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On Active Information, search, Islands of Function and FSCO/I

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A current rhetorical tack of objections to the design inference has two facets:

(a) suggesting or implying that by moving research focus to Active Information needle in haystack search-challenge linked Specified Complexity has been “dispensed with” [thus,too, related concepts such as FSCO/I]; and

(b) setting out to dismiss Active Information, now considered in isolation.

Both of these rhetorical gambits are in error.

However, just because a rhetorical assertion or strategy is erroneous does not mean that it is unpersuasive; especially for those inclined that way in the first place.

So, there is a necessity for a corrective.

First, let us observe how Marks and Dembski began their 2010 paper, in its abstract:

Needle-in-the-haystack problems look for small targets in large spaces. In such cases, blind search stands no hope of success. Conservation of information dictates any search technique will work, on average, as well as blind search. Success requires an assisted search. But whence the assistance required for a search to be successful? To pose the question this way suggests that successful searches do not emerge spontaneously but need themselves to be discovered via a search. The question then naturally arises whether such a higher-level “search for a search” is any easier than the original search. We prove two results: (1) The Horizontal No Free Lunch Theorem, which shows that average relative performance of searches never exceeds unassisted or blind searches, and (2) The Vertical No Free Lunch Theorem, which shows that the difficulty of searching for a successful search increases exponentially with respect to the minimum allowable active information being sought.

That is, the context of active information and associated search for a good search, is exactly that of finding isolated targets Ti in large configuration spaces W, that then pose a needle in haystack search challenge. Or, as I have represented this so often here at UD:

csi_defnUpdating to reflect the bridge to the origin of life challenge:

islands_of_func_chall

In this model, we see how researchers on evolutionary computing typically confine their work to tractable cases where a dust of random walk searches with drift due to a presumably gentle slope on what looks like a fairly flat surface is indeed likely to converge on multiple zones of sharply rising function, which then allows identification of likely local peaks of function. The researcher in view then has a second tier search across peaks to achieve a global maximum.

This of course contrasts with the FSCO/I [= functionally specific, complex organisation and/or associated information] case where

a: due to a need for multiple well-matched parts that

b: must be correctly arranged and coupled together

c: per a functionally specific wiring diagram

d: to attain the particular interactions that achieve function, and so

e: will be tied to an information-rich wiring diagram that

f: may be described and quantified informationally by using

g: a structured list of y/n q’s forming a descriptive bit string

. . . we naturally see instead isolated zones of function Ti amidst a much larger sea of non-functional clustered or scattered arrangements of parts.

This may be illustrated by an Abu 6500 C3 fishing reel exploded view assembly diagram:

abu_6500c3mag

. . . which may be compared to the organisation of a petroleum refinery:

Petroleum refinery block diagram illustrating FSCO/I in a process-flow system
Petroleum refinery block diagram illustrating FSCO/I in a process-flow system

. . . and to that of the cellular protein synthesis system:

Protein Synthesis (HT: Wiki Media)
Protein Synthesis (HT: Wiki Media)

. . . and onward the cellular metabolic process network (with the above being the small corner top left):

cell_metabolism

(NB: I insist on presenting this cluster of illustrations to demonstrate to all but the willfully obtuse, that FSCO/I is real, unavoidably familiar and pivotally relevant to origin of cell based life discussions, with implications onward for body plans that must unfold from an embryo or the like, OOL and OOBP.)

Now, in their 2013 paper on generalising their analysis, Marks, Dembski and Ewert begin:

All but the most trivial searches are needle-in-the-haystack problems. Yet many searches successfully locate needles in haystacks. How is this possible? A success-ful search locates a target in a manageable number of steps. According to conserva-tion of information, nontrivial searches can be successful only by drawing on existing external information, outputting no more information than was inputted [1]. In previous work, we made assumptions that limited the generality of conservation of information, such as assuming that the baseline against which search perfor-mance is evaluated must be a uniform probability distribution or that any query of the search space yields full knowledge of whether the candidate queried is inside or outside the target. In this paper, we remove such constraints and show that | conservation of information holds quite generally. We continue to assume that tar-gets are fixed. Search for fuzzy and moveable targets will be the topic of future research by the Evolutionary Informatics Lab.

In generalizing conservation of information, we first generalize what we mean by targeted search. The first three sections of this paper therefore develop a general approach to targeted search. The upshot of this approach is that any search may be represented as a probability distribution on the space being searched. Readers who are prepared to accept that searches may be represented in this way can skip to section 4 and regard the first three sections as stage-setting. Nonetheless, we sug-gest that readers study these first three sections, if only to appreciate the full gen-erality of the approach to search we are proposing and also to understand why attempts to circumvent conservation of information via certain types of searches fail. Indeed, as we shall see, such attempts to bypass conservation of information look to searches that fall under the general approach outlined here; moreover, conservation of information, as formalized here, applies to all these cases . . .

So, again, the direct relevance of FSCO/I and linked needle in haystack search challenge continues.

