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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.

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.

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).

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
gpuccio: First quick comment: I realize you have stated that functional specification is a subset of specification. The difference being that the functional specification includes parameters about the function/functionality, whereas the specification does not. That is fine as far as it goes. I'm just wondering how far it goes. It seems the only distinction here is that the specification wasn't really very specified? :) Meaning, if we loosely and vaguely define our specification then it might not be specific enough to clearly articulate the function. But if we then go on to better articulate the details, the function emerges, almost by definition. This kind of thing happens in engineering situations all the time. The boss says "Do X." He has made a specification, per your definition. But it is so vague and general, that the poor engineer has no idea where to turn. After a few more questions, the boss finally articulates the request in a bit more detail and the engineer can start to home in on what the boss really wants X to do. Finally, perhaps after some additional back-and-forth, a light will turn on in the engineer's mind and the engineer might reply, "Ah, I see. So what you really want to do is Y." To which the boss replies, "Yes, yes, that's what I've been trying to describe." Then perhaps even after a few days of initial work, some feedback and trial-and-error, they get a very good handle on exactly what it is they want the system to do. At this point they call it Z. Now we could call X a "specification" and Z a "functional specification." And maybe that has some utility (I'm not yet convinced). But really all we've seen is that X was too general, and Z is a more specific statement. Z, has more specification by definition, because it is more specific. In other words, getting from a "specification" to a "functional specification" is not, it seems in most cases, a matter of substantive or theoretical difference between the two. Rather, it is just a question of being more specific in outlining the parameters. It is just a question of having properly specified exactly what is required. So the only real distinction between the two is that one is vague/general, and the other is more specific. One is specified and the other is more specified. One is poorly defined/specified, the other is well defined/specified. One is the lazy man's description, the other is the careful engineer's description. ----- Please note I am not at this point disputing your approach, nor am I necessarily suggesting that it needs to be changed. This is a very fine nuance I am focusing in on, namely the fact that the difference between what you are calling "specification" and "functional specification" is really just one of degree -- the degree to which we have done the work and taken the time to properly specify what it is we're talking about. (This is virtually the identical issue I was critiquing Bill Dembski about in his essay on irreducible complexity.) Again, maybe there is still value to your broader point in defining the two as separate things, I'm not sure. But substantively it seems they could collapse into the same definition (call it either "specification" or "functional specification"). It is just a question of whether we have properly and adequately done the work of laying out the specification.Eric Anderson
May 5, 2014
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Piotr: You are anticipating issues which I have not yet debated in this thread, but it's OK. First of all, not all nucleotide sequences can be interpreted as protein coding. Even if we don't know the protein, there are rules to identify possible ORFs (open reading frames) in a genome: they must have a starting codon, a minimum length and a stop codon). But that's not important. The point is, with proteins we are not looking at a meaning, but at a function. Functions can be objectively defined and measured. An enzymatic function is the best example. Now, the problem is: how do we measure functional complexity in proteins? That should have been the object of a future OP, but I am glad to anticipate something now. Once we have defined a specific function, obviously we cannot measure each possible sequence to see if it is functional in that sense. The search space is too big. We will never be able to do that. Indeed, the whole universe cannot do that. But there are other ways. What do we want to know? First of all, it is useful to start from the observed functional protein (an enzyme, for example), and assume as search space the total number of sequences of that same length. There are many reasons to do that, but I will not deal with them now. So, let's assume that the search space is 20^n, where n is the number of AAs in the protein. That gives us huge search spaces even for relatively short proteins. But how do we measure the target space? That is the real problem. We have to use indirect ways. Now, a good understanding of functional protein space and of the relationship between sequence, structure and function is the best way top proceed. Unfortunately, that understanding is still limited. You may have read that Axe evaluates at 1:10^70 the number of sequences that fold. Szostak is the author of the paper you cited which is usually used to refute Axe, but believe me, that paper is completely flawed. Another way is to look at the existing proteome. The 2000 superfamilies are isolated at sequence level, and that tells us that protein function is organized in islands. The rugged landscape theories tell us that the islands are more than we could think, but that they are anyway isolated. I have given you an example of a protein, the beta subunit of ATP synthase, where 630 AAs could never change in billion of years. That should tell you how restricted and constrained the target space can be. Finally, Durston has given a simple and very good method to measure functional complexity in protein families. Please, read his paper: "Measuring the functional sequence complexity of proteins" http://www.tbiomed.com/content/pdf/1742-4682-4-47.pdf and then we can discuss it.gpuccio
May 5, 2014
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gpuccio Your answers made my my mind much clearer about what we are talking about. Just a couple of points.
