There is no brilliance in mechanism and reductionism any more.

Petrushka: I was speaking of the concept of function, not of reproductive success. You cannot mix different arguments. gpuccio

Glucose-6-phosphatase could be there for aeons, accelerating its reaction, but nobody would realize that it is a molecualr machine, unless some consious being like us realizes that it is indeed accelerating a reaction that would not normally occur, and that by a specific, sophisticated structure.

Nothing needs to realize it's there. Function is defined by reproductive success, not by measures of reaction efficiency. It's quite possible that what a chemist would call an optimal molecule would be deleterious to a living thing. Also, a coding or regulatory sequence might have multiple functions that need to be balanced. When humans encounter this kind of problem in engineering -- as in load balancing in electric power grids -- they turn to GAs. It's simply the best way to design when priorities compete. Petrushka

Got it. Thanks again GP, and to everyone else who chipped in. Food for thought there. englishmaninistanbul

Well yeah but surely we can’t just define function as “What it’s for” ie. “purpose” because that’s teleological. Inferring design based on dFSCI would then be circular.

Indeed. And I'd say that if we could really recognise purpose in biological phenomena (obviously excluding the cases where organic minds are involved), that would be enough evidence for a will behind them, rendering circular and unnecessary any argument for a designer that relies on the "recognition" of teleological functions in biology.

I know my layman’s questions must be like a child asking a mathematician what 2 + 2 is. So thank you for humouring me.

Not at all. It is a very good question and there is not a single view on this issue. The term has remained very vague and has received some attention by philosophers of biology. This is my take on it: a biological function is description in goal-oriented terms of whatever biological interaction or process someone chooses to highlight. By this, I mean "functions" are explanatory devices, rather than something that's "really there" in the organic world. This is very much like the view of John Wilkins, as I understand it. Geoxus

Petrushka: No essentialism. No essence. No philosophy. I am just saying that meaning and purpose are categories of subjective experience, not of objective things. And yet, material systems can receive a form that conveys a meaning, or realizes a purpose. Hamlet, while being a collection of ink molecules on paper sheets, is in reality a form given to written words to express a meaning. A machine is a material system whose form can realize something that has been represented as a purpose in its designer's consciousness, and that can be, often easily, recognized as a purpose by other conscious beings. IOWs, conscious contents can shape matter. And be retrieved from matter by other conscious beings. That's what we call communication. The contact between isolated conscious beings happens, at least at our common level, through material things. But in communication, there are always two conscious beings involved. Glucose-6-phosphatase could be there for aeons, accelerating its reaction, but nobody would realize that it is a molecualr machine, unless some consious being like us realizes that it is indeed accelerating a reaction that would not normally occur, and that by a specific, sophisticated structure. To us, it is obviously a biological machine. In itself, it could be not different from a stone. Only purposeful beings recognize purpose, and can describe and define it. Function can change and evolve, because conscious representations can change and evolve. Design changes and evolves. The designed form is as different as possible from an "essence". It is the temporary, often flexible crystallization of a thought and a desire. gpuccio

"What's it for" is essentialist thinking. What's it for can change and evolve. Petrushka

englishmaninistanbul: Must we go back to our old discussion? We recognize funtion in material objects, and describe it. Because we are conscious agents, and understand what purpose is. The same is true for meaning. Non conscious reality knows no meaning or purpose in itself. But conscious purposeful intelligent agents can impart to material systems specific forms, that are expressions of meaning and function: IOWs, what is first represented in the agent is outputted to a material system. Abel calls that form "semiotic information". And he distinguishes between "descriptive information", that conveys meaning, and "prescriptive information", that conveys function. The important point is that function can only be originated by a purposeful agent, and that it can only be recognized by another purposeful agent. A protein can have the most sophisticated funtion in the world, but a non conscious system would never recognize it for what it is (unless it has been programmed to do so by a conscious purposeful agent). You go round in circles, because you continue to ask for an objective definition of things that can be defined only subjectively. So yes, "what it's for" is a perfectly valid definition for a subjective perceiver, and you will never find a way to define that "what it's for" in a purely objective way. Because the objective world in itself does not contain meanings and does not contain functions. gpuccio

Of course function means “What it’s for.” That’s the meaning of the word.

