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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
Algorithm Eh:
Well, now that this has been decided, we can get right on discarding evolution and teaching creation Intelligent Design in the schools.
ID is not anti-evolution. Obviously you have no clue as to what is being debated.Virgil Cain
March 8, 2016
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Origenes @86: Feel free to reread post #65 and #70 @60 you have simply substituted "original identity" for "intrinsic identity". @70 doesn't give an explanation at all. @86 your link doesn't work; however, a cache copy seems to point to a discussion of intentionality, not objects. Origenes: How many things do we have, given that a Lego horse consists of 30 Lego blocks? There is one Lego horse. If we take the Lebo horse apart, we have 30 Lego blocks. If we look more closely, we have about 2*10^23 atoms. Each atom is composed of even smaller particles. Still, there is only one Lego horse.Zachriel
March 8, 2016
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Question designed for Zachriel: How many things do we have, given that a Lego horse consists of 30 Lego blocks? A. 30 things, namely 30 Lego blocks B. 31 things, namely 30 Lego blocks + the sum of it ("Lego horse"). C. OtherOrigenes
March 8, 2016
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Zachriel, Feel free to reread post #65 and #70. In there you will find a brief explanation of the difference between intrinsic and ascribed identity. Also here (B.Vallicella) you can find a highly relevant article, which deals with original (intrinsic) vs derived (ascribed) intentionality.Origenes
March 7, 2016
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I find it very creepy that evolution scientists try to leave subjectivity out of their view of reality. It conjures up images of scientists performing gruesome experiments on animals in the laboratory, coldly noting the facts of what happens, their emotions shut down.mohammadnursyamsu
March 7, 2016
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Origenes: You are having a great deal of trouble grasping the difference between ascribed and intrinsic identity, haven’t you? Free free to explain how you view the distinction.Zachriel
March 7, 2016
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Zachriel,
Zachriel: Rather, a typical naturalists observes the world, finds similarities and differences between various objects there, and gives them names.
Sure. You keep bringing up this trite observation as if it is relevant. But what is your point? Giving object names falls into the category "ascribed identity" — see #65 — which is in reality no identity at all. You are having a great deal of trouble grasping the difference between ascribed and intrinsic identity, haven't you?
Zachriel: You seem to think there is some sort of “ideal” horse that exists outside human experience, when, as it turns out (....).
We are not discussing my position. We are discussing naturalism and its logical consequences.Origenes
March 7, 2016
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Virgil: Yes Just as I thought, all hat, no cattle.velikovskys
March 7, 2016
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Origenes: As explained, the naturalist cannot ground the concept “horse”. Rather, a typical naturalists observes the world, finds similarities and differences between various objects there, and gives them names. You seem to think there is some sort of "ideal" horse that exists outside human experience, when, as it turns out, unless you have seen or heard about horses, you have no notion of them.Zachriel
March 7, 2016
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velikovskys: "So a intelligent designer must create both the pattern of atoms of a thing and something else which is obvious. Can ID detect this obvious something?" VC: "Yes." Well, now that this has been decided, we can get right on discarding evolution and teaching creation Intelligent Design in the schools.Algorithm Eh
March 7, 2016
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Zachriel,
Zachriel: It is a specific ordering of Legos into the shape of a horse.
As explained, the naturalist cannot ground the concept “horse”.
Zachriel: Baby naturalist: Horsey! {after making a Lego horse} O: No. You can’t say that. Baby naturalist: Horsey! {pointing}
In what way does the naive opinion of a nescient baby naturalist count as an argument?
Daddy naturalist: (… ) and therefor the universe that we observe has no purpose, no evil, no good, nothing but pitiless indifference. Baby naturalist: Daddy bad! Daddy naturalist: I have just explained to you that there is no such thing as “bad”. Baby naturalist: Daddy bad!
Question to Zachriel: how is that an argument?Origenes
March 7, 2016
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velikovskys:
So a intelligent designer must create both the pattern of atoms of a thing and something else which is obvious. Can ID detect this obvious something?
Yes.Virgil Cain
March 7, 2016
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Virgil: Obviously more than just the pattern. So a intelligent designer must create both the pattern of atoms of a thing and something else which is obvious. Can ID detect this obvious something?velikovskys
March 7, 2016
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EZ Jerad:
They don’t attempt to detect design first using Dr Dembski’s metric?
They use the EF or something very, very similar to it. Science mandates that approach but you wouldn't know that because you don't understand science.Virgil Cain
March 7, 2016
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#66 VC
Dolt. They do that by finding artifacts and other evidences left behind. But first they have to make a determination if artifacts indeed exist. They do so by finding signs of work or manufacture.
What? They don't attempt to detect design first using Dr Dembski's metric? Actually, looking for signs of a worked surface for objects like hand axes or abrader stones is done and can be a bit tricky. I've found such objects on sites and had them evaluated. Sometimes the experienced archaeologist disagree which makes sense if, say, an stone really is a hand axe but was only used once or twice on soft objects.ellazimm
March 7, 2016
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velikovskys:
If the pattern of atoms does not make a horse what did the designer design?