...2000 basic functional structures (superfamilies) in the huge search space of protein sequences... let’s say that 100 new protein structures of about 150 AAs are potentially useful in a cellular context..
I think you confine your search through all the previously found protein structures (in my opinion, "folds" may be also used here) and all the possible structures that is likely to be found (which may be estimated based on historical data) in the future. I agree with this definition. Here, I object to Piotr who said Is the following 183-base-long sequence special or not, and how on earth do you know? . We can easily check whether this sequence folds or not (well, maybe not so easily, since folding depends on temperature, pH, ligand, etc.) Nevertheless, at least in principle, we MAY check whether this sequence has the POTENTIAL to have a function (so may be special) or not. The second point I would like to talk abaout:
If an enzyme can accelerate a reaction, it can do it. It’s not because we observe the process. It is a functionality which is really in the molecule, we don’t make it up for the observed molecule
I see your point, and I agree with you to a large extent. One minor aspect I do not feel very comfortable is that we define the concepts of "enzyme" and "reaction" since they are already out there. Your suggestion may be, as I said earlier, justifiable if ours is the only life form in the universe. However, assume that we were living in a Star Wars universe, in which there were many different space-species and each had a different biomolecular structure. In that universe, a certain biomolecular organization would not be deemed to be special, since different molecular organizations would also be "functional". So I guess, here, FSI depends (though implicitly) on the uniqueness of the biochemistry of living organisms. There should be one to one mapping between enzymes and life. In this case, we would KNOW that there is a unique solution to the problem of life, so the ultimate function (life) may be reduced to a lower set of functions (structures and then coding of proteins). Thanks again for the thought provoking discussion.CuriousCat
May 5, 2014
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gpuccio: Are you sure you are dealing with anything as specific as "as a sonnet by Shakespeare" or even "a meaningful text in English"? Actually, any sequence of bases is potentially "meaningful" in the sense that it can be interpreted as a sequence of codons. Apart from being translatable it can also produce RNA, or play some other role (a binding site, an enhancer, whatever). Even if you know what protein is produced, how do you determine whether the protein has any kind of "functionality"? How do you define your target space?Piotr
May 5, 2014
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Piotr: We must distinguish between descriptive information and prescriptive information (see Abel). Pi is an example of descriptive information (it coveys a meaning). A protein gene is an example of prescriptive information (it conveys the sequence of AAs of a functional protein that can, for example, accelerate a specific biochemical reaction). A protein gene is more similar to the plan of a machine. A machine does something. Maybe I don't know how to convert the information into the machine. That's not a problem. I never said that we can always recognize the function. The design inference has 100% specificity, but low sensitivity. If a sequence of nucleotides is a protein coding sequence, the protein can be built and tested. The biochemical activity we observe, if we observe it, does not depend on our "understanding". It is there. It does not depend on us.gpuccio
May 5, 2014
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Piotr: You are a linguist. An english sonnet is made of about 600 characters. Now, I will ask: If you have a random generator of character sequences, how many do you think the probabilities are, in one attempt, of generating: a) A specific sonnet by Shakespeare? b) One of Shakespeare's sonnets? c) Any good meaningful sonnet in english? d) Any good meaningfful text of 600 characters in english? While certainly a) is lower than b (not much), and b) is lower than c) (much), and c) is lower than d) (very much), would you bet on d)? Even if you had a lot of attempts? (Let's say 10^42).gpuccio
May 5, 2014
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Correction: "But how is it even remotely relevant..."Piotr
May 5, 2014
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OK, and so? There are many special numbers, but you will never get the first, say, 100 digital figures of any of them by chance. Not if you have a list of (sufficiently few) "special numbers" in advance. But how is even remotely relevant to the discussion of function in biology? Do you expect to find the digits of π encoded in a DNA sequence? What makes a particular sequence special before you know what it does? Can you give me a list of base sequences that you know to be "special" in the sense π is special? Is the following 183-base-long sequence special or not, and how on earth do you know? ACGTAGTGGCGTTCTTCGACTGTTCCCAAATTGTAACTTATTGTTTTGTGAAAATCAAAGTTATTTCTCGATCCTTTTTATGTACGTACCATATTCTTTTAATTCTTTGGTTATTTTTCCGAAGTAGGAGTGAATAAACTTTCGTTTACGTCTTATTATTAATGATATAGCTATGCACTTTGTPiotr
May 5, 2014
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CentralScrutinizer: Thank you for your contribution.gpuccio
May 5, 2014