Going further, we may now focus:

is_ o_func2_activ_info

In short, active information is a bridge that allows us to pass to relevant zones of FSCO/I, Ti, and to cross plateaus and intervening valleys in an island of function that does not exhibit a neatly behaved objective function. And, it is reasonable to measure it’s impact based on search improvement, in informational terms. (Where, it may only need to give a hint, try here and scratch around a bit: warmer/colder/hot-hot-hot. AI itself does not have to give the sort of detailed wiring diagram description associated with FSCO/I.)

It must be deeply understood, that the dominant aspect of the situation is resource sparseness confronting a blind needle in haystack search. A reasonably random blind search will not credibly outperform the overwhelmingly likely failure of the yardstick, flat random search. Too much stack, too few search resources, too little time. And a drastically improved search, a golden search if you will, itself has to be found before it becomes relevant.

That means, searching for a good search.

Where, a search on a configuration space W, is a sample of its subsets. That is, it is a member of the power set of W, which has cardinality 2^W. Thus it is plausible that such a search will be much harder than a direct fairly random search.  (And yes, one may elaborate an analysis to address that point, but it is going to come back to much the same conclusion.)

Further, consider the case where the pictured zones are like sandy barrier islands, shape-shifting and able to move. That is, they are dynamic.

This will not affect the dominant challenge, which is to get to an initial Ti for OOL then onwards to get to further islands Tj etc for OOBP.  That is doubtless a work in progress over at the Evolutionary Informatics Lab, but is already patent from the challenge in the main.

To give an outline idea, let me clip a summary of the needle-to-stack challenge:

Our observed cosmos has in it some 10^80 atoms, and a good atomic-level clock-tick is a fast chem rxn rate of perhaps 10^-14 s. 13.7 bn y ~10^17 s. The number of atom-scale events in that span in the observed cosmos is thus of order 10^111.

The number of configs for 1,000 coins (or, bits) is 2^1,000 ~ 1.07*10^301.

That is, if we were to give each atom of the observed cosmos a tray of 1,000 coins, and toss and observe then process 10^14 times per second, the resources of the observed cosmos would sample up to 1 in 10^190 of the set of possibilities.

It is reasonable to deem such a blind search, whether contiguous or a dust, as far too sparse to have any reasonable likelihood of finding any reasonably isolated “needles” in the haystack of possibilities. A rough calc suggests that the ratio is comparable to a single straw drawn from a cubical haystack ~ 2 * 10^45 LY across. (Our observed cosmos may be ~ 10^11 LY across, i.e. the imaginary haystack would swallow up our observed cosmos.)

Of course, as posts in this thread amply demonstrate the “miracle” of intelligently directed configuration allows us to routinely produce cases of functionally specific complex organisation and/or associated information well beyond such a threshold. For an ASCII text string 1,000 bits is about 143 characters, the length of a Twitter post.

As just genomes for OOL  start out at 100 – 1,000 k bases and those for OOBP credibly run like 10 – 100+ mn bases, this is a toy illustration of the true magnitude of the problem.

The context and challenge addressed by the active information concept is blind needle in haystack search challenge, and so also FSCO/I. The only actually observed adequate cause of FSCO/I is intelligently directed configuration, aka design. And per further experience, design works by injecting active information coming from a self-moved agent cause capable of rational contemplation and creative synthesis.

So, FSCO/I remains as best explained on design. In fact, per a trillion member base of observations, it is a reliable sign of it. Which has very direct implications for our thought on OOL and OOBP.

