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 towrite 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 “Funcional information defined” I have given the following definitions:

I will try to beginintroducing 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 ofa functionfor 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 hasobjective 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 tothe 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 ofa functionfor 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 functionsare 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.