Atheism Darwinist rhetorical tactics Functionally Specified Complex Information & Organization Science, worldview issues/foundations and society

FTR: Answering ES’ po-mo antics with the semantics of “function”

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In recent days, objector ES has been twisting the concept of Wickensian functionally specific information-bearing complex organisation into post-modernist deconstructionist subjectivist pretzels, in order to obfuscate the plain inductive argument at the heart of the design inference and/or explanatory filter.

For example, consider these excerpts from the merry go round thread:

ES, 41: . . . If a conscious observer connects some observed object to some possible desired result which can be obtained using the object in a context, then we say that the conscious observer conceives of a function for that object . . . . In science, properties of the material just are, without purpose, because everybody knows purpose is subjective. Functionality comes in when you get engineerial, and then it’s more up to the “objective functionality” of the engineer than of the material . . .

KF, 42: When one puts together a complex composite such as a program or an electronic amplifier ckt or a watch or an auto engine or many other things, function is not projected to it by an observer. I wuk, or i nuh wuk, mon. Was that a bad starter motor, a run down battery, out of gas, dirty injector points and more. Was that a bug in syntax or in semantics. Was that a BJT miswired and fried, did you put in the wrong size load resistor so it sits in saturation when it was meant to be in the middle of the load line, did you put in an electrolytic cap the wrong way around, etc. Is this a heart attack triggered by a blood clot etc. Function is not a matter of imagination but observation. And you full well know that or should.

Joe, 44: Earth to E. Seigner- functionality, ie a function, is an OBSERVATION. We observe something performing some function and we investigate to try to figure out how it came to be the way it is. Within living organisms we observe functioning systems and subsystems. As for “information”, well with respect to biology ID uses the same definition that Crick provided decades ago. And we say it can be measured the same way Shannon said, decades ago.

ES, 46: To an observer it looks like cars take people to work and shopping. But most of the time cars stand in garage motionless, and sometimes they fail to start. If the observer is truly impartial, then it’s not up to him to say that the failure to start or mere standing is any less of the car’s function than the ability of being driven. The car’s function is what the car does and when the car fails to start then that’s what it does and this is its function. Of course this sounds silly, but it’s true . . .

BA, 48: It is clear to me now. You have drunk deeply from the post-modernist/constructivist Koolaid. Kairosfocus and gpuccio be advised — attempting to reason with such as E.Seigner is pointless.

Let’s first remind ourselves as to what the glorified common-sense design inference process actually does as an exercise in inductive, inference to the best current explanation on empirically observed evidence:

explan_filter

 

. . . and also, of the significance of Wickensian functionally specific, complex information and Orgellian informational specified complexity for a blind, needle in haystack search; as highlighted by Dembski et al:

csi_defn

While we are at it, let us remind ourselves of what FSCO/I looks like in the form of functionally specific organisation in the technological world:

Fig 6: An exploded view of a classic ABU Cardinal, showing  how functionality arises from a highly specific, tightly constrained complex arrangement of matched parts according to a "wiring diagram." Such diagrams are objective (the FSCO/I on display here is certainly not "question-begging," as some -- astonishingly -- are trying to suggest!), and if one is to build or fix such a reel successfully, s/he had better pay close heed.. Taking one of these apart and shaking it in a shoe-box is guaranteed not to work to get the reel back together again. (That is, even the assembly of such a complex entity is functionally specific and prescriptive information-rich.)
Fig 6: An exploded view of a classic ABU Cardinal, showing how functionality arises from a highly specific, tightly constrained complex arrangement of matched parts according to a “wiring diagram.” Such diagrams are objective (the FSCO/I on display here is certainly not “question-begging,” as some — astonishingly — are trying to suggest!), and if one is to build or fix such a reel successfully, s/he had better pay close heed.. Taking one of these apart and shaking it in a shoe-box is guaranteed not to work to get the reel back together again. (That is, even the assembly of such a complex entity is functionally specific and prescriptive information-rich.)

 

. .  . and, in the life of the cell, as the Ribosome constructs a protein (which is a functionally specific string structure) based on the coded algorithmic information in the mRNA tape:

Step by step protein synthesis in action, in the ribosome, based on the sequence of codes in the mRNA control tape (Courtesy, Wikipedia and LadyofHats)
Step by step protein synthesis in action, in the ribosome, based on the sequence of codes in the mRNA control tape (Courtesy, Wikipedia and LadyofHats)

 

. . . not to mention, the parallel in the punched paper tape reader used for older computers and NC machines:

Punched paper Tape, as used in older computers and numerically controlled machine tools (Courtesy Wiki & Siemens)
Punched paper Tape, as used in older computers and numerically controlled machine tools (Courtesy Wiki & Siemens)

 

(When things have been strawmannised and twisted into pretzels, it helps to straighten them back out again. Where also, a picture is worth a thousand words.)

However, Mr Arrington has a point.

While those caught up in po mo deconstructionist schemes are hardly likely to have a sudden change of heart on the strength of a mere blog comment or even a headlined post, the rest of us can draw lessons from what we see laid out before us. I therefore crave the indulgence of a promoted comment to headlined status, including a snippet of intensely personal history of my homeland. For, comments get buried and forgotten within hours, but a headlined post is for the record:

_________________

KF, 73: >>ES:

It may be entertaining to play semantics games with terms like function, but that simply reveals that your problem is not with science, it is with common sense reality tracing to some of the sillier bits of post-modernist radical subjectivism and deconstructionism.

Perhaps, it has not dawned on you that survival of the fittest or hill-climbing algorithms or natural selection or the like pivot on the objectivity of function. Have you gone to Panda’s Thumb, TSZ, ATBC or the like Darwinist agitator sites to challenge the core concepts of evolution based on differential reproductive success pivoting on functional differences of life-forms? I safely bet not, you are reserving such talking-points for those you object to, regardless of inconsistencies or outright incoherence.

[Ill-]Logic with a swivel.

Patently, revealingly, sadly, you have indulged in incoherent selective hyperskepticism.

And if you genuinely imagine that a stalled car with a dead engine, or a leaky roof, or a crashed computer, or a PA system that distorts sounds horribly are functionally distinct as a mere matter of subjective opinion, your problem is a breach of common sense.

Do you — or a significant other — have a mechanic? Are you a shade-tree mechanic? Do you have even one tool for maintenance? Do you recognise the difference between sugar, salt and arsenic in your cup of coffee? Between an effective prescription correctly filled and faithfully carried out when you get sick and a breakdown of that process? Etc?

I put it to you that you cannot and do not live consistent with your Lit class seminar-room talking points.

And, your evasive resort to clinging to such absurdities to obfuscate the issue of functionally specific, complex organisation and associated information, speaks loudest volumes for the astute onlooker.

Own-goal, E-S.

The bottom-line of the behaviour of several objectors over the past few days, speaks inadvertent volumes on the real balance on the merits of the core design theory contention that there are such things as reliable empirical markers — such as Wickensian FSCO/I — that are strong signs of design as key causal process.

But, many are so wedded to the totalising metanarrative of a priori Lewontinian evolutionary materialism that they refuse to heed the 2350 year old warning posed by Plato on where cynical radical relativism, amorality opening the door to might makes right nihilism and ruthless factions points to for a civilisation. Refusing to learn the hard-bought, paid for in blood lessons of history, they threaten to mislead our civilisation into yet another predictably futile and bloody march of folly. As the ghosts of 100 million victims of such demonically wicked deceptions over the past century warn us.

The folly on the march in our day is so arrogantly stubborn that it refuses to learn living memory history or the history passed on first hand to our grand parents.

Here is Sophia (personification of Wisdom), in the voice of Solomon echoing hard-bought, civil war triggered lessons in Israel c 1,000 BC:

Prov 1:20 Wisdom [Gk, Sophia] cries aloud in the street,
in the markets she raises her voice;
21 at the head of the noisy streets she cries out;
at the entrance of the city gates she speaks:
22 “How long, O simple ones, will you love being simple?
How long will scoffers delight in their scoffing
and fools hate knowledge?
23 If you turn at my reproof,[a]
behold, I will pour out my spirit to you;
I will make my words known to you.
24 Because I have called and you refused to listen,
have stretched out my hand and no one has heeded,
25 because you have ignored all my counsel
and would have none of my reproof,
26 I also will laugh at your calamity;
I will mock when terror strikes you,
27 when terror strikes you like a storm
and your calamity comes like a whirlwind,
when distress and anguish come upon you.
28 Then they will call upon me, but I will not answer;
they will seek me diligently but will not find me.
29 Because they hated knowledge
and did not choose the fear of the Lord,
30 would have none of my counsel
and despised all my reproof,
31 therefore they shall eat the fruit of their way,
and have their fill of their own devices.
32 For the simple are killed by their turning away,
and the complacency of fools destroys them
;
33 but whoever listens to me will dwell secure
and will be at ease, without dread of disaster.”

A grim warning, bought at the price of a spoiled, wayward son who fomented disaffection and led rebellion triggering civil war and needless death and destruction, ending in his own death and that of many others.

Behind the Proverbs lies the anguished wailing of a father who had to fight a war with his son and in the end cried out, Oh Absalom, my son . . .

History sorts out the follies of literary excesses, if we fail to heed wisdom in good time.

Often, at the expense of a painful, bloody trail of woe and wailing that leads many mothers and fathers, widows and orphans to wail the loss of good men lost to the fight in the face of rampant folly.

But then, tragic history is written into my name, as George William Gordon’s farewell to his wife written moments before his unjust execution on sentence of a kangaroo court-martial, was carried out:

My beloved Wife, General Nelson has just been kind enough to inform me that the court-martial on Saturday last has ordered me to be hung, and that the sentence is to be executed in an hour hence; so that I shall be gone from this world of sin and sorrow.

I regret that my worldly affairs are so deranged; but now it cannot be helped. I do not deserve this sentence, for I never advised or took part in any insurrection. All I ever did was to recommend the people who complained to seek redress in a legitimate way; and if in this I erred, or have been misrepresented, I do not think I deserve the extreme sentence. It is, however, the will of my Heavenly Father that I should thus suffer in obeying his command to relieve the poor and needy, and to protect, as far as I was able, the oppressed. And glory be to his name; and I thank him that I suffer in such a cause. Glory be to God the Father of our Lord Jesus Christ; and I can say it is a great honour thus to suffer; for the servant cannot be greater than his Lord. I can now say with Paul, the aged, “The hour of my departure is at hand, and I am ready to be offered up. I have fought a good fight, I have kept the faith, and henceforth there is laid up for me a crown of righteousness, which the Lord, the righteous Judge shall give me.” Say to all friends, an affectionate farewell; and that they must not grieve for me, for I die innocently. Assure Mr. Airy and all others of the truth of this. Comfort your heart. I certainly little expected this. You must do the best you can, and the Lord will help you; and do not be ashamed of the death your poor husband will have suffered. The judges seemed against me, and from the rigid manner of the court I could not get in all the explanation I intended . . .

Deconstruct that, clever mocking scorners of the literary seminar room.

Deconstruct it in the presence of a weeping wife and mother and children mourning the shocking loss of a father and hero to ruthless show-trial injustice ending in judicial murder.

Murder that echoes the fate of one found innocent but sent to Golgotha because of ruthless folly-tricks in Jerusalem c. 30 AD.

(How ever so many fail to see the deep lesson about folly-tricks in the heart of the Gospel, escapes me. New Atheists and fellow travellers, when you indict the Christian Faith as the fountain-head of imagined injustice, remember the One who hung between thieves on a patently unjust sentence, having been bought at the price of a slave through a betrayer blinded by greed and folly. If you do not hear a cry for just government and common decency at the heart of the Gospel you would despise, you are not worth the name, literary scholar or educated person.)

And in so doing, learn a terrible, grim lesson of where your clever word games predictably end up in the hands of the ruthless.

For, much more than science is at stake in all of this.

GEM of TKI  >>

_________________

I trust that the astute onlooker will be inclined to indulge so personal a response, and will duly draw on the hard-bought lessons of history (and of my family story . . . ) as just outlined. END

PS, Sept 30: ES has been making heavy weather over the idea of a primitive tribe encountering a can opener for the first time and not understanding its function (which he then wishes to project as subjective):

A rotating cutter can opener in action
A rotating cutter can opener in action

And, a modern development showing meshing serrated gears:

modern rotary action can opener with meshing gears (Both images HT Wiki)
modern rotary action can opener with meshing gears (Both images HT Wiki)

However, this is both incorrect and irrelevant to recognising from aspects of the can opener that exhibit FSCO/I, that it is designed:

1 –> Whether or not the primitive seeing an opener for the first time can recognise its purpose and contrivance that integrates materials, forces of nature and components into a functioning whole, that functionally specific, complex organisation for a purpose exists and is embedded in how the opener is designed.

2 –> Just by looking at the evident contrivance manifested in FSCO/I that is maximally unlikely to obtain by blind chance and mechanical necessity — as with the fishing reel above, the primitive is likely to perceive design.

3 –> The rotating gears with matched teeth set to couple together alone implies highly precise artifice to build centred disks, cut matching gearing, mount them on precisely separated and aligned centred axes, with other connected parts already demonstrates design to a reasonable onlooker.

4 –> The precisely uniformly thick handles joined in a pivot, and reflecting rectangle-based shapes would be equally demonstrative.

5 –> Where, actual intended function has not been brought to bear. (And note, we see here again the implicit demand that the design inference be a universal decoder/ algorithm identifier. That is a case of setting up and knocking over a strawman, where . . .  just on theory of computation, such a universal decoder/detector is utterly implausible. The point of the design inference is that on inductively confirmed reliable signs such as FSCO/I we may confidently identify design — purposefully directed contingency or contrivance — as key causal factor. It seems that any number of red herrings are led away from this point to convenient strawman caricatures that are then knocked over as though the actual point has been effectively answered on the merits. It has not.)

6 –> But of course, that functionality dependent on specific components and an arrangement otherwise vanishingly improbable, reeks of design and the function can be readily demonstrated, as the patents diagram shows.

7 –> Where, again, it must be underscored that, per my comment 49 to ES:

[the] ultra-modernist, ugly- gulch- between- the- inner- world- and- the outer- one [of] sophomorised Kantianism fails and needs to be replaced with a sounder view. As F H Bradley pointd out over a century ago, to pretend to know that the external world is un-knowable due to the nature of subjectivitiy . . . the denial of objective knowledge . . . is itself a claim to objective knowledge of the external world and a very strong one too. Which therefore is self-referentially incoherent. Instead, it is wiser to follow Josiah Royce’s point that we know that error exists, undeniably and self evidently. Thus, there are certain points of objective knowledge that are firm, that ground that objective truth, warrant and knowledge exist, and that schemes of thought that deny or denigrate such fail. Including post modernism, so called. Of course, that we know that error exists means we need to be careful and conservative in knowledge claims, but the design inference is already that, it is explicitly inductive on inference to best explanation on observed patterns and acknowledges the limitations of inductive knowledge including scientific knowledge. [A Po-Mo] selectively hyperskeptical focus on the design inference while apparently ignoring the effect of that same logic on science as a whole, on history, on common sense reality and on reason itself, simply multiplies the above by highlighting the double standard on warrant.

8 –> In short, we have here a case of clinging to an ideological absurdity in the teeth of accessible, well-warranted correction.

259 Replies to “FTR: Answering ES’ po-mo antics with the semantics of “function”

  1. 1
    kairosfocus says:

    PS: I regret having to showcase ES, who must be feeling a bit battered, but I believe there is a need to speak for record, not merely in a soon-buried comment. KF

  2. 2
    E.Seigner says:

    kairosfocus

    PS: I regret having to showcase ES, who must be feeling a bit battered, but I believe there is a need to speak for record, not merely in a soon-buried comment. KF

    No problem, dude. Let’s hope that this thread will become famous so I have the opportunity to deconstruct how profoundly you have misinterpreted and misrepresented me. But I will be telling it to others, not you, because your magnitude of miscomprehension is in a league of its own, something I have never seen before, evidently futile to engage with directly.

  3. 3
    kairosfocus says:

    F/N: I have added some more images to make the matter plain. KF

  4. 4
    kairosfocus says:

    ES: That one is the twist-about, turn-speech accusation. You plainly have tried to obfuscate the concept of specific, observable objective function pivoting on particular organisation, arrangement and coupling of parts, based on injecting subjectivism and semantic techniques championed in our day by the deconstructionists and other so-called post modernists . . . they are actually reductio ad absurdum ultra-modernists, with the dial firmly set on eleven, not a mere ten. When, all along, if FSCO/I was a failure as a claimed reliable sign of design as cause, a direct, credible counter example showing how the needle in haystack problem has been on observation solved by blind chance and mechanical necessity would be sufficient. And, no, given the cost of the lessons, I do not draw back from underscoring what the march of folly predictably leads to. KF

  5. 5
    kairosfocus says:

    F/N: In case the onlooker needs further warrant about the po mo absurdities ES has indulged, kindly note this comment from the merry go round thread in reply to ES’ attempt to po mo-ise English rather than acknowledge that a Shakespeare cite is patently FSCO/I but random keystrokes are not and the difference on FSCO/I reliably and correctly indicates design of the clip from Hamlet’s Soliloquy:

    20 kairosfocus September 25, 2014 at 1:21 am

    ES:

    You have failed to reckon with the issue I raised above, complexity + functional specificity tied to a given aspect, instead substituting a strawman caricature of the design inference process and resulting explanatory filter.

    Complexity by itself is generally explicable on chance.

    Toss a string of 500 H/T coins and the resulting 72 or so letter ASCII character string is complex. With all but certainty it will not spell out text in English that is contextually responsive (or evasive).

    If you come across such a string of coins with the code equivalent to the first 72 or so characters of this post, then with moral certainty, it was designed.

    This has to do with the search-space, search resource, target zone needle in haystack search challenge already highlighted to you but which you refuse to acknowledge as existing.

    Based on this from the Feser thread, it seems you are now in the unenviable position of clinging to absurdities to deny the patent but unwelcome:

    Feser thread, 314:

    E Seigner: There’s no inherent design of English in written text, but a social convention called English.

    SB: You don’t think that authors design their paragraphs?

    Reductio ad absurdum.

    Game over.

  6. 6
    StephenB says:

    kairosfocus, excellent post as usual.

    ES holds that design is projected onto the object and is not recognized as existing in the object. In other words, design is in the beholder, not in the object. We are told that ID, because of its cultural bias, projects design onto the organism; Dawkins, because of his cultural bias, projects non-design onto the organism—and that’s that. Naturally, this would rule out any kind of design inference in principle.

    With this philosophy, humans are simply not capable of inductive reasoning. An archeologist cannot detect design in an ancient hunter’s spear. Indeed, he may well project his design bias onto the rock and call it a spear, or he may project his anti-design bias onto the spear and call it a rock—and away we go. Rationality has gone out the window. This is what post-modernism has done to the human mind.

    One form of this madness goes by the name of “deconstructionism.” When an author establishes a theme with meaning and expresses that meaning in comprehensible prose, the deconstructionist takes it upon himself to project whatever meaning he chooses onto the written text. Hence, the author’s intended meaning is deconstructed and transformed into the biases and prejudices of the reader.

    Exegesis = To read out of the passage what is already there.

    Eisegesis = To read in to the passage what one chooses to be there.

  7. 7
    anthropic says:

    Thanks for the time & effort you put into this, KF! As you say, the objective (might I say function? ;)) of your disquisition is not to slam ES. Rather, it is to confront post modern thinking.

    I’m an educator who touches on worldview/philosophy issues and will use some of your thoughts in class. Bravo!

  8. 8
    Barry Arrington says:

    KF, rarely does a blog post rise to the level of literature. This one has. Thank you.

  9. 9
    E.Seigner says:

    StephenB

    We are told that ID, because of its cultural bias, projects design onto the organism; Dawkins, because of his cultural bias, projects non-design onto the organism—and that’s that.

    Both ID theory and Dawkins project design onto the organism. Dawkins has a book on it, The Blind Watchmaker. The difference between ID theorists and Dawkins is that Dawkins doesn’t admit the designer.

    Projecting some structure or pattern is a necessary precondition to make any sense of anything. Everybody does it. It’s better to know that we are doing it, instead of to be in denial and to assume that it’s all objective. For example, mathematically educated people are hard-pressed to not see a rectangle here http://www.tanveernaseer.com/w.....lusion.jpg while smaller children only see pacman shapes.

    Projection of patterns has nothing to do with postmodernism. It’s a well-studied fact of sense-perception.

    StephenB

    An archeologist cannot detect design in an ancient hunter’s spear. Indeed, he may well project his design bias onto the rock and call it a spear, or he may project his anti-design bias onto the spear and call it a rock—and away we go. Rationality has gone out the window.

    No, rationality is not out of the window. This is how rationality works. Rationality is not empirical and objective, but this doesn’t mean that it cannot work. It’s just that it’s better to know how it works. It won’t do to reject off-hand what is common knowledge in cognitive sciences.

    StephenB

    One form of this madness goes by the name of “deconstructionism.” When an author establishes a theme with meaning and expresses that meaning in comprehensible prose, the deconstructionist takes it upon himself to project whatever meaning he chooses onto the written text.

    Deconstruction means the same as reverse engineering. Youare doing the same thing under a different name. Besides, can you tell the difference between postmodernism, poststructuralism, classical structuralism, and objectivism, all of which share the concept? Nah, you are not really interested in where I am coming from. You are just interested in bashing, even when you inadvertently ridicule your own methods in the process.

  10. 10
    kairosfocus says:

    ES: In my life, I have designed many things, from text, to hand carved fishing lures for personal use, to instrumentation to microprocessor controlled systems, to degree programmes to organisations and policies. In none of these systems is the design merely a figment of my imagination. Yes, purpose is mental, concepts are mental. But once a design is effected (even as a sketch much less as an artifact) that framing has moved to objective territory, and the integrated contrivance that results is full of functionally specific, complex organisation and associated information. Which, is manifest in the soundness of the process logic and construction, as well as in the acid test of working robustly and durably. A skilled person can often reverse engineer from such an artifact to design specification by “reading” the embedded prescriptive, function specifying information. In addition, as has been repeatedly pointed out to you — but obviously has been obstinately ignored in a clinging to patent absurdity — once the relevant specifying information passes a threshold of 500 – 1,000 bits of information the likelihood that such could arise by blind chance and mechanical necessity is vanishingly small. Now, I cannot make you acknowledge sense, but in the name of blood needlessly shed because of many marches of folly, I can warn. Warn, that the poison of radical subjectivism amplified by ultramodernist fads, refuses to learn from sobering history and as Santayana warned, is doomed to repeat its worst chapters. Warn, with of all people Karl Marx, that this is why history repeats, first as tragedy then as farce. Do not make your father wail, Oh Absalom, . . . KF

  11. 11
    StephenB says:

    SB: We are told that ID, because of its cultural bias, projects design onto the organism; Dawkins, because of his cultural bias, projects non-design onto the organism—and that’s that.

    Both ID theory and Dawkins project design onto the organism.

    There you go. You might as well have said, “guilty as charged.”

    SB: We are told that an archeologist cannot detect design in an ancient hunter’s spear. Indeed, he may well project his design bias onto the rock and call it a spear, or he may project his anti-design bias onto the spear and call it a rock—and away we go. Rationality has gone out the window.

    No, rationality is not out of the window. This is how rationality works.

    Again, you might as well have said, “guilty as charged.”

    Deconstruction means the same as reverse engineering.

    Nonsense

    Deconstructionism

    “A philosophical movement and theory of literary criticism that questions traditional assumptions about certainty, identity, and truth; asserts that words can only refer to other words; and attempts to demonstrate how statements about any text subvert their own meanings: “In deconstruction, the critic claims there is no meaning to be found in the actual text, but only in the various, often mutually irreconcilable, ‘virtual texts’ constructed by readers in their search for meaning”

    or, again,

    A late twentieth-century theory of literature that concentrates on finding “ruptures” or inconsistencies in a text, thus enabling the critic to break down or “deconstruct” it. Such deconstruction consists of asserting a personally or communally relative interpretation (usually focused on power relations or class conflict in society) without claiming that any text or interpretation has objective truth or meaning. Deconstructionism is a specific kind of postmodernism, and leans heavily toward subjectivism or even nihilism.

    This is the same philosophy that you are applying to the ID debate. You are saying, in effect, that ID (or anyone else) is incapable of drawing an inference from data and can only project “a personally or communally relative interpretation” on the evidence.

  12. 12
    kairosfocus says:

    Anthropic, thanks. I suggest the NWE links will prove useful. In addition, when I taught an intro phil course, I spoke to post-/ultra- modernism here, which may prove useful. We must never ever forget that the key lessons of history were paid for in blood . . . an infinitely precious thing. Often, innocent blood like that of my grandmother’s great uncle, whose “crime” was to speak the truth in warning to a stubborn and oppressive colonial house of assembly that stirred their ire and then led them to scapegoat and judicially murder him when the explosion he sought to avert came. Five or six hundred were hanged or shot, hundreds more flogged, a thousand houses were burnt, and more. All in retaliation for a riot, admittedly a bloody one, after a petition to Queen Victoria for famine help and relief — doubtless misunderstood because of idiot advice from the same Governor Eyre who was implicated in the Irish potato famine — was foolishly answered; a riot triggered in reaction to an over the top flogging sentence against praedial larceny by men with hungry children. Sound history, we must heed, on pain of negligent homicide or worse. A lesson (one of several) literally written into my name in accordance with my family’s tradition. KF

  13. 13
    kairosfocus says:

    SB: Thanks, your amplification is well appreciated. One hopes there is enough of a spark left in ES that he will wake up from his dogmatic, indoctrination-induced slumbers. And that many others like him will wake up before the march of irrational folly and disconnect from reality has gone too far. For, folly like that predictably ends in blood. But then, warning in the face of stubborn folly is a bit of a family tradition for me. There are other cases with other members, a lot closer to home. KF

  14. 14
    E.Seigner says:

    StephenB

    There you go. You might as well have said, “guilty as charged.”