Or, it should. END

Comments
Yes, Zachriel, with Intelligent Design Evolution the evolutionary processes would be intelligent. With unguided evolution the evolutionary processes are blind and mindless, ie not intelligent.Joe
May 6, 2015
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Mung: Yes, a search guided by intelligent input will find a target more rapidly than a search not guided by intelligent input. If you mean that evolutionary processes are 'intelligent', then sure.Zachriel
May 6, 2015
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Zachriel: It’s not merely that it finds it, but that it finds it much more rapidly than random trial. Yes, a search guided by intelligent input will find a target more rapidly than a search not guided by intelligent input. I didn't realize that was even a point of dispute.Mung
May 6, 2015
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Mung: And if you mean they could manually enter the exact same string that the program had been designed to find and the program would still find it, that merits a big so what, lol. It's not merely that it finds it, but that it finds it much more rapidly than random trial.Zachriel
May 6, 2015
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Mung: I would like to see Carpathian code this wonderful weasel that can find any target. Carpathian: Wonderful Weasel cannot find any target anymore than a chicken egg could contain any bird species. I know it. And you know it. Yet you claimed:
The designer of the program included all components of Weasel into one program but nothing stops someone from removing the target string and passing it as a parameter from a console or a client on the web.
But what would be the point of that, given that the program must be provided with information about the nature of the string. And if you mean they could manually enter the exact same string that the program had been designed to find and the program would still find it, that merits a big so what, lol. I thought you had something more interesting to say. Silly me. So if someone enter's "methinks it is like a weasel" on the command line the search would still find the target? What if they entered: "methinks it is a cloud with the appearance of a Mustela nivalis"? What then? In how many places would your modular program need to be changed?Mung
May 5, 2015
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sparc, you show no evidence of even seriously reading what is on the thread right in front of you. That unresponsiveness speaks sad volumes. KFkairosfocus
May 5, 2015
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Mung: But the candidate solutions are not just randomly generated objects of no particular design. They are random mutations of (roughly) "the best so far". Mung: Let’s say that the program mutates using the uppercase characters A-Z and the space character but the target is all lower case characters. good luck with that. That's actually not a problem. It would only decrease the effectiveness somewhat, but it would still be far faster than searching by random trial. Mung: Let’s say that the length of the candidate solutions is 28 characters and I pass in a string of 128 characters [via the command line to this magical program] as the target. good luck with that. Again, not a problem, as long as mutation includes deletions and insertions.Zachriel
May 5, 2015
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Mung:
I would like to see Carpathian code this wonderful weasel that can find any target.
Wonderful Weasel cannot find any target anymore than a chicken egg could contain any bird species.Carpathian
May 5, 2015
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Yes, Carpathian, any half-wit coder can string together a bunch of modules that don't work. But that's hardly the point.Mung
May 5, 2015
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And the red herrings continue. Let's say that the program mutates using the uppercase characters A-Z and the space character but the target is all lower case characters. good luck with that. Let's say that the length of the candidate solutions is 28 characters and I pass in a string of 128 characters [via the command line to this magical program] as the target. good luck with that. I would like to see Carpathian code this wonderful weasel that can find any target.Mung
May 5, 2015
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That is what is on the table.
Too bad that obviously Dembski, Behe and Meyer are sitting at another one and don't even look over to see what's on your table.sparc
May 5, 2015
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There is no point in debating this as you could simply look at the program and see that the functions are separate and could be in three different modules. e.g. Mutate( char *Population[]); Reproduction( char *Population[]); char *Environment( char *Target, char *Population[]);
Reproduction is by intelligent Design. Mutation is part of the program with random = equally probable; and it is artificial selection, not environmental acceptance. Selection actively guiding the variants = Intelligent Design. Computers emulate people. They can just do it faster. Everything they do traces back to humans. There isn't anything about evolutionary and genetic algorithms that simulates natural selection. And one part Intelligent Design Evolution is what they model.Joe
May 5, 2015
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The steering component of my car doesn't know where it is going. It does't know where my car is going. The car doesn't know either- no matter how many times I reproduce the route. And yet my car and all of its components are intelligently designed.Joe
May 5, 2015
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Joe:
All knowledge comes from the programmer. The mutation component is part of the program.
There is no point in debating this as you could simply look at the program and see that the functions are separate and could be in three different modules. e.g. Mutate( char *Population[]); Reproduction( char *Population[]); char *Environment( char *Target, char *Population[]); Notice that the populations are passed to the modules which means we don't know what they are. Notice also that we don't know how Environment rates the Population. It might compare the strings as Dawkin's did or splice the "DNA snippets" into frogs and report the string that caused the frog's skin to turn the bluest. The modules don't know what is going on outside of them. They simply do their specific job.Carpathian
May 5, 2015
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The mutation component however, does not know what the target string is.
All knowledge comes from the programmer. The mutation component is part of the program.
This shows that mutation is completely random.
Yes, as in equally probable. I said that already.
Your are looking at Dawkins program as one single unit, but it isn’t.
I am not doing that so lay off your false accusations.
