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Functional information defined

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What is function? What is functional information? Can it be measured?

Let’s try to clarify those points a little.

Function is often a controversial concept. It is one of those things that everybody apparently understands, but nobody dares to define. So it happens that, as soon as you try to use that concept in some reasoning, your kind interlocutor immediately stops you at the beginning, with the following smart request: “Yes, but what is function? How can you define it?

So, I will try to define it.

A premise. As we are not debating philosophy, but empirical science, we need to remain adherent to what can be observed. So, in defining function, we must stick to what can be observed: objects and events, in a word facts.

That’s what I will do.

But as usual I will include, in my list of observables, conscious beings, and in particular humans. And all the observable processes which take place in their consciousness, including the subjective experiences of understanding and purpose. Those things cannot be defined other than as specific experiences which happen in a conscious being, and which we all understand because we observe them in ourselves.

That said, 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.

The purpose of this distinction should be clear, but I will state it explicitly just the same: a function is a conception of a conscious being, it does not exist  in the material world outside of us, but it does exist in our subjective experience. Objective functionalities, instead, are properties of material objects. But we need a conscious observer to connect an objective functionality to a consciously defined function.

Let’s make an example.

Stones

I am a conscious observer. At the beach, I see various stones. In my consciousness, I represent the desire to use a stone as a chopping tool to obtain a specific result (to chop some kind of food). And I choose one particular stone which seems to be good for that.

So we have:

a) The function: chopping food as desired. This is a conscious representation in the observer, connecting a specific stone to the desired result. The function is not in the stone, but in the observer’s consciousness.

b) The functionality in the chosen stone: that stone can be used to obtain the desired result.

So, what makes that stone “good” to obtain the result? Its properties.

First of all, being a stone. Then, being in some range of dimensions and form and hardness. Not every stone will do. If it is too big, or too small, or with the wrong form, etc., it cannot be used for my purpose.

But many of them will be good.

So, let’s imagine that we have 10^6 stones on that beach, and that we try to use each of them to chop some definite food, and we classify each stone for a binary result: good – not good, defining objectively how much and how well the food must be chopped to give a “good” result. And we count the good stones.

I call the total number of stones: the Search space.

I call the total number of good stones: the Target space

I call –log2 of the ratio Target space/Search space:  Functionally Specified Information (FSI) for that function in the system of all the stones I can find in that beach. It is expressed in bits, because we take -log2 of the number.

So, for example, if 10^4 stones on the beach are good, the FSI for that function in that system is –log2 of 10^-2, that is  6,64386 bits.

What does that mean? It means that one stone out of 100 is good, in the sense we have defined, and if we choose randomly one stone in that beach we have a probability to find a good stone of 0.01 (2^-6,64386).

I hope that is clear.

So, the general definitions:

c) Specification. Given a well defined set of objects (the search space), we call “specification”, in relation to that set, any explicit objective rule that can divide the set in two non overlapping subsets:  the “specified” subset (target space) and the “non specified” subset.  IOWs, a specification is any well defined rule which generates a binary partition in a well defined set of objects.

d) Functional Specification. It is a special form of specification (in the sense defined above), where the rule that specifies is of the following type:  “The specified subset in this well defined set of objects includes all the objects in the set which can implement the following, well defined function…” .  IOWs, a functional specification is any well defined rule which generates a binary partition in a well defined set of objects using a function defined as in a) and verifying if the functionality, defined as in b), is present in each object of the set.

It should be clear that functional specification is a definite subset of specification. Other properties, different from function, can in principle be used  to specify. But for our purposes we will stick to functional specification, as defined here.

e) The ratio Target space/Search space  expresses the probability of getting an object from the search space by one random search attempt, in a system where each object has the same probability of being found by a random search (that is, a system with an uniform probability of finding those objects).

f) The Functionally Specified  Information  (FSI)  in bits is simply –log2 of that number. Please, note that I  imply  no specific  meaning of the word “information” here. We could call it any other way. What I mean is exactly what I have defined, and nothing more.

One last step. FSI is a continuous numerical value, different for each function and system.  But it is possible to categorize  the concept in order to have a binary variable (yes/no) for each function in a system.

So, we define a threshold (for some specific  system of objects). Let’s say 30 bits.  We compute different values of FSI for many different functions which can be conceived for the objects in that system. We say that those functions which have a value of FSI above the threshold we have chosen (for example, more than 30 bits) are complex. I will not discuss here how the threshold is chosen, because that is part of the application of these concepts to the design inference, which will be the object of another post.

g) Functionally Specified Complex Information is therefore a binary property defined for a function in a system by a threshold. A function, in a specific system, can be “complex” (having  FSI above the threshold). In that case, we say that the function implicates FSCI in that system, and if an object observed in that system implements that function we say that the object exhibits FSCI.

h) Finally, if the function for which we use our objects is linked to a digital sequence which can be read in the object, we simply speak of digital FSCI: dFSCI.