    Or you could have dealt with the evidence: Dawkins’ book The Blind Watchmaker, the scientific knowledge accumulated in cognitive sciences, and the differences between postmodernism, poststructuralism, classical structuralism, and objectivism. But of course you are more comfortable with your preconceived ideas.

    No problem. As cognitive science says, preconceived ideas is exactly how these things work, and your behavior is proving the point. More open-minded people would be more open to evidence, but you are neatly categorizing yourself here.

  15. 15
    Mung says:

    Plants and animals really do exist. They are not projections of the human mind.

    Square circles do not exist. It is not possible for the human mind to project a square circle into non-existence.

    E.Seigner

    Projecting some structure or pattern is a necessary precondition to make any sense of anything.

    What are these projections based on? From whence do they arise? We must rule out that they arise from observation, because observation is projection.

    Further, if there is nothing there to be sensed, what triggers the act of projection?

    Perhaps this is just another mis-understanding over terms. What do you mean when you say “projecting some structure or pattern”?

  16. 16
    kairosfocus says:

    BA, thanks for some kind words. I hope our civilisation wakes up before it is too late. KF

  17. 17
    kairosfocus says:

    ES: Perhaps, you can find the time to glance here, and maybe at the Plato’s cave parable from the perspective of dealing with a manipulated public, and how sound worldviews thought can help, here — yes, The Republic. My Worldviews construction 101 here on may just open up a different path to build a saner worldview than what has been drummed into you through clever rhetoric in the name of education. You need to wake up from your dogmatic, indoctrination induced slumbers. KF

  18. 18
    kairosfocus says:

    Mung, Among other things, ES needs to realise the self referential incoherence implicit in the Kantian-style ugly gulch between the inner world and the outer one. As F H Bradley long ago pointed out, to claim that one cannot know external objective reality is an implicit holding of a very strong knowledge claim about such, its un-knowability. That is, it is self-referentially incoherent. Far sounder is the Josiah Royce claim, Error exists . . . which is undeniable and self-evident as I show in my worldview 101 here. That first self evident truth does great execution across the field of radically relativist and subjectivist views; clearing the way for a more balanced view. KF

  19. 19
    Barry Arrington says:

    KF, you are welcome. Thank you for patiently walking ES through the reasoning for the sake of the lurkers who might have been impressed and/or mislead by his sophistry. You point him to Plato – i.e., you have pointed him to reason and logic. You might as well have pointed a jackass to Mozart. They would both be equally edified.

    I take that back. The jackass would likely be more edified; perhaps he might at least take some pleasure from the soothing tones. ES takes no pleasure from instruction, and disdains correction. You see, such as ES in embracing post modernism have rejected what they call “western logic.” Of course, reason and logic are not bound by geography. There is no such thing as “western logic.” There is only “logic.” Reality is the wall you smack into when you’re wrong. Sadly, if ES’s antics are a harbinger (and I fear they are), I see our civilization heading for that wall.

  20. 20
    E.Seigner says:

    Mung

    Plants and animals really do exist. They are not projections of the human mind.

    Do you think their taxonomy is objectively real or is it man-made? Plants and animals are empirically real, but the way we categorize and classify them is open to interpretation. It has changed significantly over the millennia and still displays marked cultural differences. For example the bat is called Fledermaus in German, because it was evidently understood as a kind of mouse or mouse-like animal in the past.

    Mung

    What are these projections based on? From whence do they arise? We must rule out that they arise from observation, because observation is projection.

    We inevitably observe and perceive as we grow up, and we cannot simply store all the sense-data as it hits us. We must categorize, generalize, abstract, sort, explain, etc. All these mental actions are really subjective. Only general education keeps a kind of cohesion in place within the boundaries of one culture. Meet a person of another culture, face a different world view.

    Mung

    Further, if there is nothing there to be sensed, what triggers the act of projection?

    Assuming boldly that I understand the question, try the following. Sit in a silent pitchdark room without moving, eyes closed, for a while. Within a minute you will begin to see shapes, memories arise, you begin to plan stuff, and sitting still becomes intolerable. In a silent dark room there’s objectively nothing to hear and see, but within a minute we conjure up stuff for ourselves to perceive. What triggers this? This is what the mind is used to do. It actually requires serious practice to undo mental habits. Now, instead of denying these mental habits, it’s rational to acknowledge and study them. It helps to face reality with a clearer head.

    Mung

    What do you mean when you say “projecting some structure or pattern”?

    Come on, I even illustrated this with a picture in #9 http://www.tanveernaseer.com/w.....lusion.jpg

  21. 21
    Mung says:

    ES,

    There’s nothing to see at that link. I don’t understand. =P

    Is that your point, that there’s nothing out there, that everything is just a projection of the human mind?

    You’re not a realist?

    Are you projecting the content of the posts you read here at UD? Is that why you seems to not read the same text that I thought I wrote? But then how is it that you have any expectation that I am actually reading what you wrote?

    Given such a “projectionist” view of things how is communication even possible?

    In fact, to get back to the original issue:

    Projecting some structure or pattern is a necessary precondition to make any sense of anything.

    If I have to project some structure or pattern to see what you write and you have to project some structure or pattern to see what I write, how is communication possible?

    There has to be some structure or pattern or “form” that exists independently of what we project else how can we communicate?

    I’ll ask again, in case I just don’t understand what you mean:

    What do you mean when you say “projecting some structure or pattern”?

    Do you mean imagining some structure or pattern that isn’t really there?

    Projection of patterns has nothing to do with postmodernism. It’s a well-studied fact of sense-perception.

    Well, thank God you don’t deny sense-perception. Whew!

    So we agree that there really is something there that can be perceived by the senses.

    But it is your claim that the pattern or structure or shape of whatever it is that is out there that is being perceived is not really present in the thing being sensed?

    I have to be completely misreading you. You have someone here who isn’t out to misrepresent you, who wants to hear what you have to say and understand it on your terms. Help me out here.

  22. 22
    E.Seigner says:

    Mung

    There’s nothing to see at that link. I don’t understand. =P

    It’s an image of pacman shapes placed so that you will be hard-pressed not to “see” a square in it. But the square is not drawn in the picture, is it? If it’s not really drawn there, but you see it, then you are projecting it. Any other optical illusion conveys the same point.

    Mung

    Is that your point, that there’s nothing out there, that everything is just a projection of the human mind?

    Of course not, as should be evident from my previous comment. My point is a rather modest and common sense fact that our preconceived notions color our observations and this is something to be seriously reckoned with. For example, you might want to argue that something called “English” is objectively here on the webpages, but to determine this, one must learn the thing called “English” (it’s not my first language, by the way), so already this fairly low-profile observation depends on the background information of the observer – if the observer doesn’t know English, he will be unable to “detect” English here, so how can you say that English is *objectively* here? That we speak English here is properly called a contextual intersubjective fact rather than objective.

    Mung

    Are you projecting the content of the posts you read here at UD? Is that why you seems to not read the same text that I thought I wrote? But then how is it that you have any expectation that I am actually reading what you wrote?

    Given such a “projectionist” view of things how is communication even possible?

    Tone down your assumptions and communication becomes possible.

    Mung

    If I have to project some structure or pattern to see what you write and you have to project some structure or pattern to see what I write, how is communication possible?

    There has to be some structure or pattern or “form” that exists independently of what we project else how can we communicate?

    When we both project something we have in common, say English grammar, then communication is possible. When the text is replete with something we don’t share, such as ID-ese which is a stumbling block for me or the facts of cognitive sciences which you seem oblivious of, communication is obstructed.

    Mung

    What do you mean when you say “projecting some structure or pattern”?

    Do you mean imagining some structure or pattern that isn’t really there?

    Take a look at the image again http://www.tanveernaseer.com/w.....lusion.jpg Is the square really there? What I’m saying is not that the square isn’t there, but that projection is real and even necessary for basic communication. English grammar isn’t objectively or physically real, but it’s intersubjectively real and really enables communication. Spaces between words are just thin air, but they really help communication.

    Mung

    But it is your claim that the pattern or structure or shape of whatever it is that is out there that is being perceived is not really present in the thing being sensed?

    Are you completely unfamiliar with, for example, the claim of physics that in the nanolevel we are just atoms that constantly enter and leave the “body”, atoms who have lots of space between them so that on that level we are basically transparent and the “body” is just a higher-level construct that *seems* solid due to chemical and magnetic cohesion, but “fundamentally at the basic level” is not solid? It’s not postmodernism that came up with these things. If you are unfamiliar with this, then I must doubt if people here have seriously thought through a single scientific claim. And no, this physicalist claim is not my ultimate thesis, but it’s definitely something you should be familiar with, if *you* don’t want to seem outlandish. This physicalist claim emphasizes how profoundly mind is involved in perception, and this mental involvement is a real fact to be reckoned with, not imaginary. It’s a basic fact of cognitive sciences.

    Everything said about my connection to postmodernism in the OP is purely KF’s hallucination. Based on the few quotes he has from me there, it takes quite a leap and deliberate *projection* to draw the connection he draws. The world is not so small. My views can have totally different background connections and in fact they do.

  23. 23
    kairosfocus says:

    ES:

    Your diagram is an inadvertent example of indoctrination in action.

    You have four circles with v-nicks that just happen to be right angles and by chance happen to be perfectly aligned with the vertices and straight-line sides of a square, which our crotchety, buggy brain circuits and visual system just happen to project into a square.

    NOT!

    The odds that four equal-sized circles with right angled notches will pop up out of noise and magically find themselves perfectly aligned with the geometry of a square by blind chance and/or mechanical necessity are vanishingly small.

    The visual system, designed to spot patterns, is not being fooled, it is not projecting what is not really there, it is properly identifying a square aligned pattern and inferring the presence of a square. Actually, recognising.

    Why do I say that?

    Because I was classically trained in geometry, and so was taught that the sketches we use on paper, on chalk boards and in textbooks etc are representative.

    A point is a location, it has no size (the blob suggests the point, it is not the point). A line has length but no thickness, indeed it is the locus of a point constrained to “move” spatially based on a rule, or in more strict terms, a set of points conforming to a rule.

    So, nope, the square is there, and its presence was used to define the figure presented to us.

    But, because of dogmatic indoctrination induced resistance to recognition of design, you have mistaken the situation for an illusion.

    There are illusions that exploit the visual system’s processing through insights from Gestalt Psychology. There are after-images that can even lead to spotting coloured flags etc. There is a blind spot, covered over with a smoothing process.

    None of these suffices to support the notion that designs cannot be embedded in objects, and “read” out from them.

    Please wake up from your dogmatic slumbers.

    KF

  24. 24
    Joe says:

    E Seigner:

    Both ID theory and Dawkins project design onto the organism.

    That is your opinion and it is only an opinion.

  25. 25
    Box says:

    E.Seigner:

    If a conscious observer connects some observed object to some possible desired result which can be obtained using the object in a context, then we say that the conscious observer conceives of a function for that object…. In science, properties of the material just are, without purpose, because everybody knows purpose is subjective.

    I tend to agree with E.Seigner here. Functionality is subjective and not an objective part of an object like a car, watch, electronic amplifier or whatever.
    However it is glaringly obvious to me that these artifacts are designed and that we are capable of inferring design. “Being designed” is an objective part of these artifacts.

  26. 26
    Silver Asiatic says:

    The heart doesn’t objectively have the function of pumping blood?

    Of course, we project the idea that anything is “an object” since everything is connected to the universe, thus there are no independent objects – just a universe (there is nothing objective about the heart being separate from veins, from cells, from molecules), which is connected to an infinite multiverse, thus no independent universe.

    In a pantheist view, everything is connected to Spirit and thus there is no material universe – only Spirit.

    That certainly makes discussions a lot easier.

  27. 27
    gpuccio says:

    Box:

    If you look at my complete definitions here:

    http://www.uncommondescent.com.....n-defined/

    you will see that what I call “objective functionality” is a property of the object otself. It is the answer to the questio: “Can this object be used to effectively implement the function I have defined?” There is nothing subjective in that answer.

    Here are some of my definitions, for your convenience.

    That said, I will try to begin introducing two slightly different, but connected, concepts:

    a) A function (for an object)

    b) A functionality (in a material object)

    I define a function for an object as follows:

    a) If a conscious observer connects some observed object to some possible desired result which can be obtained using the object in a context, then we say that the conscious observer conceives of a function for that object.

    b) If an object can objectively be used by a conscious observer to obtain some specific desired result in a certain context, according to the conceived function, then we say that the object has objective functionality, referred to the specific conceived function.

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

  28. 28
    gpuccio says:

    Silver Asiatic:

    According to my definition (see previous post), the heart has the objective functionality of pumping blood if it can effectively pump it (in the right context). If it fails, it fails.

    So, a working heart has the objective functionality of pumping blood, a damaged one doesn’t.

    It is rather simple and pragmatical. And we can avoid all the philosophical questions about whether the function is in the object, or not.

  29. 29
    Box says:

    GPuccio:
    Thank you for your elucidation. I would like to make sure that I understand it correctly. Are you in accord with:

    b) If an object can objectively be used by a conscious observer to obtain some specific desired result in a certain context, according to the conceived intended function by the designer, then we say that the object has objective functionality, referred to the specific conceived function.

    ?

  30. 30
    E.Seigner says:

    gpuccio

    According to my definition (see previous post), the heart has the objective functionality of pumping blood if it can effectively pump it (in the right context). If it fails, it fails.

    So, a working heart has the objective functionality of pumping blood, a damaged one doesn’t.

    It is rather simple and pragmatical. And we can avoid all the philosophical questions about whether the function is in the object, or not.

    Actually, we cannot avoid the philosophical questions. When you label it “objective functionality” rather than mere “functionality” you are actively calling for philosophical debate on it.

    And I think Box’s question to you is intriguing 🙂

  31. 31
    gpuccio says:

    Box (and E. Seigner):

    No. I am not in accord.

    Try to understand. When we evaluate is an object exhibits dFSCI, we have only one thing: the object. That’s why I say that the design inference from dFSCI is context independent. We know nothing of the designer. We don’t even know if the object is a designed object. That’s exactly what we want to infer about.

    So, how can we know what the designer intended, is we don’t even know if the object is designed?

    Again, try to understand. My definition is completely empirical. We have an object. We, as observers, think of one or more functions for which we can use the object.

    In my post I made the example of a tablet, for which we define a function as a paperweight. Why not? let’s say that it has the correct weight ans dimensions to be used for that.

    Then, for the same object, we define the function of using it to execute a spreadsheet program and create a digital list of values on which we automatically make computations.

    This is another function fro the same object.

    Now, remember, we don’t know if the object was designed, and we don’t know, if it was designed, what it was designed for. We have only the object.

    We check, and we see that we can use well the object (the tablet) for both the functions we have defined.

    So, what can we say now? We have to compute the functional complexity fro each separate function.

    The functional complexity for a paperweight (if we define with precision which weight and range of forms we consider appropriate for the function) is not very high. IN a natural system (which we can well define, if we want to be precise) many objects can have those characteristics: a stone, for example. IOWs, we cannot infer design for a paperweight which can implement its function, because the function implies low functional information to be implemented.

    For the computer / spreadsheet function, instead, it’s all another matter. The functional complexity implied is very high. We don’t find non designed electronic computers / spreadsheets in nature. So, we can probably infer design for that kind of function, if we find an objects (the tablet) which implements it.

    As you can see, the intentions of the designer have no role in this reasoning. We can inquire about them after we have made a design inference for the object. That is perfectly correct.

    This example is very general, and includes functional specifications which are both analogic and digital, to give you an idea of the general concepts. More specific examples, with real computations, are much easier for strictly digital information. That’s why I usually debate dFSCI, and in particular its application to proteins. But, if the general ideas are clear, I can go on with digital examples.

  32. 32
    Box says:

    Gpuccio:

    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’m not sure I understand what you mean. Are you saying that we need a certain activity by a conscious observer for DNA to be objectively functional?

    BTW I do hold that parts of an organism (e.g. DNA) are objectively functional to the concerning organism.

  33. 33
    E.Seigner says:

    gpuccio

    Try to understand. When we evaluate is an object exhibits dFSCI, we have only one thing: the object.

    So, we only have one thing, the object, not the evaluator. How are we supposed to get to an evaluation of the object then? Trying hard to understand…

  34. 34
    Box says:

    Gpuccio:

    I do appreciate your post #31. Thank you. And I believe I understand the points you are making there.
    Based on my (personal) metaphysics I prefer a distinction between internal (e.g.DNA) objects and outward objects (e.g. a car) with respect to objective and subjective functionality. It follows from a huge divide between organisms and artifacts in my metaphysics. However this is of no interest to ID’s scientific ambitions. So let’s leave at that.
    I’m not quite happy with the way I worded my question in post #32. If it comes across as cynical I must inform you that this is most definitely not my intention.

  35. 35
    Dionisio says:

    #31 gpuccio

    When we evaluate if an object exhibits dFSCI, we have only one thing: the object.

    #33 E.Seigner

    So, we only have one thing, the object, not the evaluator. How are we supposed to get to an evaluation of the object then? Trying hard to understand…

    Isn’t it obvious from reading the above text that we are the evaluators?
    Are both sides in this discussion really interested in what is being discussed?
    Are both sides serious about this discussion?
    It doesn’t look like that’s the case. 🙁

  36. 36
    gpuccio says:

    Box:

    Thank you for your comments.I think I have clarified my perspective.

    Regarding #32, I simply mean that a conscious observer is needed to recognize and understand a function, define it, and then objectively verify that the object can be used to implement it. Without the function definition by the observer, the functionality of the object and the complexity needed for that functionality cannot be objectively assessed, because they are relative to a defined function.

    DNA is objectively functional, but to evaluate dFSCI for its function we must define that function and make the computation of complexity. There are various functions which can be defined for DNA (covey the information for individual proteins, convey specific regulatory information, and so on). For each of them, different complexities can be computed.

  37. 37
    gpuccio says:

    E. Seigner at #33:

    I suppose Dionisio has clearly answered you in #35. (Grazie, amico mio! 🙂 ).

  38. 38
    E.Seigner says:

    gpuccio

    I suppose Dionisio has clearly answered you in #35.

    Okay. So let’s recap:

    gpuccio: Try to understand. When we evaluate is an object exhibits dFSCI, we have only one thing: the object. That’s why I say that the design inference from dFSCI is context independent.

    Dionisio: Isn’t it obvious from reading the above text that we are the evaluators?

    ES: It was indeed obvious to me too and that’s why I asked about it. Therefore we don’t have only one thing, the object. We also have ourselves the evaluator. Therefore the design inference is not context independent, as we always carry background information in ourselves that enables evaluation. The subjective background information is always part of the context. Elsewhere you have said this about context: “As I have said many times, meaning is neither in the numbers nor in the context, but only in the consciousness of a cognizer. However, both numbers and context can generate meaning in a consciousness.” If it’s in the cognizer’s consciousness, then it’s subjective, dependent on background information based on which we evaluate.

  39. 39
    gpuccio says:

    E. Seigner:

    I don’t understand where you want to arrive. ID is science. Science is subjective, dependent on background information based on which we evaluate. Always. So is ID.

    When I say that the design detection based on dFSCI is context independent, I mean a very specific technical thing, and not a general philosophical principle. What I mean is:

    “We detect design because of properties of the object”

    as opposed to:

    “We detect design because of properties of the object and other information coming form other sources”

    For example, we could infer that an object is designed because we have a movie of the designer while he designs it, or because a book written by the designer tells us that he designed it.

    That would be design detection, but the inference of the design would be based on information which is not in the object.

    In ID, design detection is based on properties of the object itself: the functional complexity it exhibits.

    That is what I meant by “context independent”. I apologize if I was not more explicit, sometimes I probably confide too much in the creative intuition of my interlocutors, or simply in the strength of the context! 🙂

  40. 40
    E.Seigner says:

    gpuccio

    When I say that the design detection based on dFSCI is context independent, I mean a very specific technical thing, and not a general philosophical principle.

    Yes, I completely understand that you want to make it appear that you have avoided philosophical implications, but the fact is that you haven’t. In philosophy of science it’s recognized beyond question that science always derives at least from some philosophical presuppositions. You may want to minimize the presuppositions, and it’s okay to try, but you can never eliminate them. Moreover, the minimal set of assumptions embedded in your method had better be impeccably consistent. Otherwise the theory goes awry at its very foundation.

    By the way, not just science, but also philosophy is very specific and technical, and therefore requires training. Plus it’s categorical and imperative too. As a matter of principle, philosophical principles have no exceptions, only nuances. When you use terms like objective and subjective, you are inevitably treading the philosophical ground. You have nowhere to hide form this fact.

    “Objective functionality” is a philosophically suspicious concept already on the face of it. And when you want to make it appear categorically objective, it only gets more suspicious. Something like “behavior” or “operation” may be objective in the sense of “out there for everyone to see”, but *function* is what the thing does in relation to other things, and what the other things are depends on *context* where the thing happens to be. And the scope of the *context* depends on how the observer frames it. Therefore function (along with functionality, which is essentially the same thing) is not in the object and not objective. It is contextual and inevitably includes the subjective aspect.

    I have given another read to your post about functional information. In addition to what we’ve discussed, it says:

    c) Specification. Given a well defined set of objects (the search space), we call “specification”, in relation to that set, any explicit objective rule …

    Right there “objective” (the penultimate word in the quote) misplaced again. This is a philosophical category error, seriously. When you do an equivalent systemic error in computing, the program fails to run.

    It should be clear to everyone by now that my philosophy has nothing to do with wishy-washy relativist pomo as implied in the OP. Objective and subjective are clearcut absolute metaphysical categories in philosophy that shall not be infringed.

  41. 41
    Joe says:

    E Seigner:

    It should be clear to everyone by now…

    The only thing that is clear to everyone by now is that you don’t know jack about science.

  42. 42
    the bystander says:

    I have zero problem in inferring that not all Evolutionary process can be unguided, but I wouldn’t be satisfied with ID till some theory and explanation of how ID agent works is put up.

  43. 43
    gpuccio says:

    E. Seigner:

    Thank you for the comments. I think we are getting to something, not much, but something.

    Yes, I completely understand that you want to make it appear that you have avoided philosophical implications, but the fact is that you haven’t. In philosophy of science it’s recognized beyond question that science always derives at least from some philosophical presuppositions. You may want to minimize the presuppositions, and it’s okay to try, but you can never eliminate them. Moreover, the minimal set of assumptions embedded in your method had better be impeccably consistent. Otherwise the theory goes awry at its very foundation.

    I don’t want to avoid philosophical implications. It’s an essential part of my philosophy of science tha they cannot be avoided, and I have defended that position many times here.

    I just want to avoid some philosophical implication that are not appropriate, in the parts of the scientific discussion where they are not pertinent.

    I agree with the rest that you say here. However, I am convinced, without any false modesty or pride, that “the minimal set of assumptions embedded in my method” are “impeccably consistent”. You are free to think differently, and possibly to try to explain why.

    When you use terms like objective and subjective, you are inevitably treading the philosophical ground. You have nowhere to hide from this fact.

    Yes and no. I don’t want to hide form anything. But for me “subjective” and “objective” have a very definite empirical meaning. “Subjective” is anything that is experienced by the I in consciousness. “Objective” is all that we assume exists outside consciousness, and interacts with it.

    In my view, empirically, all that we experience is subjective. But I am not a solipsist, so I happily accept the inference, vastly shared by all, that objects and other subjects exist. So, my map of reality includes both subjects and objects. Those assumptions are not negotiable, for me, but I understand that some people can well refute them. Our approaches to science will therefore be different As you say, “science always derives at least from some philosophical presuppositions”. I agree, and definitely stick to mine.

    “Objective functionality” is a philosophically suspicious concept already on the face of it. And when you want to make it appear categorically objective, it only gets more suspicious. Something like “behavior” or “operation” may be objective in the sense of “out there for everyone to see”, but *function* is what the thing does in relation to other things, and what the other things are depends on *context* where the thing happens to be. And the scope of the *context* depends on how the observer frames it. Therefore function (along with functionality, which is essentially the same thing) is not in the object and not objective. It is contextual and inevitably includes the subjective aspect.

    This is simply bad reasoning, or simply you don’t understand my point. You may keep your suspicions, but in case it is only a misunderstanding, I will explain it again.

    The function is completely subjective. I, as an observer, see the object and conceive a function. Any function. I am completely free. It is a purely subjective choice. So, I see ATP synthase in bacteria and I conceive a function for it: it generates biochemical stored energy in the form of ATP from a gradient of protons. OK, I conceive that function because I see what happens in the cell, but that is not really the point. The point is: I conceive subjectively that function for that molecule.

    The second step is very important: I define the function and a way to assess it. Here, my conception is transormed in something objective. I come out with a definition like:

    “My function” consists in the ability of any molecule to generate ATP from a proton gradient in a specific cellular environment (let’s say bacteria) with a minimum efficiency of x molecules per hour per gradient unit”. Or something like that: I am not a biochemist, so I apologize for any gross imprecision in the language.

