How can you define it? 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: 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. The purpose of this distinction should be clear, but I will state it explicitly just the same: Objective functionalities, instead, are properties of material objects. But we need a conscious observer to connect an objective functionality to a consciously defined function. 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. This is a conscious representation in the observer, connecting a specific stone to the desired result. First of all, being a stone. If it is too big, or too small, or with the wrong form, etc.

And we count the good stones. It is expressed in bits, because we take -log2 of the number. What does that mean? It means that one stone out of 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. It is a special form of specification in the sense defined abovewhere the rule that specifies is of the following type: It should be clear that functional specification is a definite subset of specification.

But for our purposes we will stick to functional specification, as defined here. We could call it any other way. What I mean is exactly what I have defined, and nothing more. FSI is a continuous numerical value, different for each function and system. We compute different values of FSI for many different functions which can be conceived for the objects in that system. 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.

In that case, we say that the function implicates FSCI in that systemand if an object observed in that system implements that function we say that the object exhibits FSCI. So, FSI is a subset of SI, and dFSI is a subset of FSI. 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.

I have used the word for a specific definition, with no general implications at all. 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: 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.

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. Also, how to do statistical analysis. What do you use it for, and how? Functional information seems like a subset of information.

But what makes information functional? Or is all information functional? 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. 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: 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. 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 bits of functional information in a sequence. Probably, not even much less.

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. What a long way this argument has come. I remember when, a few years back, I first ran across Dr.

Carothers, and Jack W. Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. For a given system and function, x e. 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. Measuring the functional sequence complexity of proteins — Kirk K Durston, David KY Chiu, David L Abel and Jack T Trevors — Excerpt: We have extended Shannon uncertainty by incorporating the data variable with a functionality variable.

The resulting measured unit, which we call Functional bit Fitis 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.

Mathematically Defining Functional Information In Molecular Biology — Kirk Durston — video https: 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. The GS genetic selection Principle — David L. Abel — Excerpt: Konopka also found Shannon complexity not to be a suitable indicator of evolutionary progress over a wide range of evolving genes.

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, 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. Three subsets of sequence complexity and their relevance to biopolymeric information — Abel, Trevors Excerpt: Three qualitative kinds of sequence complexity exist: 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.

Biological Information — What is It? A Reply To PZ Myers Estimating the Probability of Functional Biological Proteins? Kirk DurstonPh. Biophysics — 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. In other words, the numbers we obtained for RecA above are exceedingly generous; the actual situation is far worse for an evolutionary search.

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: The DNA polynucleotide molecule consists of a linear sequence of nucleotides, each representing a biological placeholder of adenine Acytosine Cthymine 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. 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. Remembering that mere constraints cannot serve as bona fide formal controls, we therefore conclude that the ribosome is a physical instantiation of an algorithm. 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: Both hardware and software are prescriptive.

Quantum knowledge cools computers: New understanding of entropy — June Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory zero entropydeletion of the data requires in theory no energy at all. This is the physical meaning of negative entropy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state.

If you go any further, you will break it. 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. 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: 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 environmentthen 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.

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! 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! Are humans really beings of light? 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.

It is also interesting to note that much of the functional information in the genome is overlapping. Second, third, fourth… genetic codes — One spectacular case of code crowding — Edward N. Trifonov — video https: 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 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 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. Marks II 2, Jorge Fernandez 3 and John C. Sanford 4 — published online May Excerpt: In the last decade, we have discovered still another aspect of the multi- dimensional genome. 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. 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. 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 herethe hierarchy you outlined involving specification and function reminded me of something I wrote a while back.

Suggestions that certain complex systems are not irreducibly complex often arise from a failure to comprehensively identify the system in question.

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, PMC, Nanda and Koder write on the design of artificial enzymes. Today, a Boeing is an incredibly complex machine with over 6, 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.

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: 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! Otherwise, no inference would be necessary. Therefore, we look at configurations of matter, IOWs at forms, and we wonder: 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. But functionalityas 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. 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. Having discussed for years with our kind or less kind interlocutors, as you have done, I know them all. 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.

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.

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. Molecular Biophysics — Information theory. Relation between information and entropy: Linschitz gave the figure 9. Thus two quite different approaches give rather concordant figures. Information and Thermodynamics in Living Systems — Andy C. McIntosh — May 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.

I had not an iota of doubt. I was filled with indescribable joy. Slowly there was less fear and more joy. 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: 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. Thanks for the interesting and informative post.

The point that I do not feel comfortable is defining the function AFTER observing the function itself. In Darwinian sense though I disagreefunction is not defined beforehand, so the function, itself, is a random variable. 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.

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. This thread is very juicy. 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. That means that all my reasoning is referred here to a well defined search space, not to a generic search space. So, my definitions are referred to a known search space and a known target space: 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.

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. Now, just consider that almost 4 billion years of evolution, whatever the causal mechanism, have found about 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.

We have to sum the target spaces, while the search space remains the same. So, the probability of finding one of the useful proteins has changed of only two orders of magnitude, and it is now 1e Not a great problem, for the design inference. 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.

I get by chance the number 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: That is a correct function definition, but it is not complex: That is perfectly correct. 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. Wow, this discussion is getting really substantial. Even if humanity had never discovered Pi before, and someone produced the first digits of Pi on a Roulette wheel, that would still be a very special event whether we realized it or notbecause of the pre-existing specialness of Pi. The fact is, nobody believes this would ever happen with the probabilistic resources at hand.

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? 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. If you see question marks before 2, 3 and 5 in my post — they were meant to be square root signs.

There are many special numbers, but you will never get the first, say, 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.

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. 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 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?

But how is even remotely relevant to the discussion of function in biology? What makes a particular sequence special before you know what it does? Is the following base-long sequence special or not, and how on earth do you know?

