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Four fallacies evolutionists make when arguing about biological function (part 1)

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First of all, I want to apologize for shamelessly copying the title and structure of a recent post by VJ Torley. VJ, I hope you will pardon me: imitators, after all, are an undeniable mark of true success! 🙂

That said, let’s go to the subject of this post. I have discussed a little bit about biological function in my previous posts, and I have received many comments about that topic, some of them from very good interlocutors (I would like to publicly thank here Piotr and wd400, in particular). From my general experience in this blog during the last few years, I would like to sum up some of the more questionable attitudes and arguments which I have witnessed most frequently from the “other side” about this concept. Indeed, my purpose here is to catch not so much the specific arguments, but rather the general perspectives which are behind them, and which I believe to be wrong (that’s why I call them “fallacies” in the title).

So, here we go. First the whole list, then we analyze each individual point.

1. The fallacy of denying the objectivity of function.

2.  The fallacy of overemphasizing the role of generic function.

3. The fallacy of downplaying the role of specific function.

4. The fallacy of completely ignoring the highest form of function: the procedures.

I will deal with the first three issue in this post, and with the fourth in a later post.

1. The fallacy of denying the objectivity of function.

This attitude takes the form of an obstinate resistance to the concept itself of function, as though it were something which does not exist. So it happens that, as soon as we IDists start talking about functional specification, there is always someone on the other side ready to question: “Yes, but how do you define function?”. Or to argue that function is just a subjective concept, and that it has no role in science.

Many times I have simply answered: “Hey, just look at some protein database, like Uniprot. You will easily find, for each protein listed there, the voice: “Molecular function”. And usually there is one or more functions listed there. Is that bad science? Are you going to write to the people who run Uniprot asking them what do they mean by that word?”

rusty-185531_640The truth is that practically everybody understands perfectly what function means, and the attitude of denying the concept is just that: simple denial, motivated by the (correct) conviction that the concept itself of function is definitely ID friendly. .

However, the more sophisticated among our interlocutors will not deny function in such a gross way, but they will probably try to argue that the concept is obscure, vague, ill defined, and therefore not reliable. Here we find objections such as: “What do you mean exactly with the word?” or “To what kind of function do you refer?” or “Function can change according to how we define the context”. There is some truth in these thoughts, but in no way such objections are a real problem if we treat the concept of function correctly.

For example, in my previous post “Functional information defined” I have given the following definitions:

I will try to begin introducing two slightly different, but connected, concepts:

a) A function (for an object)

b) A functionality (in a material object)

I define a function for an object as follows:

a) If a conscious observer connects some observed object to some possible desired result which can be obtained using the object in a context, then we say that the conscious observer conceives of a function for that object.

b) If an object can objectively be used by a conscious observer to obtain some specific desired result in a certain context, according to the conceived function, then we say that the object has objective functionality, referred to the specific conceived function.

I will stick to those definitions.

So, function can be objectively defined, even if some reference to a conscious observer conceiving and recognizing it is always necessary.

It is perfectly true that different functions can be defined for the same object. There is no problem there. It is also true that functions can be stratified at different levels. Uniprot correctly lists “molecular functions”. So, for example, hexokinase has the molecular function of binding ATP and phosphorylating glucose or other hexoses, That is what I call the “local function”, the immediate biochemical effect of the molecule. But we can also say that the role of hexokinase is to start the glycolysis process and therefore contribute to the extraction of energy from food in the form of ATP, a role which would not be immediately obvious from the local function (which, instead, consumes ATP). This is a meta-function, because it describes the role of the enzyme in a wider context. We can say that the local function contributes to the meta-function.

In ID theory, local functions are specially interesting when we try to compute the functional complexity of a single protein. For that, we must refer to its immediate biochemical effect. But the meta-function is specially interesting too, when we try to analyze the complexity of a whole system of molecules, such as a protein cascades. In this kind of analysis, the concept of irreducible complexity is very important.

The important point is: denying function, or denying that it can be treated objectively in a scientific context, is a fallacy.

2.  The fallacy of overemphasizing the role of generic function.

This is generally what I call the concept of “any possible function”, which is so often invoked by darwinists as a reason to believe in the power of natural selection and of the neo-darwinian RV + NS algorithm.

The reasoning is more or less the following: as NS is not looking for anything particular, it will detect everything possible which is “useful”. IOWs, NS has no prejudices, and therefore it is very powerful, much more powerful of old good intelligent design, which is confined to intelligent options. That was one of Petrushka’s favourite arguments, but in different ways it has been proposed by many darwinist commentators here.