    Now, that is objective, because it is a verbal definition with objective procedures. It can be shared, used and reproduced by all. It’s what in a scientific paper would be part of the methods section: “We define as “my function” the ability of any molecule…”

    The third step is: I verify that the molecule I observe implements that function. That is easy. We already knew that.

    The fourth step is: I evaluate how many bits of the sequence in the protein are really necessary to implement the function (the target space) and compute the target space / search space ratio. We so that by the Durston method, or by other simple approximations. For example, for ATP synthase I have computed that the functional information is at least 1600 bits, even considering only two sequences (the alpha and beta subunit) and only the identities in AA positions. The true functional complexity of the whole molecule is probably much higher.

    The fifth step is: I choose an appropriate threshold. For biological molecules on our planet, I have suggested 150 bits as a very reasonable threshold to categorize functional information as complex or not complex. However, here with more than 1600 bits we are well beyond Dembski’s UPB of 500 bits, which is enough for any object in the whole universe.

    The sixth step is: we seriously wonder: are there any algorithmic necessity mechanisms in the system and the time span which could explain the generation of that sepcific functional molecule, beyond probability barriers.

    The easy answer for ATP synthase is: no. I will not debate the details here, because in general I see that you are not much interested in biological details. But I can do it if you request it.

    The seventh step is: I infer design as the best scientific explanation available for ATP synthase.

    That’s all. These are the facts and procedures that you must criticize. Concretely. With understandable and specific arguments.

    So, to sum up: the function is subjective. But, if we give an objective definition of it and how to assess it, the answer to the question: “Can this object be used in this specific context to implement that function?” is definitely objective, at least in the measure that is useful in science.

    Right there “objective” (the penultimate word in the quote) misplaced again. This is a philosophical category error, seriously. When you do an equivalent systemic error in computing, the program fails to run.

    See previous point. A procedure which is explicit and reproducible is “objective” in science. We can rely on it, because it will give the same results (allowing for the inevitable and acceptable errors which are always possible in any procedure) whenever we use it in controlled conditions. All empirical science is base on that kind of “objectivity”.

    For example, if I want to know if a drug is useful in healing a disease, I make experiments and record the results and analyze them. And infer conclusions which have scientific validity.

    Measuring a biochemical function in a lab in controlled conditions is much more reproducible than that.

    It should be clear to everyone by now that my philosophy has nothing to do with wishy-washy relativist pomo as implied in the OP. Objective and subjective are clearcut absolute metaphysical categories in philosophy that shall not be infringed.

    I have no problems with your philosophy. I think that you use it inappropriately in a scientific context.

  44. 44
    gpuccio says:

    the bystander:

    “I have zero problem in inferring that not all Evolutionary process can be unguided, but I wouldn’t be satisfied with ID till some theory and explanation of how ID agent works is put up.”

    I have suggested many times my possible scenario: some conscious intelligent purposeful agent, probably not physical, interacts with biological matter exactly in the way that our consciousness interacts with our body and brain: through a consciousness / matter interface, probably implemented at quantum level, so that no natural laws needs to be violated.

    It’s only a suggestion, but I find it believable and subject to inquiry.

  45. 45
    E.Seigner says:

    @gpuccio

    We have an agreement here:

    A procedure which is explicit[ly defined] and reproducible is “objective” in science. We can rely on it, because it will give the same results …

    But on both philosophical and scientific grounds I still have quibble with this:

    So, to sum up: the function is subjective. But, if we give an objective definition of it and how to assess it, the answer to the question: “Can this object be used in this specific context to implement that function?” is definitely objective, at least in the measure that is useful in science.

    Definitions are not objective. They are just definitions. Definitions and methodology are used to frame the situation so that it would become impartially experimental and empirically testable, and when this is achieved, yes, it’s called “objective” in science. However, all this defining and framing doesn’t make the procedure of defining and framing itself magically objective. The procedure itself remains subjective, but its measurable results are called scientifically objective inasmuch as they are reliably reproducible by other scientists.

  46. 46
    Joe says:

    the bystander:

    I have zero problem in inferring that not all Evolutionary process can be unguided, but I wouldn’t be satisfied with ID till some theory and explanation of how ID agent works is put up.

    So we couldn’t say that Stonehenge was designed until we knew how it was constructed?

  47. 47
    gpuccio says:

    E. Seigner:

    But I have never said that the “definition” in itself is objective in some absolute sense. What I mean is that the definition must be explicit and objective in a procedural sense.

    IOWs, I define a function (and there is no pretense at all that the function itself is “objective” in any philosophical sense). Let’s say that the function definition is a procedural convention we adopt. I define explicitly the kind of result which corresponds to an assessment of the function as present or not present.

    You see, the function in itself is not important. That’s why any observer can define any possible function, and give any possible procedure to assess its presence when the object is used in a specific context.

    This is probably the reason why many don’t understand my reasoning: they think that the function is important. No. What is important is the complexity necessary to implement the function.

    So, let’s say we have a computer program which can do something. I define that something, so that I can for any possible computer program verify if the function is present or not. It is not important what the function is: it could be ordering a list, or answering some mathematical problem given in input, or printing excerpts from a book. It’s not important.

    What is important is: how many bits do I need, at least, to have that result in my computer environment?

    So, I may have a 20 bit program which makes something very important (like giving a key to open a database) or a 1 million bit program which make something very trivial (like ordering a simple list). What is important is the minimal complexity of a program which can do what I have defined.

    The idea is that no sequence which can do something which requires a minimum complexity of n bits (let’s say 500, to stay in the UPB) will ever arise spontaneously in a real system by a random search/walk.

    So, the functions that we can subjectively conceive can be divided into “simple” and “complex” according to the number of bits that are required to minimally implement them according to an explicit assessment procedure.

    Objects which have a configuration of matter which conveys the bits necessary for a complex function are always designed (this is an empirical observation).

    Therefore, we can use functional complexity to infer that an object is designed.

    It’s very simple, as you can see. Empirical and simple.

    So, to sum up: the function definition and the procedure to assess it are subjective. That’s fine. But the observation that:

    “any function, assessed by any procedure, which requires more than n (let’s say 500) bits to be implemented is a reliable marker of design in an object that can be used to implement it”

    is an objective and reproducible observation.

    That empirical observation is the basis to use the dFSCI tool to infer design.

  48. 48
    kairosfocus says:

    TB: How design is carried out is separate from recognising that it has been carried out on signs. If you are genuinely interested in the matter, I suggest a glance at TRIZ which give a useful perspective on innovative non-routine, creative design or invention. Beyond, we already have in hand the work of Ventner et al on the world of micro-biology which already shows feasible ways to effect biological designs. KF

  49. 49
    kairosfocus says:

    ES: From the OP and discussion above, we have seen that your ultra-modernist, ugly- gulch- between- the- inner- world- and- the outer- one sophomorised Kantianism falis and needs to be replaced with a sounder view. As F H Bradley pointd out over a century ago, to pretend to know that the external world is un-knowable due to the nature of subjectivitiy . . . the denial of objective knowledge . . . is itself a claim to objective knowledge of the external world and a very strong one too. Which therefore is self-referentially incoherent. Instead, it is wiser to follow Josiah Royce’s point that we know that error exists, undeniably and self evidently. Thus, there are certain points of objective knowledge that are firm, that ground that objective truth, warrant and knowledge exist, and that schemes of thought that deny or denigrate such fail. Including post modernism, so called. Of course, that we know that error exists means we need to be careful and conservative in knowledge claims, but the design inference is already that, it is explicitly inductive on inference to best explanation on observed patterns and acknowledges the limitations of inductive knowledge including scientific knowledge. Your selectively hyperskeptical focus on the design inference while apparently ignoring the effect of that same logic on science as a whole, on history, on common sense reality and on reason itself, simply multiplies the above by highlighting the double standard on warrant. Game over, fail. Please reboot and refresh your thinking on a sounder footing. KF

  50. 50
    Dionisio says:

    47 gpuccio

    What is important is the complexity necessary to implement the function

    It would be really sad if your interlocutor doesn’t understand this. I can’t say it shorter or clearer that this.

  51. 51
    Dionisio says:

    48 kairosfocus

    How design is carried out is separate from recognising that it has been carried out on signs.

    Agree. Two completely separate issues.
    How design is carried out could be a technological secret that could only be known to others if the designer reveals it or through espionage in the case of human designs. Even reverse engineering may not reveal how design was carried out, but just what it produced, and maybe not accurately.
    Recognising that design has been carried out may require just common sense a desire to admit it.

  52. 52
    E.Seigner says:

    gpuccio

    I think this is the key passage:

    So, I may have a 20 bit program which makes something very important (like giving a key to open a database) or a 1 million bit program which make something very trivial (like ordering a simple list). What is important is the minimal complexity of a program which can do what I have defined.

    The idea is that no sequence which can do something which requires a minimum complexity of n bits (let’s say 500, to stay in the UPB) will ever arise spontaneously in a real system by a random search/walk.

    So “the minimal complexity of a program” (as weight in bits) is the crux of the matter. Simple question: Doesn’t the weight of the program depend on the programming language you use to write it?

  53. 53
    Dionisio says:

    52 E.Seigner

    What do you mean by “the weight of the program”?

    Thank you.

  54. 54
    the bystander says:

    gpuccio @44

    I have suggested many times my possible scenario: some conscious intelligent purposeful agent, probably not physical, interacts with biological matter exactly in the way that our consciousness interacts with our body and brain: through a consciousness / matter interface, probably implemented at quantum level, so that no natural laws needs to be violated.

    That line of inquiry should definitely be explored

    Joe @46

    So we couldn’t say that Stonehenge was designed until we knew how it was constructed?

    Of course not. I am asking (in many different posts) how an agent intervenes in a biological process, is there any theory of how agents work ?

    KF @48

    Beyond, we already have in hand the work of Ventner et al on the world of micro-biology which already shows feasible ways to effect biological designs

    I could find some articles about Shotgun sequencing but I couldn’t relate the material to ID agent.Sorry to be daft, but how does Shotgun sequencing explain how an agent works ?

  55. 55
    gpuccio says:

    E. Seigner:

    “So “the minimal complexity of a program” (as weight in bits) is the crux of the matter.”

    Yes.

    “Simple question: Doesn’t the weight of the program depend on the programming language you use to write it?”

    It depends on many hings. That’s why I say “minimal”. As we want to stay empirical, I will add “minimal known”. Let’s say the simplest known compiled program that can do the trick.

    To go back to proteins, one may argue in his imagination that some 50 AAs peptide could do what ATP synthase does. But the simple truth is that we know nothing that can do what ATP synthase does. And, throughout evolution, and 4 billion years of mutations, about 700 AAs in the sequence of just the alpha and beta subunits could not change, a clear indicator that they are essential to the function.

  56. 56
    Dionisio says:

    52 E.Seigner

    Did you mean “weight loss program”? 🙂

  57. 57
    Dionisio says:

    54 the bystander

    I am asking (in many different posts) how an agent intervenes in a biological process, is there any theory of how agents work ?

    Please, can you be more specific? Which biological process?

  58. 58
    Joe says:

    the bystander:

    I am asking (in many different posts) how an agent intervenes in a biological process, is there any theory of how agents work ?

    Why do you think intervention is required? Why can’t it be that organisms were intelligently designed to evolve and evolved by that design?

  59. 59
    the bystander says:

    Dionisio @57

    Please, can you be more specific? Which biological process?

    Any biological process that would defy Evolutionary explanation like complex protein structure formation, new organ development.DNA and RNA’s seeming ‘intelligence’
    Joe @58

    Why do you think intervention is required? Why can’t it be that organisms were intelligently designed to evolve and evolved by that design?

    Wouldn’t that still need an explanation of how an agent can design intelligent organism to evolve? I thought ID was about intervention and guiding complex biological/evolutionary process by ID agent.

  60. 60
    E.Seigner says:

    gpuccio

    To go back to proteins, one may argue in his imagination that some 50 AAs peptide could do what ATP synthase does. But the simple truth is that we know nothing that can do what ATP synthase does.

    Or to go back to the groups of stones, one may argue in his imagination that stones do what a circle’s ratio to its diameter does. But the simple truth is that we know nothing that can do what a circle’s ratio to its diameter does… Or am I missing something essential in your point?

    The thing is, I find #47 more full of holes than any of your previous comments. The most glaring fundamental ones we already covered in discussion just before, so I won’t go over them again.

    gpuccio

    “Simple question: Doesn’t the weight of the program depend on the programming language you use to write it?”

    It depends on many [t]hings. That’s why I say “minimal”.

    And that’s why I say – incalculable, undetectable, subjective.

  61. 61
    the bystander says:

    gpuccio

    “Simple question: Doesn’t the weight of the program depend on the programming language you use to write it?”

    It depends on many [t]hings. That’s why I say “minimal”.

    And that’s why I say – incalculable, undetectable, subjective.

    I won’t even pretend to understand what you guys are talking about. Programming language in biology? The lowest bit would be for assembly language. How does that relate to design bits ?

  62. 62
    Dionisio says:

    59 the bystander

    Any biological process […] like complex protein structure formation, new organ development.

    Do you know how they work? Can you describe any of those processes? Do you know anyone who can explain it?
    If you do, then go ahead and describe one of them. To make it easy for you, you may choose any of the over 400 examples posted in the Third Way thread News started in this blog about 4 months ago.
    Serious scientists in the ‘cutting edge’ labs around the world are working hard trying to figure out how those processes work, hence they have no time to discuss how we got those processes to begin with. First things first.
    Do you see the point?

  63. 63
    kairosfocus says:

    TB: Look here. Life engineering technologies generation 0.1 or maybe 0.01 KF

  64. 64
    kairosfocus says:

    ES: By now it is fairly obvious that you have a core that you are shielding and will not seriously examine. The problems have been identified and exposed long since, starting with the OP and onwards. I suggest you ask yourself what you are really showing by insisting on clinging to what is self referentially incoherent. KF

  65. 65
    StephenB says:

    Hi GPuccio. Thanks for your contribution. It is much appreciated.

    It appears that we may be operating from a mildly different philosophical framework. If so, there’s no problem, but let’s find out.

    Let me summarize my definitions:

    Subject = perceiver of a thing or operation
    Object = the thing or operation perceived

    Subject = the perceiver of the design
    Object – the design itself

    Accordingly, a subject (God or a human) can create an objective design or function with a subjective purpose. (Why it was intended to operate that way). Another subject can detect or perceive the design or function that was created. I am here making a sharp distinction between the subjective purpose (the reason it was designed) with the objective function (its operation),

    For example, a subject writes a paragraph with an objective design component for the subjective purpose of persuading. Another subject detects the objectively formed design and subjectively perceives the objective meaning intended.

    Similarly, the Creator designs a liver as a human organ that performs the objective function of filtering for the subjective purpose of keeping a human alive. A human can subjectively detect that objective function and provide a subjective definition for it, but the definition, it seems to me, remains subjective and the function itself remains objective. Even if no one recognized that the liver performs a function, (the one subjectively intended by the Creator) it would, nevertheless, continue to function as an objective reality because it was designed to operate that way. No human perceiver is necessary.

    Now, let’s apply this framework to the current problem under discussion.

    ES claims that the observer projects a personal or communal philosophy of design onto the object. If that person’s subjective philosophy is pro-design or anti-design, it is that projection alone that determines the answer to the question–design or not designed? In other words, for her, the subject (the perceiver) decides whether or not the artifact or organism (object) was designed. The subject who designed it or the thing itself have nothing to say about it.

    For her, it doesn’t matter if the Creator designed the human liver or if a human designed a written paragraph. In either case, she holds that a design inference cannot be made under any circumstances—period. That is because, again, for her, the design is in the perceiver, not the thing perceived. So it is with function.

    The function is, for her, not in the operation of the thing that functions, it is in the one who defines the function, that is, the subject. With this philosophy, no designs or functions can be detected. All designs and functions are projected by the subject onto the thing that is designed or functions in some way.

    If the function (as opposed to its definition) is in the observer, then the observer can decide if the function exists or doesn’t exist and the designer of the function has nothing to say about it.

    Can we detect the design in a can opener? Of course. Can we perceive its function? Of course. Are we projecting our philosophy onto the can opener? No. Does our capacity to perceive these things have anything to do with the fact that it was designed or can function in that way? No.

    The solution, it seems to me, is to replace bad philosophy with good philosophy. As far as I can tell, the only philosophical presuppositions that precede the design inference are the first rules of right reason. Yes, these do come first. However, the design process itself begins with an observation, not a philosophical projection.

  66. 66
    E.Seigner says:

    StephenB

    Can we detect the design in a can opener? Of course. Can we perceive its function? Of course. Are we projecting our philosophy onto the can opener? No.

    Of course we are projecting the idea of “can opener” onto the thing. This is because the can opener works in conjunction with cans that can be opened with such an opener. Without those cans, the can opener is a pointless object, without function.

    This point is easily seen when you go to some stone-age tribe (still found in e.g. Amazon and Papua) who have no cans and you show them the can opener. They will naturally “perceive its function” according to their own canless culture, not according to ours.

    StephenB

    The solution, it seems to me, is to replace bad philosophy with good philosophy.

    Indeed. Happy to agree on something with you. Let’s hope this is not the last time.

  67. 67
    StephenB says:

    E. Seigner

    Of course we are projecting the idea of “can opener” onto the thing. This is because the can opener works in conjunction with cans that can be opened with such an opener. Without those cans, the can opener is a pointless object, without function.

    The can opener is designed independently of the observers “projections.” It is an objective fact because someone did, in fact, design it for a purpose, which means that the design is inherent in the object. Any observer can detect its design features even without knowing its function. In the same way, I can detect the design features in a surgeon’s tool without knowing its function.

    The “idea” or “definition” of a can opener is obviously subjective. All ideas and definitions are subjective. The things that the ideas and definitions refer to are objective. Accordingly, the fact of the can opener’s existence and its inherent design are objective. A subject conceived the design for a purpose and then transformed it into an objectively real artifact with objectively real design features, which, in turn can be detected by another subject. You have it backwards. The design was not projected by the observer; it was projected by the the designer.

    This point is easily seen when you go to some stone-age tribe (still found in e.g. Amazon and Papua) who have no cans and you show them the can opener. They will naturally “perceive its function” according to their own canless culture, not according to ours.

    Members of the tribe will immediately detect the design features in the can opener, but they will not know its function or why it was designed if they have never observed a can. They will know that it is not a random conglomeration of parts and will wonder why it was designed. The one thing they will not do is try to answer that question by projecting their cultural experience onto the can opener. To do that would be to destroy intellectual curiosity and eliminate the possibility of asking about its real purpose. Only a bad philosopher or an academic would do that.

  68. 68
    StephenB says:

    SB: The solution, it seems to me, is to replace bad philosophy with good philosophy.

    ES: Indeed. Happy to agree on something with you. Let’s hope this is not the last time.

    Agreed.

  69. 69
    Mung says:

    Joe:

    So we couldn’t say that Stonehenge was designed until we knew how it was constructed?

    What makes you think Stonehenge was constructed at all? I think it was the result of numerous meteor strikes over many thousands of years that just happened to end up in the present configuration. No designer(s) needed.

    Those funny looking rocks on easter island? Pretty much the same thing with some erosion tossed in. Its’ an island, after all.

    Wait, isn’t GB an island as well?

    Well, there you have it!

    Islands attract meteor strikes.

    What other evidence do you need?

  70. 70
    Mung says:

    SB,

    I think that perhaps I begin to perceive some of the issue here, and I should not be surprised.

    ES appears to place epistemology above ontology. It’s not a can opener because the aborigines don’t know that it’s a can opener. I could be wrong. I would welcome being wrong.

    There’s nothing particularly wrong about being coy I suppose. I tend to it myself. But so much ground could be covered by allowing some generalizations.

    ES objects when people get the wrong impression (and rightly so). But statements like the following:

    Projecting some structure or pattern is a necessary precondition to make any sense of anything.

    Make me scratch my head.

  71. 71
    Mung says:

    E.Seigner:

    Projecting some structure or pattern is a necessary precondition to make any sense of anything.

    Are you saying that in order to sense something, one must first make sense of it?

    Or are you saying that to make sense of something, one must first sense it?

    Neither? Both?

    I believe that things exist in reality, independent of the human mind.

    I believe that for the human mind to “make sense” of things that exist in reality, the sensing of them comes prior to the making sense of them (assuming that we’re not just equivocating).

    But for the human mind to “make sense” of these things, they must have some characteristics or properties (form, structure, shape, pattern) that really exists.

    Projecting some structure or pattern is a necessary precondition to make any sense of anything.

    Therefore, I profoundly disagree.

    And I would really like to understand where you’re coming from and on which points we agree and on which points we differ.

    thank you

  72. 72
    Mung says:

    E.Seigner:

    Of course we are projecting the idea of “can opener” onto the thing.

    We are projecting the idea of “can opener” on to what thing? The can-opener-thing?

    We could just place the can in the fire and wait for it to explode. Then we could attempt to convince the natives that the fire isn’t really a fire, but rather a can opener.

  73. 73
    StephenB says:

    Mung:

    ES appears to place epistemology above ontology.

    I wish that it just ended there. Alas, it goes much further to the point where the epistemology crowds out the ontology altogether–where subjective philosophy devours objective existence–where what we say about things determines the essence of things–where the individual and collective mind creates the very nature of reality.

  74. 74
    SteRusJon says:

    ES

    Exchange:
    “Simple question: Doesn’t the weight of the program depend on the programming language you use to write it?”

    It depends on many [t]hings. That’s why I say “minimal”.

    Your retort:
    “And that’s why I say – incalculable, undetectable, subjective.”

    .
    In point of fact, any computer program is run at the CPU instruction level, regardless of the language it is written in. That object code can be optimized to a minimal set of CPU operations that successfully solve the problem in the particular way the program was designed to solve it. The precise amount of program bits can be calculated. Allowances can be made for possible CPU operation order flexibility. It may not be simple and easy but, in principle, it is always calculable.

    I think your comment amounts to whining. “Ah, this is too difficult to do! Can’t we just make it go away by quibbling about which part is not objective enough for my taste?”

    Stephen

  75. 75
    Mung says:

    Further on my comments @ 71.

    Humans “make sense” of things via the method of abstraction. This is in great part what sets them apart from other animals.

    But in order for the human mind to create abstractions, there must be sensible things which individually and distinctly share something in common, commonly referred to as their shape, pattern, form or structure. The denial of such universals ultimately results in self-refuting incoherence.

    Mung: Plants and animals really do exist. They are not projections of the human mind.

    E.Seigner: “Do you think their taxonomy is objectively real or is it man-made? Plants and animals are empirically real, but the way we categorize and classify them is open to interpretation. It has changed significantly over the millennia and still displays marked cultural differences.”

    If by “taxonomy” you mean their classification (categorization) into genus and species I would say that this is man-made. Taxonomy employs abstraction.

    I agree they are empirically real. It is their form, shape, structure, pattern, that permits, even encourages, their classification. If their form, shape, structure, pattern, were not objectively real, then abstraction would be impossible. But abstraction is possible.

    In spite of cultural difference about what belongs in which category, it seems to be a universal truth that humans employ abstraction in the process of categorization (taxomony).

    How is this even possible under the assumption that:

    “Projecting some structure or pattern is a necessary precondition to make any sense of anything.”

  76. 76
    the bystander says:

    Dionisio @62

    To make it easy for you, you may choose any of the over 400 examples posted in the Third Way thread News started in this blog about 4 months ago….
    Do you see the point?

    You are all over the post! Yes.I see the point – you are indicating there is no mystery in the various biological processes, but you have shown in various links how complex the biological process can be.
    It seems Evolution theory needs to be worked over. Don’t you think Darwin didn’t see the complexity of various process and that his theory was good enough for his time, but not today ?
    KF @ 63

    Look here. Life engineering technologies generation 0.1 or maybe 0.01

    The wiki page is about Human Genome Project and synthetic genes. Don’t be annoyed but I still don’t see any significance of this to how agents work.
    What do you mean by 0.1 or maybe 0.01?

  77. 77
    the bystander says:

    SteRusJon @74,

    In point of fact, any computer program is run at the CPU instruction level, regardless of the language it is written in. That object code can be optimized to a minimal set of CPU operations that successfully solve the problem in the particular way the program was designed to solve it. The precise amount of program bits can be calculated. Allowances can be made for possible CPU operation order flexibility. It may not be simple and easy but, in principle, it is always calculable.

    If any object is handed over to you, will you be able to calculate the bits required to create it ? Will everyone come with the same answer ? If not, how can that be objective? I definitely don’t see the relevance of computer programs and bit calculations in ID.

  78. 78
    E.Seigner says:

    StephenB

    Any observer can detect its [can opener’s] design features even without knowing its function.

    But what did you say just before? You said: “Can we perceive its function? Of course.” Well, of course we cannot perceive can opener’s function unless we see it in its *intended* context. It’s not up to the observer to determine what the intended context is. The observer might see it in any random context.

    StephenB

    The “idea” or “definition” of a can opener is obviously subjective. All ideas and definitions are subjective.

    I didn’t mean any random idea, but the can opener’s function as a can opener. (This requires from you the ability to understand my words in context.) So let’s conclude that we agree that it’s subjective.