So, FSI is a subset of SI, and dFSI is a subset of FSI. Each of these can be expressed in categorical form (complex/non complex).

Some final notes:

1) In this post, I have said nothing about design. I will discuss in a future post how these concepts can be used for a design inference, and why dFSCI is the most useful concept to infer design for biological information.

2) As you can see, I have strictly avoided to discuss what information is or is not. I have used the word for a specific definition, with no general implications at all.

1030743_72733179

3) Different functionalities for different functions can be defined for the same object or set of objects. Each function will have different values of FSI. For example, a tablet computer can certainly be used as a paperweight. It can also be used to make complex computations. So, the same object has different functionalities. Obviously, the FSI will be very different for the two functions: very low for the paperweight function (any object in that range of dimensions and weight will do), and very high for the computational function (it’s not so easy to find a material object that can work as a computer).

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4) Although I have used a conscious observer to define function, there is no subjectivity in the procedures. The conscious observer can define any possible function he likes. He is absolutely free. But he has to define objectively the function, and how to measure the functionality, so that everyone can objectively verify the measurement. So, there is no subjectivity in the measurements, but each measurement is referred to a specific function, objectively defined by a subject.

Comments
Piotr @ 234
The only creation design proponentsists I meet here are the occasional Jehovah’s Witnesses — a recent import from the USA.
proponentsists? can we assume you meant proponents?Dionisio
May 11, 2014
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gpuccio @ 245
But here in Italy we are usually not so fastidious about using “man” to mean “human”.
Apparently his country has been historically a so called matriarchal society, therefore men have to be careful not to say anything that women could misinterpret and disagree. There women lead and men follow. I've seen women telling their husbands or brothers to shut up and keep quiet. Really sad. Perhaps that's why he wrote @ 244:
And women too. You won’t be going places, young man, if you ignore women.
Thank God that seems to be changing as younger generations come along ;-)Dionisio
May 11, 2014
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...but because the evidence itself is not compelling by scientific standards.
:|Upright BiPed
May 11, 2014
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Piotr: Yes. Except for a couple of things: a) I don't ignore women. But here in Italy we are usually not so fastidious about using "man" to mean "human". b) I am not so young :) Regarding the evidence for the existence of God, it can be debated. I think there is great evidence, but much of it is not "scientific" in the strict sense. And I agree that believing in God is in the end a personal choice, and a personal experience.gpuccio
May 11, 2014
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Gpuccio:
My comments refer to the cultural academy of the last decades, and only to that. The bias in scientific academy in this period is not a bias of science, it is a bias of men.
And women too. You won't be going places, young man, if you ignore women. As for the rest, I myself prefer the term "empirical" and "based on evidence". Terms like "natural", "naturalistic" and "materialistic" have an antiquarian flavour and are practically devoid of meaning. In the light of modern physics words like "matter" no longer have a clear formal interpretation. We continue using them for convenience, more or less informally, but you can't build a philosophical system on vague pronouncements like "matter is all that exists". That's why I don't care for being called a "materialist" or a "methodological naturalist". In disputes, such terms are used more often as condemnatory labels than as accurate descriptions of someone's actual philosophical stance. I don't mind being called an "atheist" because I don't "believe" in god(s) (by believe I mean 'accept for cultural reasons whatever the evidence'). I find the evidence for god(s) unconvincing not because she/he/it/they are "supernatural" or "non-material", but because the evidence itself is not compelling by scientific standards. I do subscribe to a mild version of scientism. I accept that science is the best method of collecting reliable and objectively communicable knowledge about reality. I suppose we largely agree about these things.Piotr
May 11, 2014
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Piotr: My comments are not about scientists in general, or science at all times. I love scientists, and I love science. My comments are about a specific cultural situation which has been established about 50 - 60 years ago, with the advancement of the "modern synthesis" to the status of "absolute and indisputable truth" in biology, and of strong AI theory as "explanation of consciousness" in general thought. My comments refer to the cultural academy of the last decades, and only to that. The bias in scientific academy in this period is not a bias of science, it is a bias of men. One important difference with past situations is that now it is exactly the scientific academy which has the role of "priest class" and of holder of absolute truth. IOWs, scientism is the new religion of our era. And methodological naturalism is its tool. Just think of the definition itself of "methodological naturalism". From RationalWiki:
Methodological naturalism is the label for the required assumption of philosophical naturalism when working with the scientific method. Methodological naturalists limit their scientific research to the study of natural causes, because any attempts to define causal relationships with the supernatural are never fruitful, and result in the creation of scientific "dead ends" and God of the gaps-type hypotheses. To avoid these traps scientists assume that all causes are empirical and naturalistic; which means they can be measured, quantified and studied methodically. However, this assumption of naturalism need not extend beyond an assumption of methodology. This is what separates methodological naturalism from philosophical naturalism - the former is merely a tool and makes no truth claim; while the latter makes the philosophical - essentially atheistic - claim that only natural causes exist.
Now, please note (as a linguist) the ambiguity in words. "Nature" and "natural causes" are never defined. Obviously, "natural" is one of those words which have no definite meaning. What is nature? What is natural? Is human consciousness "natural"? If non physical beings exist, are they "natural"? If one god, or many gods, exist, is he (are they) natural? What distinguishes existing things or beings in natural and supernatural? Note that, according to the second paragraph, in methodological naturalism there is no assumption at all that "only natural causes exist". So, if non natural causes can exist, how do you generate the partition? And, if non natural causes can exist, why shouldn't science be interested in their effects? And so on. Then in the following statement: "To avoid these traps scientists assume that all causes are empirical and naturalistic;" (emphasis mine) The word "empirical" suddenly appears, together with "naturalistic" as though they mean the same thing. Wait a moment! We were not discussing "methodological empiricism"!, and "empirical" and "naturalistic" do not mean the same thing. Not at all. From Dictionary.com: "Empirical: derived from or guided by experience or experiment." "Naturalistic: imitating nature or the usual natural surroundings." I have taken the first meaning for both. Note the vague definition for naturalisitc (the other two definitions are no better), and the precise meaning of "empirical": "guided by experience". Note also the ambiguity of the final statement: "which means they can be measured, quantified and studied methodically" First of all, it is not clear if that is the meaning of "empirical", of "naturalistic" or both. Second, to be measured, to be quantified and to be studied methodically are not the same things. In particular, "studied methodically" has not the same meaning as "measured". So, you may think that my ideas on these things are "self-deception on my part". I don't. But obviously, being self-deceived, I wouldn't. :)gpuccio
May 11, 2014
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Methodological naturalism is the doctrine according to which science can only consider “natural” causes. As “natural” means essentially nothing, the final result is that “natural” is defined as “compatible with my present worldview, both philosophical and scientific”. That is the death of true science.
I think it's self-deception on your part. Scientists are open to philosophical and scientific worldview changes. They may resist new theories for various reasons, but evidence (if really incotrovertible, and inexplicable within the old framework) will eventually sway them. Can you imagine what it must have cost early 20th-century physicists to switch from classical mechanics plus ether theory to relativity? And before they recovered from the shock, they had to assimilate quantum mechanics. Evolutionary biology was likewise incompatible with most people's philosophical and scientific worldview. If scientists resisted novelty just because of theoretical, philosophical or ideological bias, pre-Darwin creationsism would be well and kicking.Piotr
May 11, 2014
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UB and Axel: Thank you for your friendship.gpuccio
May 10, 2014
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Piotr: Believe me, I am not pretending anything. I have my ideas about the designer, but they are my ideas, they are based on my personal worldview, and I never discuss them here. I only discuss here what is empirically based, or what, although philosophical, has important epistemological implications in a scientific debate about the things we debate here. I am not pretending anything, I believe in that attitude, and I try to practice it. OK, let's go to sleep.gpuccio
May 10, 2014
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Gpuccio: That's because although there are many religious evolutionists, I have yet to see a non-religious ID proponent. Also, the designer has so many divine attributes (unknown origin, activity over billions of years, invisibility combined with omnipresence and omnipotence) that is seems to me slightly disingenuous to pretend that you don't mean God (or at least a god) when referring to "the designer". But OK, I accept your explanation for the sake of argument. I'll comment on the mind-matter "quantum interface" tomorrow.Piotr
May 10, 2014
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Troppo simpatico, Dottore! Ma e vero. N'est-ce pas? (rhetorical, veccio). (You'll be relieved to hear I'm going to stop with the Italian, while (I hope) I'm ahead. Crazy as it sounds, Piotr, we Roman candles have been 'on the back foot' about the prevailing scientific/scientistic paradigm, since the Galileo affair. Those RC prelates and high churchmen don't miss much, but as regards evolution, so all-pervasive and hegemonic has been the latter's imposition by the multinationals, that that lacuna in their knowledge is almost certainly, imo, due to plain ignorance; as is certainly the case with many other very astute and otherwise knowledgeable people in the media, public life, etc. In the case of the RC intellectuals, indeed, part of the reason for their diffidence is precisely because most would surely prefer God to have used evolution. It would really be something, after all, for a child's scooter to change into a bicycle, then a motorbike, then a car, so far from recoiling in horror, if they were modern youngsters, they would doubtless say, 'THAT'S COOL!' Or some similar daft, but wonderfully colourful formula.Axel
May 10, 2014
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Piotr, Here is what you say GP said:
The allegation that you have to be an atheist or a “reductionist materialist” .. to accept a scientific theory is bloody demagoguery.
- - - - - - - - - - - - - - - - - 1. demagogue: a leader who makes use of popular prejudices and false claims and promises in order to gain power n. demagogue: A leader who obtains power by means of impassioned appeals to the emotions and prejudices of the populace. - - - - - - - - - - - - - - - - - - What GP actually said:
Today’s culture is strongly biased in favor of a reductionist materialist worldview. I have nothing against that (everybody can choose the worldview he likes), but it is only a philosophical position: it cannot be the foundation for scientific inquiry. ... Moreover, the reductionist materialist philosophy is recent, unsupported by specific facts, not shared by the majority of human beings, not shared by the majority of past thinkers, scientists, and philosophers. My point is: there is no reason to accept it simply because the scientific academy of the last few decades has made a religion out of it.
Upright BiPed
May 10, 2014
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Piotr: Moreover, I have given those philosophical considerations only as a premise to explain how and why the problem of consciousness matter interface, although in part philosophical, has definite scientific aspects and implications in scientific epistemology. That was done only to try to answer your request about my views on those issues. For the rest, you can see that I have tried to keep the discussion on a purely scientific plane. If someone has repeatedly referred to God, religion and religious implications, that was you.gpuccio
May 10, 2014
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Piotr: I could not care less if one is religious or atheist. A lot of religious people are reductionists and materialists if you really ask them what they think about science. Scientism is as popular among religious people as it is among atheists. Ken Miller is a good example. Reductionist materialism means that one embraces the worldview that only matter (whatever it means) exists, or (if one is religious) that only matter can be considered by scientific knowledge, and religion is something completely separated. Scientism means the doctrine that science is the supreme (maybe the only) source of true knowledge. Methodological naturalism is the doctrine according to which science can only consider "natural" causes. As "natural" means essentially nothing, the final result is that "natural" is defined as "compatible with my present worldview, both philosophical and scientific". That is the death of true science. All these positions are legitimate as personal worldviews. I don't want to label anyone. As I said, I believe that personal worldviews are a choice, and they must be respected. What I don't respect is that a personal worldview be used as the standard of science for all. I don't know the situation in your country, but here I am practically the only design proponent that I know. And I have not been imported from the USA. :) Again, it is not a question of religion. ID is a scientific theory, and a very good one. Maybe many embrace it for religious reason. That is a pity, in a sense, because it deserves to be embraced for its scientific merits only. I would really like to see atheists embrace ID for its merits. While remaining atheists, if they like. Just as Ken Miller can remain religious, and yet embrace the inconsistency of darwinian dogma. As I have said many times, my religious convictions predate my passion for ID, and have never needed ID. They are strong on their own. My passion for ID is scientific, intellectual and moral. While it is perfectly compatible with my religious views, it is not motivated by them. Unless you consider love for truth a religious view.gpuccio
May 10, 2014
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Moreover, the reductionist materialist philosophy...
Gpuccio, I know quite a number of evolutionary biologists (from Theodosius Dobzhansky, with his famous dictum, to Ken Miller) who somehow manage to reconcile their "non-reductionist" "non-materialist" religious worldview with doing science. The allegation that you have to be an atheist or a "reductionist materialist" (whatever all these -isms are supposed to mean in practice, except that you use them to label your "Darwinist" adversaries) to accept a scientific theory is bloody demagoguery. I thought you could do better than that. Like you, I live in one of the countries regarded as Roman Catholic strongholds. The only creationdesign proponentsists I meet here are the occasional Jehovah's Witnesses -- a recent import from the USA.Piotr
May 10, 2014
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Axel: Well said, vecchio mio!gpuccio
May 10, 2014
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Got ma trusty hammer with me still... looking for the next nail. A simulacrum* of a nail will do, of course! * Or 'maquette' if your scientific mindset demands it. But it just seems a bit 'over the top' to me for such a simple item!.Axel
May 10, 2014
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'..... Moreover, the reductionist materialist philosophy is recent, unsupported by specific facts, not shared by the majority of human beings, not shared by the majority of past thinkers, scientists, and philosophers. My point is: there is no reason to accept it simply because the scientific academy of the last few decades has made a religion out of it.' Moreover, vecchio*, in complete contrast to the yawning deficiencies in terms of supporting evidence of their reductionist assertions, and of RATIONAL THOUGHT on their part - of which they have the brass neck to posture as veritable paragons - the matter of irreducible complexity is simply unanswerable! It just makes no sense to me that scientists, 'above all kites and crows', should simply refuse to accept plain, scientifically and logically incontestable FACTS, instead, continuing to cling to their own conjectures and fantasies, irrespective even of whether they have been roundly, scientifically disproved. *vecchio' is 'old chap' isn't it?Axel