If you have a random generator of character sequences, how many do you think the probabilities are, in one attempt, of generating:. While certainly a is lower than b not muchand b is lower than c muchand c is lower than d very muchwould you bet on d? Even if you had a lot of attempts? 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. I never said that we can always recognize the function. If a sequence of nucleotides is a protein coding sequence, the protein can be built and tested.

It does not depend on us. Apart from being translatable it can also produce RNA, or play some other role a binding site, an enhancer, whatever. How do you define your target space?

I agree with this definition. Here, I object to Piotr who said Is the following 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. I see your point, and I agree with you to a large extent. 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. 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.

First of all, not all nucleotide sequences can be interpreted as protein coding. 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: 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. Managed forex funds australia search space is too big.

We will never be able to do that. Indeed, the whole universe cannot do that. What do we want to know? First of all, it is useful to start from the observed functional protein an enzyme, for exampleand 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. 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: 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 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 binary options prediction, the beta subunit of ATP synthase, where 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:. I realize you have stated that functional specification is a subset of specification.

That is fine as far as it goes. But if we then go on to better articulate the details, the function emerges, almost by definition. This kind of quote scottrade stock happens in engineering situations all the time.

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. So what you really want to do is Y. At this point they call it Z. 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. One is specified and the other is more specified. Please note I am not at this point disputing your approach, nor am I necessarily suggesting that it needs to be changed.

This is virtually the identical issue I was critiquing Bill Dembski about in his essay on irreducible complexity. It is just a question of whether we have properly and adequately download forex robot tfot the work of laying out the specification. OK, I agree with your comments, but remember: As I said, the existence of a complex cellular environment limits extremely the number of useful new solutions in that environment.

IOWs, you need not only write a new software procedure, but you also have to make one which may be useful in Windows 8, and compatible with the existing code! I have been thinking about this example, but I could not remember where I read it. Starting from the last paragraph on page and throughthe author tells a story attributing to Feynman. Though I, now, agree that the way you define functionality is unlike the case mentioned here before vs.

Probably, I have been too quick about the problem of specification, just to avoid being too how to make money easy for teenagers in the OP.

IOWs, a specification is any well defined rule which generates a information asymmetry stock market partition in a well defined set of objects. Now, there are many possible ways to generate a binary partition in a set of objects. Defining a function for those objects something for which they can be used is only one way.

For example, we could generate a partition by dividing sequences in compressible ordered and non compressible. I believe that Dembski sometimes uses this concept. But being compressible is not a function, but another kind of property. With Piotr, I have made an example based on meaning, and I have introduced a distinction between descriptive information meaning and prescriptive information function. I take that distinction from Abel, and I find it very useful. There is a subtle difference between meaning and function, even if they are strictly linked, and even if both can be used to specify.

But if the machine is working, a definite result happens in the outer world, even if nobody is there to understand and recognize it.

Functional information defined | Uncommon Descent

A working machine works. It needs not a conscious being to work, even if a conscious being was necessary to build it.

We can just see the results. I mean that functional specification is specification by a function, while meaning based specification is a specification based earn free nexon cash error code 51 meaning, and could be good for language.

And specification by compressibility can be good to separate ordered sequences from non ordered sequences. But in all cases, the specification must be clear, detailed ad objective. Otherwise, no reasoning can be done. Being involved in statistical analysis all the time, I am well aware of the problem of overfitting. It is certainly a serious problem, and one often not considered enough, especially in medical literature. Here, we are not modeling some result by many variables, so that random noise in those variables can be considered as a true effect if we use a dubious threshold for significance.

Here, we are just rejecting the null hypothesis that random noise can generate a very powerful, objective effect that we really observe, and we reject that hypothesis because its improbability is amazing, tens and hundreds of magnitude beyond any conventional threshold. When you get p how to borrow money from pawn shop of the order of 1e or 1e, overfitting is certainly not your major concern.

And the effect of functionality in an enzyme is not certainly a false effect, generated by random noise. The effect is there, as big as the sun. Thousand of functional proteins are not a false effect. If the appearance of design were a false effect of random noise, it would not appears in different and isolated systems. Functional information is certainly not the result of overfitting in our analysis.

Those are the only two games in town. Information asymmetry stock market of them must be true. It is the probability of obtaining the current data given rs trade counter stock check null hypothesis is correct.

The correct definition of p in hypothesis testing is the first thing I try to explain to young medical doctors as soon as I can. It is perfectly true that the number of medical doctors who correctly understands that definition is… no, I will not say it!

The use of statistic in medicine is often embarrassing, sometimes shameful. But commodity trading zero sum game is possible to use it well.

And many times it is used well, even in medicine. However, all that has nothing to do with our design inferences, which are a good example of a good use of statistics. On the distinction between Specification S and Functional Specification FS as per Eric Anderson at 38 and gpuccio at Emphasize for us what would be common between the two and what would be the specific difference between the two.

Can be argued as Eric did that the difference between 1 and 2 is more a matter of degree rather than one of substance? Pragmatic value provide specific approaches and formulas to compute FSI, FSCI, dFSCI, etc. And for the good questions, which allow the stock market collapses on october 29 1929 better clarification of aspects which I have not detailed enough.

As functional specifications are a subset of S, FS is included in S. But, if how do members make money on runescape want some specification in S which is not in FS, then you have to use some rule which is not related to a function to generate the partition.

Your example for 1 is not an example of S specification which is not an FS specification. It is an example of incomplete FS specification.

The difference between S non FS and FS is in how much money does an architect make an hour type of rule, not in the completeness of the definition of the rule. That rule generates a binary partition, but is not related to a function. Although we could define a function for a spherical stone, the specification by a geometrical form in itself makes no reference to a function, or to a how to make money on silkroad use of that form.