    StephenB

    Members of the tribe will immediately detect the design features in the can opener, but they will not know its function or why it was designed if they have never observed a can.

    Good. So your original claim “Can we perceive its function? Of course.” is overturned.

    Mung

    ES: Projecting some structure or pattern is a necessary precondition to make any sense of anything.

    Are you saying that in order to sense something, one must first make sense of it?

    Or are you saying that to make sense of something, one must first sense it?

    Neither? Both?

    Sensing is one thing, making sense is another thing, and both are needed to make sense of anything. To achieve that, one must relate the thing in one’s own mind to other similar things, to separate it from unrelated things, and/or to mentally place it in different contexts to hopefully come up with the most appropriate context. Where one “senses” the thing first may not be the appropriate context to determine its function.

    You people here think that making sense of things, “perceiving function” and “detecting design” is something totally straightforward, self-evident and uncontroversial. Well, there are totally straightforward, self-evident and uncontroversial examples to the contrary and I just discussed one more such example with StephenB. And more will follow below.

    Mung

    I believe that things exist in reality, independent of the human mind.

    I believe that for the human mind to “make sense” of things that exist in reality, the sensing of them comes prior to the making sense of them (assuming that we’re not just equivocating).

    But for the human mind to “make sense” of these things, they must have some characteristics or properties (form, structure, shape, pattern) that really exists.

    Not just characteristics or properties of the thing, but also its operation (or immobility) and context are necessary. The observer judges based on context and background information. Not everybody judges things the same way, and not everybody even senses the same way. Some people don’t see some colours, some don’t see rapid motion.

    It’s not so simple that things are out there and that’s it. When we are talking about perceiving things, then we are talking about interaction and there’s stuff that depends on the observer. No need to violently overinterpret this as if I denied the reality of things, but when you think things are out there and everybody should come to the same conclusions about them, you are obviously wrong. Do you come to the same conclusions as Darwinists when you study biology? Well, there.

    I don’t place epistemology above ontology. The problem is in that you seem to acknowledge too little role for epistemology.

    SteRusJon

    Exchange:
    “Simple question: Doesn’t the weight of the program depend on the programming language you use to write it?”

    It depends on many [t]hings. That’s why I say “minimal”.

    Your retort:
    “And that’s why I say – incalculable, undetectable, subjective.”

    In point of fact, any computer program is run at the CPU instruction level, regardless of the language it is written in. That object code can be optimized to a minimal set of CPU operations that successfully solve the problem in the particular way the program was designed to solve it. The precise amount of program bits can be calculated.

    Of course the precise amount of the program bits can be calculated, but the question is what counts as the *minimal* program. What programming language should we take? Why exactly that language and none other? Perhaps we can devise a more efficient language and the whole framework changes again…

    SteRusJon

    I think your comment amounts to whining. “Ah, this is too difficult to do! Can’t we just make it go away by quibbling about which part is not objective enough for my taste?”

    And your comment amounts to trampling your feet and insisting it is objective enough when it obviously isn’t.

    Mung

    Humans “make sense” of things via the method of abstraction. This is in great part what sets them apart from other animals.

    Now you’re talking. Indeed, when we talk about sensing as distinct from “making sense”, then other animals, even though they sense, do not even begin to *make sense*. And this is one more example how making sense of things, “perceiving function” and “detecting design” presupposes a lot from the observer.

    Mung

    In spite of cultural difference about what belongs in which category, it seems to be a universal truth that humans employ abstraction in the process of categorization (taxomony).

    Yes, every human does this, but they do it in different ways. Similarly, everyone has some morality or another, but there are differences of moral norms from society to society and differences of moral sensitivity from person to person.

    Mung

    How is this even possible under the assumption that:

    “Projecting some structure or pattern is a necessary precondition to make any sense of anything.”

    Our ability to abstract is activated in observation, thus projected when we are trying to make sense of the thing observed. The result depends on the individual ability to abstract, former familiarity with the thing, etc. All this goes under what I call projection.

  79. 79
    Upright BiPed says:

    SB: Members of the tribe will immediately detect the design features in the can opener, but they will not know its function or why it was designed if they have never observed a can.

    ES: Good. So your original claim “Can we perceive its function? Of course.” is overturned.

    What really does this have to do with anything?
    Is someone here denying that hemoglobin objectively exists, and objectively carries oxygen to replenish the body?

    If not, then the question regarding design in biology does not hinge on the objective existence of function, it’s about how the informational constraint over inanimate matter came into existence.

    ES, I’ve pointed out to you the intractable inference to design on that front.

  80. 80
    StephenB says:

    SB: Any observer can detect its [can opener’s] design features even without knowing its function.

    E. Seigner

    But what did you say just before? You said: “Can we perceive its function? Of course.” Well, of course we cannot perceive can opener’s function unless we see it in its *intended* context. It’s not up to the observer to determine what the intended context is. The observer might see it in any random context.

    You are running into difficulties with logic. We can detect the design features of a can opener without knowing its function. That doesn’t mean that we cannot perceive its function. Quite the contrary. We can perceive its function, but we may not if we don’t know why it was designed. We don’t need that same knowledge to detect design. Any rational person will know that a can opener was designed immediately upon inspection, even if they know nothing else. The same is not true of function. Recall my example of the surgeon’s tool. I can recognize the design without knowing its function. Even so, I can perceive its function once I come to understand why it was designed.

    SB: Members of the tribe will immediately detect the design features in the can opener, but they will not know its function or why it was designed if they have never observed a can.

    Good. So your original claim “Can we perceive its function? Of course.” is overturned.

    I don’t mean to be unkind, but you are going to have to work harder with your logic. The members of the tribe will not know its function if they have never observed a can, which is the scenario you set up. On the other hand, they will perceive its function if they observe a can or if someone tells them the purpose of the can opener.

  81. 81
    E.Seigner says:

    StephenB

    You are running into difficulties with logic. We can detect the design features of a can opener without knowing its function. That doesn’t mean that we cannot perceive its function. Quite the contrary. We can perceive its function, but we may not if we don’t know why it was designed.

    This is exactly the point I was making. You are running into difficulties with reading comprehension. (Note that subjective difficulties in reading comprehension are perfectly expected according to my background assumptions, while according to yours everybody should understand things the same way.)

    StephenB

    I don’t mean to be unkind, but you are going to have to work harder with your logic. The members of the tribe will not know its function if they have never observed a can, which is the scenario you set up. On the other hand, they will perceive its function if they observe a can or if someone tells them the purpose of the can opener.

    I don’t mean to be unkind, but this was precisely the point I was making, and this goes squarely against your original unconditional contention that we can perceive function, full stop.

  82. 82
    kairosfocus says:

    ES: Your can opener attempted counter example is answered in a PS to the OP, above. That is because a picture is worth a thousand words. I also note that failure to observe function on our part does not entail absence of function in an artifact. And, even when overall function based on complex, specific organisation, is poorly understood, the FSCO/I in parts is enough to point to design. KF

  83. 83
    Joe says:

    the bystander:

    Wouldn’t that still need an explanation of how an agent can design intelligent organism to evolve?

    Yes, that is separate from ID and it proves ID is not a dead-end.

    I thought ID was about intervention and guiding complex biological/evolutionary process by ID agent.

    That is a possibility but it isn’t required.

  84. 84
    E.Seigner says:

    @kairosfocus #82

    You mean this? http://www.uncommondescent.com.....Opener.jpg
    What are those lines and numbers in the image? The numbers refer to some explanatory notes, right? Why should there be explanatory notes meant to go along with the image? Because even something as basic as a can opener is not automatically self-explanatory by plain observation. It requires instruction and the image is meant as such instruction.

    I note that your failure to acknowledge the value of context and the importance of background information when it’s right there even in your own illustrations is remarkable. Definitely an ideological issue.

  85. 85
    Dionisio says:

    76 the bystander

    Apparently you did not understand my message. Sorry, my fault, I’m not a good communicator.

    In the many examples you saw in the indicated thread, one can note elaborate cellular and molecular choreographies associated with what KF calls FSCO/I and GP refers to as dFCSI.

    As you could note in most of those posts, serious scientists are very busy trying to figure out how those complex processes work. They don’t have time to think about how they appeared to begin with. IOW, OOL discussions are irrelevant to resolve their research issues at this point.
    Every new discovery reveals more FSCO/I and dFCSI that demands explanation.
    Your question about how an intelligent agent does his work seems kind of premature, in light of our lack of detailed information about the actual work of the observed processes. You might have to wait quite a while for an answer to your question. First things first.
    Did you get it now?

  86. 86
    Dionisio says:

    #85 correction

    Every new discovery reveals more FSCO/I and dFCSI that demand explanation.

  87. 87
    kairosfocus says:

    ES: More red herrings led away to strawmen. I chose a patents drawing, which will naturally be indexed. how convenient to pounce on and ignore the actual issue being highlighted! But, had you bothered to notice what was drawn out point by point from the discs and matched teeth with centred holes and aligned axes as well as the flat pieces of metal bent into rectangle based shapes and hinged at a pivot, you would have seen that the FSCO/I involved in the parts, independent of the overall function, would be enough to infer design. Perhaps, you are unaware of how hard it is to make a precise circle out of metal, cut meshing teeth and centre holes for mounting then align parallel axes at just the right separation in 3-d space . . . quite an exercise in geometry and in precision fabrication as well as dynamics of machines. Just so, the FSCO/I in text-strings in posts in this thread, in computer programs, in the PC or whatever you are reading this on, and of course in DNA, in mRNA and tRNA and in the ribosome or proteins, will be quite sufficient to confidently infer design. Save, for those locked into a prioris that lead them to cling to absurdities rather than admit that there is evidence pointing to something that does not sit comfortably with their preferred worldview. KF

  88. 88
    kairosfocus says:

    D: FSCO/I is the general form, which needs not be in digitally coded strings — cf the exploded view of a fishing reel in the OP, which can be reduced to a set of coded strings by using something like AutoCAD etc. What GP and I both call dFSCI is the latter, coded strings. DNA is an explicit code, RNA is transcribed from it, proteins are assembled based on translating the code and themselves embed the code in their amino acid sequences. So, analysis on strings is without loss of generality, WLOG. Of course, the funciton of protein strings is quite remote from the DNA code, it requires a lot of nanomachinery to transcribe, edit, transfer, set up the Ribosome, and assemble the protein, That hen needs to fold or be folded in a chaperone machine, then perhaps be augmented with enabling species and/or clustered to build a structure, etc. We have not yet touched on the post office despatch system using the intracellular highway and vesicles moved about with walking trucks — yes, walking trucks. This stuff is astonishing, awe-inspiring indeed. We have a long way to go to get near that sophistication. And as for the molecular nanotech involved, sheer genius that. KF

  89. 89
    kairosfocus says:

    F/N: Philip Johnson replies to the a priori Lewontinian materialism that is driving so much of the above, directly or indirectly through fellow traveller ideologies:

    For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them “materialists employing science.” And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) “give the appearance of having been designed for a purpose.”

    . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

    Back to a challenging transition, I already had to go out for the morning to deal with a policy paper.

    KF

  90. 90
    Silver Asiatic says:

    Because even something as basic as a can opener is not automatically self-explanatory by plain observation. It requires instruction and the image is meant as such instruction.

    Of course, you’re completely incorrect, as usual.
    There are many human beings who have suffered severe brain damage and could not recognize a can opener even with instructions. Some are in a coma and cannot respond to information. Others would not be able to see what that image is because they are lacking eyesight. Other people are not interested in science so they would not want to know of a can-opener was designed or not.

    So, obviously, the design inherently obvious in a object like a can-opener is not self-explanatory and it’s impossible to determine if it emerged naturally from random chemical reactions.

    In fact, a can-opener may be a living organism that evolved from scorpions. If you look at it quickly, there could be some homology there.

    //sarc

  91. 91
    Dionisio says:

    KF,

    Good clarification. Thank you.

  92. 92
    Box says:

    Inferring design and inferring function are two distinct operations. The second is controversial if one claims to be able to do so irrespective of context.

  93. 93
    Joe says:

    The best one could do irrespective of content is to posit a possible function or functions.

  94. 94
    kairosfocus says:

    Box, function depending on interacting integrated parts depends on the context of configurations and the materials and forces of nature. It often does not depend on an onlooking conscious observer. The living cell is not conscious, and neither is an embedded controller. That function is objective — i wuk or i nuh wuk. But, those bedevilled by a sophomorised kantian ugly gulch between inner and outer worlds tend to project that error to the world. But as has been pointed out — ignored of course — that ugly gulch concept fails its own test, it implies the strong knowledge claim about the outside world, that it is unknowable. It self-refutes. KF

  95. 95
    Box says:

    KF #94,
    DNA as an integrated part of the organism undeniably has a function IMHO. A function ultimately for the organism.
    However, a can opener is out there. It is not obviously a part of a larger whole. So, contrary to DNA, the function of the can opener is hanging in mid air, so to speak.
    Similarly, one could say that extracted DNA has lost its function, by being isolated from its context.

  96. 96
    kairosfocus says:

    Box, its completed function as a can opener, yes, but the structure, composition and functions of component parts which have context, is a legitimate focus of a design inference. For example look at the modern opener, with the inclined gearing. The meshing and working of the gear train is complex, specific and functional, sufficient to make a confident by design inference. Discs with centred holes, aligned on just right axes and with meshing co-ordinated teeth are not credible results of blind chance and mechanical necessity. The hinged rectangle based arms, even, would be enough. KF

  97. 97
    gpuccio says:

    E. Seigner at #60:

    “The thing is, I find #47 more full of holes than any of your previous comments. The most glaring fundamental ones we already covered in discussion just before, so I won’t go over them again.”

    and

    “And that’s why I say – incalculable, undetectable, subjective.”

    OK. I have tried to explain my views, but I will not debate them with you endlessly. I hate repetitions.

    Thank you for your interesting contributions.

  98. 98
    gpuccio says:

    StephenB at #65:

    I don’t think there are differences between our views on these things, only different methodologies. I will try to clarify.

    In all my discussion with E. Seigner, as in my general scientific arguments here, I try not to depend on ant specific metaphysics, as far as it is possible. That does not mean that I have not a metaphysics, but I try to make science when I make science, and metaphysics when I make metaphysics. I know that any science is more or less metaphysically based or biased, and all the rest, but just the same, let’s say that whe I make science, I try to do it in a way that to me appears the leastt biased I can do it. OK?

    Now, when I speak of function, and I say that the function we define for the object is subjective, my discourse is completely empirical and procedural.

    Bear with me with what I am saying, for a moment: I try to treat subjects as objects, in the sense that they exist objectively as subjects, and therefore I can use them objectively in a procedure.

    So, let’s say that a subject is the only type of “object” who can “recognize” a function. Or simply “conceive” it.

    It is true that the liver works independently from anyone who observes it, but again describing what happens in the liver as a function requires the conception of purpose, and only subjects have that.

    Therefore, function is “subjective” because only a subject can conceive that a series of events has a purpose, which is the only conception which can differentiate any generic series of events (which always generates results) form a functional series of events (which generates purposeful results).

    But the point is, our observer looks at a object (or material system) and “recognizes” a function in it. OK. But is he right? I mean, is that object really generating those results because a designer intended that? Or am I, the observer, only thinking that that is the case?

    In general, the observer cannot know, unless he has direct knowledge that the object was designed.

    That’s why we are discussing design detection, and in particular design detection in cases where we know nothing of the designer and the design process, and what we have is the object and the system in which the object is supposed to have originated.

    That’s why I just say that the observer “conceives” of a function for the object he is observing. And verifies that this object has the objective functionality to implement that function.

    So, in my procedure, the function is subjective because I leave the observer completely free to conceive and define any possible function for the object he is observing. Maybe those functions were designed, maybe not, Maybe he is just imagining that function, as a conscious being, for the first time. Maybe the object is not designed, and still we can conceive of a function for it, and still maybe that it has the objective functionality to implement it.

    That’s why I say that the conception of the function, and the definition of it, in my procedure, are subjective. Not because they cannot be objectively shared (they can) and used (they can), but because my observer is completely free to conceive and define any function for which the object can be used.

    But how does that connect to design detection?

    It’s easy, and you know very well.

    The point is, if an observer, any observer, can conceive a define for an object any function which:

    a) is complex enough (requires a minimum of informational bits to be implemented,

    and

    b) those bits are enough according to an appropriate threshold for the system to make any random generation of the whole sequence of bits completely unlikely

    and

    c) there is no known necessity mechanism in the system which can generate that specific information

    then we infer design as the best explanation.

    Why? because in all the cases where we can apply the procedure and verify it (because we may know independently if the object is designed or not), IOWs in all the cases in which we can scientifically test the procedure. the procedure as described has 100% specificity for designed objects (and low sensitivity).

    OK, that was a repetition, but the purpose was to clarify better what I mean when I say that, in my procedure, the function is defined as a subjective conception of the observer, while the objective functionality is the objective, repeatable assessment of whether an object can implement the previously defined function or not.

    I hope I have been clear (not for E. Seigner, I think, I have lost those kind of hopes).

    By the way, I will be very busy in the rest of the week, so I apologize in advance if I don’t answer some post by someone. I will do my best.

  99. 99
    StephenB says:

    SB:You are running into difficulties with logic. We can detect the design features of a can opener without knowing its function. That doesn’t mean that we cannot perceive its function. Quite the contrary. We can perceive its function, but we may not if we don’t know why it was designed.

    This is exactly the point I was making.

    It is not the point that you have been making at all. You have been arguing the very opposite, namely that we cannot detect design—period, that we must “project” it.

    With respect to function, you have never made the distinction that I made above (We can perceive function, but we may not). However, if you agree with the point, so much the better. We can forget about function and focus on design. .

    SB: The members of the tribe will not know its function if they have never observed a can, which is the scenario you set up. On the other hand, they will perceive its function if they observe a can or if someone tells them the purpose of the can opener.

    I don’t mean to be unkind, but this was precisely the point I was making, and this goes squarely against your original unconditional contention that we can perceive function, full stop.>

    I did not go against my original claim, which was that we can perceive function. Members of the tribe will detect design in a can opener the moment they observe it. They will likely not immediately understand its function if they have never observed a can. Nevertheless, they can understand its function when they learn about cans. Let me dramatize the point: Members of the tribe WILL (unconditionally and with no understanding of context) perceive design and they CAN (with an understanding of context) perceive function.

    To sum up, I have never said that an uninitiated tribe will immediately perceive the function of a can opener. I have said that they will immediately perceive its design. You are trying to argue that they will project their cultural biases and decide on that basis whether or not it was designed. That is false.

  100. 100
    Box says:

    KF #96: Discs with centred holes, aligned on just right axes and with meshing co-ordinated teeth are not credible results of blind chance and mechanical necessity.

    Indeed, I agree 100%. Of course it is designed.
    The function of a can opener however, can only be understood in context. Without a can being in existence, there is no function of a can opener.
    Discs with centered holes are parts of the can opener irrespective of context. On the contrary the function of a can opener is not part of the can opener irrespective of context. So the function of the can opener is ontologically distinct from the can opener. The function is an idea in the minds of conscious observers who can envision the context.

  101. 101
    Silver Asiatic says:

    Perhaps the example of a can opener is too simplistic and it doesn’t work as well as others.

    The function of an elevator, for example, is to carry people or things up or down the building.

    Now we could say, the function of the elevator can only be understood within the context of … what?

  102. 102
    kairosfocus says:

    Box: Sub-assemblies and sometimes components in their own right have function that may be readily discerned and may exhibit FSCO/I. We do not need to set out on the overall, if a component or two or a sub assembly will do. That is why for FSCO/I the protein synthesis process — obviously central to cell based life — is a key case. One that puts design at the foundation of biological life, from microbes to man. One that, as it pivots on codes, algorithms and NC machines, is a signpost pointing to language-using intelligence implicated in the design process. One that, once a priori materialist blinkers are removed, is readily understood in an information age. One that puts the chalenge squarely to such: kindly, show us on empirical observation, a comparable case of such FSCO/I and particularly dFSCI and associated NC execution machinery, coming about by blind chance and mechanical necessity on the gamut of our solar system or observable cosmos. An in fact decisive case. That is why, predictably, when it is on the table — as in the OP — it is ALWAYS ducked or diverted from by objectors. And of course, let us hear some explanation of how codes and algorithms and execution machinery only have imagined, projected function, how the machine-readable object codes disappear into blind chemistry etc (notice, the telling echo of what happens to conscious mind under evolutionary materialism). KF

  103. 103
    kairosfocus says:

    PS: A gear is almost as iconic, that seemingly humble disc with a centred hole and meshed teeth that transmits power, synchronisation and regulatory control, requiring astonishing precision and alignment to do so well. (Ever got sand into the gear assembly of a fishing reel such as the one pictured above?) KF

  104. 104
    Box says:

    KF #102: That is why for FSCO/I the protein synthesis process — obviously central to cell based life — is a key case.

    Again, I agree 100%. The cell is an excellent context for the protein synthesis process – which is obviously functional for the cell. I stated something very similar in post #95. However a not-in-context can opener is not part of such a context – only in our minds. Unfortunately I have to repeat myself, because you have ignored this point once again.

    SA #101: The function of an elevator, for example, is to carry people or things up or down the building.

    Now we could say, the function of the elevator can only be understood within the context of … what?

    I don’t see much difference with the can opener example. One could compare the elevator with the can opener and “people and things” with the can.

  105. 105
    kairosfocus says:

    Box: think components and interactions, as already noted. We do not need function of the whole. For an elevator the motor and cable assembly would be enough, much less the floor programming system. KF

  106. 106
    Box says:

    KF: “(…) the motor and cable assembly would be enough (…)”

    Enough .. to do what?

  107. 107
    Daniel King says:

    Now we could say, the function of the elevator can only be understood within the context of … what?

    If you can’t answer that all by yourself, dear Asiatic, you need to go back to elementary school.

  108. 108
    StephenB says:

    GPuccio @98, Thank you very much for the clarification. I understand now why you define function in subjective terms and why you differentiate it from objective functionality. This helps immensely. Our arguments are eminently compatible, but as you say, the methodologies are quite different. In order to avoid confusion for the poor reader, I will substitute your term, “objective functionality” for my term “function” and your term “function” for my term “perception of function.” This way we will be using words that mean the same thing when we argue. Thanks for taking time out to explain.

  109. 109
    kairosfocus says:

    Box, an elevator has a motor-cable assembly that moves it. It is easy to see the function and FSCO/I content. Same, with the gear assembly on can openers and the code in DNA as well as the associated nanotech execution machines. Focussing on such components is sufficient to ground a design inference without worrying over grand contexts. KF

  110. 110
    Mung says:

    Mung:

    But it is your claim that the pattern or structure or shape of whatever it is that is out there that is being perceived is not really present in the thing being sensed?

    E.Seigner:

    Are you completely unfamiliar with, for example, the claim of physics that in the nanolevel we are just atoms that constantly enter and leave the “body”, atoms who have lots of space between them so that on that level we are basically transparent and the “body” is just a higher-level construct that *seems* solid due to chemical and magnetic cohesion, but “fundamentally at the basic level” is not solid? It’s not postmodernism that came up with these things. If you are unfamiliar with this, then I must doubt if people here have seriously thought through a single scientific claim. And no, this physicalist claim is not my ultimate thesis, but it’s definitely something you should be familiar with, if *you* don’t want to seem outlandish. This physicalist claim emphasizes how profoundly mind is involved in perception, and this mental involvement is a real fact to be reckoned with, not imaginary. It’s a basic fact of cognitive sciences.

    I am familiar with the claim but find it a tad incoherent. Your use of scare quotes for “body” are instructive.

    There must be something there, for there to be something for atoms to “enter” and “leave.”

    The fact that we cannot see the atoms “entering” and “leaving” that body is hardly an argument for us imagining a body that is not really there but is rather a consequence of our “projection.” In fact, out failure to sense those atoms entering and leaving mitigates against your argument for he non-existence of real (mind-independent) shape, form, pattern or structure.

    Projecting some structure or pattern is a necessary precondition to make any sense of anything.

    On the contrary, the necessary precondition is that structure or pattern exists independently of what humans think about those structures or patterns

    Do bacteria “project” some structure or pattern in order to “make sense” of things, or is “making sense” of things a purely human (mental/intellectual) activity?

  111. 111
    E.Seigner says:

    Mung

    There must be something there, for there to be something for atoms to “enter” and “leave.”

    And how can you tell something’s there? By your own perception, by your own mind. So, in order for something to be there, you have to see and feel and study and make sense of it. Otherwise you would be talking about a tree falling in the forest that nobody saw.

    Mung

    The fact that we cannot see the atoms “entering” and “leaving” that body is hardly an argument for us imagining a body that is not really there but is rather a consequence of our “projection.”

    The scientific argument I brought has been actually observed. So much for your respect for scientific observation. I count this as a serious point against you.

    But the more serious point against you is this. It’s common sense that aggregate things, by virtue of their being aggregates, are a sum of their parts and, if one has reductive tendencies, one would say that the parts are what are really there and the aggregate is but a sum of the parts. You are reductive another way. You take it uncritically what you see, and you assume (i.e. project) that everybody should automatically perceive the same way, no mind allowed. Now, this denunciation of the activity of the mind in perception is a hallmark of materialist philosophy which I firmly reject. It’s pretty amusing to see how scriptural literalists and atheist materialists have the exact same ontology.

    Mung

    In fact, out failure to sense those atoms entering and leaving mitigates against your argument for he non-existence of real (mind-independent) shape, form, pattern or structure.