Now, I hate quoting myself again, but if you look at the above definscrapyardition of “function”, you will see that everything can be functional in some context. Function is not a rare thing, because, as already said:

If a conscious observer connects some observed object to some possible desired result which can be obtained using the object in a context, then we say that the conscious observer conceives of a function for that object.”

Now, as we can conceive of a lot of desires (that is certainly a very human prerogative), functions are very easy to get. In any context, we can use practically anything to obtain some result. That’s why I rarely throw away anything because, you know, “it could be useful, sooner or later”.

Does that reinforce the darwinist concept that “any possible function” is relevant?

Not at all. Quite the contrary. Just because possible functions are everywhere, it is easy to see that only some specific functions are really relevant in a specific context.

home-office-336377_640So, if I go to my attic, I can maybe find some use for any kind of junk that I may find there. But, if I happen to find a forgotten working computer there, I can certainly use it in a very specific way.

So, I would say that there is a great difference between finding some piece of wood which could perhaps be adapted to some use, and finding a working computer. The piece of wood is an example of “any possible function”, while the computer is an example of specific, complex function.

And, as anyone should understand, even if I find 1000 pieces of wood in my attic, that will not give me a working computer. IOWs, simple generic functions do not naturally add to a complex specific function.

So, why am I saying that darwinists tend to overemphasize the role of generic function?  The reason is simple: generic function is all they have, all they can deal with. Their only “engine of variation”, which is RV, can only, at best, generate simple generic function, nothing more. So, what do we do when we have only such and such?   We overemphasize the importance of such and such. Not because it is important, but because it is the only thing we have. An old fallacy, but always a common one.

3. The fallacy of downplaying the role of specific function.

The simple truth is that, especially in a system which is already complex, functional changes usually require complex interventions. Indeed, the addition of a truly new function to an existing complex system requires not only the complexity implicit in the function itself, but also the complexity necessary to integrate the new function in the existing system.

As already said, in the biological context there are two different ways to look at functions: what I call the “local function”, IOWs, the immediate biochemical activity of the molecule, and the “meta-functions”, IOWs, the general results of the activity of that molecule in the whole system.

Let’s take a molecule as an example: ATP synthase. A classic.

It is a very good example, because:

a) It is a very old molecule, already present in LUCA, before the archaea-bacteria divergence, almost 4 billion years ago.

b) It is a very complex molecule: it is made of two different parts, F0 and F1, each of them made of many subunits, and each subunit is a complex protein.

c) It is a very functional protein, indeed a wonderful molecular machine which transforms a proton gradient into stored biochemical energy in the form of ATP, working very much like a mill.old-windmill-96688_640

d) It is a very conserved protein. Let’s take only the subunits alpha and beta, which make most of the F1 part. a multiple alignment between: the human protein, the archaea protein (methanosarcina barkeri) and the bacterial protein (E. coli) showed 176 identities for the alpha subunit and 202 identities for the beta subunit. A total of 378 perfectly conserved aminoacid positions in just two of the many subunits of the molecule, along the whole tree of life.

e) Its local function is very clear: it synthesizes ATP from the energy derived from a proton gradient, transforming the flow of H+ ions into a mechanical rotation which in turn couples the phosphate molecule to ADP.

f) Its meta-function is equally clear: it generates the energy substrate which makes all cellular life possible: ATP.

Now, 378 identities after about 4 billion years during which all possible neutral mutations had time to happen mean just one thing: those 378 AAs must be there, and they must be what they are for the molecule to work.

This is a very good example of a very specific and complex function. In a complex context (cellular life), where the function is useful because there are a lot of individual processes whic h depend on ATP to exist. It is not the piece of wood in the attic. It is a supercomputer, an amazing molecular machine.

Well, are darwinists  curious, concerned or worried because of such specific complex functions which can be found in the old attic of OOL? Not at all. They are confident that they can be readily dealt with. There is an appropriate tool, usually called “the just so story”. For a good example, just read the Wikipedia section about ATP synthase, the part under “Evolution of ATP synthase”. Have fun.

The problem is: complex functional proteins simply cannot be explained. So, why should we think that they must be explained? After all, we can find so many generic functions in our attic: small variations in a gene which can give antibiotic resistance through one or two AA mutations, small changes in the affinity of an existing esterase which confer a nylonase activity through a couple of mutations, the selective spread in specific populations of the heterozigote state of drepanocytosis (one mutation) which gives some resistance to malaria. With all those good pieces of wood which can be used to fix some old chair, who cares about those stunning supercomputers which crowd our attic? They are just there, let’s not be fastidious about the details.