I believe that FS is more useful than generic specification for design inference in biology for two reasons:. Meaning is the other fundamental conscious experience, and it is equally good to detect design, but it is more appropriate for objects with descriptive information language. Function is the natural specification for software and biological molecules. Instead, specification based on compressibility, while valid, is less useful in our contexts as a design detection tool.

Compressibility can be connected to conscious experiences, but the link is less obvious. Moreover, order and compressibility have another hindrance: This is an aspect I have not yet discussed in this thread, but it is obviously part of the design detection procedure excluding necessity.

Being naturally humble, I hope my essay has significant value for all three of them. It seems that I had an indirect contribution while sleeping: Very briefly, I should say that I agree with gpuccio on the use of P-values in the scenario related with proteins.

However, I emphasize the importance of uniqueness once again, and I slightly disagree with gpuccio who says that this has nothing to do with design inference. Say that we have a maze, in which we put a rat. Rat may choose left L or right R directions. How can we test the hypothesis that the movements choosing L or R of the rat is random or not?

One way is to assume say that Ho: The thing is as the sequence gets larger larger, P-value will get smaller, so we reject the randomly moving rat hypothesis. So, are we justifed in performing the test in the above presented manner? My answer is a reserved no. The rat stock market prediction for the week of course choose a L-R pattern, and the specific chosen path would be a highly unlikely choice as the sequence gets larger.

However, there are two reservations:. If we can how to apply sph reit ipo or assume that this is cme futures trading strategy ONLY path that leads to the exit, then this is a special path.

I think gpuccio would call and I agree this path a functional path. In this case, we MAY be justifed in this hypothesis test. When it comes proteins-life case, this path may correspond to folded proteins, I think.

Life is not only a transformation of 2-d coding to function, in this ncb bank saudi arabia exchange rate to india Darwinists would be more justified in their views.

We cannot because folding at least under some conditions is a MUST. So the paths which lead to life as we know up this day consists of finite number of functional entities. This is why I insist jquery select option set selected index the uniqueness of paths leading to life.

Otherwise, the hypothesis test presented above would not work, in my opinion. The other is more controversial and maybe irrelevant to the current topic, but may be relevant to the general ID-Darwinism controversy.

However, mouse makes a couple of wrong turns, does LRLLLRLRR an additional LR added but finds the exit at the end. Can we still use the above hypothesis test? Not directly, but in the following way we may, I guess. We may consider all the paths which do not lead to the exit and which lead to exit making with some wrong turns in between, and then see where the current observation lies.

For a low P-value, we would say that this is not random. So, why do I call this controversial? Unfortunately, life is not a single exit as presented here. Say, there are cheese pieces along buy shares in charlton athletic way to the exit, so the immediate aim of the mouse may not be to get out of the maze but first eat these cheese pieces, then get out.

So it may unnecessarily from the point of view of a person who thinks exiting the maze is the first aim visit many additonal paths. This is a mistake many Darwinists make, I think. They assume that they know the mind of God who they do not believeand say that if this were a guided process, this and that would not have happened, which is actually a bad hypothesis test, in my opinion. I am not sure I understand what you mean here. Why would the p value get smaller? How are you getting a p value here?

What is the H0 hypothesis? If there are only a few sequences that reach the exit, and the rat easily finds the exit, then we can reject the Hypothesis that it is moving randomly if that is our null hypothesis. We still have to try to explain how the rat found the exit route: IOWs, rejecting the null hypothesis does not automatically support an alternative hypothesis.

That is another methodological problem which is often misunderstood. IOPWs, rejecting that null hypothesis just means rejecting that the rat is moving randomly, but does not explain automatically how it finds the route. Therefore, if the way is long enough, we can safely reject the null hypothesis of a random movement.

Rejecting the null hypothesis does not make sense. But is there are nodes, and still the rat finds the exit in one attempt, the probability of that is about 1e If still moneymaker strain review rat finds the exit, I would definitely reject the null hypothesis. The rat is not moving randomly. The scenario is similar to the problem of protein function.

Overfitting has nothing to do with this situation. Observing the result after it has happened has no relevance. Finding the exit is a well defined special result, and nothing changes if we define it before or after it happens.

What other special result could the poor rat get? General considerations on life have no relevance too. Finding a AAs long proteins which is an enzyme, and accelerates a reaction which in nature is extremely difficult and slow, or just would not happen, is like finding the exit with hundreds of nodes.

It will never happen by chance. The null hypothesis northwestern mutual stock market chance can very safely be rejected.

For what it is worth, the concept of dFSCI has always been very clear to me and IMHO it is the most productive version of the specified complexity argument. Meaning, if we loosely and vaguely define our specification then it might not be specific enough to clearly articulate the function.

That is precisely the distinction that dFSCI is trying to make and that is why it will be the most productive approach in demonstrating the implausability of what the non-design proponents are trying to say…. By leaving the observer completely free to define any function he likes, we are no more interested in how many different functions can be found.

One single function which is also complex will be enough for the design inference. If there are ONLY A FEW sequences that reach the exit, then we reject the null hypothesis that rat is moving randomly.

However, the way a Darwinist thinks is different from a person who sees the universe in teleological perspective. As a molecular biology analogy, they may have a point on the other hand, for a real life engineering situation this thinking is stp forex brokers list stupidity.

It is humans that give a special meaning to all heads case, how to understand stock market philippines this is not something randomly occurring in our daily lives.

Now, you may say that what if this specific sequence is functional objective function. Say that we toss a dice times and the resulting sequence somehow creates a key and this key opens a door. Still no, unless we know that tossing other sequences will not open a door. We have but one advantage over Darwinism, biology tells us that most of the other sequences will not open a door, and will not have a function.