    And again you are uncritical of your own sense-perception when you should be scientifically investigative and carefully non-reductive. As to the non-existence of real shapes etc. I never gave such an argument. You are overinterpreting even when I already warned you of this.

  112. 112
    Box says:

    KF:

    Box, an elevator has a motor-cable assembly that moves it.

    Why are you telling me this?

    It is easy to see the function and FSCO/I content.

    By studying a motor-cable assembly – in isolation – it is easy to see the function of an elevator? Or do you mean by studying a motor-cable assembly – in isolation – we can infer the function of the motor-cable assembly? Both statements are obviously wrong.

    Same, with the gear assembly on can openers and the code in DNA as well as the associated nanotech execution machines.

    Their functions are also easily identifiable without context?

    Focussing on such components is sufficient to ground a design inference without worrying over grand contexts.

    For the fourth time: I do not deny the design inference. I’m talking about identifying function and its ontological status. Don’t tell me not to worry over “grand contexts”, because without them it is impossible to identify function.

  113. 113
    kairosfocus says:

    Box

    I think we are having a framing issue.

    I am saying that we do not need to focus on overall function of a whole system, if we can find in it subsystems, parts or components that we can readily spot and isolate function and specified complex organisation to achieve function of the part.

    Where, motors are a blatant case.

    (And I have in mind the undeniable motors in the cell, in the flagellum obviously but also in ATP synthase which is central to life function and pervasive across the world of cell based life as ATP is the energy battery molecule.)

    If a part of a whole is credibly designed, then that creates a drastic shift to the way we should look at evidence of design elsewhere in the system as a whole.

    So also, with seeing a tape data storage system, transcription and editing, code and algorithm use, and a NC machine that uses same to synthesise the major workhor4se class of molecules, the proteins.

    The rhetorical tactics to distract from this, speak volumes.

    KF

  114. 114
    kairosfocus says:

    Mung, we are seeing undermining of the law of identity, A is A, with its immediate corollaries, LNC and LEM. Those who do so do not understand that if you undermine first principles of right reason, you undermine rationality. Actually you show that whatever led you to try that is profoundly irrational and should be abandoned. KF

  115. 115
    Silver Asiatic says:

    Box

    Their functions are also easily identifiable without context?

    I’m not necessarily disagreeing with you, but what context is there required to understand the function of an elevator? You said:

    One could compare the elevator with the can opener and “people and things” with the can.

    For the can opener, you wondered what function it would have if there were no cans, and that seems ok because with no cans, there’s nothing to open.

    Now, however, we compare that with the elevator — what if there were “no people and things”? How could you have a working elevator if there were no people? Who would be around to observe it and determine its function?

  116. 116
    kairosfocus says:

    SA (& Box):

    KINDLY, NOTICE . . .

    One of the big debate tactics we have to deal with is reframing.

    Moving to can openers and elevators feeds an attempt to obfuscate the meaning of function, and to allow room to wedge in talking points along the lines of it’s subjective and hopelessly vague. Translated, we have loaded up on metaphysical issues so we can play the merry go round.

    But, something that is specific, easily seen and outright obvious blows up that game.

    A strategically pivotal example that brings out what a wider concept means, is hard to deal with if you want to duck, dodge, slip-slide and go in circles.

    And, to get away from its point, you have to use a givaway tactic: the red herring distractor led away from the original topic, to a conveniently set up strawman.

    If you doubt me simply scroll up to the OP and see what is actually being discussed now by contrast. How did we get here, from there? Red herrings side tracked us.

    Gears and motors are very familiar objects. Computer storage media slightly less so, especially tapes, paper or magnetic. But a picture or two work wonders, being worth a thousand words.

    Where also, it is hard to deny the observable functionality of a motor and how its rotor and stator interact to give function, coupled to a load by a shaft. It is no accident that a synonym for physical work in engineering contexts is, shaft work.

    It is very hard to play oh, that’s only an analogy so I can ignore it games when you are confronted by a motor. Especially motors that, on the usual geochronology, were around a long time before we came along to observe and think about such.

    As in, the flagellum and ATP synthase. (Please, watch the videos.)

    FSCO/I in action, and as something that it is very hard to play context hop scotch rhetorical games with.

    In particular, try to say to a person of reasonable common sense that the functionality of such a motor is a mere subjective projection unto the external world across an unbridgeable gulch between the inner and outer worlds.

    No, that’s a motor. Period.

    Next, a gear and gear train are like that. A tad of reflection will show that gears need to be precisely centred and have meshing teeth, with just the right spatial separation and orientation, implying tight controls on the axles and shafts they sit on.

    Very soon, we are deep into FSCO/I.

    And we understand gears and their function enough to see that sophomoric kantian ugly gulch rhetorical games are a non-starter.

    As for data tapes, transcription, transfer, threading into read heads, and running NC machines off them, that we can follow.

    Presto, protein synthesis. (Please watch the video, and yes that’s simplified.)

    Now, we come back.

    The subjectivist po mo obfuscation of what the objective functionality of a motor, a gear a control tape or a NC machine controlled by the tape have all gone, poof.

    We see relevant cell based life cases.

    Where FSCO/I is present and points strongly to design.

    On well grounded induction, not projected imaginary question-begging.

    Despite rhetoric games.

    And now we see key parts showing strong signs of design.

    That shifts the context of evaluating other aspects and the whole, decisively.

    which is why it is stoutly resisted to the point of reductio ad absurdum.

    Let us pity those left clinging to absurdities.

    They think they have no other choice.

    But they are wrong.

    Just, are they willing to take the hits that come with going with evidence pointing where many have no wish to go?

    KF

  117. 117
    Box says:

    KF #113: I am saying that we do not need to focus on overall function of a whole system, if we can find in it subsystems, parts or components that we can readily spot and isolate function and specified complex organisation to achieve function of the part.
    Where, motors are a blatant case.

    Indeed, in many cases we can limit our focus to parts of a subsystem and postulate that the latter is the complete context. So, forget about the function for the can opener in a larger context, let’s focus instead on the function of the discs with centered holes with respect to the can opener, which is declared to be the complete context.
    I’m ok with this modest approach, which is in accord with the basic point I was making – we need context in order to be able to identify function.
    Stating the obvious: the function of the can opener remains unresolved by focusing on components.

    Silver Asiatic #115, my basic point is that we need context (people, things, a building) in order to be able to identify the function of the elevator. Similarly, letters need words to receive their meaning/functionality. IOW functionality is a top-down thing.

  118. 118
    kairosfocus says:

    Box, the effectiveness of FSCO/I as an empirically reliable sign of design does not pivot on resolving purpose and function of any one thing or all things without limits. If the modest part is good enough it is good enough. KF

  119. 119
    E.Seigner says:

    Silver Asiatic

    Now, however, we compare that with the elevator — what if there were “no people and things”? How could you have a working elevator if there were no people? Who would be around to observe it and determine its function?

    The fact is that when nobody enters the elevator and pushes the buttons the elevator will not move and the observer will remain clueless of its function. This again emphasizes how indispensable context is to observation. The function can be identified when the approach is systemic so that the context is acknowledged, but the systemic approach is completely up to the observer, not to the object.

  120. 120
    StephenB says:

    E. Seigner

    The fact is that when nobody enters the elevator and pushes the buttons the elevator will not move and the observer will remain clueless of its function.

    It doesn’t matter whether or not the observer can immediately identify the elevator’s function. What matters is that any observer at all–even in the absence of context–will immediately know that the elevator was designed and that it has a function of some kind.

  121. 121
    E.Seigner says:

    StephenB

    It doesn’t matter whether or not the observer can immediately identify the elevator’s function. What matters is that any observer at all–even in the absence of context–will immediately know that the elevator was designed and that it has a function of some kind.

    Which is totally trivial. When inclined this way, we find function and design everywhere. Can you name a thing that has no design or function? Thought so.

    If you want to call it *specified* information, then the specific function matters. And the specific function depends on context. Otherwise you are conjuring up a fuzzy smokescreen of pomo antics.

  122. 122
    StephenB says:

    SB: It doesn’t matter whether or not the observer can immediately identify the elevator’s function. What matters is that any observer at all–even in the absence of context–will immediately know that the elevator was designed and that it has a function of some kind.

    Which is totally trivial.

    Trivial? First you say that it is false, now you say it is trivially true. Please affirm one position and negate the other.

    When inclined this way, we find function and design everywhere. Can you name a thing that has no design or function? Thought so.

    I can think of millions of things that have no design. How about the pattern my coffee makes on the floor after I spill it?

    Which is totally trivial. When inclined this way, we find function and design everywhere. Can you name a thing that has no design or function? Thought so.

    If you want to call it *specified* information, then the specific function matters. And the specific function depends on context. Otherwise you are conjuring up a fuzzy smokescreen of pomo antics.

  123. 123
    StephenB says:

    SB: It doesn’t matter whether or not the observer can immediately identify the elevator’s function. What matters is that any observer at all–even in the absence of context–will immediately know that the elevator was designed and that it has a function of some kind.

    E. Seigner

    Which is totally trivial.

    Trivial? First you say that it is false, now you say it is trivially true. Please affirm one position and negate the other.

    When inclined this way, we find function and design everywhere. Can you name a thing that has no design or function? Thought so.

    I can think of millions of things that have no design. How about the pattern my coffee makes on the floor after I spill it?

  124. 124
    E.Seigner says:

    StephenB

    Trivial? First you say that it is false, now you say it is trivially true. Please affirm one position and negate the other.

    You thought I said it was false? Then you have not been paying attention. I say: It’s false to say context is unnecessary to determine function.

    StephenB

    I can think of millions of things that have no design. How about the pattern my coffee makes on the floor after I spill it?

    So, coffee has no function?

    Let’s forget about floor and spilling. They are context and context is irrelevant according to OP and all followup comments by you and KF. For once try to be consistent and follow your own rules.

    Still, a fortune teller sees quite a meaningful pattern even there. It’s just you with totally ad hoc approch here which changes as your mood changes.

  125. 125
    Silver Asiatic says:

    The fact is that when nobody enters the elevator and pushes the buttons the elevator will not move and the observer will remain clueless of its function.

    True, if I don’t take any time to understand what you’re saying, then your words are meaningless. If your words are meaningless, then you have nothing to say. If you have nothing to say, you have no knowledge to communicate.
    People with no knowledge are what we call “ignorant”.

    So, if I don’t attempt to understand you, that means you are ignorant.

    Again, if everything is designed, then the word design is meaningless since it cannot be distinguished from its opposite. If everything has function, then the word function is meaningless since it also cannot be distinguished from its opposite.

  126. 126
    Box says:

    KF #118: Box, the effectiveness of FSCO/I as an empirically reliable sign of design does not pivot on resolving purpose and function of any one thing or all things without limits. If the modest part is good enough it is good enough.

    Modesty may very well be misplaced with regard to the function of parts of an organism. I would like to argue that we can indeed identify function of the integrated parts of an organism.

    The organism is an encompassing context par excellence. My eyes, arms, legs, organs are all subordinate to the whole that I am. The function of my eyes is to extend external vision to me. IOW the function is relative only to “me”. I am the exterior circle in the ripple effect of functionality. I am the complete and final context of the function of my eyes. I am a real living context.
    Surely such a encompassing context is absent for a can opener. The can opener is out there – isolated. That’s why the possibility of identifying function for a can opener is doubtful.

  127. 127
    kairosfocus says:

    Box, you have to remember the deeply indoctrinated, confused onlooker. One has to creep before one walks, much less runs or flies or swims. KF

  128. 128
    kairosfocus says:

    PS: Again, you shift context. For the can opener, we do not need to pose hypotheticals about primitives coming agcross one and whatnot. All we need to do is to focus on the meshing gears in the Swing Away type. That alone is sufficient, and the very meshing of gears in action is an easily demonstrated functionality that is replete with FSCO/I and is a strong sign of design. So BTW would be the textual info on the opener. Do not allow yourself to be pulled away from what is direct and sure to ground of a determined objector’s choosing — chosen, because he imagines he can throw up such a fog of obfuscation that he can get away with his talking points in the resulting cloud of confusion and maybe polarisation.

  129. 129
    Box says:

    KF:

    Unfortunately, as so often, I’m barely able to grasp small parts of what you mean. “Hypotheticals about primitives coming across one and whatnot” and “meshing gears in the Swing Away type” do not ring a bell nor does it seem possible to look it up in a dictionary.
    May I suggest, considering your concern with the “deeply indoctrinated, confused onlooker”, that you modify your writing accordingly?

  130. 130
    kairosfocus says:

    Box, pardon

    Swing Away is a common “name” brand of Can Openers, and the name is inscribed on the units.

    Cf Ace Hardware advert here. Notice the meshing, carefully aligned gears.

    Primitive people such as unreached tribes in New Guinea, are the audience used to try to suggest that can openers do not have objective functionality but such is projected unto them.

    A hypothetical, is a thought exercise situation, not one that credibly has happened and demands a response.

    KF

  131. 131
    kairosfocus says:

    PS: Testimonial

    Comments about Swing-A-Way® Can Opener (407WH):

    I was turned on to the Swing-Away as a young adult by my older sister. Knowing her demand of quality I went out and bought one. I still own it, 22 years later and it is as dependable as ever. You will never need to own another. Form follows function, and this utensil is a work of art!

    Bottom Line Yes, I would recommend this to a friend

  132. 132
    Box says:

    KF:

    Thank you for the clarifications. Now, please explain why you told me (post #129) “again, you shift context”. Also, I never used the ‘unreached tribes in New Guinea argument’, so why do you bring it up?
    Lastly, I have told you ad nauseam that I’m a huge fan of the design inference, so why do you keep pounding me with arguments for design as if I state otherwise?
    In post #126, I’m presenting my view on functionality with regard to an organism as a living context. Obviously, you don’t have to agree or even be intersted, but a derogatory remark like “again, you shift context” is uncalled for.

  133. 133
    StephenB says:

    The existence of design and context

    I hold that any observer can immediately apprehend a can opener’s design in the absence of context. Thus, the subjectivist’s argument against ID can be safely discounted. One does not need context to detect design. An uninitiated member from an ancient tribe will detect design even in the absence of context.

    The existence of function and context

    Further, I hold that the observer can, regardless of (or in the absence of) context, immediately apprehend the existence of some kind of function, in a can opener that is, the fact of its objective functionality. The uninitiated tribe member will know that it was designed to do something.

    The essence of function and context

    Finally, I hold that the observer will not, immediately (without context) apprehend the essence of the function in a can opener. The uninitiated tribe member will not, in the absence of context, know exactly what the can opener does. In all likelihood, he will only know that it was designed to do something.

  134. 134
    StephenB says:

    E. Seigner

    You thought I said it was false? Then you have not been paying attention. I say: It’s false to say context is unnecessary to determine function.

    You are the one who has not been paying attention. If that is all there was to it, I would not have been nearly so critical. Your original claim was that context is necessary to detect the presence of DESIGN. That is demonstrably false.

    SB: I can think of millions of things that have no design. How about the pattern my coffee makes on the floor after I spill it?

    So, coffee has no function?

    Are you cuckoo? I didn’t say that coffee has no function. I said, in response to your naive challenge that literally everything is designed, that the “pattern” of spilled coffee on the floor was a good example of something that was not designed. The pattern was caused by natural laws and epistemological chance–not design.

    Let’s forget about floor and spilling.

    Let’s not forget about it. It was an answer to your challenge. Acknowledge the refutation so that we can move on.

    They are context and context is irrelevant according to OP and all followup comments by you and KF. For once try to be consistent and follow your own rules.

    Context is irrelevant to design detection. It is not necessarily irrelevant to function, though it can be. You haven’t been paying attention or else you do not bother to read what I write.

    Still, a fortune teller sees quite a meaningful pattern even there. It’s just you with totally ad hoc approch here which changes as your mood changes.

    This is more of the same “projection” nonsense. For you, the mind is about manufacturing reality. For everyone else, the mind is about understanding reality.

  135. 135
    E.Seigner says:

    StephenB

    If that is all there was to it, I would not have been nearly so critical. Your original claim was that context is necessary to detect the presence of DESIGN. That is demonstrably false.

    As we have learned in the exchange with GPuccio, function is one of the hallmarks of design. No function, no design, according to him.

    As to the importance of context, I have seen only plain assertions against it, no demonstration. Only some attempted examples that prove the opposite. Your #133 is a list of plain unevidenced faith claims.

    StephenB

    I didn’t say that coffee has no function. I said, in response to your naive challenge that literally everything is designed, that the “pattern” of spilled coffee on the floor was a good example of something that was not designed.

    But if coffee still has function, then surely it has design too.

    The “naive challenge” charge is weird. Do you feel ready to argue with Aquinas about it? According to Aquinas, yes, literally everything is designed, in at least two senses: 1. All things are created. 2. All things have a structure.

    Your objection only works if you use “design” in some idiosyncratic meaning. I use it in the dictionary sense, synonymous to structure and pattern.

    StephenB

    Let’s not forget about it. It was an answer to your challenge. Acknowledge the refutation so that we can move on.

    I may easily concede that you have refuted GPuccio’s view that function implies design. I found his claims incoherent anyway. As I do yours…

    StephenB

    Context is irrelevant to design detection. It is not necessarily irrelevant to function, though it can be. You haven’t been paying attention or else you do not bother to read what I write.

    …such as here. What are you saying? Are you saying yes or no? And yes or no to what? What is the supposed relationship between function and design? And how can you confidently without any evidence say context has no impact in determining function and design (as you do in #133), when the thread evinces specific examples to the contrary? And why such vehement disregard for the uncontested facts in other sciences and even in common-sense experience?

  136. 136
    StephenB says:

    E. Seigner

    As to the importance of context, I have seen only plain assertions against it, no demonstration. Only some attempted examples that prove the opposite. Your #133 is a list of plain unevidenced faith claims.

    It is not a statement of faith to say that a paint pattern caused by an explosion in a paint factory can easily be distinguished from the paint pattern caused by an artists rendition of the Mona Lisa. It is a fact of experience that these kinds of design inferences are made every day. No other living human being that I have ever heard of would question the point.

    Any rational person would laugh his head off at your thesis, namely the idea that one group of people may “project” design on the explosion and another group may project non design on the Mona Lisa on the grounds that their cultural biases prompted them to do so. The burden of proof is on you to defend such a bizarre philosophy. It is not on me to prove what everyone except yourself already knows.

    SB: I didn’t say that coffee has no function. I said, in response to your naive challenge that literally everything is designed, that the “pattern” of spilled coffee on the floor was a good example of something that was not designed.

    But if coffee still has function, then surely it has design too.

    Please reread the my comment above your comment since it is obvious you didn’t comprehend the point.

    The “naive challenge” charge is weird. Do you feel ready to argue with Aquinas about it? According to Aquinas, yes, literally everything is designed, in at least two senses: 1. All things are created. 2. All things have a structure.

    So what? That doesn’t change anything. Matter was designed to have an atomic structure. However, matter can be redesigned into new forms. Thus, the created matter called sand can be redesigned into a sand castle. That process leaves design clues. Also, God could have first designed matter and then redesigned it into a DNA molecule. That, too, leaves clues.

    Your objection only works if you use “design” in some idiosyncratic meaning. I use it in the dictionary sense, synonymous to structure and pattern.

    Design

    [“Design a plan or drawing produced to show the look and function or workings of a building, garment, or other object before it is built or made.”]

    or again,

    [“purpose, planning, or intention that exists or is thought to exist behind an action, fact, or material object.

    This dictionary definition fits in perfectly with both my examples. Spilled coffee or scattered paint produces no designed patterns. The issue is, are the parts arranged or not arranged.

    The one thing you will not find in the dictionary is design conceived as a projection of a personal cultural bias. That wierd conception of design belongs to you exclusively.

    I may easily concede that you have refuted GPuccio’s view that function implies design. I found his claims incoherent anyway. As I do yours…

    No, you may not concede that I have refuted GPuccio’s view, because you understand neither argument. Function does, indeed, imply design. Anywhere you find a function, you can safely conclude that it was designed. However, you could not conclude design from function if they were, as you want to argue, one and the same thing.

    What are you saying? Are you saying yes or no? And yes or no to what? What is the supposed relationship between function and design? And how can you confidently without any evidence say context has no impact in determining function and design (as you do in #133), when the thread evinces specific examples to the contrary? And why such vehement disregard for the uncontested facts in other sciences and even in common-sense experience?

    I didn’t say that context has no impact in determining function.

    I quote myself:

    “Finally, I hold that the observer will not, immediately (without context) apprehend the essence of the function in a can opener. The uninitiated tribe member will not, in the absence of context, know exactly what the can opener does. In all likelihood, he will only know that it was designed to do something.”

    What is it about the word “not” that you don’t understand?

    Your problem is exactly as I described it early on. You don’t read meaning “out” of the passages as the author intended. You read “into” them anything that you please. You did it three times on this one post. This fatal trait is, no doubt, related to your goofy thesis that observers read design into the artifact from the perspective of their cultural biases.

  137. 137
    Box says:

    StephenB #133: Further, I hold that the observer can, regardless of (or in the absence of) context, immediately apprehend the existence of some kind of function, in a can opener that is, the fact of its objective functionality. The uninitiated tribe member will know that it was designed to do something.

    Watch at youtube: Useless Machine 1.1 🙂

  138. 138
    Upright BiPed says:

    >>Can you name a thing that has no design or function?

    >>the pattern my coffee makes on the floor after I spill it

    >>Let’s forget about floor and spilling

    >>Let’s not forget about it. It was an answer to your challenge.

    >>you have refuted GPuccio’s view that function implies design

    😐

    It would be funny if he wasn’t actually serious.

  139. 139
    StephenB says:

    Box,

    Interesting. A machine that was designed to serve no practical purpose. It does, however, do something, namely open and close. It is not totally without function. There is a process.

    I gather that you disagree. No problem. Still, the bigger and more important question remains: Would you at least agree that the design (not function) can be detected even in the absence of context.

  140. 140
    E.Seigner says:

    StephenB

    It is not a statement of faith to say that a paint pattern caused by an explosion in a paint factory can easily be distinguished from the paint pattern caused by an artists rendition of the Mona Lisa.

    An explosion in a pasta factory is also different from an explosion in a paint factory, and all paintings are different. Even printed reproductions of the same painting are different at microlevel. Your point was?

    StephenB

    Any rational person would laugh his head off at your thesis, namely the idea that one group of people may “project” design on the explosion and another group may project non design on the Mona Lisa on the grounds that their cultural biases prompted them to do so. The burden of proof is on you to defend such a bizarre philosophy. It is not on me to prove what everyone except yourself already knows.

    The answer is easy. Savages may see in Mona Lisa just a burning material, nothing else. What purpose does a painting have for a stone-age civilization (provided that function is a sign of design, which you alternately affirm and deny as suits your purposes)?

    StephenB

    Matter was designed to have an atomic structure. However, matter can be redesigned into new forms. Thus, the created matter called sand can be redesigned into a sand castle. That process leaves design clues. Also, God could have first designed matter and then redesigned it into a DNA molecule. That, too, leaves clues.

    Clues such as? Let me guess: The clue of a designed thing is design 😀

    Since nobody has provided a scientific method to detect design thus far, I can safely conclude nobody ever will. It’s been vehemently asserted that it’s mathematically calculable, but we are still revolving around examples like Mona Lisa, paint factories, sand castles, spilled coffee, etc. Enough.

  141. 141
    StephenB says:

    E, Seigner

    An explosion in a pasta factory is also different from an explosion in a paint factory, and all paintings are different. Even printed reproductions of the same painting are different at microlevel. Your point was?

    I have already articulated (and dramatized) the point, which as usual, you ignored. All rational people will recognize and admit that the painted Mona Lisa screams design and that the scattered paint from the explosion does not.
    SB: Any rational person would laugh his head off at your thesis, namely the idea that one group of people may “project” design on the explosion and another group may project non design on the Mona Lisa on the grounds that their cultural biases prompted them to do so. The burden of proof is on you to defend such a bizarre philosophy. It is not on me to prove what everyone except yourself already knows.

    The answer is easy. Savages may see in Mona Lisa just a burning material, nothing else. What purpose does a painting have for a stone-age civilization (provided that function is a sign of design, which you alternately affirm and deny as suits your purposes)?

    The savages will recognize the design immediately. They need not know the purpose of the design to know that it was designed. The one thing they would not do is conclude that the painting was the product of law and chance. No savage could ever be a stupid as a Darwinist.

    Also, I have never denied that function is a sign of design. Quite the contrary. This most recent claim of yours is, by the way, more evidence that you read things into what people write and don’t bother to apprehend the meaning in the text. Why do you so shamelessly misrepresent what people say.

    I quote myself @136

    Function does, indeed, imply design. Anywhere you find a function, you can safely conclude that it was designed.

    Can you defend your claim by showing where I said that function is not a sign of design? Of course not. You are just blowing smoke again.

    SB: Matter was designed to have an atomic structure. However, matter can be redesigned into new forms. Thus, the created matter called sand can be redesigned into a sand castle. That process leaves design clues. Also, God could have first designed matter and then redesigned it into a DNA molecule. That, too, leaves clues.

    Clues such as? Let me guess: The clue of a designed thing is design

    Notice how you completely ignore the refutation and change the subject. Everything is designed at the first level where God produces the raw materials for design, but not at the second level where those raw materials are used to make new designs. Contrary to your claim, not everything s designed at the second level. Aquinas would certainly not say that it was. Thus, you are refuted again—in spite of your attempt to evade the point.

