Origenes: What interests me is what the ideal naturalist — who acts in perfect accord with the logical consequences of naturalism — does. The use of the term "ideal" and "perfect" are probably ill-chosen, however, we understand that you think logically consistent naturalism can't treat conglomerates as real objects. A naturalist can see clumping of matter as a real phenomenon, and consider it as an object. A simple example is a molecule of sodium chloride, which has an existence, in most naturalist philosophies, above and beyond that of the individual sodium and chlorine atoms. That's because there is a relationship between the atoms when in molecular form that is not there when in atomic form. You're actually arguing that a logical naturalist can't recognize a cake as an object independent of the sugar and flour of which it is made.Zachriel
March 14, 2016
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Zachriel: Are you really claiming that a naturalist doesn’t see sodium chloride as a distinct object, or a cake for that matter.
No, that's not what I'm claiming. It's rather disappointing to notice that you still don't understand my argument. I'm not interested in what the average dime-a-dozen naturalist does and doesn't do. Nor am I interested in the activities of "baby naturalists" {#71, #79}. What interests me is what the ideal naturalist — who acts in perfect accord with the logical consequences of naturalism — does.Origenes
March 14, 2016
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Origenes: Six bottles of beer have another shape, weight, impact, structure and what not, than one bottle of beer. Gee whiz, Origenes. We've already agreed that many groupings are strictly formal. What about sodium and chlorine? Are you really claiming that a naturalist doesn't see sodium chloride as a distinct object, or a cake for that matter.Zachriel
March 14, 2016
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Zachriel, Six bottles of beer have another shape, weight, impact, structure and what not, than one bottle of beer. That still doesn't mean that 6 equals 1.Origenes
March 13, 2016
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Origenes: Six bottles of beer have properties that are quite distinct from one bottle of beer. However that doesn’t make six bottles of beer one single item. Perhaps. However, a six-pack has only a single barcode, while sodium and chlorine have distinctly different properties than sodium chloride.Zachriel
March 13, 2016
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Zachriel, Six bottles of beer have properties that are quite distinct from one bottle of beer. However that doesn't make six bottles of beer one single item.Origenes
March 13, 2016
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Origenes: Obviously we have to draw the line somewhere and obviously it’s a matter of agreement between reasonable people. Obviously, reasonable people, naturalist and otherwise, agree we can observe that matter clumps into things we call objects, and that these objects have properties that are emergent, that is, properties that can only be found in the clump, and not in the components. Everyone agrees that ordinary table salt is sodium chloride, but table salt has properties that are quite distinct from those of sodium and chlorine.Zachriel
March 12, 2016
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Aleta,
Aleta: Treating salt as if were one thing when it’s really 52 elementary particles but each bottle of beer is a bottle of beer, not 10^30 elementary particles, isn’t consistent, (…)
Obviously I agree. However in order to discuss this topic we have to pretend that there is a basic level somewhere — we either stop with a bottle of beer, with elementary particles or with fermions and bosons. Obviously we have to draw the line somewhere and obviously it's a matter of agreement between reasonable people. By the same token someone may object to your assessment that salt consists of 52 elementary particles, and proposes 10^300 fermions (not to mention even more 'strings') instead. It’s utterly irrelevant to my argument, which you fail to address.
Aleta: I can’t make much sense out of Origenes’ points.
How is this trivial matter related to the points I make?
Aleta: and I don’t see him putting forth any consistent set of principles in play here.
What kind of consistent set of principles do you have in mind regarding this ‘what-is-the-basic-level-issue’?
Aleta: Well, I dropped into this discussion, but think I’ll drop back out.
Well good for you! However, I do hope that you understand that your semantic point does not in any way undermine the substantive points I have made.Origenes
March 11, 2016
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Origene @ 136
Your observation points to a related problem: infinite regress. If parts consist of parts, which in turn consists of parts, which in turn … and so forth.
But the infinite regress of parts stops at fundamental particle level, because there are no more particles (parts) to discern.Me_Think
March 11, 2016
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Well, I dropped into this discussion, but think I'll drop back out. I can't make much sense out of Origenes' points. Treating salt as if were one thing when it's really 52 elementary particles but each bottle of beer is a bottle of beer, not 10^30 elementary particles, isn't consistent, and I don't see him putting forth any consistent set of principles in play here. I do agree with this, though:
it will never reach any point labeled “last stop, all off” (or rather “starting point” for all destinations). By the same token, if it has to move down to smaller and more fundamental components of reality than even fermions or bosons, it won’t ever know whether it has reached the “basement level” of reality.