However, we have a another problem. A Darwinist may argue that those doors are not aligned side by side, but they are one in another. So other doors call it A1, A2. And if you happen to open another door maltese puppies for sale uk kent it B in the first instance, different doors B1, B2. In summary, objective functions have not been clearly defined previously how can it be for a random process?

I think it was Stephen Gould who said something like it is only due to chance that humans instead of dolphins, or other creatures rule the earth this might be an awful quotation but I cannot find the exact words right nowwhich shows that the path and existing status of sequences and functions could have been different. If this is the case or dominating view in sciencethen I do not think we are justified in the hypothesis test we are arguing above. On the other hand, you already suggested a solution here.

Now, we see that fold is a preexisting entity in Platonic sensewhich depends only on the fundamental laws of nature. Though function itself is like a fluid, whose existence depends on the existence of other functions and may change again from a Darwinist perspective fold is not.

This means in my opinion: It may not currently have any function in the whole nature. Or in an alternative path that could have been taken by evolution, it would have a function.

So a random non-functional sequence would be functional in an alternative evolution history. I think I have written too much, and I may have bored people if anyone bothered to read up to this pointso I stop here and not say anymore for this discussion.

One last unscientific point: I find the existence of high low indicator forex protein fold a miracle; the connection between a protein and its function another miracle.

An apparently unlikely result may have a mundane explanation. Regarding folding, in SCOP 2. While foldings is the fundamental grouping, superfamilies are still a completely sequence isolated grouping, based mostly on structure and function. Foldings would be good too, and probably also kumpulan indikator forex mt4, although between families you could sometimes find some possible vague evolutionary connection.

There is no absolute connection between the length of a sequence and a p value. A p value must be referred to some definite result, for which we can build H0 and some alternative hypothesis. So, if we have a bit sequence, there is no p value about it in itself.

It is just a sequence that we can get randomly. The probability of getting a generic bit sequence by random events each generating 1 bit is 1. But, if we have a digit sequence and we ask for the probability of generating that sequnce after we have defined it, it is 1: This is an example of pre-specification.

The sequence has nothing peculiar, but it becomes peculiar becuase we know it in advance. And if we ask the probability of getting a sequence of 1s or 0s, the probability is 2: The peculiarity is there anyway. The concept of corporation tax deduction unapproved share options is specially apt to be binary option methods standards and work design bullet tool to detect design, because it is obviously connected to one of the two fundamental experiences of conscious beings: Singapore airline stock market due to order is often but not always generate by algorithms.

That is not true of complexity due to function prescriptive information or to meaning descriptive information. Those types of complexity are scarcely compressible, and cannot be generated by simple algorithms. I have not dealt with this part in detail, in this thread, but it is an important part. It includes explaining why protein sequences can never be generated by NS acting on RV. I must have forgotten to add the emphasis lancashire grid for learning maths targets the first quote.

It was meant for the following paragraph:. A sonnet written on a piece of paper presumably has a function. We might say its function is to express an idea or sentiment or thought. Its function might be to convey information. For example, this sentence has a function. Quote true that highly repetitive sequences do not allow us to infer design, in and of themselves.

They are terrible examples of how to infer design, except in very limited cases. Particularly when we see sequences that are functional, meaningful, that have independent specification apart from the odds of generating the sequence itself.

The repetitive sequence fails the design filter because it is not complex. Any old random sequence fails the design filter because it is not specified. Both aspects are required. Scientifically, there is no alternative to describe the mechanics of the event except in a traditionally materialist sense. On the other hand, if coins appeared out of thin air in a carefully controlled and observed environmentthen an alternative scientific explanation like a quantum anomaly on a macro-scale would be wildly speculative and ultimately unsatisfactory.

As I have tried to argue, all three can be valid specifications, but it is useful to understand their differences:.

So, specification by order needs special attention to exclude any known algorithmic cause. As Piotr has correctly stated, a heads sequence can well be the result of an unfair coin. Moreover, biological molecules are machines: If and when we find sonnets in DNA, obviously, my statements could be falsified. But I believe that a more specific terminology can only help. But the point is exactly that: Please, read again my statement about gas molecules.

Ordered states all the molecules in half the space of the container are in no way more unlikely than each individual state where the molecules are dispersed quite equally in all the space of the container.

But the number of states of the second type is infinitely more numerous than the number of ordered states. You are right that heads could be the result of an unfair coin. Ordered states can be the result of necessity. But, if we are sure that the coin is fair, and that the system is truly random, then we will never see heads.

Realistically, heads warrant one and only one explanation: Probably, it is designed for fraud. Or it is simply not random because it was designed to be random, but by a bad designer. You see, design is always there in some way! Nobody would ever believe that the result is really sheer luck not even darwinists: Constrained sequences are no good for forex cuanto es un lote. But they can never be generated by simple algorithms which is the distinguishing feature of ordered sequences.

Otherwise, by the same token, we should never see any of the following:. And yet we shall see one of them if we flip the coin times. False negative type one. False negative type two. I forex peso to canadian dollar no idea if the nucleotide sequence you offered has any function.

And at present I have no means and no desire to find out. So, I will not infer design for it. I am not sure I understand what you are saying here. Could you please explain better what kind of specified sequence we will see flipping the coin?

A unique sequence, not a class of sequences. Nobody can tell that in the general case, anyway, even if they think they can. Yes design is there, but so too a materialist explanation of the physical processes. And BTW, many of them pivot on the difference between recessions and stagflations with creative destruction at work. I have had to be brushing off some economics. And some thermodynamics [for Geothermal energy development — looks like so far 2 MW potential identified here], a bit of mechanical analogue computing [fascinating subject, led me to glance at gunnery at Jutland and Dreyer vs Argo.

As in AutoCAD etc. If deep enough, a solar system or observed cosmos scope blind search is maximally implausible as a good explanation compared with design.