Well yeah but surely we can't just define function as "What it's for" ie. "purpose" because that's teleological. Inferring design based on dFSCI would then be circular. Obviously "function" can't be defined as "the effect of an entity on it's environment" because that would include nuclear isotopes, harking back to our previous discussion. On the other hand if Wikipedia is to be believed (which I doubt, because the article I linked to is a particularly dubious one) materialists only allow function as a "teleonomic" way of delineating that which directly or indirectly increases an organism's fitness. Which must be bunk, because that would mean that if you find a function that's redundant or unnecessary, and you can't work out what it was good for in the past, you can't call it a function. Nobody over at UNIPROT says "Ah you've discovered a protein function have you? You must work out how it contributes to fitness, otherwise we can't put it on the system." So what is the exact definition of function? I know my layman's questions must be like a child asking a mathematician what 2 + 2 is. So thank you for humouring me. englishmaninistanbul

englishmaninistanbul: Of course function means “What it’s for.” That's the meaning of the word. The quoted question: “What is function?” he asks. “What does it mean?” A gene that is important for survival in one species may have become redundant in a closely related strain, for instance, even though the sequence is identical. is simply silly. If a gene is important in one context, and redundnat in another, that simply means that its function is required in the first case, and non necessary in the second. In no way it means that it has lost its function. On the other hand, if a gene mutates and is no more able to accomplish its biological function, then we can say that it has lost it. I suppose that even babies understand those not too smart distinctions... Babies, yes, but apparently not darwinists. The loss of commons sense seems to be the main result of defending wrong ideas. gpuccio

Thanks GP. I suppose then that in that context "function" basically means what we all know it to mean: "What it's for." Teleology. You can run but you can't hide. :) englishmaninistanbul

Yes, the definition of “gene” does vary according to who is asked and the context. This is hardly new. That is why Dawkins talks about this extensively in the 35 year old book “The Selfish Gene” (and it was hardly new then). “I am using the word gene to mean a genetic unit that is small enough to last for a large number of generations and to be distributed around in the form of many copies. This is not a rigid all-or-nothing definition, but a kind of fading-out definition, like the definition of ‘big’ or ‘old’. The more likely a length of chromosome is to be split by crossing-over, or altered by mutations of various kinds, the less it qualifies to be called a gene in the sense in which I am using the term.” “What I am doing is emphasizing the potential near-immortality of a gene, in the form of copies, as its defining property. To define a gene as a single cistron is good for some purposes, but for the purposes of evolutionary theory it needs to be enlarged. The extent of the enlargement is determined by the purpose of the definition. We want to find the practical unit of natural selection. To do this we begin by identifying the properties that a successful unit of natural selection must have. In the terms of the last chapter, these are longevity, fecundity, and copying-fidelity. We then simply define a ‘gene’ as the largest entity which, at least potentially, has these properties. The gene is a long-lived replicator, existing in the form of many duplicate copies. It is not infinitely long-lived. Even a diamond is not literally everlasting, and even a cistron can be cut in two by crossing-over. The gene is defined as a piece of chromosome which is sufficiently short for it to last, potentially, for long enough for it to function as a significant unit of natural selection.” goodusername

englishmaninistanbul: From the UNIPROT site: Myoglobin, human (P02144): Function: Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles. Glucose-6-phosphatase, human (P35575): Function: Hydrolyzes glucose-6-phosphate to glucose in the endoplasmic reticulum. Forms with the glucose-6-phosphate transporter (SLC37A4/G6PT) the complex responsible for glucose production through glycogenolysis and gluconeogenesis. Hence, it is the key enzyme in homeostatic regulation of blood glucose levels. Catalytic activity: D-glucose 6-phosphate + H2O = D-glucose + phosphate. Glycyl-tRNA synthetase, human (P41250): Function: Catalyzes the attachment of glycine to tRNA(Gly). Is also able produce diadenosine tetraphosphate (Ap4A), a universal pleiotropic signaling molecule needed for cell regulation pathways, by direct condensation of 2 ATPs. Catalytic activity: ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly). And so on. Well, how is it that people here have all those difficulties in identifying protein functions, while biologists do that all the time? gpuccio

“What is function?” he asks. “What does it mean?” A gene that is important for survival in one species may have become redundant in a closely related strain, for instance, even though the sequence is identical. Does that make it a gene in one species and not in the other?

That strikes me as a rather good question. Wikipedia (the font of all wisdom bwahaha) defines Function (biology) as follows:

A function is the reason some object or process occurred in a system that evolved through a process of selection.

So of course whoever wrote that would probably say that a design inference based on dFSCI was self-contradictory, since you can only define function with reference to "selection" (natural selection, I'm assuming). I feel a bit like a tourist asking for directions from the locals, but I hope you will indulge me: What exactly is the definition of "function" in "digital functionally specified complex information"? In a nutshell? Is there anything that goes beyond "whatever helps the organism to survive"? englishmaninistanbul

And you refined the idea of natural selection such that evolutionary biologists wouldn't agree with it. Bravo... Joe

He cited Mark Gerstein of Yale as his authority for claiming that we don’t know what a gene is any more.

We never knew what a gene was/is. "Gene" was introduced as a theoretical term to explain observed patterns of inheritance. In searching for the elusive gene, DNA was discovered. So now DNA becomes the central focus of the science. The term "gene" remains as a left-over that helps us understand older scientific literature, and that is still useful for informal imprecise discussions. For precise scientific discussions, DNA and sequences within the DNA are the proper referents. That sort of refinement of ideas is the way science is supposed to work. Neil Rickert