There should have been three separate components: Reproduction, Mutation and Environmental Acceptance.
Reproduction is by intelligent Design. Mutation is part of the program and it is artificial selection, not environmental acceptance. Selection actively guiding the variants = Intelligent Design.Joe
May 5, 2015
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Joe:
Selection actively guides the variants.
Very true. The mutation component however, does not know what the target string is. During a run, a character matching the target string sometimes gets turned into a non-matching character. This shows that mutation is completely random. Your are looking at Dawkins program as one single unit, but it isn't. Programmers sometimes get slapped on the wrist for putting too much functionality in one file when it really should be spread out across multiple components. Dawkin's Weasel incorporates all functionality into one file but that was simply a case of quickly getting it done. There should have been three separate components: Reproduction, Mutation and Environmental Acceptance.Carpathian
May 5, 2015
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The mutation component does not know what the target string is and thus does not know which character should be modified.
You say that as if it means something. The mutation component is always actively guided towards a solution. That is the very important part. The mutations happen when programmed to happen and then the variants guided as programmed. Selection actively guides the variants.Joe
May 5, 2015
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Joe: The designer of the program included all components of Weasel into one program but nothing stops someone from removing the target string and passing it as a parameter from a console or a client on the web. The mutation component does not know what the target string is and thus does not know which character should be modified. It modifies any character without regard to the target.Carpathian
May 5, 2015
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The designer of the program knew what the target was and that knowledge was programmed in. The program was intelligently designed to reach that target. Remove the intelligently programmed knowledge and weasel would still be running unable to find the target. Also "random" wrt GAs (like weasel) just means an equal probability of occurring. It does not mean accidental or unplanned. The debate is about the latter, ie random as in accidental or unplanned.Joe
May 5, 2015
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Mung:
But the candidate solutions are not just randomly generated objects of no particular design.
In Weasel, random is exactly what they are. The mutation component may make one string less acceptable and another more acceptable to the "environment". This is not a problem since the less acceptable one will not be allowed to reproduce and mutate. Despite mutational setbacks, the solution string eventually appears in the "environment" despite the fact that the mutating component does not know what the target string should be.Carpathian
May 5, 2015
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P^5S: Let's try a sample chapter:
6 SYSTEMS BIOLOGY OF CELL ORGANIZATION The first few chapters of this textbook laid the foundation for understanding cell structure and function. We learned that life depends on organic molecules, which form the building blocks for macromolecules such as proteins, nucleic acids, and carbohydrates. In addition, we considered cell organ-ization at a higher level. Cells contain complex structures such as membranes, chromosomes, ribosomes, and a cytoskeleton. Eukaryotic cells have organelles that provide specialized com-partments to carry out various cellular functions.
In short, complex specifically functional organisation of the cell based on interaction of correct, correctly arranged parts is a basic fact of life. Just as the OP describes. And just as the acronym FSCO/I describes. FSCO/I is real and it is relevant to biology from the molecular nanotech of the cell on up. Where there is a debate, is on the design inference on this form of CSI. Fine, if you want to debate that do so. Don't try to pretend that FSCO/I is a dubious notion cooked up by some dismissible IDiot we can cyberstalk or stalk on the ground and smear with all sorts of false accusations, year after year, or enable such outrages and pretend that nothing is going on or that it is to object to such that is wrong. If you try to debate it, recognise that FSCO/I can be reduced informationally by creating a descriptive language based on addressing the nodes-arcs pattern with a structured string of Y/N q's. So, we can reasonably assign a value for functionally specific info to it. Further, recognise that once you deal with the constraints of multipart interactive, specific function, you are clustering a relatively narrow range of possible configs, as opposed to any arbitrary clumped or scattered arrangement. Thus, if you are trying to suggest arriving at FSCO/I via blind chance and mechanical necessity, you are dealing with blind needle in haystack search. Where when the info content hits or exceeds 500 - 1,000 bits, you are looking at searches of the type in the OP: at 1,000 bits, 1 straw sampled from a haystack that would dwarf the observed cosmos. No wonder we have a trillion member inductive sample where FSCO/I reliably comes about by intelligently directed configuration, design. If you doubt me, start with the Internet, then go on to nuts, bolts, gear trains etc. So, design is an inductively warranted best current causal explanation of FSCO/I. WHERE -- ABSENT A PRIORI IMPOSITION OF EVOLUTIONARY MATERIALISM -- THERE IS NO SERIOUS COMPETING EXPLANATION. (My caps lock stuck by accident, but I'll leave that.) That is what is on the table.kairosfocus
May 5, 2015
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Zachriel is a hoot. A population module and an oracle and "the population module knows nothing about the workings of the oracle." So what? This is ground already covered and Zachriel wants to cover it again. The population module is generator for potential solutions (candidate solutions) to the problem. IOW, it helps traverse the search space. But the candidate solutions are not just randomly generated objects of no particular design. Zachriel:
Zachriel: The notion of a fitness landscape entails that there is a defined relationship between the replicators and the landscape…
And just how and where is this relationship defined? Zachriel:
An evolutionary algorithm typically consists of two modules; the evolving population and an oracle. The oracle can be simple, such as in Weasel, or it can be complex, such as a simulation of the natural environment. The key is that the only contact between the two parts is the return of a fitness value from the oracle when evaluating the elements of the population.
And that's nothing more than a red herring and is only part of the story.Mung
May 5, 2015