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Piotr: OK, and so? There are many special numbers, but you will never get the first, say, 100 digital figures of any of them by chance. There are many ways in which all the molecules of a gas in a container could stay in half the space of the container, leaving absolute void in the other half of the container. But that will never happen, as the second law of termodinamics tells us. Why? Because there are so many more, hugely many more, ways in which the molecules are diffused almost equally in all the space of the container. And there are so many more, hugely many more, real numbers which are not special at all. As the search space increases exponentially, there is no chance at all that the target space linked to order, function or meaning can increase adequately. The probabilities of ordered or functional states diminish inexorably, and very early they become an empirical impossibility. Please, see also my post #23. When we speak of hundreds of orders of magnitude of complexity, what does it matter if the target space is a few orders of magnitude greater because we sum the functional events?gpuccio
May 5, 2014
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If you see question marks before 2, 3 and 5 in my post -- they were meant to be square root signs.Piotr
May 5, 2014
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@gpuccio:
That is perfectly correct. Why? Because pi is a special number with a special meaning whose definition does not change before and after we observe that result.
But how many "special numbers" are there? If π qualifies, so presumably do 2π and π/2, and perhaps the binary representation of π, and of course Euler's number e, and the Golden Ratio φ; and Jean-Claude Perez can assure you that (3-φ)/2 is also very special. So are ?2, ?3, ?5, and 9046503395561 (it's the 314159265359th prime, and we have already established that the number 314159265359 is special). Oh, yeah, and there are constants in physics too, like the fine structure constant α = 0.00729735257, and its reciprocal 137.035999074.Piotr
May 5, 2014
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gpuccio: Because pi is a special number with a special meaning whose definition does not change before and after we observe that result.
Exactly. Even if humanity had never discovered Pi before, and someone produced the first 500 digits of Pi on a Roulette wheel, that would still be a very special event whether we realized it or not, because of the pre-existing specialness of Pi. The fact is, nobody believes this would ever happen with the probabilistic resources at hand. If, after such an event occurred, we discovered Pi, we would immediately conclude the Roulette wheel's output was not random- someone rigged the game! That would be the rational conclusion. So the question is, with regards to certain biological features, such as OOL and protein domains is, how special were the events leading to them? That is, is the number of chemical pathways that could lead to OOL as we know it large or small compared to all possible chemical events? The smaller that number of pathways, the more special they are. And what sort of impediments might such pathways face? What sort of chemical affinity or resistance? "It's all chemistry" (as Evolve likes to spout) answers nothing. One needs to show the precise pathway(s) that chemical interactions could have tread into order to build the first replicator that is stable and complex enough to develop into what we observe. The OOL theoreticians are light years away from any sort of complete picture. Good luck to them. Given certain lack of chemical affinities (as Meyer explains in Signature of the Cell), it appears downright ridiculous to me to think it wasn't "rigged." But time will tell if the anti-ID crowd can fund their promissory notes. Thanks for all your great posts, gpuccio.CentralScrutinizer
May 5, 2014
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Wow, this discussion is getting really substantial. The old Wendy's commercial question 'where's the beef?' seems to be addressed here ;-) Thanks.Dionisio
May 5, 2014
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CuriousCat: Now, your first objection. Is it correct to define the function AFTER observing the function itself? And the answer is: yes, provided that the function is well defined. You see, if the function is well defined objectively, without any post-hoc reference to the real sequence of bits, then it is perfectly correct to define it after having observed it. Let's make an example. I get by chance the number 83436952. The I say: "Well, let's define a function for that number. I set my lock combination exactly that way, and then I define the function as being the key for my lock". That is not allowed. That is building an ad hoc function for a random sequence after having observed it. In this case, the only correct definition for the function is: "any number which I can set as a key for my lock". That is a correct function definition, but it is not complex: a lot of numbers will be functional. But let's say that I observe the number 3.14159265359, and I say: "Hey, these are the first 11 decimal figures of pi!". And I define the function (well, in this case it's a meaning more than a function, but let's not be fastidous :) ) as "the first eleven decimal figures of pi". That is perfectly correct. Why? Because pi is a special number with a special meaning whose definition does not change before and after we observe that result. IOW, the definition is wholly independent from what we observe. Our observation is just a trigger to recognize a function which can be objectively defined at any time, and remains always the same. If an enzyme can accelerate a reaction, it can do it. It's not because we observe the process. It is a functionality which is really in the molecule, we don't make it up for the observed molecule. That will be enough, for now.gpuccio
May 5, 2014
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CuriousCat: Thank you for your intervention, and for your very good and thoughtful objections. I will try to answer you, even if that means anticipating some concepts about the design inference. First of all, you can see that, as I have defined them, FSI (and therefore dFSI) are not subject to your second objection. I quote myself:
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.