May 10, 2014
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Dionisio: Mille grazie a te per le gentili parole!gpuccio
May 10, 2014
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BA: A simple chart indeed! Thank you. It reminds me of a chart I used once for a presentation about cell cycle control and oncogenesis, which was about the c-myc transcription factor and its many interactions with other factors. The graph was so crowded that the authors had added the following comment: "Please, don't discover any new interactions, because there is no more space left!" :)gpuccio
May 10, 2014
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gpuccio, you may appreciate this: chart - This is the biosynthesis pathway for the 20 standard amino acids . They had to exist before LUCA was there. How could natural mechanisms explain the origin of amino acids, the building blocks of life ? http://genomebiology.com/2008/9/6/R95/figure/F1 In the following video, Dr. Axe discusses his 'conversion experience' after studying the biosynthetic pathways necessary to make the tryptophan amino acid Nothing In Molecular Biology Is Gradual - Doug Axe PhD. - video http://www.metacafe.com/watch/5347797/bornagain77
May 10, 2014
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gpuccio @ 223
Science is the search for truth about empirical observations, and cannot be bound to a specific philosophy.
Eccellente!!! Mile grazie.Dionisio
May 10, 2014
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Piotr at #224: I agree with you. The superfamily grouping is probably too large. Indeed, the SCOP definition explicitly acknowledges that, much more than the Wikipedia page:
The different major levels in the hierarchy are: Family: Clear evolutionarily relationship Proteins clustered together into families are clearly evolutionarily related. Generally, this means that pairwise residue identities between the proteins are 30% and greater. However, in some cases similar functions and structures provide definitive evidence of common descent in the absense of high sequence identity; for example, many globins form a family though some members have sequence identities of only 15%. Superfamily: Probable common evolutionary origin Proteins that have low sequence identities, but whose structural and functional features suggest that a common evolutionary origin is probable are placed together in superfamilies. For example, actin, the ATPase domain of the heat shock protein, and hexakinase together form a superfamily. Fold: Major structural similarity Proteins are defined as having a common fold if they have the same major secondary structures in the same arrangement and with the same topological connections. Different proteins with the same fold often have peripheral elements of secondary structure and turn regions that differ in size and conformation. In some cases, these differing peripheral regions may comprise half the structure. Proteins placed together in the same fold category may not have a common evolutionary origin: the structural similarities could arise just from the physics and chemistry of proteins favoring certain packing arrangements and chain topologies.
I use the superfamily concept just to be fair versus darwinists. The problem is that, if there is structural and functional similarity, one could always argue that sequence homology has been eroded in time by neutral variation. However, I cannot believe that in extreme cases like Rec A and the beta subunit of ATP synthase, because the homology is completely absent, while the two proteins are strongly conserved individually in time. So yes, in that case I would speak of design convergence. :)gpuccio
May 10, 2014
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Piotr: So, that was just a premise, to get to the point: let's assume that non physical conscious beings can exist, that it is not correct to exclude them a priori, and that they could be considered as the designer(s) of biological information. Then, we can address the important question which you yourself suggested: how can a non physical conscious being design material things? Does he need magic? To answer that, let's consider again our favorite model: human beings and human design. I have said that I reject strong AI theory. However, I have no reasons to impose my personal worldview. So, let's try to remain empirical as much as possible. Let's say that we accept consciousness and its representations as a fact, and we don't try to explain it and them. We just accept that subjective representations exist, and that they are linked to the process of design. At the same time, we know that in humans subjective representations are linked to the physical world, in both senses: as perceptions of the outer world, and as actions which reach the outer world. Design is based on the second type of connection, but it certainly uses also the first type (as when we draw something that we are observing and therefore representing in our consciousness). Now, my point is: of we understand how our conscious representations are outputted to the material object in the process of human design, that can be a good model for biological design, at least as a starting point. That brings us to very old problems: the hard problem of consciousness (Chalmers), the problem of free will, and so on. Old stuff, important stuff. Now, I just want to express my model, without pretending to solve those problems (provided that you too don't pretend to solve them). :) As I believe in free will, true libertarian free will, not the parody of compatibilism, I think that we must ask ourselves (as many have done): does the existence of free will violate mechanical deterministic laws? And the answer is: not necessarily. You may be aware of models of the mind-brain interface which are based on quantum mechanics. The idea is simple, and extremely similar to ID considerations. We know from physics that the universe must not be necessarily considered as wholly deterministic (unless you are a die hard Einsteinian). Quantum wave function collapse (at least in most interpretations of quantum