Well, that’s enough for the moment. We will discuss the “procedures” fallacy in next post.

 

 

 

Comments
gpuccio, some great comments here - I'm looking at writing a paper on some of this, regarding frameshifts, would be very keen for your input and/or to cite you if that's okay, email address is my username at gmailgenome.guy.82
September 23, 2016
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gpuccio, Check this out - really juicy: http://events.embo.org/15-kinetochore/ Can't miss that event.Dionisio
April 6, 2015
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Interesting papers: http://www.cell.com/cell/abstract/S0092-8674(15)00241-X http://www.cell.com/molecular-cell/abstract/S1097-2765(14)00523-1 http://www.cell.com/cell/abstract/S0092-8674(14)00866-6 http://www.cell.com/trends/cell-biology/abstract/S0962-8924(14)00118-4 http://www.cell.com/trends/cell-biology/abstract/S0962-8924(14)00135-4Dionisio
March 14, 2015
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gpuccio https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-520543Dionisio
October 21, 2014
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gpuccio https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-514898Dionisio
September 16, 2014
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Wow! The same comment got posted twice with identical time stamp. Maybe I pressed the 'post' button twice? double tapped or double clicked ? Oh well, sorry for that. :(Dionisio
September 6, 2014
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Still don't quite understand why they use these words 'surprising' and 'unexpected' so often in their reports. What were they expecting? Something else? Check this out: https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-513588Dionisio
September 6, 2014
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Still don't quite understand why they use these words 'surprising' and 'unexpected' so often in their reports. What were they expecting? Something else? Check this out: https://uncommondescent.com/evolution/a-third-way-of-evolution/#comment-513588Dionisio
September 6, 2014
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p.s. The iPad example wasn't mine. I think it was Dr. John F.X. Knasas, professor of Philosophy at the University of St. Thomas in Houston who mentioned it in his epistemology class last spring. I really liked it and managed to remember it somehow. Not quite a miracle, but close. :-)tgpeeler
July 18, 2014
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Vivid and SB, thanks for the feedback. i was beginning to think the post was so bad it wasn't worth a response from anyone! Now I would like to hear from MF or Pietro...tgpeeler
July 18, 2014
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tgp @477. Thanks for providing a good summary of first principles. Yes, the reasoning process starts with the facts of sense experience, not from axioms or assumptions or presuppositions. Yes, statements about identity are the basis for understanding what must be true and what must be false. If A is not B, then it is false to say that A is B. Yes, understanding what must be true and what must be false is the basis for syllogistic reasoning. Logic depends on the Law of non-contradiction.StephenB
July 17, 2014
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TGPEELER BTW I really like the iPad analogy well done. Vividvividbleau
July 17, 2014
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TGP Excellent post as to why reason informs the evidence and not the other way around. Of course there are those who have argued that no one can be certain that it is you that is existing maybe it is an illusion. One former poster insisted that it is impossible to know anything with 100% certainty. Of course he was uncertain if that was certain :) By your writings I think we have been influenced by the same person regarding these matters. No doubt there is much muddled thinking in the areas you address. I don't think it is coincidental that you have not got some feedback from the evidentialists that has far as I can tell thinks evidence takes precedence over reason. The devil is always in the details. Once you start getting into those devilish details surprise surprise they don't want to discuss things anymore. Take MF
If you can imagine something then it is logically possible.
You would assume that the opposite would be true as well. That is if you can't imagine something it is not logically possible. So I asked him this
And this has been one of my main points all along. Assuming you are correct about this( see VJT).If it is correct you have argued forcibly that it is not logically possible that something springs from nothing.Please imagine for all of us “nothing”
Unfortunately all of a sudden he doesn't want to talk about it anymore. Hmmmm Vividvividbleau
July 17, 2014
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Hmmm...tgpeeler
July 17, 2014
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I have read through most of this thread with great interest. The discussion concerning the principles of "right reason" I found particularly illuminating, in several ways. Even though better men and better minds than me have made the first principles case I'd like to take a shot at it. I've been meaning to do this anyway but the discussion here has provided a nice foil. I will consider this a trial run to be refined based upon the conversation that follows, if any follows. I start, pre-reflectively, with the awareness that things exist. I exist. The world around me exists. The keyboard upon which I am typing exists. The computer screen upon which I cast my gaze exists. And so forth. As I begin to think about this the first thing that I become aware of is that everything that exists, is what it is. That is, everything is identical with itself. Everything