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What utter drivel- GAs ACTIVELY search for the solution they are designed to find. They use actual selection which is contrary to evolutionism's mechanisms.Joe
May 5, 2015
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Mung:
Carpathian: In the case of Dawkin’s Weasel program, the algorithm doesn’t know the answer.
Mung: So?
It means that despite not knowing what the "target" is, the algorithm can find it. The feedback from the "environment", (string comparison), for a string or "DNA snippet" is simply die versus reproduce. The string that is evaluated is not a part of the algorithm itself. Zachriel explains it well in #189.Carpathian
May 5, 2015
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Carpathian: In the case of Dawkin’s Weasel program, the algorithm doesn’t know the answer. Mung: So? An evolutionary algorithm typically consists of two modules; the evolving population and an oracle. The oracle can be simple, such as in Weasel, or it can be complex, such as a simulation of the natural environment. The key is that the only contact between the two parts is the return of a fitness value from the oracle when evaluating the elements of the population. In other words, the population module knows nothing about the workings of the oracle, and the only information it receives is through the fitness function. The oracle can be simple or exceedingly complex. Mung: Why a string? Because an evolutionary algorithm is a simple model of genomes, which can be represented by an evolving population of strings. Mung: Let me tell you why. Because the programmer knew that the desired solution was a string of a certain length composed of specific letters in a specific order and found a way to code that into the program. That's not necessarily the case. While Weasel uses strings of a given length, a population can be composed of strings of arbitrary length.Zachriel
May 5, 2015
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PPPPS: Just for hammering the point home:
http://www.ncbi.nlm.nih.gov/pubmed/18202877/ Theory Biosci. 2004 Jun;123(1):3-15. doi: 10.1016/j.thbio.2004.03.001. Evolution of cell division in bacteria. Trevors JT1. Author information Abstract Molecular evolution in bacteria is examined with an emphasis on cell division. For a bacterial cell to assemble and then divide required an immense amount of integrated cell and molecular biology structures/functions to be present, such as a stable cellular structure, enzyme catalysis, minimal genome, septum formation at mid-cell and mechanisms to take up nutrients and produce and use energy, as well as store it. The first bacterial cell(s) capable of division must have had complex cell and molecular biology functions. At this stage of evolution, they would not have been primitive cells but would have reached a threshold in evolution where cell division occurred in a regulated manner.
But, but, but the drum-beat of objections and dismissals MUST go on . . .kairosfocus
May 5, 2015
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PPS: And despite posting hiccups and web vanishing, let us continue:
http://www.ncbi.nlm.nih.gov/pubmed/18762901/ Naturwissenschaften. 2009 Jan;96(1):1-23. doi: 10.1007/s00114-008-0422-8. Epub 2008 Sep 2. The riddle of "life," a biologist's critical view. Penzlin H1. Author information Abstract To approach the question of what life is, we first have to state that life exists exclusively as the "being-alive" of discrete spatio-temporal entities. The simplest "unit" that can legitimately be considered to be alive is an intact prokaryotic cell as a whole. In this review, I discuss critically various aspects of the nature and singularity of living beings from the biologist's point of view. In spite of the enormous richness of forms and performances in the biotic realm, there is a considerable uniformity in the chemical "machinery of life," which powers all organisms. Life represents a dynamic state; it is performance of a system of singular kind: "life-as-action" approach. All "life-as-things" hypotheses are wrong from the beginning. Life is conditioned by certain substances but not defined by them. Living systems are endowed with a power to maintain their inherent functional order (organization) permanently against disruptive influences. The term organization inherently involves the aspect of functionality, the teleonomic, purposeful cooperation of structural and functional elements. Structures in turn require information for their specification, and information presupposes a source. This source is constituted in living systems by the nucleic acids. Organisms are unique in having a capacity to use, maintain, and replicate internal information, which yields the basis for their specific organization in its perpetuation. The existence of a genome is a necessary condition for life and one of the absolute differences between living and non-living matter. Organization includes both what makes life possible and what is determined by it. It is not something "implanted" into the living beings but has its origin and capacity for maintenance within the system itself. It is the essence of life. The property of being alive we can consider as an emergent property of cells that corresponds to a certain level of self-maintained complex order or organization.
But, the beat must go on and on . . .kairosfocus
May 5, 2015
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PPS: And some more of the same,
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4092032/ C R Biol. 2011 Jan; 334(1): 1–5. Published online 2010 Dec 30. doi: 10.1016/j.crvi.2010.11.008 PMCID: PMC4092032 NIHMSID: NIHMS561755 Thermodynamic perspectives on genetic instructions, the laws of biology, diseased states and human population control J. T. Trevors corresponding author and M. H. Saier, Jr. This article examines in a broad perspective entropy and some examples of its relationship to evolution, genetic instructions and how we view diseases. Many knowledge gaps abound, hence our understanding is still fragmented and incomplete. Living organisms are programmed by functional genetic instructions (FGI), through cellular communication pathways, to grow and reproduce by maintaining a variety of hemistable, ordered structures (low entropy). Living organisms are far from equilibrium with their surrounding environmental systems, which tends towards increasing disorder (increasing entropy). Organisms must free themselves from high entropy (high disorder) to maintain their cellular structures [--> i.e. cellular, functional organisation] for a period of time sufficient enough to allow reproduction and the resultant offspring to reach reproductive ages. This time interval varies for different species. Bacteria, for example need no sexual parents; dividing cells are nearly identical to the previous generation of cells, and can begin a new cell cycle without delay under appropriate conditions. By contrast, human infants require years of care before they can reproduce. Living organisms maintain order in spite of their changing surrounding environment, that decreases