Though it seems WmAD used it waaaaay back. That stretches the space to organic chem structures, leading to functionally co-ordinated clusters. Do we understand the gamut of the space of chemical possibilities, the energetics and where it points? Again, local isolation is a killer. The seas of non-function are vastly beyond. If superposed on our galactic neighbourhood, such would turn up as straw with all but certainty, on the standard results for blind, random samples.

If I came across a line of ordinary coins, all H, I would for good reason tied to the relative statistical weights of the all 1 state vs the dominant cluster of near in no particular order, I fortis stock buy or sell with empirical certainty conclude design.

And for excellent reason. The cases relevant to design put this toy case — only 3. And BTW if a maze required turns in a specific and singular pattern, a figure chartiste forex that ran it with all but certainty is not doing so by blind trial and error.

I would suspect a scent trail.

In any sequence consisting of two symbols there only two possible in which all H or all T appear. Assuming each symbol is equi-probable, as the length of the sequence increases the probability of the sequence being all H or all T decreases. Take two huge sided die, each face of equal dimensions. Inscribe each face with a number from 1 through Tossing each die individuallytimes how rupert murdoch makes money to indicate that no number is more likely to appear than any other.

Mung, Binomial, sharp peak near evens. Hate to say it but the chemist did a better job than all the physicists! A state nearno particular order has vastly more statistical weight than all-H and is vastly more likely. The valid form of law of averages. I have a link here somewhere to that Nash text. I shall have to shell out the dollars! Nothing that would cause us to pause and question its origin?

Nothing that would give us reason to think that something else might be in play besides pure random draw? Each single one of them is unique. Humans see them as special because we are particularly good at detecting patterns and regularities in our anvironment.

What do you mean? When we compute a probability of one event, the first thing where can i buy juzo compression stockings must do is defining well the event. There is no difference if the event is one sequence or a class of sequences. You cannot use this post-hoc. KF and Mung have given excellent explanations of how we reuters exchange rates south africa generalize to well defined levels of order.

Indeed, it is extremely likely that some of that will be there. As you certainly know. But, for each well defined class of events, we can compute a probability and a binomial probability distribution success — non success for repeated attempts.

The simple fact is, for very large search spaces, you will never get peculiar sequences that belong to extremely unlikely classes. You will always get non peculiar sequences, which become peculiar only if you pre-specify them by giving explicitly, bit by bit, all or great part of the information in the sequence see a. IOWs, for large search spaces you never get ordered, largely compressible results by chance. You can obviously get them by necessity, but I have already discussed that.

I suggest that you carefully consider the interventions of KF and Mung in the previous few posts. I think we have to start form that, for further discussion on this point. Work has its priorities, like sleep…. Thank you for your excellent intervention, in spite of all your other duties. I really appreciate it. Very good thoughts, and very useful in the specific context is your post designed? For a H sequence, there never will be, empirically, a false positive.

It will always be explained by some necessity or design explanation. Well, if we can safely exclude algorithmic explanations, they do demonstrate design. I agree that, for regular patterns, it is more difficult to exclude algorithmic explanations. But that is very easy when meaning and function, rather than order, are the specifying rule. But that does not mean that the functionality for being detected as a pattern or as a meaning, or as a function is not objectively in the object see my initial distinction in the OP: I knew it would come useful sooner or later!

Popped back by, thanks. Though there is none so blind as one who will not see. You may need to note you use a comma for the decimal marker. Us anglophones use a dot, perhaps raised. My HP 50 gives the choice of course. Mapou, yes, transfinite nos — infinities — are all over modern math, and you may want to look at the recent rise of nonstandard analysis which builds on and regularises ideas in Newton etc regarding calculus foundations.

I think it is more intuitive than the limits formulation, and just as rigorous now. What we cannot do is instantiate a transfinite, step by step, e. I usually try to remember, but it is easy to err. We use the comma as decimal marker, and the dot as thousands separator! And the explanatory filter takes care of regular patterns in nature. Specify the sequence before hand and then flip a coin to match it. Tell us how long it takes you. Before I tackle your reply to 66, let me add a small comment to my post 90 by way of introduction.

This is true of a physical coin flipped in the usual way. You have to know its context. Any sequence specified beforehand any exact prediction of the throws is equally unlikely.

Lotto players practically never bet on sequences like 1, 2, 3, 4, 5, 6 ; they go to great pains to make the bet as random-looking as possible, e. Remember, the specification must generate a binary partition in the search space. What are we speaking of? Mutations in existing genomes? A good understanding of the system is fundamental to evaluate what algorithmic mechanisms may be included in its starting state.

Foe example, if we are evaluating OOL, reproducing beings are not a part of the initial system. But if we are explaning evolution of species after OOL, we can consider reproduction as an already existing algorithm, and accept it as part of the starting condition of the system. The system starts at time 0, and we analyze the events that can happen or happen in the system from time 0 to time t. That is important to evaluate the probabilistic resources of the system. They depend on the time span and the number of states tested in the system per unit of time.

They represent the number of different states number of attempts that the system can reach in the time span, and for a random system with a uniform probability distribution of the states, they are important to establish the threshold of complexity in order to reject the null hypothesis if a random origin of what we observe.

All these components are fundamental parts of the reasoning. Some of them were not introduced in the OP because the purpose of the OP was limited to the definition of functional information, and it did not deal with the whole procedure of design inference.

OK, any specification which specifies a single sequence generates the same partition, and has the same probability. OK, we know where we stand. Sorry, but I again have other things to do. Not with respect to flipping coins. If it were regukar then it would occur quite often. Yet it never does. It is certainly debatable whether we are simply imposing meaning or whether it objectively exists.