    Since nobody has provided a scientific method to detect design thus far, I can safely conclude nobody ever will. It’s been vehemently asserted that it’s mathematically calculable, but we are still revolving around examples like Mona Lisa, paint factories, sand castles, spilled coffee, etc. Enough.

    I explained the difference between a formal scientific design inference and an informal design inference long ago. I used examples of the informal design inference to expose your nonsensical epistemology of design projection and the insane idea that an observer will project his anti-design bias onto a spear and call it a rock, or project his pro-design bias onto a rock and call it a spear. Everyone, except you, knows that such a scenario is ridiculous. I am confident that my readers and your readers know it.

    To your claim that no one has produced a scientific method for design, I can only laugh out loud. Kairosfocus dedicated this post to that very point and you completely ignored it. No doubt you didn’t even read it. Unbelievable.

  142. 142
    Box says:

    StephenB,

    StephenB #139: Interesting. A machine that was designed to serve no practical purpose. It does, however, do something, namely open and close. It is not totally without function. There is a process. I gather that you disagree.

    Not sure. Do you agree that ideally and ultimately must define function of designed objects in terms of usefulness for an agent (user)? I hold that we must; what else would function mean? Of course “usefulness for an agent” needs further definition.
    What may follow is the question: If some designed object is absolutely useless for any agent, does it have function?
    BTW including an agent in the equation of function obviously does in no way imply the absurd notion of E.Seigner that function is entirely subjective. One can choose not to use a can opener, but one cannot choose that it is useless to open cans. Similarly, one cannot project into a can opener that it actually functions as remote control.

    StephenB #139: Still, the bigger and more important question remains: Would you at least agree that the design (not function) can be detected even in the absence of context.

    Of course I do. The following line by WJM is a classic: “Anyone who argues that a battleship’s combination of directed specificity and/or complexity is not discernible from the complexity found in the materials after an avalanche is either committing intellectual dishonesty or willful self-delusion.”

  143. 143
    StephenB says:

    SB: Interesting. A machine that was designed to serve no practical purpose. It does, however, do something, namely open and close. It is not totally without function. There is a process. I gather that you disagree.

    Box

    Not sure.

    OK

    Do you agree that ideally and ultimately must define function of designed objects in terms of usefulness for an agent (user)? I hold that we must; what else would function mean? Of course “usefulness for an agent” needs further definition.

    I suppose there are two ways to approach it. If we go strictly by the dictionary definition, then I would be inclined to say that we could go either way.

    Function

    “an activity or purpose natural to or intended for a person or thing.”

    That doesn’t help much: Is it activity or purpose. We are trying to decide which one and they offer us a choice with the word “or.” If they has said “and,” the matter would be settled.

    They example suggests purpose:

    “bridges perform the function of providing access across water”

    but the synonyms appear to open it up for both ways:

    “responsibility, duty, role, concern, province, activity, assignment, obligation, charge; task, job, mission, undertaking, commission”

    It reminds me of the story of two groups of workers on opposite sides of a river. The first group took raw materials like stones and built beautiful structures, sending them to the other side of the river in completed form. The group across the river used demolition tools to tear all the objects down into raw parts and dust. Then they sent it back to the other side as raw materials to begin the process all over again.

    Did each group perform a function? Obviously, the entire enterprise was futile, but the behavior appeared to be goal oriented. I guess it depends on your perspective.

    At the moment, I am inclined to say that purpose is not necessary to function, however, I don’t hold that opinion very firmly and can easily be persuaded otherwise.

    From a broader perspective, though, even this apparently useless machine could have a purpose. It could, for example, be the intention of the builder to dramatize his creativity or to present a riddle for design thinkers, in which case it would seem to have a purpose after all.

    What may follow is the question: If some designed object is absolutely useless for any agent, does it have function?

    Right. That is the question.

    BTW including an agent in the equation of function obviously does in no way imply the absurd notion of E.Seigner that function is entirely subjective. One can choose not to use a can opener, but one cannot choose that it is useless to open cans. Similarly, one cannot project into a can opener that it actually functions as remote control.

    Yes.

  144. 144
    Mung says:

    E.Seigner:

    Both ID theory and Dawkins project design onto the organism. Dawkins has a book on it, The Blind Watchmaker. The difference between ID theorists and Dawkins is that Dawkins doesn’t admit the designer.

    What is it about this “organism” that leads BOTH Dawkins AND the ID theorist to “project design onto the organism”?

    If both come to the same conclusion, even though from such opposite view points, perhaps there is something THERE that is in fact objective.

    E.Seigner:

    Projecting some structure or pattern is a necessary precondition to make any sense of anything.

    There must be something objectively there to be made sense of.

  145. 145
    Box says:

    StephenB,
    Thank you for your insights. One quick follow-up question. Do you agree that function is (ultimately) related to a person and not a thing? You did not address this in your previous comment and I’m particularly curious to find out what your position is.

    IMHO it doesn’t make sense to state that a can opener is functional for a can. Ultimately a can opener is functional (useful) for a person who wants to open a can. Similarly, DNA is ultimately useful for an organism. A person is always the most outward circle of the ripple effect invoked by functionality.

  146. 146
    Mung says:

    Box @ 137.

    LMAO!

    Was the useless machine the thing with the human looking finger?

  147. 147
    Mung says:

    IMO, the box was designed to illustrate the concept that for every action there is an equal and opposite reaction.

  148. 148
    Mung says:

    E.Seigner:

    Since nobody has provided a scientific method to detect design thus far, I can safely conclude nobody ever will.

    Taken at face value, this is a non-sequitur.

    As such, it is highly implausible that “nobody has provided a scientific method to detect design thus far” is in fact a premise in your argument.

    But in case I am wrong, would you care to share your reasoning?

  149. 149
    Vishnu says:

    E.Seigner: Since nobody has provided a scientific method to detect design thus far, I can safely conclude nobody ever will.

    Even if that were true – you haven’t demonstrate that it is – how do forensic technicians detect design or intent?

    When blood is splattered on a wall, why would anyone think that it was “designed” or an artifact of an intentional action?

    Now, just to clue you in, abductive reasoning is not necessarily “scientific”, but it is useful. In fact, it is absolutely necessary for the survival of humans, include you. (I’m assuming you’re a human.)

    “Science” isn’t everything. “Science” is merely one tool in the toolbox that humans use. Humans are more intelligent than science. In case you haven’t noticed, we invented it.

  150. 150
    Box says:

    Mung #146,

    No, what you saw was part of a useful consciousness / matter interface 🙂

  151. 151
    StephenB says:

    Box

    Thank you for your insights.

    I always appreciate both your questions and your well-thought-out convictions.

    One quick follow-up question. Do you agree that function is (ultimately) related to a person and not a thing? You did not address this in your previous comment and I’m particularly curious to find out what your position is.

    I think that an organism has a function (objective) and it used by a person (subjective).

    IMHO it doesn’t make sense to state that a can opener is functional for a can. Ultimately a can opener is functional (useful) for a person who wants to open a can.

    I think that there is a “what” and a “for,” answering the questions, what does it do? and for who(m)? Put another way, I think it functions as a thing and for a person. Or, again, I think function is a feature of and in the thing (its objective functionality) that is conceived, built, defined, understood, and used by the person (subjective). [***Subject conceives, designs, and builds objective functionality in a thing (organism, artifact) that comes to be understood and perceived by another subject].

    Similarly, DNA is ultimately useful for an organism. A person is always the most outward circle of the ripple effect invoked by functionality.

    I would be inclined to use the same formula as above. GPuccio also makes the distinction between the subjective and objective component, though he proceeds a little differently: You and I are discussing what is while he is discussing how we come to know it.

  152. 152
    kairosfocus says:

    ES:

    Since nobody has provided a scientific method to detect design thus far, I can safely conclude nobody ever will.

    All you are doing is reiterating a denial in the face of evidence. Speaks volumes.

    Pause for a moment and glance up to OP.

    Notice, the flowchart and linked infographic on why FSCO/I is maximally implausible to be found by blind chance and mechanical necessity?

    Right there, head of the discussion.

    Next, empirical data and induction.

    We have in hand all around us trillions of cases of FSCO/I that we directly observe the cause of. Consistently, FSCO/I is the result of design — intelligently directed contingency. (And no, we have no reason to confine such possible intelligence to humans.)

    In addition, this is the only plausible solution to the needle in haystack challenge.

    Per inductive argument — by which evidence summed up in premises supports a conclusion, and particularly inference to best explanation on reliable sign, FSCO/I is a reliable index of design.

    So, we are epistemically well-warranted to conclude that FSCO/I is a diagnostic sign of design.

    Does this provide absolute, deductive proof or certainty beyond all possibility of doubt?

    No.

    So, you have failed to prove . . . tada!

    Not so fast, pahdnuh.

    We are here dealing with inductive warrant, the basic means of establishing reliability of scientific (and a lot of other) knowledge claims. Such are incapable of absolute proof, but are widely seen as reliable and useful, given inherent limitations of our knowledge and reasoning. Known for centuries.

    So, to exert a double standard on warrant in order to reject the design inference approach, is a case of selective hyperskepticism.

    No great surprise.

    Please, pause, and think again.

    KF

  153. 153
    Box says:

    StephenB #151,
    Thank you for the clarifications. I have to ponder on the profound objective – subjective distinction that you eloquently offer.

    Some initial thoughts semi-related to this issue:
    In an organism we witness harmonized functional connectedness –all the parts function in harmony and are subordinate to the whole. BTW all this is in stark contrast with e.g. my chaotic collection of kitchen appliances. If we attempt to explain the functional harmony of the countless parts of organism we must suppose it originates from the level of the whole organism. A bottom-up explanation, from the level of the parts, for the observed harmony takes us into the realm of absurdity. Order is imposed – and specific functionality is demanded – from above; that is, from the organism / person.
    So, at least in biology, there is a definite hierarchy in the relation (not bottom-up) and no sharp devide between objective and subjective.

  154. 154
    E.Seigner says:

    StephenB

    I have already articulated (and dramatized) the point, which as usual, you ignored. All rational people will recognize and admit that the painted Mona Lisa screams design and that the scattered paint from the explosion does not.

    What design? Do you mean that Mona Lisa doesn’t spring up by chance or that it doesn’t evolve by itself from natural causes? How are paint factories any different? Are you saying that paint factories spring up by chance and evolve by themselves from natural causes? I will get back to you when you begin to make sense.

    Vishnu

    Even if that were true – you haven’t demonstrate that it is – how do forensic technicians detect design or intent?

    They don’t. Does it say in their job description that they are supposed to detect design? Does anyone of them talk about detecting design? And really, the question is how ID theorists detect design, not how some unrelated people do it. And the more fundamental question is what it even means to detect design.

    Mung

    There must be something objectively there to be made sense of.

    To share a basic concept with you: Observation is the subject facing the object. There’s both an object and a subject in observation and this is irreducible. Somehow you people think observation is all-objective because there’s an object, whereas in reality, if there’s no subject, there’s no observation in the first place. Moreover, the way you go about observation – carelessly, with no regard to methodical interpretation of the facts so as to ensure reliable reproducible results – can only be called subjective. We have had tons of discussion by now, but even the most basic distinctions have not been clarified. Basic distinctions such as design versus non-design. Somehow the distinction should be “obvious” and those who don’t uncritically accept it are “selectively hyperskeptical” or “stupid like Darwinists”.

    What should be obvious is that when ID theory is a fringe minority movement, then “design detection” is evidently far from obvious. If you disagree with this, then that’s your subjective opinion. I prefer to call things as they are.

  155. 155
    Joe says:

    LoL!@ E Seigner! Of course forensic scientists and technicians detect design- murder is a form of design. Any crime is a form of design. BTW ID uses basically the same techniques as forensic science, SETI and archaeology

  156. 156
    kairosfocus says:

    ES, one’s behaviour becomes selectively hyperskeptical when one exerts a double-standard on warrant to shut out what one does not wish to take seriously. As has been documented above: inductive reasoning — including abduction — is a major foundation for science. It is a self-refuting position, and the onward level of global skepticism the OP has to address is even moreso. The implicit notion that one cannot know the external world but projects subjective thoughts unto it, is by direct implication a very strong knowledge claim about the external world. It refutes itself. Instead, one could start from the undeniably true claim, error exists, and from that one can build from the possibility of truth, knowledge and error, a sounder worldview. This is relevant to doing science, but also to much more than science. And, to point this out is not to denigrate you or your intelligence, it is to provide an opportunity for you to make a needed fresh start. KF

  157. 157
    kairosfocus says:

    PS: ES, the distinction between design, chance and mechanical necessity as causal factors is ancient and well-established. Such are not on trial, we are. With lawlike regularity, the sun and Moon rise and set across the face of the sky and the stars at night vary with the seasons, also guavas and apples fall at 9.8 N/kg from trees. These are connected, and the study of these by Newton as a young student transformed the world. About a century later, the analysis of pressure of a gas pointed to molecules moving around at high speed, and across C19 – 20, statistical thermodynamics emerged, pivoting on the chance-based random behaviour of such. Temperature came to be understood as an index of the average random energy per molecule per degree of freedom. And all along, mechanical necessity was associated with low contingency of outcomes on similar starting conditions. High contingency of outcomes on similar initial conditions could be stochastically distributed, reflecting chance. It could be credibly intelligently directed, reflecting design. Which is a manifestation of a very common phenomenon and experience, intelligence. Next, FSCO/I is a key example of a phenomenon — such as the text of your post just above — that is not plausible or empirically observed on chance, but is frequently seen on design. In this context, trying to obfuscate well known, readily understood and familiar concepts in order to try to blunt the force of evidence pointing to design in contexts that many are not comfortable with is not a healthy sign. The price being paid to reject it, however, is an inadvertent sign of how strong the case is.

  158. 158
    Mung says:

    E.Seigner:

    To share a basic concept with you: Observation is the subject facing the object. There’s both an object and a subject in observation and this is irreducible.

    Of course, the object is also a subject, but let’s leave that aside for now.

    To assert something about observation, as you have, is to assert certain things about what it means for something to be a subject and to assert certain things about what it means for something to be an object.

    For a subject to observe an object, there must be something objectively there. If there is in fact nothing there to be observed, then by your own admission it’s not an object. And no one here is claiming the reality or objectivity of non-objects.

    E.Seigner:

    Somehow you people think observation is all-objective because there’s an object, whereas in reality, if there’s no subject, there’s no observation in the first place.

    You cannot possibly be so naive.

    Your claim can be reduced to the assertion that absent a subject observing an object, nothing can exist.

    Moreover, the way you go about observation – carelessly, with no regard to methodical interpretation of the facts so as to ensure reliable reproducible results – can only be called subjective.

    You’ve lost sight of your argument.

  159. 159
    Joe says:

    E Seigner:

    And the more fundamental question is what it even means to detect design.

    It means we have A) eliminated entire classes of possible causes, B) determined a causal class, which C) tells us how to proceed with the investigation. The strongest thing ID offers to biology is that opens up the likelihood that there is immaterial information, ie not DNA, RNA, AA, guiding biological processes and determining form.

  160. 160
    Mung says:

    E Seigner:

    And the more fundamental question is what it even means to detect design.

    On the contrary, the more fundamental question, as we have shown, is what it evens means to detect anything at all.

    In different words, the more fundamental question, as we have shown, is what it evens means to project anything at all.

  161. 161
    Vishnu says:

    E. Seigner,

    Vishnu: how do forensic technicians detect design or intent?

    E. Seigner: They don’t. Does it say in their job description that they are supposed to detect design? Does anyone of them talk about detecting design?

    Yes. That’s their job. They work with prosecutors to create a hypothesis (which they typically call a “theory”) of the crime based on the evidence. Abductive reasoning is an integral part of this process, is it is with ID, and forms the basis of all hypothesis creation.

    And really, the question is how ID theorists detect design, not how some unrelated people do it. And the more fundamental question is what it even means to detect design.

    SETI is attempting to detect design based on “coded information” on signals from space. Why do you suppose that is? Since we find coded information in the DNA/ribosome system, why should we not abductively reason that an intelligent source is the best inference given what we currently know about physics, chemistry, coded information systems, and intelligence?

  162. 162
    drc466 says:

    E.Seigner:

    You are on a beach. You see sand. Is it intelligently designed?
    Farther on, you see a smooth rock generically shaped. Is it intelligently designed?
    Couple more steps. You see an oddly-shaped lump of sand sticking up above the sand around it. Is it intelligently designed?
    Farther. Now you see an exquisitely detailed sandcastle. Is it intelligently designed?
    Still farther. You see another rock, triangular in shape, with what looks like possibly tool-marks on two sides. Is it intelligently designed?
    Again, more. You find a watch, still running. Is it intelligently designed?
    More steps. You find a paperclip. Is it intelligently designed?
    A few more steps. You find the stone heads of Easter Island. Are they intelligently designed?
    Almost there. You find an obviously complex structure with knobs and switches and weird protrusions you can’t identify, made of a material you don’t recognize. Is it intelligently designed?
    Final steps. You find a pamphlet entitled “Intellectual Honesty and the Art of Self-Deception”. Do you read it?

  163. 163
    Mung says:

    Meanwhile, E.Seigner continues to project.

    Fortunately, projection only requires a blank screen. One might, mistakenly, think that projection obviates the need for reality.

  164. 164
    E.Seigner says:

    Meanwhile, I’ve been reading up on this blog how you calculate FSCO/I. You came closest here http://www.uncommondescent.com.....on-of-csi/ but the conclusion you reached was hatred and vilification, not a solution to any of the problems.

    By now I have a solid picture of ID theorists and their community:

    – ID theorists loudly insist that complexity, specification, design, etc. prove something and are calculable, but
    – There’s no agreement on the definitions and nobody has made any actual calculations, except feeble inconclusive ones
    – Upon requests to back up their claims they turn to insults

    The short answer to the question how to calculate FSCO/I is: You don’t. The long answer is loudmouthing and ridicule. After several rounds, at least this much is scientifically settled.

    And I even haven’t asked you to calculate anything. I came here to participate in threads on other topics. You are doing this ID thing to yourself and you fail miserably. Like Barry who brought up two strings that were supposed to prove something, but which ended up proving the opposite – calculably so. This was not the best case, but it is the most prominent one.

    I’d rather you didn’t embarrass yourselves so much. Be more humble (which is what you ask of others after all) and find some other topic.

  165. 165
    Upright BiPed says:

    Like Barry who brought up two strings that were supposed to prove something, but which ended up proving the opposite

    I would drive me crazy if, over and over again, the defense of my beliefs was forced to rely on rhetoric. I honestly don’t know how you people do it, but you do it well.

  166. 166
    E.Seigner says:

    Upright BiPed

    I would drive me crazy if, over and over again, the defense of my beliefs was forced to rely on rhetoric. I honestly don’t know how you people do it, but you do it well.

    You mean I rely on rhetoric to defend my beliefs? The OP and the whole thread is a fine example that nobody actually cares what my beliefs are. All you do is exemplify yet another case of projection of beliefs that have nothing to do with me. Just like Barry who called me materialist after I had been discussing Thomist theology for a month. This definitely required some projection on his part, don’t you think?

  167. 167
    Upright BiPed says:

    You ask: “Can you name a thing that has no design or function?”

    A valid answer comes: “the pattern my coffee makes on the floor after I spill it”

    You respond “But if coffee still has function, then surely it has design too.”

    In this exchange, and dozens of others, you clearly demonstrate that you have no desire to understand squat.

    – – – – – – – – – – – –

    Barry posted two sequences of symbols; one that is gibberish (which he called “random”) and another with full specification to any English-speaking human adult. Even though it was painfully obvious to all rational people what the meaning of the sequences were (as well as Barry’s description of them), literally tens of thousands of words were produced for no reason other than to obfuscate the issue in place of dealing with it. And here you are, victory in hand, holding this farce up as a failed test of ID.

    – – – – – – – – – – –

    As I said, I don’t know how you do it.

  168. 168
    E.Seigner says:

    Upright BiPed

    You ask: “Can you name a thing that has no design or function?”

    A valid answer comes: “the pattern my coffee makes on the floor after I spill it”

    You respond “But if coffee still has function, then surely it has design too.”

    In this exchange, and dozens of others, you clearly demonstrate that you have no desire to understand squat.

    The purpose of the exchange was to get to the definition of design. According to most definitions I encountered early on, human-made was “clearly and demonstrably” supposed to mean design and to deny it meant to be “selectively hyperskeptical”. Therefore: Does coffee drink grow on trees? Does it get into the cup by itself and spill itself? Evidently, by examples like this we are not getting any closer to what is meant by design, and it’s preposterous to call it clearly demonstrated when your definition of design is an obfuscation by design in itself.

    Upright BiPed

    Barry posted two sequences of symbols; one that is gibberish (which he called “random”) and another with full specification to any English-speaking human adult.

    Except that the randomness/design was supposed to be demonstrably measurable and the specification was supposed to be obvious without context. None of which has been the case.

  169. 169
    gpuccio says:

    E.Seigner at #164:

    Your 3 points:

    1) ID theorists loudly insist that complexity, specification, design, etc. prove something and are calculable

    True.

    2a) There’s no agreement on the definitions

    Wrong. There is a lot of agreement on the general concepts, and many disagreements on specific details or procedures, as it is completely natural in human thgought and in science. ID is a scientific theory, indeed a scientific paradigm, not a party line.

    2b) and nobody has made any actual calculations, except feeble inconclusive ones.

    Wrong. I have offered calculations for specific proteins. They are not feeble, and they are not inconclusive. You are free to believe differently, of course. But simply stating your imaginations does not make them true.

    3) Upon requests to back up their claims they turn to insults.

    Wrong. I don’t think I have turned to insults. I have tried to answer in detail all your “arguments”. As far as it was reasonable. I cannot spend my whole life answering someone who does not want to listen.

    Maybe some ID proponent recurs to insults. It is equally true that a lot of anti IDists recur to insults. In some anti ID blogs, insult is the absolute rule. That is simply an interesting hint about human nature, and not certainly about ID or neo darwinism or any other human philosophy. People recur to insult about practically everything.

    But I would never say that “I have a solid picture of anti-ID theorists and their community” and that the solid picture is that “Upon requests to back up their claims they turn to insults”. That would be an offensive lie. It would be an offensive lie against people like Mark Frank, Piotr, wd400, and a lot of others, for which I have esteem and respect.

    Maybe you should reflect a moment on what “humble” means.

  170. 170
    E.Seigner says:

    gpuccio

    I have offered calculations for specific proteins. They are not feeble, and they are not inconclusive. You are free to believe differently, of course. But simply stating your imaginations does not make them true.

    You mean the other post you linked to, right? I disagree, but not based on belief. I disagree based on the fact that you did not have any rigorous definitions to form a sensible hypothesis to clarify what you were supposed to be calculating there in the first place. Lack of definitions makes your calculations actually and factually inconclusive. You stuffed “objective” where it didn’t belong and you imagined by this you made it objective…

    gpuccio

    But I would never say that “I have a solid picture of anti-ID theorists and their community” and that the solid picture is that “Upon requests to back up their claims they turn to insults”. That would be an offensive lie. It would be an offensive lie against people like Mark Frank, Piotr, wd400, and a lot of others, for which I have esteem and respect.

    So you see, people can sensibly disagree about ID. This is yet another sign among others by which you should be able to understand that it’s not as conclusive as it appears to you.

    And by all means tell where did Shallit go wrong in his calculations? Do you have better calculations? Thus far Barry has been spreading the message that it was wrong of Shallit to calculate at all.

  171. 171
    gpuccio says:

    E.Seigner:

    Very interesting. So:

    1)

    “I disagree based on the fact that you did not have any rigorous definitions to form a sensible hypothesis to clarify what you were supposed to be calculating there in the first place. Lack of definitions makes your calculations actually and factually inconclusive. You stuffed “objective” where it didn’t belong and you imagined by this you made it objective…”

    OK. that is what you think. And I think you are wrong. Very wrong. And I think that not based on belief, but on the fact that you do not understand my definitions and you do not understand the clear meaning of my words, explicit and defined, including the context in which I use “objective”.

    And you seem not to understand a very simple truth about human nature and condition: people may disagree about things (see later).

    2)

    “So you see, people can sensibly disagree about ID. This is yet another sign among others by which you should be able to understand that it’s not as conclusive as it appears to you.”

    This is really a pearl! So, you are saying that people can disagree about ID. What a news!

    I am sorry to inform you of something that maybe you should have already noticed in your life, unless you live on Mars or any other place which is not this unfortunate planet: people can disagree about everything.

    Do you think nobody ever disagreed with Einstein about his relativity theory, or Bohr about quantum mechanics?

    Now, let’s say that Bohr goes to the shop to buy some food, and that the dealer says: “Mr Bohr, you know, I really disagree with you about quantum mechanics, therefore it’s not as conclusive as it appears to you”. What a tragedy for science.

    3)

    “And by all means tell where did Shallit go wrong in his calculations? Do you have better calculations? Thus far Barry has been spreading the message that it was wrong of Shallit to calculate at all.”

    The point is simple. Barry has shown a clear example of positive design inference. Correct positive design inference. And of a string for which no design inference based on meaning could be done.

    That is a perfect example of correct application of the design inference. In the Shakespeare passage, a huge quantity of functional information was connected to a detectable English meaning. In the other string, that was not true.