I think that will forever be the case for our most fundamental level of reality. But that seems to be an entirely different subject.Aleta
March 11, 2016
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All this talk of beer is making me thirsty.algorithm A
March 11, 2016
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Me_Think, Your observation points to a related problem: infinite regress. If parts consist of parts, which in turn consists of parts, which in turn ... and so forth. Rosenberg puts it like this:
The multiverse theory seems to provide an opportunity seized upon by wishful thinkers, theologians, and their fellow travelers among the physicists and philosophers. First they ask, “If our universe is just one of many in a multiverse, where did the multiverse come from? And where did the multiverse’s cause come from, and where did its cause come from?” And so on, ad infinitum. Once they have convinced themselves and others that this series of questions has no stopping point in physics, they play what they imagine is a trump card, a question whose only answer they think has to be the God hypothesis. It is certainly true that if physics has to move back farther and farther in the regress from universe to multiverse to something that gave rise to the multiverse, to something even more basic than that, it will never reach any point labeled “last stop, all off” (or rather “starting point” for all destinations). By the same token, if it has to move down to smaller and more fundamental components of reality than even fermions or bosons, it won’t ever know whether it has reached the “basement level” of reality.
---- Zachriel, you have become more and more unresponsive. Glancing up through your last posts, I see nothing that merits a response.Origenes
March 11, 2016
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Origenes: When a naturalist “treats” six bottles of beer as one, two or three items, does he seriously hold that such a treatment is related to reality? The naturalist cashier treats a six-pack as a single item, while treating six separate bottles as six items. She may even suggest you get a better deal buying a six-pack rather than six separate bottles of beer. Origenes: I mean, a naturalist would still understand that there is a difference between reality and fiction, right? Sure. And perhaps you could argue with the cashier that your six separate items should be treated as one item, while everyone waiting in line is treated to the spectacle. However, some collections of items have real existence to (most) naturalists, including the collection of atoms that make up a rock, a star, or a rock star. Origenes: “Naturalism holds that there is nothing over and beyond the level of elementary particles.” That is incorrect. A naturalist recognizes that there are collections, which often have properties emergent from the collection. (Technically, naturalism is independent of atomism. Someone doesn’t have to believe that things are made up of atoms, or even know what atoms are, to think that everything supervenes on the natural.)Zachriel
March 11, 2016
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Origenes @ 133 Let me add one more dimension to this: The number of parts an object is made of would depend on what you use to see the object/person. With your eyes, you can see 1 human being, with a microscope you see more parts, with electron microscope, you may see even more parts. similarly, if you are far off, you can see a group , with binoculars you can see 3 persons in the group, with a better binocular you may see 1 person, with an even better binocular you may see the face of one person. IOW the parts someone sees depends on the instrument he/she uses to see it. Ofcourse, there is also the intention of the person - a decent guy may see all the parts, while some guys may concentrate on only some parts.Me_Think
March 11, 2016
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Aleta,
Aleta: What is the difference between a theist and a naturalist in recognizing a bottle of beer as an object?
I argue continually that there is no difference. Theists and naturalists have the same view on inanimate objects.
Origenes: I hold that naturalists and theists can agree on that 6 bottles of beer are 6 items total — and not 7.
It’s surprisingly important to my argument to stress that 6 bottles of beer are 6 items. My point is that it’s not an accurate description of reality when we, theists and naturalists alike, speak of “one set of beer” and refer to 6 bottles of beer. Since there exists no actual distinct entity, which is one thing and is called “one set of beer”. What actually does exist are six bottles of beer.
Aleta: A really simple example. Sodium is an element with 11 electrons, 11 protons, and 12 neutrons (34 parts), and chlorine is an element with 17 electrons, 17 protons, and 18 neutrons (52 parts). Together they make one molecule of salt. Salt is something that exists in the world and it is composed of elementary particles. Neither the theist or the naturalist would disagree about this, I don’t think.
“Salt” is in fact not one thing, just like “one set of beer” is not one thing. Sure, we may treat a salt molecule as if it is one thing, but in reality it is 52 things. Similarly we may treat “one set of beer” as if it is one thing, but in reality it is 6 things.