mechanics) is a true example of intrinsic probabilistic realities. The probabilities in quantum mechanics are not just a way to describe deterministic systems with too many variables, like in conventional statistics. They are an intrinsic property of reality at that level. But quantum probabilities are random systems. They cannot generate order and functional information, as we have discussed. Unless they are guided. To achieve specific configurations (Abel's "configurable switches"), according to conscious representations. Without violating deterministic laws (no magic, no miracle). Without apparently violating probabilistic laws (the functional result is the range of possibilities, after all), and at the same time strongly violating them (the functional result is so improbable that it would never happen without the guidance of the conscious being). This violation without violation, this miracle without miracles, is at the core of a quantum theory of the mind. It's ID all the way. In humans, that would happen mainly in neuronal cells. Small quantum deviations from utter randomness can well explain guided neuronal function. The outputs of the mind to the brain are no more deterministic: they follow quantum patterns guided by consciousness. In biological design, the same thing may happen. The consciousness of the designer can interact with biological matter at quantum level, guiding events, like mutations, which are intrinsically random, and therefore are an optimal interface for conscious intervention. Why do you think that I am such a great fan of transposons, and of genes modeled by transposon activity? Well, I think that can be enough, for the moment.gpuccio
May 10, 2014
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@Gpuccio: Re: superfamilies This is the definition of "superfamily" from Wikipedia:
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is based on structural alignment and mechanistic similarity even though no sequence similarity is evident.
I wonder to what extent standard classifications stand up to the ideal declared in the first sentence. If two extremely well-conserved proteins have a similar structure and function, but the homology is not supported by the sequence analyses, convergence is at least a distinct possibility. If so, they are not really members of the same superfamily despite being "officially" regarded as such for classificatory convenience. It's again a terminological question. If you demand that a superfamily should be a clade, sequential evidence should be decisive. Top be sure, the use of BLAST to disprove homology is risky (after all, homology doesn't equal similarity); cladistic analyses taking into account other members of the putative superfamily would be necessary. I have no idea if they nave been conducted. If not, the classification must be taken with a grain of salt. (Linguists have similar problems too. Traditional classification of languages into families often confuse genetic groupings with typological or even geographical ones. We have a hard time sorting out the resulting confusion.)Piotr
May 10, 2014
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Piotr: Profiting of a moment of calmness, I will try to give you a brief outline of what I think about the physical implementation of biological design. Please, consider that this issue is at present highly speculative, but potentially open to many empirical approaches. a) ID is about the inference of design, in particular for biological information. It is perfectly true that, to infer design, it is not necessary to know any details about the designer (nature, purposes, times and modalities of implementation), because the design inference is independent from all that, and depends only on the observation of complex functional information and on its empirical connection with the process of design. If we infer design, we are only inferring that the specified form in the observed object was inputted into the object from the conscious purposeful representations of a conscious being. In particular, what we know of the process of design is derived from the observation of human design. b) That said, it is equally true that, if we infer design, even tentatively, as an explanation for biological information, things do not stop there. There are a lot of legitimate question that arise, and that must be scientifically addressed, as far as it is possible. The most obvious questions are: - Who is the designer - One or many designers? - What is the purpose of the design process? - When was the design implemented? - How was the design implemented? - What are the design strategies used? - Is the design process slow and gradual, or "punctuated"? Some of these questions are easier, some are really difficult. I would say that the most empirically approachable is: when was the design implemented? Given the type of inference we have defined here for design (inference from complex functional information) there is a simple procedure to identify the times of design: whenever we have appearance of new complex functional information, we can infer an act of design. From all the discussions we have had here, you can therefore understand that I believe that at least every time a new basic protein domain, or superfamily, appears in natural history, I infer design. Obviously, OOL and the appearance of eukaryotes, and the cambrian explosion are examples of huge inputs of new complex functional information in a relatively small window of time. But my approach is to infer design also for less amazing events, according to the procedure I have detailed. I would like to consider now the obvious problem: who is the designer and how does he design things? The only things which are really requested of the designer are: 1) To be a conscious, intelligent, purposeful being. That is necessary because design always originates from conscious, meaningful, purposeful representations. 