is what it is. In my entire experience I have never seen one thing that is something other than what it is. (Leaving aside for the moment that I may be confused or ignorant about what that is, exactly, which is an epistemological issue and not an ontological issue.) Thus, I can be certain that things do in fact exist, and that things are identical with themselves. I exist. There can be no question of that. If I didn’t exist then I couldn’t say that I did. If I didn’t then no one is typing this post. Clearly this is absurd so our starting point is upon the firmest possible ground. Things exist and they are what they are. This is called the Law of Identity and it is The First Principle. Without the Law of Identity there is nothing. No existence, no identity, nothing. So it seems that I have connected with a universal truth. That things are and that things are what they are. I did not assume this to be true. I did not start from some a priori or arbitrary or assumed starting point. I started with the evidence that the universe presented to me. I started with the data. It seems obvious that intellectual integrity demands that we account for ALL of the data. Science seems to be about the data, or it should be, anyway. So what could be more fundamental than this data? That things exist. I also think that this illustrates a confusion in philosophy (and science) that runs deep and wide in epistemological issues (and who am I to say but I will anyway) and that is a failure to understand that all knowledge begins in the senses. It ends in the mind but it begins in the senses. We sense particulars and we generalize or abstract based upon those particulars. What I am saying is that even deduction is induction, in the end. The First Principle of Identity, which encompasses two concepts, that of Being or existence, and Identity; that a thing is and must be what it is, is an eternal and universal truth, an a priori truth, but we discover it by means of experiencing the world through our senses. How else could it be? The notion of "a priori" truth has been conflated with the notion of "a priori" knowledge. There is "a priori truth," i.e. "a priori principles," but we come to an awareness of them by means of sense experience, in an "a posteriori" fashion. What else becomes apparent based upon this Law of Identity? If I say that something is what it is, that is just a “short cut” way to saying that it is not what it isn’t. Instead of saying, Hi, I’m not KF, and not Upright BiPed, and not SB, or well you get the point, I say Hi, I’m Tom. In other words, when I say that something is, at the same time, in the same mental act, I am also saying what it is not. To say what something is, is at the same time to also say what it is not. Now we have the Law of Noncontradiction. I can’t say that something is AND isn’t, because to say what something is, is to say what it isn’t. It’s absurd to say that I am me and that I am not me. I understand this clearly and distinctly, to use a phrase from Descartes. I cannot be confused about this. I can deny this principle in my arguments or in my conversation but when I do I only demonstrate to the world that I am an irrational or ignorant or unthoughtful person. For what could be more foolish than to claim that I am and that I am not? Remembering that this principle, which we have discovered, not invented or created, we have discovered by “the scientific method” of analyzing data, the data of existence. The other thing that falls out of this is the Law of the Excluded Middle. As I think about something being or not being, I realize that there is no third option. There is no tertium quid or middle option. Thus “excluded middle.” Thus we have the "First Principles" of "right reason," the Laws of Identity, Noncontradiction, and Excluded Middle, which have been inferred from the data of existence. These principles are falsifiable. All it takes is one instance or example to make them not so. So for Mark Frank or Piotr, or anyone else, all you have to do is show some data, one datum, even, of something that isn’t what it is, or is and is not at the same time, or that falls into a third category beyond is or isn’t. In the meantime, you’ll forgive me and “us” for considering these laws of thinking, or principles of right reason, or First Principles, inviolable. Since it is literally inconceivable to think that something is and isn’t, I think we are on pretty solid ground for our starting point. What’s the big deal with the starting point? Well, if I start in the wrong place, even though I get my facts right and reason properly from then on, I am guaranteed to end in error. Two examples should suffice to illustrate this. The first one is a logical example. Consider the following syllogism: All dogs are reptiles. Rover is a dog. Therefore, Rover is a reptile. This syllogism is valid. That means that the structure of the argument guarantees the conclusion. It doesn’t guarantee that it is true, that’s not what valid means. It means that the conclusion necessarily follows from the premises. One can see this by constructing a simple Venn diagram. If dogs are reptiles and Rover is a dog then Rover IS a reptile. But dogs are mammals, not reptiles. So even though I have my data correct (Rover is a dog) and I reasoned correctly, that is to say validly, my conclusion is not only wrong it is guaranteed to be wrong because I started in the wrong place. I started with a faulty premise. The second example is less abstract. Say I give someone directions to my home. Say I assume that the person will be leaving from their office. Say that person is actually leaving from home, which is a different place than their office. Will they get to my home if they follow the directions exactly? No. They will not. Thus the importance of the STARTING POINT. Now, here’s the payoff. If one starts with