order according to the second law of thermodynamics. These events actually work together since living organisms create ordered biological structures by increasing local entropy. From a disease perspective, viruses and other disease agents interrupt the normal functioning of cells. The pressure for survival may result in mechanisms that allow organisms to resist attacks by viruses, other pathogens, destructive chemicals and physical agents such as radiation. However, when the attack is successful, the organism can be damaged until the cell, tissue, organ or entire organism is no longer functional and entropy increases. . . . . Atoms are ancient relics of the hypothesized Big Bang (Matsuno, 2008) and can be used to construct life forms under the control of FGIs (functional genetic instructions). Living organisms are programmed by FGIs, which flow through a biochemical communication pathway involving DNA--> RNA--> proteins, to instruct cells how to assemble into living organisms. They are programmed to grow and reproduce by maintaining a variety of hemistable, ordered structures (low entropy state) (Schrodinger, 1944). They are far from equilibrium with their surrounding environment, which tends towards increasing disorder (Dolev & Elitzur, 1998). This is achieved by absorption of energy, from our thermonuclear sun, which provides the energy for the conversion of inanimate material into living organisms. This occurs on our planet with conditions commensurate with the maintenance of the life forms that comprise our singular biosphere system (Dolev & Elitzur, 1998; Gatenby & Frieden, 2007). Researchers have devoted time and effort to defining and understanding the characteristics of life, from the atomic to the biospherical levels of organization (Penzlin, 2009; Schrodinger 1944) and in more recent years the possibility of synthetic single-celled life. Biology can therefore be viewed as the study of life (and death) at all levels of biological organization . . . Science relies on the fundamental laws of thermodynamics in addition to the knowledge that: (1) the cell is the basic unit of life; (2) life arises only from life; (3) a cell is the only living structure that can grow and divide (Trevors, 2004), and (4) functional genetic instructions flow along a cellular communication pathway to provide the instructions for the challenges from entropy, with reproduction as the normal outcome. Although natural selection prevents many individual organisms from reproducing, others must succeed if a species is to survive, even though all individuals within a species die, generally just not at the same time.
The presence of the pattern of thought captured in the acronym FSCO/I should be abundantly apparent. But, the beat goes on and on and on . . .kairosfocus
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PS: Just as a fresh perspective on complex biological, coded functional information, we may wish to ponder:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3319427/ Journal ListTheor Biol Med Modelv.9; 2012PMC3319427 Theor Biol Med Model. 2012; 9: 8. Published online 2012 Mar 14. doi: 10.1186/1742-4682-9-8 PMCID: PMC3319427 Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems David J D'Onofrio,corresponding author1 David L Abel,corresponding author2 and Donald E Johnson3 Bioinformatics has opened up the field of molecular biology through the use of computer science and statistics. Data mining of genetic information includes discovering relationships between individual DNA sequences and variability in disease [1]. More importantly, the application of computer science will contribute to identifying intricate complex data and algorithmic structures that are part of the biological processes that manage and maintain metabolic functions of the cell. Biological organisms are considered to be controlled and regulated by Functional Information (FI) [2-8]. FI comes closer to expressing the intuitive and semantic sense of the word "information" than mere Shannon combinatorial uncertainty or reduced uncertainty (poorly termed "mutual entropy"). The innumerable attempts that have been made to reduce the functional information of genomics and molecular biology to nothing more than physical combinatorics and/or thermodynamics will fail for reasons best summarized in the peer-reviewed anthology entitled The First Gene: The Birth of Programming, Messaging and Formal Control [9]. "Functional Information (FI)" has now been formalized into two subsets: Descriptive Information (DI) [7] and Prescriptive Information (PI) [7,10,11]. This formalization of definitions precludes the prevailing confusion of informational terms in the literature. The more specific and accurate term "Prescriptive Information (PI)" has been championed by Abel [12-16] to define the sources and nature of programming controls, regulation and algorithmic processing. Such prescriptions are ubiquitously instantiated into all known living cells [13]. PI either instructs or produces formal function [12] in such a way as to organize and institute a prescribed set of logic-gate programming choices. Without such steering of physicochemical interactions by "Choice-Contingent Causation and Control" (CCCC) [17-19], metabolic pathways and cycles would be impossible to integrate into a cooperative and holistic metabolism. The Organization (O) Principle [19] states that nontrivial formal organization can only be produced by CCCC. [--> Cf OP] Maynard Smith [20] argued that bioinformation is both specific and intentional. Maynard Smith also pointed out in this same paper the irreversibility of information transfer. Information moves only from signal to response, not in the reverse direction. He argued that genetic information implies the possibility of misinterpretation or error. Maynard Smith also considered genetic information to be undetermined by cause-and-effect necessity. But he considered genetic information to be gratuitous (not called for by the circumstances: unwarranted) [20]. Jablonka [21] argues that life is dependent upon semantic information, and that Shannon "information" is insufficient to explain life. She emphasizes, as does Adami [22], the importance of "aboutness." Aboutness relates to meaning which in biology relates to biofunction. Jablonka [21] also argues that semantic information can only exist with living or designed systems. "Only a living system can make a source into an informational input." On page 588 Jablonka emphasizes the function of bioinformation. Thus the joint authors of this paper are not alone in our emphasis on the formal nature of life's many control mechanisms. A closer examination of Prescriptive Information (PI) has led to a dichotomy in its definition to differentiate between 1) what are prescribed data, and 2) what are prescribed algorithms. As the concepts of computer science are applied to the cell, it is necessary to deconstruct information structures to identify and differentiate data from algorithms. 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 . . .