Aleta: Aha. Reading more carefully, I see that part of the problem is Origene’s definition of naturalism. A more accurate definition of would be that naturalism holds that all things that exist are composed of the basic constituents (elementary particles and forces) of the material world.
There is an inaccuracy loaded into this definition. “Things that exist are composed of [parts]”. IOWs there is one thing that is many things. There is the inaccuracy. Right there. Upon reflection it doesn’t make sense. There is “one set of beer” that is composed of “six bottles of beer”.
1 = 6
Is there in reality a distinct entity, which is one thing and is called “one set of beer”? No, there is not. In reality there are six bottles of beer.Origenes
March 11, 2016
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Aha. Reading more carefully, I see that part of the problem is Origene's definition of naturalism.
“Naturalism holds that there is nothing over and beyond the level of elementary particles.”
and in 13, he wrote,
There exist no entities over and beyond the level of elementary particles.
These are not accurate statements. In fact they load the definition with the exact conclusion that is being contested. A more accurate definition of would be that naturalism holds that all things that exist are composed of the basic constituents (elementary particles and forces) of the material world. Assuming we subsume all the complexities of quantum particles, fundamental forces, and other elements of modern physics into the phrase "elementary particles'", this can be shortened to
Naturalism holds that all things that exist are composed of elementary particles.
This definition accurately reflect the fact that the properties of these elementary particles are such that they combine to make discernable wholes of which they (the particles) are the most elementary parts. A really simple example. Sodium is an element with 11 electrons, 11 protons, and 12 neutrons (34 parts), and chlorine is an element with 17 electrons, 17 protons, and 18 neutrons (52 parts). Together they make one molecule of salt. Salt is something that exists in the world and it is composed of elementary particles. Neither the theist or the naturalist would disagree about this, I don't think. P.S. Let me make it clear that I know that the theist will say that naturalism is false, but that is not the topic of the discussion. We are discussing an accurate description of how people, both theists and naturalists, perceive and think about inanimate wholes and their parts.Aleta
March 10, 2016
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re 130: But what about a six pack of beer, or a bicycle, or a rock I understand that a theist believes there is more to life than the material world. But you are making claims about inanimate objects, and I think we need to understand that first. You seem to be making blanket claims about differences between theists and naturalists in being able to recognize parts and wholes in general. That’s what I would like to understand. In 121, you wrote,
Under naturalism, “objects” don’t exist as distinct entities but are instead nothing over and beyond the parts — they “exist” in the same way as a mereological sum of six bottles of beer “exist”.
That statement is about all objects, not just organisms. Post 111 doesn’t explain why you think this is true. So back to my original question: what is the difference between a theist and a naturalist in recognizing a bottle of beer as an object?Aleta
March 10, 2016
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Aleta, Tell me what you find unclear about post #111. I believe the answer to your question is in there. "Naturalism holds that there is nothing over and beyond the level of elementary particles." As we all know a theist does not agree. According to theism a human being is more than his (physical) parts. Therefor theism can ground the term "human being" — under theism "human being" refers to an actual existing entity — and the naturalist cannot.Origenes
March 10, 2016
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Origenes, please explain how the problems of identifying what is an object is different for a theist than it is for a naturalist. How does a theistic perspective make these issues not a problem for the theist that you describe as a problem for the naturalist? I would like to ask some more questions about the general philosophical issue of wholes and parts, but I first need to understand why the issues are different for the theist than the naturalist.Aleta
March 10, 2016
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Zachriel, When a naturalist "treats" six bottles of beer as one, two or three items, does he seriously hold that such a treatment is related to reality? Or is such an arbitrary "treating" activity some sort of thought exercise? Like ... "suppose for a moment that we don't have six items, but have one item instead"? or "no, let's make that two items!". I mean, a naturalist would still understand that there is a difference between reality and fiction, right? Right?Origenes
March 10, 2016
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Origenes: What I’m not interested in is in “treating” six bottles of beer as if they are one item.
http://www.walmart.com/ip/Budweiser-Beer-12-fl-oz-6-pack/10984460 "$6.47 at Portland"Daniel King
March 10, 2016
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Origenes: What I’m not interested in is in “treating” six bottles of beer as if they are one item. A formalist view is that we can treat any arbitrary grouping as a set. The naturalist view is that there are good reasons to treat certain groupings as objects, for instance, matter clumps into distinct objects called stars.Zachriel
March 10, 2016
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Zachriel,
Zachriel: (...) treating a set as a whole, (...)