the awareness that things exist, as certain a fact as there can possibly be, one that is universally known and one that is literally undeniable, then one is on solid ground for all further intellectual endeavors. If, on the other hand, one starts from the assumption, say, that “the natural (or physical or material) world is all there is, then one is possibly starting from error. The statement “the natural world is all that exists” doesn’t contradict itself so it could be true and it could be false. Further investigation is required. But one can see immediately that whatever else commends this statement, because it is not certain, it is not a good starting point. In other words, “the natural world is all that exists” should be a conclusion to an argument, not its starting point. It’s time for one more bit of reflection. Is there anything else that I know for sure other than that things exist and that they are what they are and that they can’t both be and not be and that they are either? As it turns out, there is something else that I know. I know that things change. They change in many kinds of ways. Everything ages. Colors fade. Muscles get stronger or weaker. Leaves fall. Living things die. Point made, I trust. So What? Well if something changes it is reasonable to ask why it changes, is it not? And if I ask that question, I realize that there are only two sources of change. Either the change can be accounted for by what the thing is or what it is not (Law of Identity). In other words, we will, we must, find the cause of the change in either the nature of the thing or something other than the thing (an external force) acting on the thing. Given the Laws of Identity, Noncontradiction, and Excluded Middle, those are the only possible sources of the change. In the case of my existence, I can reason thusly. I have not always existed. There was a time that I did not exist, that time before I was born. So it must not be my nature to exist. In other words I am a contingent being. That is, it’s possible that I not exist. This is proven by the fact that for virtually all of the existence of the universe I did not exist. A modus tollens argument is suggested. If it were my nature to exist, then I would have always existed. But I did not always exist. So it’s not my nature to exist. But since I do, in fact, exist, existence must be something I have since it’s not something I AM. But if it is something I have rather than something I am, from where did I get my existence? What CAUSED me to come into being? What is the source of my existence? Well it’s my parents, of course. But upon further reflection, I realize that my parents did not always exist, either. And their parents. And so on. So we have the specter of an infinite regress of causes for my existence. So is it possible for my existence to be explained by this implied infinite regress? And if not, why not? In any case, it seems clear, unavoidably clear, that there is a cause of my existence. Again, this isn’t something dreamed up out of nowhere or something that comes from revealed theology or from a dusty philosophy book, this notion arises as a result of considering the data. The facts of existence and change. Let’s talk about the infinite regress. This can be a bit abstract so I’ll start with a concrete example and then we’ll transfer the concept to existence or being in general. Let’s say I want to borrow KF’s iPad. Being the generous guy that he is, he would lend it to me but alas, he doesn’t have one. Being a friend he says, that’s ok, I’ll get one from Upright, he’ll lend you one. But Upright doesn’t have one either. So he says to KF, I’ll go check with SB, he’ll have one. But he doesn’t either, and so on. The infinite regress is set in place. We always need to go back “one more” to find the iPad. Well, ask yourself this, will Tom ever get his iPad? No, I will not. Why? Because every “cause” in the chain of causes that will result in my having an iPad is, on its own, incapable of giving me the iPad because none of them have one, either. So it matters not that there are a hundred “causes” in the chain without an iPad or an infinite number of causes in the chain without an iPad, none of those causes can provide an iPad because NONE OF THEM HAVE AN IPAD. So what we need to terminate this regress of causes for me to get my iPad is someone that has an iPad and doesn’t need to get it from someone else. Just one guy in the chain with an iPad terminates the infinite regress and I get my iPad. In the same way, I cannot get my being or existence from an infinite series of “causes” that do not have being to give. Whose own being is bestowed upon them by another. At some point we MUST come to a cause, or if you prefer, a Cause, that has being to give. In other words, we must come to a cause that IS BEING. And since the nature of this Being is to exist it is necessary that It must exist. This is logically necessary given the certain existence of contingent beings. Again, we are driven by the data of existence and change. It’s logically possible, I suppose, that nothing could exist. But given the fact of any contingent being it is now logically certain that a Necessary Being exist. In other words, everything that contingently exists is actually proof that a necessary Being, one Whose nature it is TO BE, exists. This is just scratching the surface but I'm sure it's enough to offer food for thought.tgpeeler
July 16, 2014
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kairosfocus:
Where, a straight line is still just that . . . as in, LOI: A is A and not NOT_A, a plane is still flat (think, Complex Plane based on R x R if you don’t know what that is), and polygons and circles still have well known meanings so — pretzel-twisting notwithstanding — square circles (think the functional representations in the Plane as given, as muscle behind ordinary meanings) are still good examples of impossible beings.