Emphasis added. That means that all my reasoning is referred here to a well defined search space, not to a generic search space. And later:
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).
So, my definitions are referred to a known search space and a known target space: ideally, each item in the search space should be tested for the function. That's what is implied in the definition. Obviously, I am well aware that in any real context, if the search space is very big, that cannot be done. But there are indirect ways to measure functional information, for example in the protein search space (see Durston). However, I have reserved those aspect of the discussion for a future post. For the moment, I want to specify: a) That my definiton is relative to some specified function, not to any possible function. I will deal with the "any possible function" perspective, often raised by darwinists, when I will discuss the design inference for proteins. The FSI value is the improbability of getting that function in that system and in that search space, by one attempt and with a uniform probability distribution. I can anticipate that the "any possible function" argument is not valid, because in a neodarwinian perspective what we need is: - a function which is useful in the complex context of the existing cell - a function which is coordinated (in terms of quantity, sequence and location and regulation) with the complex context of the existing cell - a function which is so useful that it confers detectable reproductive advantage, and can be expanded and fixed by NS. That reduces the space of candidate functions a lot. Now, just consider that almost 4 billion years of evolution, whatever the causal mechanism, have found about 2000 basic functional structures (superfamilies) in the huge search space of protein sequences. And that new superfamilies appear at a constantly slower rate. We will see, when we debate the design inference for proteins, that even if many new complex functions were potentially available in a specific context, the result would not change much. For example, let's say that 100 new protein structures of about 150 AAs are potentially useful in a cellular context (which, IMO, is highly unlikely), and that each of them has a functional complexity of 300 bits, and therefore a probability of being found of 1e-90. So, we have a search space of 1e195 (20^150), and we are assuming a target space of about 1e105. Let's say that we want the probability of finding one of the 100 functional proteins, instead of the probability of finding one specific protein. We have to sum the 100 target spaces, while the search space remains the same. So, the total target space will be 1e105*10^2=1e107. So, the probability of finding one of the useful proteins has changed of only two orders of magnitude, and it is now 1e-88. Not a great problem, for the design inference. More in next post.gpuccio
May 5, 2014
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This thread is very juicy. I'm taking my time to read it carefully, so that I can digest it well. The main subject discussed here is very important to my current project, so I'm enjoying this discussion. Thanks. :)Dionisio
May 5, 2014
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gpuccio, Thanks for the interesting and informative post. I'm looking forward to reading the rest of this discussion. There is one point I would like to mention, related to the "functionality" concept. You say:
b) The functionality in the chosen stone: that stone can be used to obtain the desired result.
You also add:
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.