And, the beat goes on and on and on . . .kairosfocus
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sparc: Why are you unresponsive to what Dembski stated in one of his main works, in discussing that in the biological context the specification in question in CSI is functional: "Biological specification always refers to function"? Similarly, why are you unresponsive to the specific citation from Meyer that refers to "specified or functional information (especially if encoded in digital form)"? Especially, as both have been specifically cited to you above? Let me cite Dembski again, from the cite that appears most recently above at comment no. 148 just yesterday morning (rather coincidental with it's coming from p. 148 f in NFL . . . ); for your information:
p. 148:“The great myth of contemporary evolutionary biology is that the information needed to explain complex biological structures can be purchased without intelligence. My aim throughout this book is to dispel that myth . . . . Eigen and his colleagues must have something else in mind besides information simpliciter when they describe the origin of information as the central problem of biology. I submit that what they have in mind is specified complexity [[cf. here below], or what equivalently we have been calling in this Chapter Complex Specified information or CSI . . . . Biological specification always refers to function. An organism is a functional system comprising many functional subsystems. . . . In virtue of their function [[a living organism's subsystems] embody patterns that are objectively given and can be identified independently of the systems that embody them. Hence these systems are specified in the sense required by the complexity-specificity criterion . . . the specification can be cashed out in any number of ways [[through observing the requisites of functional organisation within the cell, or in organs and tissues or at the level of the organism as a whole. {Dembski cites:} Wouters, p. 148: "globally in terms of the viability of whole organisms," Behe, p. 148: "minimal function of biochemical systems," Dawkins, pp. 148 - 9: "Complicated things have some quality, specifiable in advance, that is highly unlikely to have been acquired by ran-| dom chance alone. In the case of living things, the quality that is specified in advance is . . . the ability to propagate genes in reproduction." On p. 149, he roughly cites Orgel's famous remark from 1973, which exactly cited reads: In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . And, p. 149, he highlights Paul Davis in The Fifth Miracle: "Living organisms are mysterious not for their complexity per se, but for their tightly specified complexity."] . . .” p. 144: [[Specified complexity can be more formally defined:] “. . . since a universal probability bound of 1 [[chance] in 10^150 corresponds to a universal complexity bound of 500 bits of information, [[the cluster] (T, E) constitutes CSI because T [[ effectively the target hot zone in the field of possibilities] subsumes E [[ effectively the observed event from that field], T is detachable from E, and and T measures at least 500 bits of information . . . ”
(It would be appreciated if you were to explain to us why this is apparently unacceptable to you as pointing out that in the biological world, we address the functionally specified subset of complex, specified information, instantly making it reasonable to use an acronym for a stock descriptive phrase that describes the explicit and implicit cases of such biologically functional, information-rich specified complexity. Namely, again, FSCO/I = functionally specific complex organisation and/or associated information. BTW, why have you been consistently unresponsive to the repeated explanation or expansion of the acronym?) Likewise, FYFI, here is Meyer as cited to you just yesterday at 148, in his response to Falk's hostile review of Signature in the Cell, 2009:
For nearly sixty years origin-of-life researchers have attempted to use pre-biotic simulation experiments to find a plausible pathway by which life might have arisen from simpler non-living chemicals, thereby providing support for chemical evolutionary theory. While these experiments have occasionally yielded interesting insights about the conditions under which certain reactions will or won’t produce the various small molecule constituents of larger bio-macromolecules, they have shed no light on how the information in these larger macromolecules (particularly in DNA and RNA) could have arisen. Nor should this be surprising in light of what we have long known about the chemical structure of DNA and RNA. As I show in Signature in the Cell, the chemical structures of DNA and RNA allow them to store information precisely because chemical affinities between their smaller molecular subunits do not determine the specific arrangements of the bases in the DNA and RNA molecules. Instead, the same type of chemical bond (an N-glycosidic bond) forms between the backbone and each one of the four bases, allowing any one of the bases to attach at any site along the backbone, in turn allowing an innumerable variety of different sequences. This chemical indeterminacy is precisely what permits DNA and RNA to function as information carriers. It also dooms attempts to account for the origin of the information—the precise sequencing of the bases—in these molecules as the result of deterministic chemical interactions . . . . [[W]e now have a wealth of experience showing that what I call specified or functional information (especially if encoded in digital form) does not arise from purely physical or chemical antecedents [[--> i.e. by blind, undirected forces of chance and necessity]. Indeed, the ribozyme engineering and pre-biotic simulation experiments that Professor Falk commends to my attention actually lend additional inductive support to this generalization. On the other hand, we do know of a cause—a type of cause—that has demonstrated the power to produce functionally-specified information. That cause is intelligence or conscious rational deliberation. As the pioneering information theorist Henry Quastler once observed, “the creation of information is habitually associated with conscious activity.” And, of course, he was right. Whenever we find information—whether embedded in a radio signal, carved in a stone monument, written in a book or etched on a magnetic disc—and we trace it back to its source, invariably we come to mind, not merely a material process. Thus, the discovery of functionally specified, digitally encoded information along the spine of DNA, provides compelling positive evidence of the activity of a prior designing intelligence. This conclusion is not based upon what we don’t know. It is based upon what we do know from our uniform experience about the cause and effect structure of the world—specifically, what we know about what does, and does not, have the power to produce large amounts of specified information . . .