BTW, gpuccio has already addressed the false positives issue. That is a large part of the reason for the explanatory filter, to eliminate false positives. They are interesting, but they are not really pertinent for the empirical reasoning that I want to pursue. Now, everything has form, but probably the most common use of the word is to mean that we give form to something, or transmit a form, and idea.

In that sense, information is a message between conscious beings, and its transmission happens by giving a form to some material object the vehicle of information. In that strict sense, all information is designed. Shannon is interested essentially in the signal — noise relationship, but he does not deal with the nature of the signal IOWs with what is meaning or function. That is a fundamental achievement, and the scientific world will have to acknowledge that simple fact, sooner or later.

May I throw something on the pile? In this process, information is the contingent and incomplete abstraction being represented, but in common conversation we refer to the material representation itself as the information.

As the only observable manifestation that information, this common usage of the term is entirely natural. Piotr is talking about coming across the pattern of H in a row and what we might initially presume.

Namely, that it was the result of a law-like process, such as an unfair coin. He is exactly right, that this would be the first and correct place to start. Joe is talking about the pattern of H and what we might suspect, after we have eliminated the possibility of a law-like process; in other words, after having confirmed the coin is fair, has been fairly flipped, etc.

Then, at that stage of the game, Joe is right that we would be suspicious and would not likely ascribe the event to chance. They are talking past each other because they are focusing on different time slices of the explanatory filter. Incidentally, this is part of the reason a highly repetitive pattern like H in a rowis a poor example for design detection. I wish Sal had never brought it up or got people thinking along those lines. It would be much less confusing to use an example that is not readily amenable to explanation from a law-like process.

Rather than H in a row, it would be more helpful to think of examples like the coins being flipped to form a binary representation of the digits of pi or the first verse of a Shakespearean sonnet, or the first prime numbers in order, etc. May the perpetrator who first unleashed that confounded term on the unsuspecting world be tormented by their conscience for eternity.

I absolutely agree, even if Sal has all the reason to insist on the heads: I suspect that many prefer order because they want to avoid dealing with the concepts of meaning and function. Seriously, there is an important advantage in dealing with meaning and especially function for the specification.

They have the formal properties of a random sequence to a certain pointbut they are designed. Their functional value in no way can be generated algorithmically, because it implies understanding, complex links with different contexts, you name it. And even if we could, the algorithm would be infinitely more complex than the final sequence. Not once, but again and again, and again and again and again. In particular, it will contain every sonnet by Shakespeare encoded in UTF Can objects, even if nothing is known about how they aroseexhibit features that reliably signal the action of an intelligent cause?

But what about things nobody has ever seen being designed, and so their design has to be inferred? The examination of the object itself does not yield reliable conclusions. For example, a relatively simple nondeterministic algorithm can easily produce something that superficially imitates a real language: Biniba boncianla den diani yali n den tieni tisiga ni.

Bin den diani ke li ta yemma leni yabi n den la leni binuni hali micilima n den wani ti mama gi go twa tipo bimawanggikaba. Seeing that on a cave wall I would immediately infer some agency put it there and it was not the result of necessity and chance.

The explanatory filter would flow very fast- almost suddenly. That is why context matters in the case pf heads in a row. That is not a regular pattern, in that context. To me Piotr was saying that heads in a row is regular because it is repetitive.

Taken in context, highly repetitive patterns are not regular. The question is not whether every sequence has the same statistical probability of arising through random means, though some would like to assert that this is a key issue.

You use the explanatory filter every day, as does everyone else, whether they know it or not. And we do not need to know beforehand where the artifact came from. Yes, we need to recognize it as an artifact. In certain cases we might even need to know something basic about its function in order to decide the artifact is something worth studying. The explanatory filter is not primarily geared toward identifying whether something is an artifact worth studying.

It is not even in the business of determining function. The explanatory filter is geared toward inferring the most likely origin of the artifact. He focuses, rightly, on the question of origin. Then you conflated that question with questions about whether we are dealing with an artifact in the first place or whether we know what function it plays. Piotr- your comment in 66 is moot.

We observe DNA in living organisms. We observe it being replicated. We observe it being transcribed. We observe mRNA get processed, edited and spliced. We observe functionality, that is structures doing work, ie providing a function. Spontaneous generation of DNA appears to be a no go. The Information in Life. Shannon Information — Channel Capacity — Perry Marshall — http: And the genetic code, despite its inability to evolve once it is in place, is found to be optimal:. Biophysicist Hubert Yockey determined that natural selection would have to explore 1.

The maximum amount of time available for it to originate is 6. Put simply, natural selection lacks the time necessary to find the optimal universal genetic code we find in nature. When the researchers calculated the error-minimization capacity of the one million randomly generated genetic codes, they discovered that the error-minimization values formed a distribution. All of these codes fall within the error-minimization distribution.

Dawkins on the Tree of Life — and Another Dawkins Whopper — March Excerpt: Any mutation in the genetic code itself as opposed to mutations in the genes that it encodes would have an instantly catastrophic effect, not just in one place but throughout the whole organism.

If any word in the word dictionary changed its meaning, so that it came to specify a different amino acid, just about every protein in the body would instantaneously change, probably in many places along its length. Unlike an ordinary mutation…this would spell disaster. By any measure, Dawkins is off by an order of magnitude, times a factor of two.

Examples include protein address codes [Ber08B], acetylation codes [Kni06], RNA codes [Fai07], metabolic codes [Bru07], cytoskeleton codes [Gim08], histone codes [Jen01], and alternative splicing codes [Bar10]. Johnson — Programming of Life — pg. Evolution by Splicing — Comparing gene transcripts from different species reveals surprising splicing diversity.

On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. Deciphering the splicing code — May Excerpt: The code determines new classes of splicing patterns, identifies distinct regulatory programs in different tissues, and identifies mutation-verified regulatory sequences.