As far as I can see, and Mung pointed out and you agreed, you want to quantify "objective functional information", so that later you can employ a hypothesis test for the existence of design. The point that I do not feel comfortable is defining the function AFTER observing the function itself. In Darwinian sense (though I disagree), function is not defined beforehand, so the function, itself, is a random variable. To explain things a little bit further, let's take the example of stones on the beach. We may define a certain a function, find the resulting Shannon entropy for that specified function and amazed at that value, but that would be, I think, a biased experiment. To be really amazed at that value, I believe we should (somehow) compute (and/or compare) this value to those computed for all the possible specified functions (the total function space) which have been realized and which will be realized in the universe. In other words, for a specified function we may have high FSI value, but this does not guarantee a highly unlikely process, because the function space is also (quite possibly) infinite (or very huge). For instance, if we can guarantee that a single biochemical path exists for the existence of life, then your reasoning is, I believe, sound. Then, we can compute FSI of the ordering of molecules, and so on. However, we cannot guarantee the existence of single ordering of molecules, which will yield life (or something like life). Logically, it may be some other combination(s) of molecules which may produce other types of life(s). Hence, functional space is unknown. I think a single high FSI value (though it indicates the unlikeliness of that event) does not take this factor into consideration.CuriousCat
May 5, 2014
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BA (and Evolve, if you are there): The interesting thing is that random variation in genomes, which is supposed to be the engine which generates new functional information in neodarwinism, is not even the working of biochemistry, but the working of errors in biochemistry. Indeed, the molecular machines which duplicate the information in DNA are supposed to duplicate it exactly. But no machine can work perfectly, so errors happen, once in a while. Those errors are the origin of random variation. They happen randomly, because they are errors, Biochemistry is algorithmic. Therefore, if biochemical machines worked perfectly and algorithmically, genomic information would always remain the same (if there were no design intervention). So, form a neo darwinian point of view, it's not all chemistry, it's all errors in chemistry! Expressed that way, it sounds a little foolish, doesn't it? :)gpuccio
May 5, 2014
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Eric Anderson, but of course, how could I have forgotten 'Mr. 'Just Chemistry' Evolve' recent denial of information in the cell :)
"It’s all chemistry, Eric." https://uncommondescent.com/chemistry/we-have-a-live-one-folks-information-redux/
No, Mr. Evolve, it certainly is NOT all chemistry, 'It's all Information':
“a one-celled bacterium, e. coli, is estimated to contain the equivalent of 100 million pages of Encyclopedia Britannica. Expressed in information in science jargon, this would be the same as 10^12 bits of information. In comparison, the total writings from classical Greek Civilization is only 10^9 bits, and the largest libraries in the world – The British Museum, Oxford Bodleian Library, New York Public Library, Harvard Widenier Library, and the Moscow Lenin Library – have about 10 million volumes or 10^12 bits.” – R. C. Wysong http://books.google.com/books?id=yNev8Y-xN8YC&pg=PA112&lpg=PA112 'The information content of a simple cell has been estimated as around 10^12 bits, comparable to about a hundred million pages of the Encyclopedia Britannica." Carl Sagan, "Life" in Encyclopedia Britannica: Macropaedia (1974 ed.), pp. 893-894
For calculations, from the thermodynamic perspective, please see the following site:
Molecular Biophysics – Information theory. Relation between information and entropy: - Setlow-Pollard, Ed. Addison Wesley Excerpt: Linschitz gave the figure 9.3 x 10^12 cal/deg or 9.3 x 10^12 x 4.2 joules/deg for the entropy of a bacterial cell. Using the relation H = S/(k In 2), we find that the information content is 4 x 10^12 bits. Morowitz' deduction from the work of Bayne-Jones and Rhees gives the lower value of 5.6 x 10^11 bits, which is still in the neighborhood of 10^12 bits. Thus two quite different approaches give rather concordant figures. https://docs.google.com/document/d/18hO1bteXTPOqQtd2H12PI5wFFoTjwg8uBAU5N0nEQIE/edit Information and Thermodynamics in Living Systems - Andy C. McIntosh - May 2013 Excerpt: The third view then that we have proposed in this paper is the top down approach. In this paradigm, the information is non-material and constrains the local thermodynamics to be in a non-equilibrium state of raised free energy. It is the information which is the active ingredient, and the matter and energy are passive to the laws of thermodynamics within the system. As a consequence of this approach, we have developed in this paper some suggested principles of information exchange which have some parallels with the laws of thermodynamics which undergird this approach.,,, http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0008 - Dr Andy C. McIntosh is the Professor of Thermodynamics (which is, I believe, the highest teaching/research rank in the U.K.) at the University of Leeds. Quantum Information/Entanglement In DNA – short video https://vimeo.com/92405752