Yes, and we also have the problem of having two definitions for a non-Eulidian square and a non-Eulidian circle. It should be obvious that a large non-Euclidian square, which is alleged to have both the qualities of a square and a circle, cannot be the same kind of thing (square) as a small non-Euclidian square, which does not have all those same qualities. It should be equally obvious that a large non-Euclidian circle, which is alleged to have both the qualities of a circle and a square, cannot be the same kind of thing (circle) as a small non-Euclidian circle, which does not have all those same qualities.StephenB
July 14, 2014
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Mark Frank @454- RE a specific ID testable hypothesis: Darwinism, Design and Public Education page 92: 1. High information content (or specified complexity) and irreducible complexity constitute strong indicators or hallmarks of (past) intelligent design. 2. Biological systems have a high information content (or specified complexity) and utilize subsystems that manifest irreducible complexity. 3. Naturalistic mechanisms or undirected causes do not suffice to explain the origin of information (specified complexity) or irreducible complexity. 4. Therefore, intelligent design constitutes the best explanations for the origin of information and irreducible complexity in biological systems. And then there are the specific hypotheses borne from "The Privileged Planet"Joe
July 14, 2014
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UB:
I maintain that in order to organize the original living cell, a coordinated system must arise that includes two sets of arrangements of matter to bridge and preserve the physicochemical discontinuity between an informational medium and its resulting effect upon translation. One set must encode form, while the other set must establish what the physical result of that encoding will be. The system must preserve this necessary discontinuity because inexorable law would otherwise limit the system to only those effects that can be derived from the material properties of the medium itself, making informational constraint on the system impossible to obtain. And because the discontinuity is preserved, a local independence from physical determinism is created – resulting in functional effects that are not derivable from inexorable law; they are only derivable from the organic systems that translate information. Lastly, in order to originate life on earth, this system must arise from within a non-information (inanimate) environment, with the details of the system’s construction being encoded in the very information that the system makes possible.
Useful summary, pivoting on elements of a comms system and how they work together. The we didn,t agree and pretzel twisted beyond recognition so let's move on tactic fails. But, it reveals another worrying fallacy of evo mat ideology: Throw up inough dust, fuss and confusing smoke and distractins then pretend the problems have gone away. Indeed, the latest seems to be, we have contained the design movement, have created enough confusion and polarisation, it is dying, the problem is over. Even were that so, "the blood of thy brother crieth up from the ground . . . " KFkairosfocus
July 14, 2014
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Piotr: Pardon but the first pivotal issue is whether design theory is helpful in moving science towards finding the truth about origins based on empirical evidence and known causal factors. It passes that test, evolutionary materialist ideology hampered schools of thought don't. Second, has it produced significant work over the years and especially in fairly recent times, despite dirty tactics ruthless opposition; again, yes. Third, with peer review showing the kind of ugly underside that is increasingly popping up, appeal to authority is not primary, the issue is, has reasonable work been done, is more being done, is there promise and is there reasonable publication -- including books, papers, proceedings etc. All of that, too has been happening, and it is noteworthy that different theories have different ranges of focus, so not only biology but informatics, computing, astrophysics and cosmology are relevant, as well as broader work in phil of sci. And btw, resort to schoolyard namecalling taunts is a sure sign you have lost on the merits. Where, a straight line is still just that . . . as in, LOI: A is A and not NOT_A, a plane is still flat (think, Complex Plane based on R x R if you don't know what that is), and polygons and circles still have well known meanings so -- pretzel-twisting notwithstanding -- square circles (think the functional representations in the Plane as given, as muscle behind ordinary meanings) are still good examples of impossible beings. So also, we see the importance of first principles of right reason, modes of being and causality in sound thought including for science. For instance, equivocation violates law of identity. The evolutionary materialist fallacy problem continues to be a material issue, right from first principles of right reason on up. KFkairosfocus
July 14, 2014
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gpuccio, That's indeed a very interesting analogy by Gil Dodgen. Thank you for bringing it to my attention here.Dionisio
July 13, 2014
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Mark, You have made repeated attempts to reposition the dialogue as 'old hat'. Your attempts are as transparent as they can possibly be. This is evidenced by the simple fact that you never mention any key details (any details whatsoever) of this imagined rebuttal of the semiotic evidence presented. Our last encounter…
UB, I know you think that there is some kind of symbolism going in a cell. You are wrong.