    So, we infer design for the Shakespeare passage, and not for the other string. That is a perfectly correct positive inference. I don’t understand why you and Shallit seem not to understand it.

    Can you provide a false positive to falsify the procedure?

    The fact that our non inference of design for the first string is a false negative or a true negative is irrelevant. However, just to make you understand, I will clarify that it is a true negative for the function “having a correct English meaning”. The first string was never designed for that.

    If you define the function as “being recognizable as a string typed on a keyboard without any intention to get a meaningful string” then the first string is probably recognizable for that function. It is very likely that strings randomly typed on a keyboard are recognizable because of the physical constraints generated by the typing tool (the keyboard). That has nothing to do with a design inference based on a conscious intentional meaning or function, implemented by a complex series of designed bits. The only thing you recognize here is the necessity constraints in the random system which generated the string (the keyboard and the random typist).

    But I doubt that you will accept even these simple ideas. If you and Shallit do not understand the basic concept of ID and of design detection (the complexity linked to a definable function), then there is no hope.

  172. 172
    Joe says:

    E Seigner is either willfully ignorant, deluded or dishonest as FCSI/O has been measured wrt biology and that was in peer-review.

  173. 173
    E.Seigner says:

    gpuccio

    “And by all means tell where did Shallit go wrong in his calculations? Do you have better calculations? Thus far Barry has been spreading the message that it was wrong of Shallit to calculate at all.”

    The point is simple. Barry has shown a clear example of positive design inference. Correct positive design inference. And of a string for which no design inference based on meaning could be done.

    That is a perfect example of correct application of the design inference.

    Perfect example of correct application of the design inference how? Barry’s case is not based on the calculation of FSCO/I (even though the original context was about the mathematical proof, not mere assertion), so what is it based on? How can you claim it’s correct and even a perfect example of correct application without any calculation and even without definition of the terms?

    gpuccio

    The fact that our non inference of design for the first string is a false negative or a true negative is irrelevant. However, just to make you understand, I will clarify that it is a true negative for the function “having a correct English meaning”. The first string was never designed for that.

    How did you compute or detect the function “having a correct English meaning”? I know: You didn’t. You simply assume it’s obvious and should be uncritically accepted, even though we were supposed to be objectively calculating something. Sorry, but yours is a clear case of a foregone conclusion.

    I have been faced with nonsense like this here all along. A little above, someone said spilled coffee was an obvious case of randomness, while some time earlier a messed-up room with disappeared jewellery was supposed to be an obvious case of design and – get this – none of the cases require any proof, calculation, or definition. They are supposed to be self-evident. All this clearly conveys the message that nobody has any idea what they are talking about, but you are quick to jump to conclusions and declare them obvious. And anyone who cites lack of evidence and lack of definitions is denounced as selectively hyperskeptical. Good grief.

    As to “The fact that our non inference of design for the first string is a false negative or a true negative is irrelevant”, well, if the distinction between design and non-design is real, isn’t it highly relevant that it be reliably determined? The whole OP tries to make the case how design inference is supposedly objective and reliable, not subjective and unreliable. Yet as Aquinas (and any other classical theologian) implies – correctly in my opinion – creation in its entirety and totality is designed, so there is no logical way to distinguish design from non-design and therefore *all* your negatives are false. Consequently, the distinction between design and non-design is empirically indeterminable and does not exist for any practical purpose. Which means ID theory is just an exercise in sophistry. Your statement “The fact that our non inference of design for the first string is a false negative or a true negative is irrelevant” along with utter subjectivity of function and specification makes ID theory utterly irrelevant. And it won’t help to blame Aquinas for employing po-mo antics, as KF does. Such a turn was ridiculous from the beginning.

    gpuccio

    But I doubt that you will accept even these simple ideas. If you and Shallit do not understand the basic concept of ID and of design detection (the complexity linked to a definable function), then there is no hope.

    Indeed, I won’t accept ideas that involve foregone conclusions and category errors, no matter how simple or complex. I prefer real distinctions and logical concepts with demonstrable practical utility, thanks.

  174. 174
    Joe says:

    E Seigner:

    How did you compute or detect the function “having a correct English meaning”?

    It’s called knowledge of the English language. Are you really that simple?

  175. 175
    Upright BiPed says:

    >> “Can you name a thing that has no design or function?”

    >>> “the pattern my coffee makes on the floor after I spill it”

    >> “coffee still has function” … “I won’t accept category errors” … “there is no logical way to distinguish design from non-design” … “I have been faced with nonsense like this here all along”

  176. 176
    kairosfocus says:

    ES,

    the string in question is ASCII English text, which has a readily identifiable size in bits, at 7 bits per character. It is functionally specific [any arbitrary at-random string is not] and is well beyond 72 – 143 characters. 500 – 1,000 bits.

    The design inference on Chi_500 or Chi_1000 is obvious:

    Chi_500 = I*S – 500, bits beyond the solar system threshold for FSCO/I

    (Cf discussion here on in context . . . note biological cases in point per the Durston Info metrics)

    String 1: approx 500 characters, no specification (any arbitrary string would have done as well, I would have recommended sky noise or Zener noise driving a digital string generator) so S = 0, the DEFAULT:

    Chi_500(S1) = (500 x 7 bits/char) * 0 – 500 = – 500 bits, the default threshold meaning not specific and so baseline.

    String 2: approx 500 characters, recognisable, grammatical English text, so per observed specificity and functionality, S = 1:

    Chi_500(S2) = (500 x 7) * 1 – 500 = 3,000 bits beyond the solar system threshold

    The design inference using this metric model first discussed publicly in 2011, says S1 is not designed, and S2 is.

    As expected.

    And per testimony of the source, S1 is not designed, it comes from haphazard keyboard typing similar to:

    kiynptld52jpdw9msqauiak4kotvdiu . . .

    Even, were this a case of an actually designed case, the want of recognisable specific functionality would lead to a false negative which is acceptable. We are not trying to create a universal decoder algorithm.

    The second string is notoriously a famous passage from Shakespeare.

    The design inference does exactly what it is intended to do. And in fact the Chi_500 or 1000 expression is the reduction of much of the flowchart in the OP above to a metric model.

    Yes, it pivots on observing functional specificity, which can be a challenge.

    So what, that challenge of observational anchorage is common for all sorts of sciences. Right now for instance I am using Solow’s growth model to look at long waves in economics to identify what is driving the global economy forward form the current Kondratiev- Schumpeter long wave trough, in order to give sensible policy advice. And decades ago in Physics class, I recall the semi-empirical mass model of Weisacker, which brought forth the nuclear shell model, which was anchored to empirical observations.

    Someone once objected to beyond-threshold metrics so I note that the photoeffect expression is a case of just that, one that helped win a Nobel Prize.

    But of course, when you all were publicly presented with a metric model on measuring FSCO/I, you played at obfuscation and refused to attend to it or its effectiveness.

    KF

  177. 177
    kairosfocus says:

    PS: I count 535 chars for S1, and S2 the same, at least in the version I found.

  178. 178
    gpuccio says:

    E. Seigner:

    “How did you compute or detect the function “having a correct English meaning”? I know: You didn’t. You simply assume it’s obvious and should be uncritically accepted, even though we were supposed to be objectively calculating something. Sorry, but yours is a clear case of a foregone conclusion.”

    OK, I did not compute it because it is obvious and for brevity, but as you request it, let’s discuss it.

    The Shakespeare passage is 535 characters long, and has a correct English meaning.

    Now, let’s start computing the search space. I will consider an alphabet of 30 characters (including essential punctuation). So, the search space is 30^535. That is about 2622 bits.

    I suppose we can accept a threshold of 500 bits as UPB. Indeed, Barry did not have 14 billion years and all the quantistic states of the universe to effect a computation of the string, so I would say that a very conservative threshold of 300 bits could be considered more than enough to infer design.

    So the simple fact is, we can safely infer design is the number of sequences of 535 characters which have a correct English meaning is lower than 2^2322, IOWs lower than (about) 10^771. Which is a number greater than the quantistic states of the universe from the beginning to now.

    Now, I am rather sure that the number of sequences of 535 characters which have a correct meaning in English is much, much lower than that. Do you really doubt it?

    However, can I demonstrate that? Not explicitly and not now, and I am not really interested in trying. I suppose that a linguist (Piotr, where are you?) together with a mathematician could try some good approximation of the computation. In the past, I have suggested a very simple reasoning which shows clearly how the target space/search space ration must necessarily become lower as the string length increases, so one could start with some shorter string value and then extrapolate.

    I am not really interested in that because my interest is in applying design detection to proteins. For proteins, the Durston method is at present the best way to approximate the target space/search space ratio. The target space/search space ratio must always be approximated by some indirect method for long sequences, because a direct estimation is beyond any realistic possibility. So, the method will be different for meaningful language, for functional software and for functional proteins. But in general, it will be found that beyond a certain length the ratio is definitely below any reasonable threshold. For example, out of 35 protein families in the Durston paper, 28 are definitely beyond my suggested biological threshold of 150 bits of functional complexity. The 7 protein families which have lower functional complexity are invariably short proteins (33-80 AAs).

    Let’s say that I will gladly infer design for any language string which has a correct English meaning and is at least 1000 bit long (205 characters). I defy you or anyone else to produce a false positive which was generated in any random character generating system on our planet (please, bring the evidence, otherwise I will not believe it! 🙂 ).

  179. 179
    gpuccio says:

    E. Seigner:

    I am realizing that perhaps when you said:

    ““How did you compute or detect the function “having a correct English meaning”?

    maybe you were not asking how I did compute the target space/search space ratio (which is the real problem in the procedure), which is what I discussed in my previous post. Maybe you meant: “How did you decide that the function was there?”.

    That is much easier. The function is defined as “having a correct sense in English”. Any English speaker who can read the string, and understand it, and explain its meaning, can verify that the function is present. The detection of the function is a binary value: either it is present or it is not. I agree that we should define the function in more detail, so that the observer has no doubts about the requisites which are requested. That can easily be done. I did not do it for brevity.

  180. 180
    E.Seigner says:

    gpuccio

    I am realizing that perhaps when you said:

    ““How did you compute or detect the function “having a correct English meaning”?

    maybe you were not asking how I did compute the target space/search space ratio (which is the real problem in the procedure), which is what I discussed in my previous post. Maybe you meant: “How did you decide that the function was there?”.

    Exactly. And this unfortunately makes your previous comment moot.

    gpuccio

    The function is defined as “having a correct sense in English”. Any English speaker who can read the string, and understand it, and explain its meaning, can verify that the function is present.

    Which is context and a bunch of subjective factors thrown in. There’s “verification” only after a host of subjective prerequisites are met, which brings it closer to “expert assessment” rather than “verification”.

    gpuccio

    The detection of the function is a binary value: either it is present or it is not.

    Context is always present. Always without exception. Individual subjective factors are to be acknowledged and minimized, not ignored or amplified. This is so in philosophy of language.

    http://media-cache-ak0.pinimg......7b9142.jpg

    Don’t get me wrong. I actually appreciate how you are trying to explain these things. Not your fault that the theory is indefensible 🙂
    Now there’s also this awesome comment by HeKS, clarifying the procedure more methodically than I’ve ever seen before. It emphasizes several key points that I have myself identified despite irrational denial by the theorists here. It explicitly states the inevitable. Of course, when everything is so lucidly laid out, then also the fundamental flaws of the theory stand out screaming. If you want, I can bring up some points from that comment. However, this only makes sense if you have yourself read it and completely agree with it.

  181. 181
    gpuccio says:

    E. Seigner:

    “Context is always present.”

    You always make trivial statements that are completely irrelevant to what I have said. My compliments.

    My point is that the detection of the function is a binary value: either it is present or it is not, according to specific and explicit rules to assess its presence. So the context is there, but it is completely repeatable.

    You simply ignored, as it is your custom, my statement: “I agree that we should define the function in more detail, so that the observer has no doubts about the requisites which are requested. That can easily be done. I did not do it for brevity.”

    For an enzyme, I have given the very explicit example of an explicit definition which is absolutely repeatable:

    “Any protein which, in the specific lab condition such and such, can accelerate the specific reaction A so that it takes place at least at the rate X.”

    Given that definition, any lab can assess any protein for the presence of the function, or not. Which makes it a binary variable whose value can be objectively determined in a completely repeatable way.

    But please, go on making trivial statements which are irrelevant. It’s your way, it seems.

    Regarding HeKS’comment, I have read it, and while I probably agree on many things, I cannot say that I “completely agree with it”. So, it’s your choice. As you could not answer my points directly, you can try to do that indirectly. Your choice. I will answer accordingly.

  182. 182
    gpuccio says:

    E. Seigner:

    By the way, my “previous comment” is not “moot” only because it answered something different from what you had asked. It remains valid and makes many important points, completely relevant to the discussion.

    At first, I had thought you had proposed a more interesting question. That was not the case. I apologize.

  183. 183
    Upright BiPed says:

    ES at 168:
     

    The purpose of the exchange was to get the definition of design.

     
    The purpose of the exchange was to defend your personal interpretation of creation – that all things were designed and therefore it is impossible even in principle to tell design from the non-design. You are willing to defend this interpretation into abject absurdity.
     

  184. 184
    Mung says:

    E.Seigner:

    The purpose of the exchange was to get to the definition of design.

    Your definition of design is your own projection of your own definition of design. Isn’t that your point?

    Are you asking us to adjust your projection?

  185. 185
    Mung says:

    ES:

    Don’t get me wrong. I actually appreciate how you are trying to explain these things. Not your fault that the theory is indefensible

    That’s just you projecting your subjective opinion on the facts. None of us are obligated in any way to conform to your subjective projections.

  186. 186
    Mung says:

    E.Seigner:

    By now I have a solid picture of ID theorists and their community:

    You have a solid projection. We should cheer? Whether your projection is in fact a “solid picture” is doubtful.

    Don’t allow the incoherence of your position bother you in the least.

  187. 187
    HeKS says:

    @gpuccio #181

    I noticed that you said you didn’t completely agree with my description of the logic of the methodology involved in calculating CSI. Can you specify where you disagree? Do you think I’ve made some mistake somewhere? If so I’d be interesting in knowing where you think I’ve gone wrong since, if I have, I don’t want to continue repeating the mistake.

    Take care,
    HeKS

  188. 188
    Mung says:

    E.Seigner complains about our projections of ES. Repeatedly. They are mistaken (so sez ES). But why they are mistaken (wrong/not factual) remains a mystery.

    E.Seigner appears to ascribe to a position which holds that our projections ought to be subject to some external reality. Dare we say, to something objective?

  189. 189
    kairosfocus says:

    ES: Pardon a newsflash — not.

    As there are entire professions based on it, it is not in our gift to define design, which ID uses in the very ordinary sense of intelligently/ purposefully directed contingency. Where intelligence is inferred from creativity, ability to understand and solve problems using creativity, insightfully creative use of mind etc, as IQ tests routinely show. Purpose comes out of credibly goal-directed behaviour reflecting activities and resource deployments towards a relevant target.

    Anyway, here is that humble, materialism leaning generic source, Wiki:

    Design is the creation of a plan or convention for the construction of an object or a system (as in architectural blueprints, engineering drawings, business processes, circuit diagrams and sewing patterns).[1] Design has different connotations in different fields (see design disciplines below). In some cases the direct construction of an object (as in pottery, engineering, management, cowboy coding and graphic design) is also considered to be design.

    More formally design has been defined as follows.

    (noun) a specification of an object, manifested by an agent, intended to accomplish goals, in a particular environment, using a set of primitive components, satisfying a set of requirements, subject to constraints;
    (verb, transitive) to create a design, in an environment (where the designer operates)[2]

    Another definition for design is a roadmap or a strategic approach for someone to achieve a unique expectation. It defines the specifications, plans, parameters, costs, activities, processes and how and what to do within legal, political, social, environmental, safety and economic constraints in achieving that objective.[3]

    Here, a “specification” can be manifested as either a plan or a finished product, and “primitives” are the elements from which the design object is composed.

    Again.

    In short, sadly, it seems that you are again living up to the seemingly harsh evaluation in the title line for this thread. Unfortunately, it has shown itself all too apt and that is why I did not revise it on second and third thought.

    The zero concessions to IDiots policy is plainly failing.

    And BTW, here is the UD glossary under the resources tab:

    Design — purposefully directed contingency. That is, the intelligent, creative manipulation of possible outcomes (and usually of objects, forces, materials, processes and trends) towards goals. (E.g. 1: writing a meaningful sentence or a functional computer program. E.g. 2: loading of a die to produce biased, often advantageous, outcomes. E.g. 3: the creation of a complex object such as a statue, or a stone arrow-head, or a computer, or a pocket knife.)

    Intelligence – Wikipedia aptly and succinctly defines: “capacities to reason, to plan, to solve problems, to think abstractly, to comprehend ideas, to use language, and to learn.”

    Information — Wikipedia, with some reorganization, is apt: “ . . that which would be communicated by a message if it were sent from a sender to a receiver capable of understanding the message . . . . In terms of data, it can be defined as a collection of facts [i.e. as represented or sensed in some format] from which conclusions may be drawn [and on which decisions and actions may be taken].”

    Intelligent design [ID] – Dr William A Dembski, a leading design theorist, has defined ID as “the science that studies signs of intelligence.” That is, as we ourselves instantiate [thus exemplify as opposed to “exhaust”], intelligent designers act into the world, and create artifacts. When such argents act, there are certain characteristics that commonly appear, and that – per massive experience — reliably mark such artifacts. It it therefore a reasonable and useful scientific project to study such signs and identify how we may credibly reliably infer from empirical sign to the signified causal factor: purposefully directed contingency or intelligent design. Among the signs of intelligence of current interest for research are:

    [a] FSCI — function-specifying complex information [e.g. blog posts in English text that take in more than 143 ASCII characters, and/or — as was highlighted by Yockey and Wickens by the mid-1980s — as a distinguishing marker of the macromolecules in the heart of cell-based life forms], or more broadly

    [b] CSI — complex, independently specified information [e.g. Mt Rushmore vs New Hampshire’s former Old Man of the mountain, or — as was highlighted by Orgel in 1973 — a distinguishing feature of the cell’s information-rich organized aperiodic macromolecules that are neither simply orderly like crystals nor random like chance-polymerized peptide chains], or

    [c] IC – multi-part functionality that relies on an irreducible core of mutually co-adapted, interacting components. [e.g. the hardware parts of a PC or more simply of a mousetrap; or – as was highlighted by Behe in the mid 1990’s — the bacterial flagellum and many other cell-based bodily features and functions.], or

    [d] “Oracular” active information – in some cases, e.g. many Genetic Algorithms, successful performance of a system traces to built-in information or organisation that guides algorithmicsearch processes and/or performance so that the system significantly outperforms random search. Such guidance may include oracles that, step by step, inform a search process that the iterations are “warmer/ colder” relative to a performance target zone. (A classic example is the Weasel phrase search program.) Also,

    [e] Complex, algorithmically active, coded information – the complex information used in systems and processes is symbolically coded in ways that are not preset by underlying physical or chemical forces, but by encoding and decoding dynamically inert but algorithmically active information that guides step by step execution sequences, i.e. algorithms. (For instance, in hard disk drives, the stored information in bits is coded based a conventional, symbolic assignment of the N/S poles, forces and fields involved, and is impressed and used algorithmically. The physics of forces and fields does not determine or control the bit-pattern of the information – or, the drive would be useless. Similarly, in DNA, the polymer chaining chemistry is effectively unrelated to the information stored in the sequence and reading frames of the A/ G/ C/ T side-groups. It is the coded genetic information in the successive three-letter D/RNA codons that is used by the cell’s molecular nano- machines in the step by step creation of proteins. Such DNA sets from observed living organisms starts at 100,000 – 500,000 four-state elements [200 k – 1 M bits], abundantly meriting the description: function- specifying, complex information, or FSCI.)

    And more . . .

    Sitting there all along on this and every UD page, for years.

    KF

  190. 190
    gpuccio says:

    HeKS at #187:

    First of all, I want to say that I appreciate very much your detailed arguments about design detection. I don’t think it’s a problem of being right of wrong. There are probably some differences between the way I would express the concepts and the way you express them. I am certainly happy to discuss these aspect with you, so I will try to explain where I would use some different formulation.

    1) The first point is that I usually express the concept of dFSCI (my subset of CSI, which is defined as digital and functionally specified) as a means to refute the random origin of a string in a traditional scenario of Fisherian hypothesis testing.

    You say:

    “Rather, a measure of the improbability of some event, pattern, etc., is directly connected to a specific chance hypothesis that seeks to explain the event, and it is only valid in relation to that particular chance hypothesis used to make the calculation.”

    I completely ahree with that. But in my hypothesis testing scenario, there is only one random hypothesis (it is usually called H0 in Fisherian hypothesis testing): the hypothesis that the effect we observe is explained by random events, according to some probability distribution.

    Now, I agree that we always have to deal with some specific context. Indeed, in my reasoning, I always point out that we are trying to explain some observed effect (the digital string with its digital sequence which implements a well defined function) in a specific context: a well defined system, with specific probabilistic resources, and a definite time span.

    So, we observe the string and we know that it originated in a definite time span in a definite system where definite random events happen, and therefore the probabilistic resources of the system can be evaluated quantitatively. These are the observed facts.

    The question is: can the random events taking place in this system, in this time span, explain the specific string we observe?

    At first, we accept this random hypothesis as our H0. Then we compute the probability of the observed result (the functional string) if we accept H0 as true. If the probability is extremely low, we reject H0.

    Now, as you can see, we have only one random hypothesis (the null hypothesis H0), and we can have one or more alternative explanations (H1, H2…), which we will consider once we have decided that we reject H0.

    The probability of the observed event (the functional string) must be considered under two aspects:

    a) The probability of the functional string given the search space. That corresponds to the ratio target space/search space. IOWs, the functional definition generates a binary partition in the search space: strings with the function and strings without the function. The ratio target space/search space is a measure of that probability, assuming a uniform probability distribution of the states (which is completely reasonable, for reasons that I will not discuss here for brevity).
    This probability corresponds to the probability of getting a functional state in a single attempt: IOWs, each time a new state is achieved. That includes any possible type of random variation events. -log2 of the probability is the functional complexity in bits (what Durston calls fits).

    The functional complexity (dFSI) of a protein corresponds to that probability. For example, in Durston’s paper, the functional complexity of beta-lactamase is 336 bits. That corresponds to a probability of finding a functional beta-lactamase in one attempt (in a random walk from an unrelated state) of 1:2^336 (about 1:10^99).

    b) But certainly the system can perform much more than one random attempt in the time span. That’s what we call the probabilistic resources of the system: the number of different states that can be reached in the system in the time span.

    I have made a very gross computation that the maximum number of different states reached by a biological context on our planet in the whole time span of its existence is about 120-130 bits (2^130 different states).

    Now, the probability of getting at least one success in 2^130 attempts, given a probability of success in one attempt of 1:2^336, is about 1:10^62. That expresses the probability of the observed event if we accept H0 (the classical p value).

    Now, with all respect of our Bayesian friends (Mark first) who are suspicious about classical Fisherian hypothesis testing, a p value of 1:10^62 should convince even the most skeptical reasonable individual that H0 must be rejected (neo darwinists are not included 🙂 ).

    So, let’s say that we reject H0 for beta lactamase in the system and time span of biological life on our planet: it could not arise randomly. Now, we have to consider alternative explanations.

    I would stop here for the moment, and wait for your comments.

  191. 191
    kairosfocus says:

    GP: Excellent as usual. I would only add that a functionally organised thing can per AutoCAD etc be reduced to coded strings as we do with PCs routinely. So, discussion on dFSCI and strings is a key first case and arguably is WLOG. KF

  192. 192
    gpuccio says:

    KF:

    You are perfectly right. As you know, I just profit from the simple fact that protein coding genes are already in digital form 🙂

  193. 193
    Mark Frank says:

    Gpuccio
     

    Now, with all respect of our Bayesian friends (Mark first) who are suspicious about classical Fisherian hypothesis testing, a p value of 1:10^62 should convince even the most skeptical reasonable individual that H0 must be rejected.

    The lowness of the p value is irrelevant as to whether you dismiss h0. As you know all outcomes are equally improbable.  What matters is whether h1 or h2 can give a better explanation – including how plausible h1 and h2 are.  This is why pure Fisherian hypothesis testing has been discarded for decades even by non-Bayesians. Even the most elementary statistics textbooks demand that you also make it clear what h1 is. Only that way can you decide what the rejection region is. If it is a one-tailed test then it doesn’t matter how extreme the result is towards the other tail,  h0 will not be dismissed because h1 does not provide a better explanation.

  194. 194
    gpuccio says:

    Mark:

    I don’t agree with you. H1 can simply be that there is some unknown different non random explanation. H0 as a random explanation can certainly be rejected if it is really so unlikely.

    That’s what is always done in medicine. You detect possible connection between variables, even if you don’t know at present how they are connected. But you simply reject the hypothesis that the connection is due to random sampling, if you have a p value, say, of 10e-9 or lower. Nobody would attribute that result to an effect of random sampling.

    I don’t understand what you mean when you say that “As you know all outcomes are equally improbable.” Let’s say that you have two sets of values of two variables, and that a linear regression analysis shows a p value of 10e-10. Everybody would reject H0, even if we have no detailed theory about how the two variables are connected. Here H1 can be that one of the variables is the cause of the other, and H2 can be that there is a third variable connected to both, and so on, Maybe we have no clues to which is the best explanation.