Quote:
Earth’s crammed with heaven, And every common bush afire with God; But only he who sees, takes off his shoes, The rest sit round it and pluck blackberries. - Elizabeth Barrett Browning Kirsten Powers’ Reluctant Journey from Atheism to Christian - 2013 Excerpt: Powers doesn't recall what Kathy Keller taught on that day, but when she left the Bible study she knew everything had changed. "I'll never forget standing outside that apartment on the Upper East Side and saying to myself, 'It's true. It's completely true.' The world looked entirely different, like a veil had been lifted off it. I had not an iota of doubt. I was filled with indescribable joy.",,, "Everywhere I turned, there He was. Slowly there was less fear and more joy. http://crossmap.christianpost.com/news/fox-news-kirsten-powers-reluctant-journey-from-atheism-to-christian-6355
Verses, and music:
Exodus 3:5 "Do not come any closer," God said. "Take off your sandals, for the place where you are standing is holy ground." John1:1-4 In the beginning was the Word, and the Word was with God, and the Word was God. He was with God in the beginning. Through him all things were made; without him nothing was made that has been made. In him was life, and that life was the light of all mankind. Casting Crowns - The Word Is Alive - Live http://www.youtube.com/watch?v=X9itgOBAxSc
bornagain77
May 5, 2014
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dgw: You are perfectly right, and I agree with each single word you have written in your post. Enzymes are the best model for biological functional complexity. The reason is simple. Enzymes are in a sense the most easily understood biological machines. Their function can be very easily defined in terms of the biochemical reaction that they accelerate, and of how much they accelerate it, and it is very easy to define an objective way to measure that function in standard lab conditions, and to fix a minimal threshold of function to be detected if we want to express the measurement in binary form. The concepts remain valid for all functional proteins, but for enzymes the application is really straightforward.gpuccio
May 4, 2014
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Eric: Thank you. Of course, I am aware of the recent discussions here about the information problem, and of your very active and very good role in them. That's exactly one of the reasons that stimulated me to publish this post, because this is really a central issue for ID, and the more we discuss, clarify and deepen it, the better for us. :) Behe's irreducible complexity is another fundamental concept, and it is obviously linked to the concept of functional complexity, but I think that it is a meta-concept. Indeed, irreducibly complex system could be viewed as systems where many different parts, each of them exhibiting high functional complexity, contribute to a higher meta-function, which could not be implemented if even one of the complex parts did not exist. In that case, the total functional complexity for the meta-function is obviously obtained by summing the individual functional complexities of the parts in bits (IOWs, multiplying the individual probabilities).gpuccio
May 4, 2014
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Dionisio: Thank you!gpuccio
May 4, 2014
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BA: Thank you for your excellent contributions. Of course, Dembski, Abel, Durston and many others are the absolute references for any discussion about functional information. I think and hope that my ideas are absolutely derived from theirs. My only purpose is to detail some aspects of the problem. And you are perfectly right about the inconsistent objections that are routinely made about this concept, especially by different exploitations of the potential ambiguity of the word "information". Having discussed for years with our kind (or less kind) interlocutors, as you have done, I know them all. :)gpuccio
May 4, 2014
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Mung:
So gpuccio is not out to define information, nor to differentiate functional information from non-functional information, but rather to develop a definition of functional information that is objective. As far as I know this is all that is required in order to allow it to be useful in science.