You don't seem to grasp the argument .... at all. I'm interested in what is. What I'm not interested in is in "treating" six bottles of beer as if they are one item. Treating things as if they are something that they are not is not an argument. Your 'treating-argument' does not make sense at all. Why not "treat" two bottles of beer as one item and "treat" the other four bottles of beer as one item, so you have two items total? Stop it.
Origenes: There are six bottles of beer.
Zachriel: Then it’s six items in the checkout lane.
Ok. So, I take it that the "mereological sum" is out - does not exist. Reread #111. If you still have questions, do let me know.Origenes
March 10, 2016
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Origenes: For the record, is it your argument that six bottles of beer are one object because “it” has “its” “own” “emergent properties”? Sure it does. A six-pack has it's own container, for instance. Origenes: If so, why do you not arrive at a total of 7 items? It's no different than treating a set as a whole, except that in formalism, sets can be arbitrary, while in nature, there are often good reasons to treat multiple components as a single object, particularly if they exhibit properties that are not exhibited by the components. Origenes: For the umpteenth time: there is no six-pack, there never was. There are six bottles of beer. Then it's six items in the checkout lane. Perhaps you aren't suited for the job of a cashier.Zachriel
March 10, 2016
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Zachriel @122,
Origenes: In both these examples it is absurd to refer to an additional “mereological sum” and thus arrive at a total of 7 items.
Zachriel: No, but six items can be treated as a single object, and most naturalists agree that this corporate object may have a natural existence with its own emergent properties.
For the record, is it your argument that six bottles of beer are one object because “it” has “its” “own” “emergent properties”? If so, why do you not arrive at a total of 7 items? How about two bottles of beer, does “it” have “its” “own” “emergent properties” as well?
Zachriel: There is nothing inconsistent about treating each beer in a six-pack as an object, and treating the six-pack as an object. You don’t end up with seven objects.
For the umpteenth time: there is no six-pack, there never was. There are six bottles of beer. Allow me to rephrase what you just said:
Zachriel: There is nothing inconsistent about treating each beer in a six-pack of six bottles of beer as an object, and treating the six-pack six bottles of beer as an object. You don’t end up with seven objects.
If there is “nothing inconsistent” about treating six bottles of beer as one object, why don’t you arrive at a total of 7 items? And while we are at it, why not treat (whatever that means) three bottles of beer as one object and add two more items?Origenes
March 10, 2016
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Aleta: What if I show up to buy one bottle of beer, and the clerk says. “Sorry, that is actually 10^30 elementary particles. You’ll have to get in the other line” Origenes: He would have a point. But no job as a cashier. Origenes: In both these examples it is absurd to refer to an additional “mereological sum” and thus arrive at a total of 7 items. No, but six items can be treated as a single object, and most naturalists agree that this corporate object may have a natural existence with its own emergent properties. There is nothing inconsistent about treating each beer in a six-pack as an object, and treating the six-pack as an object. You don't end up with seven objects. You end up with either six objects or one object depending on the level of analysis. It's no different than any other set, formal or naturalistic. You've already indicated that there is at least one naturalist, working as a cashier, that has no problem making this distinction.Zachriel
March 10, 2016
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Aleta, Me_think & Zachriel,
Aleta: What if I show up to buy one bottle of beer, and the clerk says. “Sorry, that is actually 10^30 elementary particles. You’ll have to get in the other line”?
He would have a point. However, for the sake of this discussion please pretend that the level of elementary particles does not exist and that one bottle of beer is one item.
Zachriel: In any case, there is nothing about naturalism that prevents the recognition of objects in the world.
Aleta: I agree. I would like Origenes to explain why he thinks otherwise.
Under naturalism, "objects" don't exist as distinct entities but are instead nothing over and beyond the parts — they "exist" in the same way as a mereological sum of six bottles of beer "exist". I have spelled out my reasoning as clearly as I can in post #111. Which part of my reasoning is in need of explanation?
Me_Think: Just curious – what is the ‘mereological sum’ of a human being?
A 'human being' is the 'mereological sum' of the parts that constitute a human being. More generally formulated, the term "mereological sum" is used to appeal to the intuition that a human being, contrary to 6 bottles of beer, is more than his (physical) parts.Origenes
March 10, 2016
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Aachriel writes,
In any case, there is nothing about naturalism that prevents the recognition of objects in the world.
I agree. I would like Origenes to explain why he thinks otherwise.Aleta
March 10, 2016
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