2) To be able to output those representations to material objects. Note that in point 1 there is no implication that the biological designer must be God, or a god, or that he must be omnipotent, or good, or any other connotation. When I say that ID is scientific, and not religious, I really mean that. However, as I have said, our model of design is human design. Except for bizarre scenarios, which I will not consider, nobody really thinks that humans were the biological designers. The hypothesis of aliens, instead, is perfectly reasonable, and compatible with ID. I don't like that hypothesis, and it has an obvious limit (does not explain the origin of the aliens), but it is a valid ID scenario. However, I will not deal with that, for the moment. It is not my scenario, and probably not yours. So, we are left with a simple question: what kind of conscious being can the biological designer be? I have always frankly admitted here at UD that the most reasonable hypothesis is: a conscious intelligent purposeful being who is not physical. That is the minimal credible requirement, because indeed if physical designers had been around throughout natural history, we would probably have some physical trace of that fact. What about conscious non physical beings? Well here is the central point of the ideological war that has been built around ID. Today's culture is strongly biased in favor of a reductionist materialist worldview. I have nothing against that (everybody can choose the worldview he likes), but it is only a philosophical position: it cannot be the foundation for scientific inquiry. Instead, that specific worldview has become dogma, and is considered as the necessary standard for science. See, for example, the ad hoc concept of "methodological naturalism". I reject that position. Science is the search for truth about empirical observations, and cannot be bound to a specific philosophy. Moreover, the reductionist materialist philosophy is recent, unsupported by specific facts, not shared by the majority of human beings, not shared by the majority of past thinkers, scientists, and philosophers. My point is: there is no reason to accept it simply because the scientific academy of the last few decades has made a religion out of it. I believe, like many others today and in the past, that consciousness is not generated by material configurations of matter, and is not necessary linked to the. IOWs, I completely reject the position usually called "strong AI theory". More in next post.gpuccio
May 10, 2014
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gpuccio @ 215
Maybe. But in italian the phrase works that way! We are probably less precise about double negations, italians are compliant people. :)
un italiano vero! eccellente! Keep writing mio caro amico, you do it very well. I'm learning quite a bit from your OPs and the follow-up comments. May God bless you, doctor. P.S. back to my head-scratching study sessions, trying to understand things you already know well. BTW, got a good amount of helpful information from the links you provided. They were quite a boost! Mile grazie!!! Now reviewing the description of the spindle apparatus mechanisms operating on the intrinsic asymmetric divisions. The more I look at this, the more it seems like science fiction. What a fascinating story! Anyway, can't make much progress on the software development project until I get the story main scenario and choreography clear. This is fun!Dionisio
May 10, 2014
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BA: Thank you for your contributions. A lot of interesting stuff there.gpuccio
May 10, 2014
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Moreover, proteins are far more complicated, and antagonistic to Darwinian claims, than most Darwinists imagine, or would prefer, them to be: Acrobatic Protein Stars in Two Gymnastic Events - July 2012 Excerpt: "We showed that RfaH refolds, which is a big enough deal already. You would think this is impossible. That's what you're told in school," says Ohio State microbiologist Irina Artsimovitch,,, Though the process happens in seconds, Artsimovitch likened the refolding (of a single protein to a completely different fold pattern) to "having a knitted sweater that you rip out and then knit into a sweater with a different pattern." http://www.evolutionnews.org/2012/07/acrobatic_prote_1062541.html The Gene Myth, Part II - August 2010 Excerpt: “It was long believed that a protein molecule’s three-dimensional shape, on which its function depends, is uniquely determined by its amino acid sequence. But we now know that this is not always true – the rate at which a protein is synthesized, which depends on factors internal and external to the cell, affects the order in which its different portions fold. So even with the same sequence a given protein can have different shapes and functions. Furthermore, many proteins have no intrinsic shape, taking on different roles in different molecular contexts. So even though genes specify protein sequences they have only a tenuous (very weak or slight) influence over their functions. ,,,,So, to reiterate, the genes do not uniquely determine what is in the cell, but what is in the cell determines how the genes get used. Only if the pie were to rise up, take hold of the recipe book and rewrite the instructions for its own production, would this popular analogy for the role of genes be pertinent. Stuart A. Newman, Ph.D. – Professor of Cell Biology and Anatomy http://darwins-god.blogspot.com/2010/08/gene-myth-part-ii.html Physicists Discover Quantum Law of Protein Folding – February 22, 2011 Quantum mechanics finally explains why protein folding depends on temperature in such a strange way. Excerpt: First, a little background on protein folding. Proteins are long chains of amino acids that become biologically active only when they fold into specific, highly complex shapes. The puzzle is how proteins do this so quickly when they have so many possible configurations to choose from. To put this in perspective, a relatively small protein of only 100 amino acids can take some 10^100 different configurations. If it tried these shapes at the rate of 100 billion a second, it would take longer than the age of the universe to find the correct one. Just how these molecules do the job in nanoseconds, nobody knows.,,, Their astonishing result is that this quantum