I am so glad that you have completely appreciated my point! The problem is that the word "information" means too many things for too many people. Rather then debating the different meanings, I have just tried to give an operational definition of a particular aspect. In a sense, we could say that true information is only designed information: a message of meaning and purpose which is passed from a conscious being to another one, through some physical transmission system. That is true, but how could it help in a discussion about design detection. It would simply be self-referential. We could never argue that designed information is a clue to design! The simple truth is, when we want to infer design, we don't know in the beginning if what we are observing is designed. Otherwise, no inference would be necessary. Therefore, we look at configurations of matter, IOWs at forms, and we wonder: is this designed? Is this intelligent, intentional, consciously originated information? So, we must start with an open mind, and accept that any configuration we observe could be designed information. Function in itself cannot help us, because, as I have said, we can always find some function for something. That's why it is important to remember that function is a product of consciousness, it is not in the object itself, or in its configuration. But functionality, as I have defined it, is objective, even if in relation to a function objectively defined by a conscious subject. But, again, functionality in itself is not enough. Many non designed things are functional for simple functions. But functionality for complex functions is the real thing. :)gpuccio
May 4, 2014
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Perhaps progress could be made on this topic by considering enzymes as biological embodiments of functional information. Their function is to catalyze a reaction. They are far more effective than chemical catalysts and they have a complex molecular structure. Metabolic pathways rely on a sequence of enzymes to efficiently transform components. In a recent publication, PMC3443871, Nanda and Koder write on the design of artificial enzymes. They comment: Today, a Boeing 747 is an incredibly complex machine with over 6,000,000 parts. As such, computers have become indispensable in the aerospace industry. Although much smaller in size, the mechanistic complexity of enzymes and challenges associated with their design (Box 1) argue that they are as sophisticated as passenger airliners, and it is expected that computational methods in chemistry and biology will promote a similar revolution in the design of artificial catalysts. They go on to describe means of improving enzymes using design techniques and directed evolution. Directed evolution implies a target in mind, the result is an enzyme with an improved design that meets their purpose.dgw
May 4, 2014
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gpuccio: Thanks for the OP. I hope to be able to think through this in more detail and respond in the next day or so with some thoughts. In the meantime (and with apologies for linking to my own piece here), the hierarchy you outlined involving specification and function reminded me of something I wrote a while back. It was focused specifically on Behe's concept of irreducible complexity (as complemented by Dembski's writings), but has some relevance to this discussion:
One of the principal challenges with the concept of irreducible complexity is defining a system’s basic function within a particular environment, and thus determining the irreducible core. Suggestions that certain complex systems are not irreducibly complex often arise from a failure to comprehensively identify the system in question. (Emphasis added.)
http://www.researchgate.net/publication/26409309_Irreducible_Complexity_Reduced_An_Integrated_Approach_to_the_Complexity_SpaceEric Anderson
May 4, 2014
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BA77:
. . . and when I pointed this work out to Darwinists, many die-hard evolutionists would deny that information even existed in a cell. If a Darwinists admitted information was in the cell, then he try to say information is generated using Claude Shannon’s broad definition of information. They did this since ‘non-functional’ information bits may be considered information in his broad definition of information.
You mean like the example discussed here: https://uncommondescent.com/chemistry/we-have-a-live-one-folks-information-redux/#comment-498779 :)Eric Anderson
May 4, 2014
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It is also interesting to note that much of the functional information in the genome is overlapping. At the 7:55 mark of the video, Trifonov makes reference of up to '13 codes' in the genome:
Second, third, fourth… genetic codes - One spectacular case of code crowding - Edward N. Trifonov - video https://vimeo.com/81930637
In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, "Reading only one message, one gets three more, practically GRATIS!". And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. Also of note, at the 10:30 minute mark of the preceding video, Dr. Trifonov states that the idea of Dawkins' selfish gene 'inflicted an immense damage to biological sciences', for over 30 years: In the following paper, it is mathematically demonstrated what is intuitively obvious. Namely, that the probability of finding overlapping functional sequences, by unguided processes, is vastly more improbable than finding that rare single functional sequence by unguided processes.
Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Montañez 1, Robert J. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 – published online May 2013 Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. We now know that DNA sequences are typically “ poly-functional” [38]. Trifanov previously had described at least 12 genetic codes that any given nucleotide can contribute to [39,40], and showed that a given base-pair can contribute to multiple overlapping codes simultaneously. The first evidence of overlapping protein-coding sequences in viruses caused quite a stir, but since then it has become recognized as typical. According to Kapronov et al., “it is not unusual that a single base-pair can be part of an intricate network of multiple isoforms of overlapping sense and antisense transcripts, the majority of which are unannotated” [41]. The ENCODE project [42] has confirmed that this phenomenon is ubiquitous in higher genomes, wherein a given DNA sequence routinely encodes multiple overlapping messages, meaning that a single nucleotide can contribute to two or more genetic codes. Most recently, Itzkovitz et al. analyzed protein coding regions of 700 species, and showed that virtually all forms of life have extensive overlapping information in their genomes [43]. http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0006
bornagain77
May 4, 2014
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gpuccio, I'm so glad to read this interesting OP you've written, as well as the follow-up comments it has provoked. Good job! Thanks.Dionisio
May 4, 2014
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