Uncommon Descent Serving The Intelligent Design Community

Functional information defined

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

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).

OLYMPUS DIGITAL CAMERA

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
Dr. Durston, has extended his work here:
(A Reply To PZ Myers) Estimating the Probability of Functional Biological Proteins? Kirk Durston , Ph.D. Biophysics - 2012 Excerpt (Page 4): The Probabilities Get Worse This measure of functional information (for the RecA protein) is good as a first pass estimate, but the situation is actually far worse for an evolutionary search. In the method described above and as noted in our paper, each site in an amino acid protein sequence is assumed to be independent of all other sites in the sequence. In reality, we know that this is not the case. There are numerous sites in the sequence that are mutually interdependent with other sites somewhere else in the sequence. A more recent paper shows how these interdependencies can be located within multiple sequence alignments.[6] These interdependencies greatly reduce the number of possible functional protein sequences by many orders of magnitude which, in turn, reduce the probabilities by many orders of magnitude as well. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search. http://powertochange.com/wp-content/uploads/2012/11/Devious-Distortions-Durston-or-Myers_.pdf
And Dr. Abel, Dr. Johnson and company, extended functional information to include prescriptive information here:
Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems - 2012 David J D’Onofrio1*, David L Abel2* and Donald E Johnson3 Excerpt: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine (A), cytosine (C), thymine (T) and guanine (G). This quaternary system is analogous to the base two binary scheme native to computational systems. As such, the polynucleotide sequence represents the lowest level of coded information expressed as a form of machine code. Since machine code (and/or micro code) is the lowest form of compiled computer programs, it represents the most primitive level of programming language.,,, An operational analysis of the ribosome has revealed that this molecular machine with all of its parts follows an order of operations to produce a protein product. This order of operations has been detailed in a step-by-step process that has been observed to be self-executable. The ribosome operation has been proposed to be algorithmic (Ralgorithm) because it has been shown to contain a step-by-step process flow allowing for decision control, iterative branching and halting capability. The R-algorithm contains logical structures of linear sequencing, branch and conditional control. All of these features at a minimum meet the definition of an algorithm and when combined with the data from the mRNA, satisfy the rule that Algorithm = data + control. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm.,,, The correlation between linguistic properties examined and implemented using Automata theory give us a formalistic tool to study the language and grammar of biological systems in a similar manner to how we study computational cybernetic systems. These examples define a dichotomy in the definition of Prescriptive Information. We therefore suggest that the term Prescriptive Information (PI) be subdivided into two categories: 1) Prescriptive data and 2) Prescribed (executing) algorithm. It is interesting to note that the CPU of an electronic computer is an instance of a prescriptive algorithm instantiated into an electronic circuit, whereas the software under execution is read and processed by the CPU to prescribe the program’s desired output. Both hardware and software are prescriptive. http://www.tbiomed.com/content/pdf/1742-4682-9-8.pdf
And then there is also non-local 'Quantum Information' in a cell of which classical information is found to be a subset:
Quantum Information/Entanglement In DNA - short video https://vimeo.com/92405752 Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm Quantum Entanglement and Information Quantum entanglement is a physical resource, like energy, associated with the peculiar nonclassical correlations that are possible between separated quantum systems. Entanglement can be measured, transformed, and purified. A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. The general study of the information-processing capabilities of quantum systems is the subject of quantum information theory. http://plato.stanford.edu/entries/qt-entangle/ Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html
It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure 'quantum form' is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement 'effect' in biology possibly be explained by a material (matter/energy) 'cause' when the quantum entanglement 'effect' falsified material particles as its own 'causation' in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the material particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various 'special' configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! Yet it is also very interesting to note, in Darwinism's inability to explain this 'transcendent quantum effect' adequately, that Theism has always postulated a transcendent component to man that is not constrained by time and space. i.e. Theism has always postulated a 'living soul' for man that lives past the death of the body. And then there is also 'photonic information' in the cell:
Are humans really beings of light? Excerpt: "We now know, today, that man is essentially a being of light.",,, "There are about 100,000 chemical reactions happening in every cell each second. The chemical reaction can only happen if the molecule which is reacting is excited by a photon... Once the photon has excited a reaction it returns to the field and is available for more reactions... We are swimming in an ocean of light." http://viewzone2.com/dna.html
etc.. etc.. etc...bornagain77
May 4, 2014
May
05
May
4
04
2014
06:48 PM
6
06
48
PM
PDT
What a long way this argument has come. I remember when, a few years back, I first ran across Dr. Durston's work on functional information,
Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak: Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define 'functional information,' I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions. http://www.pnas.org/content/104/suppl.1/8574.full Measuring the functional sequence complexity of proteins - Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors - 2007 Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable. The resulting measured unit, which we call Functional bit (Fit), is calculated from the sequence data jointly with the defined functionality variable. To demonstrate the relevance to functional bioinformatics, a method to measure functional sequence complexity was developed and applied to 35 protein families.,,, http://www.tbiomed.com/content/4/1/47 Mathematically Defining Functional Information In Molecular Biology - Kirk Durston - video https://vimeo.com/1775160