transition model fits the folding curves of 15 different proteins and even explains the difference in folding and unfolding rates of the same proteins. That's a significant breakthrough. Luo and Lo's equations amount to the first universal laws of protein folding. That’s the equivalent in biology to something like the thermodynamic laws in physics. http://www.technologyreview.com/view/423087/physicists-discover-quantum-law-of-protein/ Watching a protein as it functions - March 15, 2013 Excerpt: When it comes to understanding how proteins perform their amazing cellular feats, it is often the case that the more one knows the less one realizes they know. For decades, biochemists and biophysicists have worked to reveal the relationship between protein structural complexity and function, only to discover more complexity.,,, A signaling protein usually responds to a messenger or trigger, such as heat or light, by changing its shape, which initiates a regulatory response in the cell. Signaling proteins are all-important to the proper functioning of biological systems, yet the rapid sequence of events, occurring in picoseconds, had, until now, meant that only an approximate idea of what was actually occurring could be obtained.,, The team identified four major intermediates in the photoisomerization cycle. ,,, By tracking structurally the PYP photocycle with near-atomic resolution, the team provided a foundation for understanding the general process of signal transduction in proteins at nearly the lightning speed in which they are actually happening. http://phys.org/news/2013-03-protein-functions.htmlbornagain77
May 10, 2014
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Piotr: Very good. I am a great fan of clear definitions (as anybody can see from the titles of my 2 OPs). So, I am grateful that you ask me to define better my terms. Let's try. Premise: the divergence between archaea and bacteria is the first one we can detect from the existing proteomes. At present, we can infer nothing about what happened before from the observation of the existing proteomes. OK? a) LUCA. We call LUCA the living beings that existed immediately before that divergence (let's assume 3 billion years ago), and from which that divergence happened. b) What we don't know about LUCA. We don't know for how long it existed. If it was a single species or a pool of different organisms. If there were simpler ancestors. And so on. c) What we know about LUCA. It was more or less a prokaryote. It had a lot of the basic functions of a prokaryote, functions which are shared between archaea and bacteria. d) HGT is certainly a complication, but not to the point that the above facts can be doubted. e) Now, let's call protein information in LUCA all the information that is shared between archea and bacteria. f) In particular, if some protein, like those two I have cited, still present high homology today between archaea and bacteria, like our two examples, we can be rather certain that that protein was already in LUCA as an ancestor of both the bacterial and the archaeal form. In particular, if the homology is still very high, like in our two examples, we can be rather certain that the LUCA ancestor was essentially the same thing as the modern proteins in the modern proteome, and the differences can be easily explained as the effect of neutral evolution with conserved structure and function. g) What can we say if two proteins, of the same superfamily, but completely different between themselves, were both present in LUCA? This is the case of Rec A and the beta subunit of ATP synthase. You object that: "You are partly confusing the two notions of shared ancestry yourself. Note that you say that related genes had diverged “already in LUCA”. That means that LUCA had an ancestor in which both genes had a single source. I want to make the distinction clear to avoid quibbling about terminology." That's OK. But in reality I said that: "Therefore, it is clear that not only the superfamily was already present in LUCA, but that it was already diversified at least in these two different proteins, always in LUCA." Emphasis mine. I did not really mention "divergence". However, this is a good occasion to clarify: 1) The first divergence we observe is the archaea bacteria divergence. 2) Were there divergences before? That is part of what we don't know. Maybe. But it is at least strange that, if there was an evolutionary history of OOL, and then an evolutionary history from FUCA to LUCA, no earlier divergences can be observed today. THat is ib itself an argument in favor of my hypothesis that LUCA is FUCA. If one does not accept that, the lack of any detectable earlier divergence can be explained only in two ways: 1a) A long and complex evolutionary history (which generated life and then brought form FUCA to LUCA) happened without any divergence at all (very strange). 2a) There were divergences, but they are no more detectable. Even stranger, if you consider that we clearly detect the divergence between bacteria and archaea, which took place 3 billion years ago. Previous divergences should have already been cancelled in LUCA, because otherwise they should be still detectable (unless you think that nature selectively cancels divergences 3.2 billion years old, and respetcs divergences 3 billion years old). But is those divergences were alredy cancelled in LUCA, then they were created and canceled in a window of a few hundred million years. Why? 3) What can we say of Rec A and the beta subunit of ATP synthase? THat they are two different proteins, of the same superfamily, with no sequence homology, and that they were both in LUCA. Frankly, the explanation that they diverged form a single ancestor does not seem very promising. Looking at their complete sequence separation, I would prefer an explanation based on independent design. The structural and functional affinity, which is the reason for the classification in the same superfamily, would then be the consequence of functional constraints in the design. The problem, however, is open to enquiry and discussion.gpuccio
May 10, 2014
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