If you'd like to establish a response that mirrors your blanket denial, then why don't you address the comments made:
I maintain that in order to organize the original living cell, a coordinated system must arise that includes two sets of arrangements of matter to bridge and preserve the physicochemical discontinuity between an informational medium and its resulting effect upon translation. One set must encode form, while the other set must establish what the physical result of that encoding will be. The system must preserve this necessary discontinuity because inexorable law would otherwise limit the system to only those effects that can be derived from the material properties of the medium itself, making informational constraint on the system impossible to obtain. And because the discontinuity is preserved, a local independence from physical determinism is created – resulting in functional effects that are not derivable from inexorable law; they are only derivable from the organic systems that translate information. Lastly, in order to originate life on earth, this system must arise from within a non-information (inanimate) environment, with the details of the system’s construction being encoded in the very information that the system makes possible.
Upright BiPed
July 13, 2014
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Dionisio: Some time ago, here at UD, Gil Dodgen expressed a similar concept very well. I invite you and all who may be interested to read this old post: "ID and the Trajectory of Observational Resolution" https://uncommondescent.com/intelligent-design/id-and-the-trajectory-of-observational-resolution/ I paste here the conclusion:
The proper analogy would be that with increasing telescope power and other sophisticated analytical capabilities, we could observe that the canals on Mars were supported by suspension bridges, that the water was redirected to hydroelectric plants equipped with generators, that there was a power grid that distributed the power all over the planet, and that there were sophisticated software programs that controlled the distribution of the electrical power and synchronized it all. This is what we observe in living systems, only raised to the Nth power — and N is very large.
Very good thought! Thank you, Gil.gpuccio
July 13, 2014
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458 Mark Frank
I am sorry. I didn’t mean the text was confusing. I am confused because...
...it's hard to understand how an ignorant 'Joe Smoe' can make the experts to admit they don't know how to answer fundamental questions in their own area of expertise. Well, that's how things are in modern biology these days. Bad news for some folks out there: it ain't gonna get easier. As more outstanding questions get answered by the ongoing research, new questions will be raised. This revelation process will keep shedding more light on the complex biological systems, resulting in the strengthening of the evidences that support the ID paradigm. The party is just starting. The fun part is still ahead ;-)Dionisio
July 13, 2014
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#462 UB
I’ve approached both Mark and Piotr with this semiotic model of translation, and both have flatly rejected the discussion. One simply says I’m wrong, and the other doesn’t want to talk about it.
I am not sure which one I am! I am sure you are wrong but on the few occasions we discussed it the debate became tedious and repetitive. Life's too short for that. I see a couple of complaints above about people dropping out of debates. The fact is that no one is ever going to concede and the debate has to stop some time. There are healthier things to do, both physically and mentally, than keep repeating old arguments on the Internet.Mark Frank
July 13, 2014
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Piotr, I am very familiar with the paper. You should have reflected on it for a moment before you posted it.Upright BiPed
July 13, 2014
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Piotr: I suppose you are making our point here. Have you been well "vaccinated"? :)gpuccio
July 13, 2014
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Upright BiPed Here's some more by Marcello Barbieri:
In the Editorial of the very first Issue of this Journal I wrote that Biosemiotics rests on two basic principles. The first is the idea that semiosis belongs to life, i.e., that it does not exist in inanimate matter; this differentiates biosemiotics from Pansemiotics, the doctrine that accepts the existence of semiosis even in the physical world. The second principle is the idea that semiosis and meaning are natural entities; this divides biosemiotics from the doctrine of ‘intelligent design’, and from all other doctrines that maintain that the origin of life on Earth was necessarily due to a supernatural agency. ... We need to get vaccinated against Pansemiotics as we have been against Intelligent Design. They are the Scylla and Charybdis of Biosemiotics, and only if we pass consciously through them we can, like Odysseus, reach the open sea of our voyage of discovery.
"The Scylla and Charybdis of Biosemiotics" Biosemiotics 1/3, December 2008, pp. 281-284Piotr
July 13, 2014
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Piotr: Again, you are unfair. They "boast" what they can. It's just to prove that we exist. But it's not easy. Research is done in a network of thought. You cannot do research when you are alone and banned. Your attempt to state that ID is unable to do scientific research because of some defect in the theory is ridiculous. There are a lot of reasons for the difficulty of having abundant ID research (the lack of biologists with an ID commitment is one of them). There are many reasons why most people in ID are from other fields (mathemathics, informatics, engineering, medicine). I am sure that you believe that you know very well the reason for that, but believe me, you are wrong. The real reason is a shame for the scientific world, and I doubt that you would ever admit it.gpuccio