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. Yet, Shannon information completely fails to explain the type of information being dealt with in molecular biology:
Mutations, epigenetics and the question of information - Excerpt: By definition, a mutation in a gene results in a new allele. There is no question that mutation (defined as any change in the DNA sequence) can increase variety in a population. However, it is not obvious that this necessarily means there is an increase in genomic information.,, If one attempts to apply Shannon’s theory of information, then this can be viewed as an increase. However, Shannon’s theory was not developed to address biological information. It is entirely unsuitable for this since an increase of information by Shannon’s definition can easily be lethal. http://creation.com/mutations-epigenetics-information The Evolution-Lobby’s Useless Definition of Biological Information - Feb. 2010 Excerpt: By wrongly implying that Shannon information is the only “sense used by information theorists,” the NCSE avoids answering more difficult questions like how the information in biological systems becomes functional, or in its own words, “useful.”,,,Since biology is based upon functional information, Darwin-skeptics are interested in the far more important question of, Does neo-Darwinism explain how new functional biological information arises? http://www.evolutionnews.org/2010/02/the_evolutionlobbys_useless_de.html The GS (genetic selection) Principle – David L. Abel – 2009 Excerpt: Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes. Konopka’s work applies Shannon theory to known functional text. Kok et al. (71) also found that information does not increase in DNA with evolution. As with Konopka, this finding is in the context of the change in mere Shannon uncertainty. The latter is a far more forgiving definition of information than that required for prescriptive information (PI) (21, 22, 33, 72). It is all the more significant that mutations do not program increased PI. Prescriptive information either instructs or directly produces formal function. No increase in Shannon or Prescriptive information occurs in duplication. What the above papers show is that not even variation of the duplication produces new information, not even Shannon “information.” http://www.bioscience.org/fbs/getfile.php?FileName=/2009/v14/af/3426/3426.pdf Programming of Life - Information - Shannon, Functional & Prescriptive – video https://www.youtube.com/watch?v=h3s1BXfZ-3w Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors Excerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, http://www.tbiomed.com/content/2/1/29 Biological Information — What is It? - published online May 2013 - Werner Gitt 1*, Robert Compton 2 and Jorge Fernandez 3 http://www.worldscientific.com/doi/pdf/10.1142/9789814508728_0001
bornagain77
May 4, 2014
May
05
May
4
04
2014
06:47 PM
6
06
47
PM
PDT
Q:
Functional information seems like a subset of information. But what makes information functional? Or is all information functional?
All information is functional. So functional information is not a subset of information. I actually deleted some material I started to post earlier in which I asked what is non-functional information, lol! 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.Mung
May 4, 2014
May
05
May
4
04
2014
06:06 PM
6
06
06
PM
PDT
Querius:
Functional information seems like a subset of information.
Well, just to be fastidiously precise: Specified information is a subset of information. Functionally specified information is a subset of specified information. Digital functionally specified information is a subset of functionally specified information.gpuccio
May 4, 2014
May
05
May
4
04
2014
05:49 PM
5
05
49
PM
PDT
Querius: Everything can be functional, if we find a way to use it. The point is, some things can be used for very special functions. Machines are specially efficient to do things. Even simple tools can do things that natural objects cannot do. Efficiency at specific functions usually depends on specific forms. The more a form is specific, the more its functional information is high. In this sense, information just means some kind of form. In that sense, everything has information, but this is not a semiotic meaning of the word. Always in this sense, everything has some functional information, because everything has a form that can be used for something. But in most cases the functional information of natural objects is very low: many objects can perform the functions that are possible for those natural objects. It's like in my examples of the stone: a stone can be used to do many things, but all those things can be done by many stones. No really strict functional constraint is necessary. Instead, take a machine, like an engine. The things that an engine can do, you cannot do them with stones or other natural objects. You need a special configuration of matter, a configuration which is designed and does not occur naturally. With digital sequences, the reasoning is easier, because it is easier to compute the target space/search space ratio. As we already know (but I will debate it in detail in a future post) no random process in the whole universe can ever generate 500 bits of functional information in a sequence. Probably, not even much less.gpuccio
May 4, 2014
May
05
May
4
04
2014
05:44 PM
5
05
44
PM
PDT
Mung: It's a good idea. I will see what I can do. :) I perform a lot of medical data analysis with R, which is open source and can be used by anyone. At first it is not very user-friendly, but it is a wonderful software, with packages which allow almost anything, and it is completely free. I find very useful to use it by a graphical interface, which in the beginning simplifies the work very much (I would recommend R Commander). My interest for biological databases and procedures of bioinformatics is mainly motivated by my involvement in ID, even if I must say that being a medical doctor certainly helps. The resources are freely available on the Internet (for example, UNIPROT, BLASTP at nlm, SCOP, PDB). OK, I hope I can post something more detailed in the future.gpuccio
May 4, 2014
May
05
May
4
04
2014
05:34 PM
5
05
34
PM
PDT
So far, so good. Functional information seems like a subset of information. But what makes information functional? Or is all information functional? Just asking. -QQuerius
May 4, 2014
May
05
May
4
04
2014
05:31 PM
5
05
31
PM
PDT
Hi gpuccio, When you can find the time I'd love to see you create some OPs on basic bioinformatics research: What are the tools and databases you use? What information can be derived from them? How does that assist in the argument for intelligent design? Nothing necessarily expansive or detailed, perhaps spread them out over several OPs. Basically looking for introductory level material so that readers (myself included) can perform the same research and obtain the same results. You know, science! ;) Also, how to do statistical analysis. I've seen you reference the R language. What do you use it for, and how? Where can we find your source code? Do you have an account on GitHub? Thanks!Mung
May 4, 2014
May
05
May
4
04
2014
05:24 PM
5
05
24
PM
PDT
1 8 9 10

Leave a Reply