Why are you further unresponsive to Orgel's focus on specified complexity as a characteristic of cell based life that distinguishes it -- in a specifically OOL context -- from crystals and random polymers? Also, to Wicken's apt point that wiring diagram, information rich function is involved in the organisation found in that general context? (Both of these were also cited to you specifically.) Further to this, why have you been so unresponsive to the commonplace fact that simply the s-t-r-i-n-g-s of text in this discussion thread and more generally (surely you know how important this type of data structure is . . . ) are a form of wiring diagram organisation? Likewise, why have you been unresponsive to the patent fact that, it is an utter commonplace for parts to work together to create a functional result based on how they are arranged and coupled together, e.g. in electrical/ electronic circuits, or the sort of engineering diagrams commonly called exploded views and also wireframes? Why have you been unresponsive to the widespread fact that such a nodes and arcs mesh may be reduced informationally to a structured sequence of Y/N q's, i.e. to a binary digit (= bit) based description, such as one may see with AutoCAD etc, or more mathematically with the approach Orgel took of speaking to length of the descriptive string as quantifying the information involved. Have you taken note that since 2005 Trevors and Abel have distinguished and discussed in the peer reviewed literature for strings -- directly involved in D/RNA and implied by wiring diagram functional organisation -- ordered, random and functional sequence complexity. Which in turn reflects the following contrast from Thaxton et al in The Mystery of Life's Origin, 1984 -- the very first technical work that sparked the rise of design theory, which builds on Orgel and Wicken:
1. [Class 1:] An ordered (periodic) and therefore specified arrangement: THE END THE END THE END THE END Example: Nylon, or a crystal . . . . 2. [Class 2:] A complex (aperiodic) unspecified arrangement: AGDCBFE GBCAFED ACEDFBG Example: Random polymers (polypeptides). 3. [Class 3:] A complex (aperiodic) specified arrangement: THIS SEQUENCE OF LETTERS CONTAINS A MESSAGE! Example: DNA, protein.
Where, the same authors go on to say:
Yockey7 and Wickens5 develop the same distinction, that "order" is a statistical concept referring to regularity such as could might characterize a series of digits in a number, or the ions of an inorganic crystal. On the other hand, "organization" refers to physical systems and the specific set of spatio-temporal and functional relationships among their parts. Yockey and Wickens note that informational macromolecules have a low degree of order but a high degree of specified complexity. In short, the redundant order of crystals cannot give rise to specified complexity of the kind or magnitude found in biological organization; attempts to relate the two have little future. [NB: The name should be Wicken.]
They go on to comment: "the redundant order of crystals cannot give rise to specified complexity of the kind or magnitude found in biological organization; attempts to relate the two have little future." Thirty years later this has been fully justified. Now, sparc, you have been a critic of design thought in and around UD for years. I cannot believe that the above has escaped your notice all this time; your purpose is plainly rhetorical, and the facts as repeated to you are obviously inconvenient to where you want to go. I will simply point out, therefore, that the above conclusively shows that the concepts and context addressed by the acronym FSCO/I have been at the heart of design thought for 30 years, were originally built on considerations brought to the table by Orgel, Wicken and Yockey et al, and have in fact been highlighted by both Dembski and Meyer as noted. Further to all this, the phrase is descriptive of a common, easily observed pattern. One that appears in text of comments of this thread of discussion, and also in things like fishing reels, petroleum refineries, watches, engines, electronic circuits and software. All of which are abundantly familiar in a high tech age. Some of which are exemplified in the OP above. Trillions of cases altogether. FSCO/I is objectively real and not a mere fairy-tale figment of some dismissible IDiot's imagination. That you find it so hard to acknowledge that patent reality that is literally staring you in the face when you read the text of comments or compose comments of your own simply underscores its cogency and inductive force that obviously strongly points where you desperately do not want to go. Consistently, reliably -- and for reasons connected to the need for actively, intelligently inserted functional information and linked organisation (as the OP you are also largely unresponsive to discusses) -- such FSCO/I is a reliable sign of intelligently directed configuration as cause. AKA, design. Now, if you want to challenge such an inductively grounded conclusion, the path is obvious. Provide a counter example that credibly shows that nope FSCO/I is also adequately caused by blind chance and/or mechanical necessity. Which, in any case is needed to warrant claims commonly made from an evolutionary materialist perspective regarding OOL and OOBP. If, such are to meet the vera causa test of causal adequacy. The problem of course is patent. In the teeth of a trillion member base of cases, you cannot provide such cases. Dozens of attempts to do so in and around UD for years have consistently come up as instead inadvertently showing intelligently directed configuration with requisite complex specified information and/or linked organisation -- typically functionally specific -- thus being again and again showed to be strong and reliable signs of design. But, equally obviously, for reasons connected to the ideological dominance of evolutionary materialist thought on origins science -- and this descriptive term traces ultimately to concepts discussed by Plato in The Laws Bk X, FYI -- that is not a welcome result. Hence, the current semantics games, unresponsiveness to evidence and refusal to acknowledge that, on the record, these concepts have long been a part of the design theory discussions. So, while it is not a little annoying to have to deal with such drumbeat unresponsiveness to cogent evidence, the very fact of such rhetorical patterns on the part of objectors to design theory inadvertently underscores the substantial force of the design inference on FSCO/I and broader CSI. (Which of course has in its turn come in for endless drumbeat repetition of talking points in objection. And, it is not coincidental that the best way to ground the reality of the general concept is through functionally specific cases, especially those based on digital code strings and obvious wiring diagrams.) I am confident that the astute onlooker will be able to see the balance on the merits, thus why it is reasonable and empirically warranted to speak of FSCO/I as a patent empirical reality and strong sign of design as cause. KFkairosfocus
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