Obviously more than just the pattern.Virgil Cain
March 7, 2016
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However, specific conglomerations of atoms do make a horse. Virgil: And another unsubstantiated claim by Zachriel. We love how Zachriel always cries when others do so and yet all Zachriel ever does is spew unsubstantiated claims. Talk about not knowing one’s place… If the pattern of atoms does not make a horse what did the designer design? An abstract idea of horsieness?velikovskys
March 7, 2016
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Zachriel:
However, specific conglomerations of atoms do make a horse.
And another unsubstantiated claim by Zachriel. We love how Zachriel always cries when others do so and yet all Zachriel ever does is spew unsubstantiated claims. Talk about not knowing one's place...Virgil Cain
March 7, 2016
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Origenes: The reason is that there is no intrinsic “horse” identity to a collection of Lego blocks. Um, a Lego horse is not a horse. It is an object, however, even to a naturalist. It is a specific ordering of Legos into the shape of a horse. Origenes: Just like there is no intrinsic “human” identity to a conglomerate of atoms. Have no idea what that means. However, specific conglomerations of atoms do make a horse.
Baby naturalist: Horsey! {after making a Lego horse} O: No. You can't say that. Baby naturalist: Horsey! {pointing} O: Quit saying that! Baby naturalist: Horsey! Horsey!
Zachriel
March 7, 2016
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Zachriel,
Origenes: However there is nothing intrinsic to that Lego structure that is a “horse”.
Zachriel: Well, that’s probably because a Lego horse is not a horse in fact.
No, that’s not the reason at all. The reason is that there is no intrinsic “horse” identity to a collection of Lego blocks. Just like there is no intrinsic “human” identity to a conglomerate of atoms.
Zachriel:However, a particular arrangement of organic molecules is a horse in fact, as most naturalists would agree.
Given naturalism, such an agreement would constitute a clear example of naively ascribed identity. Lego blocks or atoms, under naturalism, there is in fact no horse ….Origenes
March 7, 2016
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Zachriel:
However, a particular arrangement of organic molecules is a horse in fact, as most naturalists would agree.
And yet those same naturalists cannot explain the existence of a horse.Virgil Cain
March 7, 2016
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Algorithm Eh:
I must have missed the groundbreaking paper about humans designing life from scratch.
I must have missed the groundbreaking paper about mother nature designing life from scratch. The concept can't even be tested. However we can test the concept that life was intelligently designed.
I think the term you were looking for is that the “modification”‘of life forms is possible. Darwin wrote extensively in a little book he wrote. Maybe you have heard about it.
Darwin's ideas cannot be tested. However, thanks to genetic algorithms we can directly observe the power of evolution via intelligent design.Virgil Cain
March 7, 2016
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Origenes: However there is nothing intrinsic to that Lego structure that is a “horse”. Well, that's probably because a Lego horse is not a horse in fact. However, a particular arrangement of organic molecules is a horse in fact, as most naturalists would agree.Zachriel
March 7, 2016
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Algorithm Eh:
Archaeologists study human history
Dolt. They do that by finding artifacts and other evidences left behind. But first they have to make a determination if artifacts indeed exist. They do so by finding signs of work or manufacture. The henge on Pluto would also be evidence of manufacture
We agree that humans are very good at identifying things build by other humans.
We are also good at identifying things built by other intentional agencies. We do that because we have a good understanding of cause and effect relationships. We know what mother nature is capable of and we know what intentional agencies can do with nature.Virgil Cain
March 7, 2016
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Zachriel,
Zachriel: To most naturalists, a Lego horse is a specific configuration of Legos, one which can be pointed to, named, and considered as an object.
You seem unable to make a distinction between ascribed identity and intrinsic identity. Yes we can ascribe [“point to”, “name” and “consider”] “horse” to a Lego structure. However there is nothing intrinsic to that Lego structure that is a "horse". IOWs "horse" would be a "derived" identity (from an external source, namely us) and not an "original" identity. If there is no original identity, then the Lego horse is in fact nothing over and beyond Lego blocks — simply because there is no identity that makes it one thing. IOWs there is no horse in reality, we can only ascribe (project) oneness ("horse") to what is in fact nothing over and beyond a conglomerate of Lego blocks. Similarly naturalism cannot ground (intrinsic/original) identity wrt a conglomerate of atoms — like "human being".Origenes
March 7, 2016
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Origenes: Again, does a certain shape endow something with the status “distinct entity”? What part of "yonder pile of rocks" do you not understand? Origenes: This recognition is unrelated to their philosophy and its logical consequences, which is being discussed here. You seem to want to ascribe views to naturalists when a cursory examination of the literature shows that nearly all naturalists hold a contrary view. Origenes: Naturalism, physicalism, materialism and atomism have roughly the same meaning. No. Naturalism is independent of atomism. Someone doesn't have to believe that things are made up of atoms to think that everything supervenes on the natural. Origenes: There is no “it” which “possesses” (or uses) “its own” properties. An attentive naturalist rejects these projections of personhood. We're not talking about personhood, but a pile of rocks.