July 13, 2014
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UB: Thank you. That is a good example of the "banning" I referred to, and of the dogma of methodological naturalism in action.gpuccio
July 13, 2014
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GPuccio: ”2) Have you noticed that the few “official” papers which deal with the concept of functional information, or with any ID related concept, have to explicitly declare that they have nothing to do with ID?” ...
The First Step Towards Unification The various schools of biosemiotics developed their approaches independently and went along separate roads for at least three decades, from the late 1960s to the end the 1990s. Eventually, however, contacts were established and people started talking to each other and comparing notes. The first steps toward unification came in 2004, at the fourth Gathering in Biosemiotics organized by Anton Markoš in Prague. Jesper Hoffmeyer, Claus Emmeche, Kalevi Kull, Anton Markoš and Marcello Barbieri decided that what was uniting them —the introduction of meaning in biology— was far more important than their divisions. Up until then, Barbieri had referred to the science of biological semiosis as semantic biology ,or biosemantics, whereas Markoš had called it biohermeneutics , but they both agreed to give up their favourite names and to adopt the term Biosemiotics that Thomas Sebeok had been campaigning for with so much passion and vigour. That is when biosemiotics really came of age. It happened when people decided to work together not because they had identical ideas but because they accepted to put their differences aside in the interest of a greater goal. The existence of semiosis in life does not exclude, in principle, the existence of semiosis in inanimate matter, but the unifying idea of Prague was the concept, proposed by Thomas Sebeok, that “life and semioisis are coextensive”, i.e. that “semiosis exists in all living beings and only in living beings”. This became ‘the foundational principle’ of biosemiotics, and it was precisely its acceptance that realized the first step towards unification. It must be underlined that this principle is a scientific hypothesis because it is falsifiable (a single example of semiosis in inanimate matter would immediately falsify it). Today there are still differences between the schools, but there is also a ‘minimal unity’ in the field because of two basic principles, or postulates, that are accepted by virtually all biosemioticians. (1) The first postulate is Thomas Sebeok’s idea that “life and semioisis are coextensive”. This implies that semiosis appeared at the origin of life, and sharply differentiates biosemiotics from ‘pansemiotics’ and ‘physiosemiotics’, the doctrines that semiosis exists also in inanimate matter and therefore everywhere in the universe. It also differentiates it from the views that semiosis exists only in animals or only in humans beings. (2) The second postulate is the idea that signs, meanings and codes are natural entities. This sharply divides biosemiotics from the doctrine of ‘intelligent design’, and from all other doctrines that maintain that the origin of life on Earth was necessarily the product of a supernatural agency. -- A Short History of Biosemiosis, Marcello Barbieri Biosemiotics 2:221–245 DOI 0.1007/s12304-009-9042-8
Anyone even remotely read in semiosis recognizes that the first postulate given above is derived directly from intractable material evidence, while the second postulate is entirely socio-political, without any material foundation whatsoever. And Barbieri knew fully well that ID does not posit a supernatural agency when he wrote those words. It was pure non-science. Neither Mark Frank nor Piotr will enter (in earnest) a conversation about semiosis. It does not profit them in the way that square circles and the math of poker does. I maintain that in order to organize the original living cell, a coordinated system must arise that includes two sets of arrangements of matter to bridge and preserve the physicochemical discontinuity between an informational medium and its resulting effect upon translation. One set must encode form, while the other set must establish what the physical result of that encoding will be. The system must preserve this necessary discontinuity because inexorable law would otherwise limit the system to only those effects that can be derived from the material properties of the medium itself, making informational constraint on the system impossible to obtain. And because the discontinuity is preserved, a local independence from physical determinism is created – resulting in functional effects that are not derivable from inexorable law; they are only derivable from the organic systems that translate information. Lastly, in order to originate life on earth, this system must arise from within a non-information (inanimate) environment, with the details of the system’s construction being encoded in the very information that the system makes possible. I’ve approached both Mark and Piotr with this semiotic model of translation, and both have flatly rejected the discussion. One simply says I’m wrong, and the other doesn’t want to talk about it.
“It’s always very refreshing to be able to just make a clean break, start over again with something you’re completely ignorant about” … “that’s very exhilarating; nothing’s expected of you because you’re a novice; and, with luck, you come up with something that other people were saying was impossible because they know too much.” – Physicist/Geneticist Semour Benzer
Upright BiPed
July 13, 2014
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