Second Genetic Code Revealed — May Excerpt: The paper is a triumph of information science that sounds reminiscent of the days of the World War II codebreakers. Their methods included algebra, geometry, probability theory, vector calculus, information theory, code optimization, and other advanced methods. One thing they had no need of was evolutionary theory,, http: A non-functional DNA sequence is hardly distinguishable from a functional one. A single point-mutation may disable a gene and turn it into junk, though the rest of the sequence looks exactly like it did before.

DNA may yield a functional product — an RNA or a protein that actually does something useful in terms of reproductive success. It may also yield a useless product e. Just sit back and contemplate the design. The alternative is to inquire how it really evolved. This thread is about clarifying the concept of functional information.

The current sub-topic on the table is how a given sequence can bear an observable and reliable inference to design. In commentyour questions and challenge deal with the issues of functionality and sequence structure. My response presents the actual representations in question which effectively subsumes both of your questions, and renders them moot. How do your justifications square with the experience of the first person to chance upon a crop circle?

Was he wrong to infer design even though no one informed him as to how it arose and he had no idea what its function was? I have never said that. The context is important for the design inference, not to define a function for the object.

It should be clear from all that I have said here that an observer can define any function for the object he observes, and the context in which the object arose is not necessary for that.

Probably, what you mean is that sometimes observing the object in its environment can help to recognize a possible function for it. If I study a protein in its cellular context, I can have indications of what it does. I could probably understand what it does even by a patient research in the lab, but direct experiment on a cellular environment can often be a more direct way.

That is not true. In my simple example of the beach, I have no need to know anything of the context to understand that I can use certain stones to chop food. And even with proteins or protein genes, there are many ways to understand the function. If I find an english sonnet on a sheet of paper, the only thing I need to understand its meaning is that I understand english. As our understanding of the biochemical properties of proteins increases, we may be able to understand the functions of even a new protein with a top down approach.

Imagine I find an object on Mars, and I have no idea of how it works, and even its inner stricture is completely mysterious to me, but I can see that it is made of many parts connected in patterns. Is it so difficult to hypothesize that what I have found is some kind of designed tool to measure time? No, it would be based on my understanding that it is useful to measure time for intelligent conscious beings. This is a fundamental point. That experience is really basic to understand design, indeed even to define it.

If we recognize a function, we recognize it. It just means that we realize that the object can be used to obtain some result. Certainly, we must understand how the object must be used. For a protein coding gene, we must be aware of the genetic code. Maybe in many cases we will not understand the function. But in many others we will. The cases where we recognize the function, and can measure its complexity, will be cases of true positives.

The cases where we cannot recognize the function which is indeed there will be false negatives. The cases where we recognize no function because there is none will be true negatives. Anyway, there will be no false positive, if we apply correctly the procedure. OK, my non inference of design is a false negative. How do I decide which it is? You can decide, because you know how that sequence originated. But I am not interested in knowing if my negatives are true or false, because i know that my procedure is not sensitive, and there will be a lot of false negatives anyway.

Therefore, I will never use my procedure to exclude design in objects. Why is my verse so barren of new pride, So far from variation or quick change? Why with the time do I not glance aside To new-found methods, and to compounds strange? Why write I still all one, ever the same, And keep invention in a noted weed, That every word doth almost tell my name, Showing their birth, and where they did proceed? For as the sun is daily new and old, So is my love still telling what is told. But we understand english.

Nothing else is needed to understand the meaning. A remarkable meaning, I would add. What is the total complexity of the sequence? The length is characters including spaces. The search space is more than bits. What is the target space?

But, according to some simple reasoning I have applied to language some time ago, I am absolutely confident that, with a search space of bits, the functional complexity of a sequence in good english is certainly more than bits.

I need to know, as I have already stated clearly:. The physical system, the time span and the probabilistic resource of the system: That is the answer I want to find. But I need to know where the proteins originated the systemin what time span, and what are the random variations which can take place in that system in the time span the probabilistic resources.

The only purpose is to evaluate if the null hypothesis can be rejected. That is completely false. I can try to understand that by myself. Or you can say that to me, if you know it. It does not matter. If I recognize a function, by myself or with your help, I will try to compute its complexity and, if the complexity is high enough to reject the null hypothesis, I will reject it. If no algorithmic explanation of the sequence in the system is known, or even plausible, I will infer design.

And believe me, I will have no false positives. I am well aware that protein engineering, both top down and bottom up, has made great progress.

I am aware of those small results. And I am sure that, in time, we will be able to engineer proteins very well. In no way I am trying to diminish the capabilities of humans to design proteins, which are indeed a very good argument for the design theory.

Again, I am not trying to underestimates these results. And I see no potential limitations to our protein engineering abilities. We just need more time.

That remains true even if we engineer perfect proteins. The algorithm will be extremely complex, it will require a lot of intelligent premises and a lot of highly directed computational power. I look forward to reading your next post on this highly interesting subject. Mile grazie mio caro amico. Ja mieszkam w Gda? Gdzie w Polsce mieszkasz? First, old proteins evolve and undergo selection, and selection is not random. Even de novo proteins do not have to be entirely random. After all, a good proportion of our junk DNA consists of former functional sequences like decaying pseudogenes, disabled and fragmented ex-genes that used to encode for viral proteins, etc.

You may ask about the very first proteins, at the beginning of life as we know it. I have no idea how they originated, but totally random self-assembly is not a likely solution, and no modern OOL hypothesis known to me takes such a possibility seriously.

Once we get life working and evolving, nothing originates from scratch any more. New structures are built on pre-existing ones. Calculating the probability of the formation of functional proteins as if they had no history is absurd. Purely random origin is not so much the null hypothesis as a straw man. Mieszkam w Poznaniu i pracuj? Perhaps I have expressed myself badly. I apologize for coopting you in my reasoning!