N: Do you see yonder pile of rocks? O: You mean the one that's almost in the shape of a horse? N: Yes, that's the one. O: You can't mean that pile of rocks, because you reject that rocks can form a separate object. N: Huh? I'm talking about that pile of rocks right there {pointing}. O: Your philosophy means you can't point with your finger, which is made up of atoms. N: You're as silly as Hamlet looking at clouds.
Origenes: it’s important to notice that, those properties you speak of, are fully dependent on the atoms. An emergentist would claim the properties are emergent, and in many cases, we can show how properties emerge from the collective physical behavior of the components. Origenes: Just like a Lego horse consists of nothing over and beyond Lego blocks. To most naturalists, a Lego horse is a specific configuration of Legos, one which can be pointed to, named, and considered as an object.Zachriel
March 7, 2016
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KairosFocus: "In this case, humans would not be available candidates for an icehenge on the Dwarf Planet known as Pluto." Agreed. "The obvious conclusion any archaeologist would make with moral certainty is, design." No, there is not a credible archaeologist who would jump to this conclusion. Archaeologists study human history. We have already agreed that your Plutonian Stonehenge is not of human manufacture. "In short, the confinement of design inferences to humans as an objection is a strawman tactic." Your unsubstantiated opinion is duly noted. Unless, of course, you have some real example to present. And, your propensity to falsely label the arguments made by anyone who disagrees with you (eg. falsely labelling it a strawman) is also duly noted.Algorithm Eh
March 6, 2016
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j-mac writes, in reply to my statement that "Atheists are not angry at God. Among other things, why would one be angry at a being that one does not believe exists?
Well Aleta, ideally, the atheists would have to prove that there is no God by proving that the universe and life came into existence without a need for God or ID. Most respected atheists I know are actually agnostic due to the issues mentioned by me. Unless you have some evidence to prove your atheistic view one way or another, you can only claim to be an atheist. You can’t prove your stand as to why you are an atheist, scientifically speaking. You can only say that it is your choice but that would not stand any argument here though….
Hmmmm. You are changing the subject. I have what I consider good reasons for being an atheist (and especially in not believing in any of the gods invented by mankind), and I've been in discussions here at UD about that. But the original statement was that atheists were angry at God, and that was what I was replying to. I'm not an atheist (of the form that I am) because of any anger, any more than I think you are a believer out of fear of there not be an imposed purpose in your life. It's not appropriate or constructive to ascribe beliefs to people based on your thoughts of what their motivations ought to be, rather then being willing to learn what they themselves see as the foundation of their beliefs.Aleta
March 6, 2016
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Zachriel,
Origenes: Nonresponsive. In the midst of a mountain range a pile of rocks can look like a horse but that fact doesn’t extend a “distinct entity” to this pile of rocks.
Zachriel: Of course it can. Naturalist: Do you see yonder pile of rocks that’s almost in the shape of a horse?
Again, does a certain shape endow something with the status “distinct entity”? What are you talking about?
Entity (noun) Something that exists apart from other things, having its own independent existence. [Cambridge Dictionaries Online]
Zachriel: A pile of rocks in the shape of a horse isn’t a horse — of course. However, most naturalists can easily recognize a large solid-hoofed herbivorous ungulate domesticated mammal of the genus Equus as a horse, even though it is made up of atoms.
This recognition is unrelated to their philosophy and its logical consequences, which is being discussed here. Naturalists can do all sorts of things (e.g. being moral), which according to their philosophy doesn’t make sense or should not even be possible. That’s not being discussed here.
Zachriel: Again, naturalism doesn’t imply atomism,
Naturalism, physicalism, materialism and atomism have roughly the same meaning.
Zachriel: (…) but given atomism, an object is the observed clump of atoms that has its own distinguishing properties.
First, be careful of your wording here. There is no “it” which “possesses” (or uses) "its own" properties. An attentive naturalist rejects these projections of personhood. Second, it’s important to notice that, those properties you speak of, are fully dependent on the atoms. As philosophers say these properties supervene on the atoms. And by this is meant that that given the state of the atoms, there is only one way that any structure, property or “mental property” can be. IOWs there is zero wiggle room — zero “distance” if you will — for the conglomerate wrt to the level of elementary particles. Or yet IOWs the conglomerate is no “distinct entity” wrt to the elementary particles, but is instead produced by it for 100%. Just like a Lego horse consists of nothing over and beyond Lego blocks.Origenes
March 6, 2016
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"Baloney. Atheists are not angry at God. Among other things, why would one be angry at a being that one does not believe exists?" Well Aleta, ideally, the atheists would have to prove that there is no God by proving that the universe and life came into existence without a need for God or ID. Most respected atheists I know are actually agnostic due to the issues mentioned by me. Unless you have some evidence to prove your atheistic view one way or another, you can only claim to be an atheist. You can't prove your stand as to why you are an atheist, scientifically speaking. You can only say that it is your choice but that would not stand any argument here though....J-Mac
March 6, 2016
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