Beware, now I will only give a brief outline of the reasoning. For my definition of what design is, please see here:. If it is higher than our threshold, we say that the object exhibits dFSCI for that system. We observe carefully the object and what we know of the system, and we ask if there is any known and credible algorithmic explanation of the sequence in that system. Usually, that is easily done by excluding regularity, which is easily done for functional specification. However, as in the particular case of functional proteins a special algorithm has been proposed, neo darwininism, which is intended to explain non regular functional sequences by a mix of chance and regularity, for this special case we must show that such an explanation is not credible, and that it is not supported by facts.

That is a part which I have not yet discussed in detail here. The necessity part of the algorithm NS is not analyzed by dFSCI alone, but by other approaches and considerations. However, the short conclusion is that neo darwinism is not a known and credible algorithm which can explain the origin of even one protein superfamily. It is neither known nor credible. And I am not aware of any other algorithm ever proposed to explain without design the origin of functional, non regular sequences. That means that as far as we know design is the best scientific explanation of what we observe.

So, to sum up, dFSCI is necessary to evaluate and eventually reject the role of RV, both as the only cause of what we observe and as part of the specific neo darwinian algorithm. Other considerations are needed for that. There are other aspects of your last posts which I want to discuss, obviously, but I wanted first to give you a complete scenario of what we are debating here. Piotr, Apparently Polish language-specific characters are not recognized by the text processor here.

Also, the mechanisms behind the genotype-phenotype association. Also the mechanisms behind neurological processes. Also, the detailed mechanisms behind physiological processes. Is this something you or someone you know could provide helpful information or point to sources? Yet IDists have said how to test for design and other design-centric venues have shown us the importance of determining design is present.

Now THAT is your ignorance showing. Design is based on our KNOWLEDGE of cause and effect relationships. OTOH darwinian and neo-darwinian evolution are based on our ignorance.

The Hands of Olsen

I want detailed coherent comprehensive step-by-step descriptions. Next time you visit Gdansk, stop by for herbata or kawa. The only algorithmic part is the chronological and most probably causal, relationship between the conscious representation and the form in the material object. Again, you can find the details in my post about design:. The origin of dFSCI from conscious agents, and only from conscious agents, is absolutely grounded in innumerable empirical observations.

We have not yet debated this aspect here, but we certainly will, before the end of it. The design inference is a strong, positive empirical inference. For a simple answer, please look at my post 23, part of which I paste here for your convenience:.

But more info is still required, hence any help is highly welcome and appreciated. You may contact me at dshared ymail. Pardon, but kindly cf. If you have to try to argue that design is so vague it can be dismissed speaks volumes.

Just as a quick clue, every comment in this thread manifests dFSCI, and that is instantly recognisable. As another quick note, as indicated already, all that is required, BTW, for the design inference, is LOCAL isolation of islands of function in the config space, as that brings up fine tuning beyond the search capacity of relevant resources; cf. BTW, too, that speaks to cosmological fine tuning, and to just what it takes to set up a tack-driver of a rifle and a shooter able to make good use of it.

At bits, Solar system is overwhelmed [a 1 straw sample to a 1, LY cubical haystack], at 1, observed cosmos is simply drowned out to effectively zero — no time to smoke a calculator on the calc this morning. The presence of ever so many singleton proteins and the isolation between fold domains fits right in here.

Sorry to be so short, gotta go now, back to G-T power and T-s diagrams, binary vs flash plants etc. Is the sampling of the genetic pool from from generation to generation, by a combination of selection and drift, an algorithm? Are mutations, recombination, linkage, the history of the genome reflected in its structure, inbreeding, migration, environmental variation, etc. Where did the number come from? The universe of aperiodic polymers and their potential functions is vast.

You can also try to see if an artificial genetic algorithm can produce functional complexity — of a kind neither designed nor predicted, by the programmer — under selective pressure. It can, as has been demonstrated, and the functionality achieved in this way is like that found in nature but not in human products: I teach linguistics, and my opinions expressed here are those of a dilettante interested in biology.

But this blog is visited from time to time by professionals who would probably be able to help you. Gdansk is a wonderful place — one of my favourite cities. Next time I go there we can try to fix a meeting. The explanatory filter is not primarily in the business of determining whether we have function.

It is interested in inferring the likely origin. Function is often either self-evident, or empirically observable, or can be gleaned after some study and research. Then the question is: What is the most likely explanation for its origin? It is performing its task properly. You are absolutely right that if we discover or are told about a complex, functional system, then we can infer design. That is the whole point.

Mutations, recombinations, frameshifts, deletions, inversions, you name it. The result of random variation is that new states appear. The probabilistic resource of RV can well be describes as the total numeber of new states that can be generated in a system, in a time span.

As I have tried to do. There is nothing messy in that. So, it does not change the probabilities. Each new state still has the same probabilities to expand, There is no relationship with function. While deleterious new states are preferentially eliminated.

This kind of process is algorithmic in relation to the function of the new state it depends on it. But it can act only on those variations new states which confer a reproductive advantage or disadvantage. Simple anitibiotic resistance is a good example. That is not true for complex language which depends on the meaning to be expressedand it is not true for complex functionalities which sepend on the function to be expressed. Least of all it is true for proteins, which are separated in isolated islands of sequences and structures as can be seen in the SCOP classificationand cannot be deconstructed into simpler additive steps which are individually not only functionalbut also naturally selectable.

They are based on the work of Behe and Axe. They are based on the SCOP classification of proteins. They are based on papers like the rugged landscape paper:. The relative fitness of the wild-type phage, or rather the native D2 domain, is almost equivalent to the global peak of the fitness landscape.

Explorations in design space: IEEE Transactions on Evolutionary Computation 3: The application of RV followed by intelligent selection IS is a design strategy.