    Still, no scientist with a sound mind would accept H0 as an explanation.

  195. 195
    kairosfocus says:

    MF, all INDIVIDUAL outcomes may be improbable, but there is a world of difference between straw and needle, and as straw is the overwhelming bulk a blind chance and necessity search will predictably [and given the ratio of possible sample size to number of possible configs, all but absolutely certainly . . . with utter empirical reliability] pick straw. The same applies to clustering microstates in statistical thermodynamics, which grounds the second law and that reasoning is connected. In short after any number of opportunities to know more accurately and many corrections, you have again knocked over the same strawman caricature. KF

  196. 196
    kairosfocus says:

    GP: That sampling challenge is what underlies the tests you speak of and the inconsistency we see here is yet another mark of selective hyper-skepticism. KF

  197. 197
    gpuccio says:

    KF:

    Thank you for the comments.

    I really cannot understand how Mark so completely denies the foundations on which all scientific inference is based. According to his reasoning, I could simply deny the law of gravitation if I just considered it a very unlikely explanation in my map of reality, because after all the events where the movements of objects are apparently connected to mass and distance are as improbable as any other configuration, so why bother to hypothesize strange attractions for which we have zero evidence, or even stranger effects of curve space?

  198. 198
    gpuccio says:

    Mung at #188:

    Objective???

    You are really a naughty boy! There is always a context… 🙂

  199. 199
    Mark Frank says:

    Gpuccio

    I don’t agree with you. H1 can simply be that there is some unknown different non random explanation. H0 as a random explanation can certainly be rejected if it is really so unlikely.
    That’s what is always done in medicine. You detect possible connection between variables, even if you don’t know at present how they are connected. But you simply reject the hypothesis that the connection is due to random sampling, if you have a p value, say, of 10e-9 or lower. Nobody would attribute that result to an effect of random sampling.

    First – let’s not confuse sampling and the underlying hypothesis. H0 is not “due to random sampling”. H0 is something like: “the probability of any character appearing at a given position in the string is the same and independent of all other positions” or “the treatment makes no difference to the probability of recovery”. You may think you simply reject h0 but there is a always an assumption about h1. This may be implicit or even unconscious, but has to be there or there is no justification for rejecting H0.

    For example:

    Suppose you want to do a clinical trial into a new treatment (T) for alleviating hay fever. So you do a RCT on 1,000 patients. Half of them get T for a month, followed by a placebo for a month; the other half the other way round. You then ask patients were they more comfortable under the first or second treatment. You don’t give the option of “no difference” so they have to decide (I am grossly simplifying things but the reasoning can be extended to more realistic trials).

    The result can be presented as a string 1,000 units long marked T or P. Every single possible string has exactly the same probability under H0: 2^1,000. So how do you decide which strings are grounds for rejecting H0? Traditionally we reject H0 if there are a large amount of Ts or Ps – but we would also reject it if there were exactly 500 Ts followed by 500 Ps – or if it corresponded to the Champerowne sequence.  What’s the justification? You could say we reject H0 if the resulting string matches any special pattern. But for any string how do you know it doesn’t match a pattern? Perhaps it is the binary equivalent of a poem in Sanskrit. In fact it is quite possible that every string matches some pattern – there infinitely many patterns to choose from. The answer is actually fairly obvious – if resulting string has 700 Ts we reject H0 because that string is much more likely if T works (that is your H1), if the string is 500 Ts followed by 500 Ps we reject it because it is much more likely to be explained by some fiddling with the results (that is your H1). However, if it happens to be the binary equivalent of poem in Sanskrit we do not reject it because there is no plausible H1 connecting the poem to the outcome.

    According to his reasoning, I could simply deny the law of gravitation if I just considered it a very unlikely explanation in my map of reality, because after all the events where the movements of objects are apparently connected to mass and distance are as improbable as any other configuration, so why bother to hypothesize strange attractions for which we have zero evidence, or even stranger effects of curve space?

    I don’t see at all how this follows from my reasoning. The observed movement of objects is far more likely given the H1 of Newton’s laws than it would be if they were in some (to be defined) sense random.

  200. 200
    kairosfocus says:

    MF: In relevant cases there are often many ways for an object to be in relevant functional clusters of states. The problem is, there may be far, far more for it not to be; as is so for FSCO/I — relatively few ways for reel parts to make a viable reel, many more for them to not. As a consequence, a blindly sampled state or set of states up to the atomic capacity of the solar system or observed cosmos, can only sample so small a fraction that the outcomes will reliably reflect the bulk of the pattern. And the classic Fisherian testing typically identifies a far skirt as a zone of interest then asks in effect, for reasonable sampling tries, what will we likely see. Answer the bulk, and it becomes so unlikely to pick up the far skirt that way that with a relevant degree of confidence, we may suggest whether or no the null hyp –we are in the far skirt by chance typically — is not credibly true. As is a commonplace. KF

  201. 201
    gpuccio says:

    Mark:

    I am afraid that you misunderstand many things.

    You say:

    “First – let’s not confuse sampling and the underlying hypothesis. H0 is not “due to random sampling”.”

    You don’t understand.

    Let’s suppose that we have, for example, two samples, and that we do observe a difference between them in the values of some measured variable.

    We call the observed difference “the effect size”, and quantify it in some ways. It can be a difference in mean and distribution.

    Or, if we compare two continuous variables, the effect is their correlation, and the effect size can be measured, for example, by the R square value in linear regression.

    If we observe no relevant effect, there is no game.

    But, if we observe an effect whose size is relevant for our purposes (clinical, methodological, or whatever), then we wonder:

    “Is the effect we observe a real effect, that we have to explain in some way, or is it only the result of random variance?”

    Usually, in clinical experiments, the random variance we refer too is the random variance in the original population from which the samples were taken.

    So, our H0 is that the two samples are from some homogeneous population (for the variable we are considering), and that other factors do not make any difference.

    So, any difference observed in our two samples is due to the random variance of the original population. That is H0. It is the hypothesis that what we observe is explained by random variation.

    The p value is a blending of the effect size and of the numerosity of the samples. It tells us how likely it is to observe the effect that we are observing (or a greater one) if H0 is true.

    If the p value is very low, and the effect size is relevant for us, we can rather safely reject H0 (the lower the p value, the safer the rejection).

    That has nothing to do with H1, H2, and so on.

    If we reject H0, we know that we are (most likely) observing a true effect, and not only a pseudo effect. That effect we must try to explain. And there may be many possible explanations for it. The choice between explanations is usually not so much a question of probability, but a methodological evaluation: how well does our explanation explains, given all that we know? It is a cognitive choice, and not a probability.

    In your example of the RCT, I really don’t understand what you are saying. What has the string to do with it? In that case, we are interested in how many patients have a sense of improvement when they take the treatment, compared with how many patients have it when tehy take placebo. It is a very easy evaluation, just a 2×2 table which can be evaluated by a chi square test for independence: is the binary variable treatment/no treatment independent from the binary variable improvement/no improvement? Again, a very low p value will tell us that the two variables are most likely connected. The effect size here is simply a comparison between proportions.

    What has that to do with design detection?

    In design detection, our effect is the functionality in the string, and our effect size is measured by the bits of functional information linked to that function.

    Our H0 is that the particular string we observe, with its functional sequence, arose as the result of random variation in the system.

    If our p value for that hypothesis is really low (like in the example of beta lactamase), we can very safely reject H0.

    It’s as simple as that.

  202. 202
    Mark Frank says:

    Gpuccio

    Do you really think I don’t understand basic statistical methods? What you need to understand is the fundamental assumptions underlying these methods – why they work (and sometimes don’t). I clearly did not explain it well at my first attempt. I will try again tomorrow.

  203. 203
    gpuccio says:

    Mark:

    I think according to what I see. If you say wrong things, I think that you have a wrong understanding (I have full confidence in your good faith and seriousness).

    I have tried to explain clearly my points. I do believe they are correct and they work. You say you did not explain well your points, and you will do that tomorrow. I am waiting.

  204. 204
    StephenB says:

    GPuccio, just in case my earlier message got lost in the shuffle, I wanted to thank you again for clarifying your approach and the reasons for it. It makes perfect sense to me. I understand now why you define function in subjective terms and why you differentiate it from objective functionality. I make the same distinction with different words for different reasons. You are right. It is simply a difference in methodologies (and temporary objectives)

  205. 205
    gpuccio says:

    Stephen,

    Thank you! I am so happy that we understand each other well. 🙂

  206. 206
    gpuccio says:

    Mark:

    While I wait for your clarifications, I will try to sum up the key points (IMO):

    H0 is a null hypothesis. Its essence is that some effect that we observe (in general, some form of apparent regularity or rule) is not true: it can be explained by some kind of random fluctuation on the system, which has no real causal relationship with the supposed regularity or rule that we believe we are observing.

    IOWs, as what we observe is only a pseudo-effect, it is not a reproducible aspect of reality. That means that we cannot make any prediction based on it, because in a different sample it will disappear.

    To be credible as an explanation (IOWs, to accept that there is no other explanation needed for what we observe) the null hypothesis must have explanatory power: that means that the random variance in the system must be great enough to be able to generate the observed configuration with some probability. We are discussing a random explanation, and the key of randomness is probability. A random explanation which is utterly improbable has no explanatory power. IOWs, it is not an explanation at all.

    Therefore, the rejection of H0 depends exclusively on its lack of any credible explanatory power. An explanation where what we observe has only 10e-62 probabilities of happening by chance is not an explanation at all. IOWs it must be rejected, and other explanations, not based on random events, must be searched.

    H1 (or any alternative hypothesis) is all another matter. The rejection of H0 is never in itself an affirmation of H1, unless H1 is formulated as the logical alternative to H0 (for, example, in very general terms, as “What we observe is not the result of random variation in the system”).

    If H1 is a specific explanation (for example, A is the cause of what we observe) it must be evaluated on its own merits and explanatory power. Here, probability is no more the measure, because H1 is not a probabilistic explanation. While you, as a Bayesian, can certainly attribute some probability to H1, H2 and so on, the fact remains that even those probabilities depend on the specific explanatory merits of the different hypotheses, and not on their probabilistic properties, because they are not explanations based on probability distributions.

    For example, I may offer as explanation that A is the cause of what we observe. Then, I must ask:

    a) Is it logically consistent that A can cause what we observe? IOWs, are there logic contrdictions in my explanation?

    b) Is it empirically credible that A is the cause of what we observe? IOWs, is there some empirical support to my explanation?

    c) Are there better non random explanations fpr what we observe?

    All those questions are not in themselves probabilistic, although you can, if you like, assign probabilities to the answers (I would not do that, because as you know I am not a Bayesian).

    For me, those questions are methodological and cognitive questions, which require answers based on cognition and intuition, and not on probability.

    So, to sum up:

    1) H0 is an intrinsically probabilistic explanation, and it is rejected (or not rejected) according to its intrinsically probabilistic explanatory powers.

    2) H1, H2 and so on are alternative, causal explanations for what we observe. They are evaluated for their own explanatory merits, and we choose what is the best explanation (in the present context) according to that evaluation.

    Of course, that choice is in some measure a personal choice, but it can certainly be shared and be a matter of intellectual confrontation.

    [–> ED: minor typo cleanup, KF]

  207. 207
    Mark Frank says:

    Gpuccio

    I will try to explain this as concisely as I can but it the comment will be a lot longer than I would like.

    First let me explain the rather strange test statistic that I used. I wanted to create a test statistic that was an ordered set of Bernoulli trials to make it as close as possible to the kind of “string” that is routinely discussed in ID. I admit that the usual way of testing if a treatment works would be to simply give the treatment to one population and the placebo to another  and use something like a chi squared test.

    Now let me try to explain the problem with classic Fisherian hypothesis testing. This is very hard to do without a picture so bear with me.

    Take a simple Student’s t-test for comparing the means of two unmatched samples. The value of the test statistic (what you call the effect size) could vary from minus infinity to plus infinity. H0 is:  the two samples are drawn from the same population and therefore the two samples have the same population mean. Suppose we get fairly large positive effect size x (I can’t be bothered to do the maths).  It makes no sense to talk of the probability of that particular value. It is single point in an infinite range. So we have to use it define a rejection region – an interval in the range of possible effect sizes – and calculate the probability of the effect size falling into the rejection region – we call that probability the p-value. Typically we define the rejection region, as you did, as any value more extreme than x. But in this case there are two extremes – very low and very high. Sometimes we use both (a two-tailed test) and sometimes we use just one (a one-tailed test). We will get different p-values according to which choice we make. How do we justify the choice? By deciding what H1 is. Is H1: population X has a greater mean than population Y? Or is it: population X is different from population Y. So under one H1 we may reject H0 and under another we may not. That is why every good statistics text book insists you make H1 explicit as well as H0.

    But it goes further than this. Why should the rejection region be extremes at all? The observed effect size will fall into infinitely  many different intervals with widely varying p-values. What if our interest is in detecting fraud in the trials – we think the experimenter might have been trying to show that the treatment has no effect. In this case we will be looking to see if the effect size is suspiciously close to zero. There is a very low probability that the two sample means should be extremely close to zero even if they are drawn from the same population. So you might define a rejection of region of “at least as close to zero as the effect size”.  What if the effect size is measured in days to recovery from diagnosis and the treatment under test is administered two days after diagnosis. We might well reject H0 if the sample effect size were suspiciously close to two days even if this is not a particularly extreme value. So we might define a rejection region of “at least as close to 2 days as the sample effect size”. And so on. In all these cases the justification of the rejection region is determined by H1.

    Please understand that I fully accept that in the vast majority of cases we will reject H0 based on a rejection region “at least as extreme as”. I just want to argue that in doing so we are implicitly assuming a certain H1 which in odd cases may be different. This assumption becomes key when you extend the argument to ID.

    This all deals with a continuous case because most of the examples you offered were continuous. Of more relevance to ID  is where the test statistic is a discrete value such as the number of times the Democratic candidate comes top of the polling list (to use Dembski’s example). But I will offer this for the moment and if time allows extend it to the discrete case later.

  208. 208
    Mark Frank says:

    GP

    A very quick response to #206. I don’t see at all why H0 is statistical and H1 are not. It is extremely common for H1 to be an explanation in its own right with its own pdf e.g. it might just be an alternative population mean.

    More importantly – you write:

    An explanation where what we observe has only 10e-62 probabilities of happening by chance is not an explanation at all.

    As explained in #207 what we observe can have any probability depending on the rule we use to define the rejection region. It is not an observation that has a probability but a range defined by the observation. That range is often (but not always) “more extreme”. The choice of that range can only justified by assuming an alternative hypothesis.

  209. 209
    gpuccio says:

    Mark:

    I agree with some of the things you say in your post #207 (not all). Anyway, I think they are really irrelevant, especially if applied to ID.

    Let’s begin with the two tailed/one tailed problem. That is essentially a problem of methodology, and it depends on what we are interested in, what we consider relevant, rather than on our explanation of what we observe.

    As I have said, we have to decide in advance what effect size we consider relevant. That is valid both for the size of the effect and for its direction. It is a problem of what we are interested in, not of how we explain it. It has nothing to do with H1.

    In general, if our purpose is to understand, and we have no pre-commitments, a two tailed test will give the highest guarantees.

    Regarding your discussion about “detecting fraud in the trials”, I don’t know, I am not an expert in detecting trials, and I suppose a specific methodology is needed, but again the problem is not in H1, but in the question we have when we approach the problem.

    You say:

    “There is a very low probability that the two sample means should be extremely close to zero even if they are drawn from the same population.”

    I suppose you are saying that there is a very low probability that the difference between two sample means should be extremely close to zero. Of course, it would be very suspicious if, say, two sample means of two samples with 100 values each and some reasonable variance were exactly the same, up to the tenth decimal digit. That would smell, very simply, of a strange stupidity in the author of the fraud! So, if we want to detect stupid frauds, that would be a good method. For normal frauds, we need something better.

    However, what has that to do with design detection? In design detection, our question when we decide if we reject H0 is very clear and very simple. I repeat it for you:

    Can the effect we observe be reasonably explained as the result of random variation in the system? IOWs, given the system, the time span, and the probabilistic variation in the system, what are the probabilities of having such an effect?

    The rejection region can be easily defined as the probability of having at least one success in n attempts (the total number of new states tested in the time span), each of them with probability p of success. In this case, success is the appearance of a protein coding gene for the specific functional protein we are observing.

    So, as you can see, our H0 and our rejection region are well defined, without any detail about alternative hypotheses.

  210. 210
    gpuccio says:

    Mark at #208:

    You say:

    “I don’t see at all why H0 is statistical and H1 are not. It is extremely common for H1 to be an explanation in its own right with its own pdf e.g. it might just be an alternative population mean.”

    What do you mean?

    H0 is an intrinsically statistical explanation, because it assumes that the effect we observe has no other cause than random events in the system which are not causally connected to the effect. IOWs, we observe the effect only because, by chance, many independent variables which have no cause and effect relationship with the observed effect happened to generate a configuration which simulates the effect.

    Let’s say that we have a sample of 100 males and a sample of 100 females, and we measure a continuous variable A in both groups. We find that A is higher in males, both its mean and its general distribution.

    So, is A dependent on sex?

    Our H0 is that the two variables are independent, and that the higher values in males are simply explained by the normal variance of the variable in the original population, and by the random variance in sampling.

    OK, if our p is 0.01, we can discuss. After all there is one probability in 100 that the two variables are really independent.

    But if our p is 10e-20, who would still believe that the two variables are really independent? Not I.

    WE may have no idea of why A is higher in males, but anybody in a sane mind will be empirically sure that it is higher in males, whatever the explanation.

    It’s as simple as that.

  211. 211
    Mark Frank says:

    GP at #209 Let’s get straight to the ID example. This relates directly to my #199.

    Can the effect we observe be reasonably explained as the result of random variation in the system? IOWs, given the system, the time span, and the probabilistic variation in the system, what are the probabilities of having such an effect?
    The rejection region can be easily defined as the probability of having at least one success in n attempts (the total number of new states tested in the time span), each of them with probability p of success. In this case, success is the appearance of a protein coding gene for the specific functional protein we are observing.
    So, as you can see, our H0 and our rejection region are well defined, without any detail about alternative hypotheses.

    Let as assume that we are talking about a string of DNA 100 base pairs long and the effect is one particular configuration.  “Random variation” presumably means any of the four base pairs is equally likely at any point in the string and are independent of each other – which is our H0. Your problem, as you well know, is that every possible string is equally likely under H0. They each have a probability of 4^100 in one trial (I will ignore multiple trials for the moment). So you have to explain why some strings are justification for rejecting H0 and others are not.
    The classic ID response is that the strings that justify rejection are specified (in your case functionally specified). But for any given string:
    * You don’t know for certain that it is not specified in some way (maybe not functionally but perhaps it is a coded representation of a Sanskrit poem)
    * If you think of all the different ways string can be specified it is reasonable to suppose that most, if not all, strings are specified in some way
    So now you have to explain why your particular specification is grounds for rejection while other specifications are not. If there was a plausible alternative explanation why that particular string was created (e.g. it was the result of combining two existing strings) then that would clearly be a justification for rejecting H0 – but that would be an H1. Your challenge is to explain why H0 would be rejected for that particular string without using an alternative explanation.

  212. 212
    Mark Frank says:

    GP at #210
    You say:

    H0 is an intrinsically statistical explanation, …..

    My point was not that H0 is not statistical – just that H1 is also statistical – so this paragraph is irrelevant.

    Let’s say that we have a sample of 100 males and a sample of 100 females, and we measure a continuous variable A in both groups. We find that A is higher in males, both its mean and its general distribution.
    So, is A dependent on sex?
    Our H0 is that the two variables are independent, and that the higher values in males are simply explained by the normal variance of the variable in the original population, and by the random variance in sampling.
    OK, if our p is 0.01, we can discuss. After all there is one probability in 100 that the two variables are really independent.

    I hope that was careless error. There is a probability of 0.01 of seeing a result as least as extreme if the two variables are really independent. That is quite a different thing. But I assume you know that.

    But if our p is 10e-20, who would still believe that the two variables are really independent? Not I.

    It depends on how the rejection region was defined. I have already shown that the rejection region can be defined in different ways depending on your H1. However, I admit that if the region was defined as “more extreme” and it was this low a probability I would reject H0. But the important thing is to understand why. Otherwise you may transfer the same logic to other situations such as ID where it does not follow (see previous comment). There are an infinite number of other rejection regions with just as low a probability. Why is the extreme region grounds for rejection and not say the very thing slice around zero which is just as low a probability? The reason is very straightforward. The extreme value is more likely if the variables are dependent than if they are independent, while that is not true of the central slice. There is nothing difficult about this but you must recognise the logic before you can transfer it to another case or you will go badly wrong.

  213. 213
    gpuccio says:

    Mark:

    “There is a probability of 0.01 of seeing a result as least as extreme if the two variables are really independent.”

    OK, that is more correct. 🙂

    So, I think that we agree enough on the statistical details, after our clarifications. Now, I will try to answer your #211 about the application to ID.

  214. 214
    gpuccio says:

    Mark:

    OK, here is the important point.

    In my discussions about dFSCI, I have always made it clear that I deal with a specifically defined function, and I compute the probability of getting that functionality in an object by random variation in the system. You must, for now, accept this as a procedure. I am not, for the moment, inferring anything from it.

    So, if I have an enzyme which catalyzes some specific reaction, I define the function (giving if necessary detailed ways to measure it in controlled conditions), and then I try to compute how many sequences of AAs of the same length can implement the function. I call functionally specified information (dFSI) in the observed object (the protein which implements the function) the ratio target space/search space (or better, -log2 of that ratio).

    OK? These are definitions, nothing more. As you know, I believe that the values given in the Durston paper are good approximations of that measure.

    As you can see, all my reasoning is specific to one functional definition. I am not considering all possible specifications. I am considering one definite functional specification. And I am computing the minimum number of bits necessary to implement it, at the best of our understanding.

    OK?

    So, I have a number. For example, for beta lactamase, according to Durston’s data, I can say that the functional specification is 336 bits.

    What does that number mean?

    It expresses the probability of getting one functional string by a single variation event, in a random search/random walk, starting from an unrelated state. If no other non random factors intervene, and assuming an uniform distribution of the probability of all possible states in the random search/random walk.

    OK?

    Now, we know that the protein emerged in a system in a time span. We can grossly compute the probabilistic resources of the system in the time span. The total number of attempts (new states reached).

    So we can compute the probability of obtaining at least one success in that system, only as the result of random variation, with those probabilistic resources: for beta lactamase, it is about 1e-62. That is the p value for our observed result (a protein which implements the defined function) in our system, if our H0 (only random variation) is true. This value is referred to the function: beta lactamase. Success is defined as the presence of that function, and the probability is computed by the binomial distribution.

    OK?

    Now, my point is, any time that any specific functional definition (you can define all the functions you like) requires a sufficiently high number of bits to be implemented (has a sufficiently high functional specification), IOWs exhibits dFSCI, so that the value of its dFSI is so big that it is vastly greater than the probabilistic resources of the system, and the p value computed in the way I have described is extremely small (1e-62 certainly qualifies), then we can safely reject random generation as an explanation, and, if no other credible explanation based on reasonable necessity “contributions” is available, we can safely infer design.

    I know your objection. You say that we should consider “all possible functions” or “all possible specifications”, and that my procedure does not work.

    I have two different ways to counter that.

    The first is that, even if it were true (and it is not) that there are so many possible functions (useful in the context, which means naturally selectable, for our context) that finding some functional sequence becomes reasonably likely, the specific sequences we observe remain however extremely unlikely.

    So, let’s say that we have a target space of many “naturally selectable functions” (!!!). OK, let’s suppose that for a moment. The whole target space has a probability of being found, in one attempt, say of 150 bits, which would put it borderline with my proposed threshold for a biological system. OK, let’s say that it is possible that in the course of natural history that target space may be hit a few times.

    A subset of that target space is our beta lactamase, with its individual probability of 336 bits. Of course, as you can understand, that is really a tiny fraction of the whole target space. The target space, indeed, is made almost entirely of much simpler proteins, which are functional and much more likely.

    So, even if the target space is luckily hit a few times in the course of natural history, what proteins will be found? Certainly the simpler ones, not certainly the “complex” beta lactamase, which is only a super-tiny part of the target space.

    And I am not discussing proteins like ATP synthase, or dyneins, whose functional complexity ranges in the thousands of bits, and which would be a super-tiny part of any set of proteins as likely as beta lactamase!

    And yet, those are exactly the proteins which we found abundantly represented in the existing proteome.

    IOWs, if a functional result is really unlikely, it is perfectly correct to reason about the probability of getting that specific result. The fact that some simpler functional results, with different and simpler functions, may certainly exist, is no help in explaining that we find that specific complex function implemented in the proteome.

    My second type of answer is much more simple and empiric: the procedure works.

    If we apply exactly my procedure to any possible functional sequence which is designed, and has enough functional specification, I will detect design correctly in all cases in which I detect it, without any false positive (and possibly with many false negatives). I am always ready to accept that challenge. You simply cannot offer any example of a false positive.

    So, I will recognize any passage in correct English of sufficient length, and I will never be fooled by randomly generated sequences of characters. Even if in theory some sequence of characters could be specified in who know what way, that does not change the simple fact that I will recognize the designed English passages of sufficient length, and I will never be wrong.

    The procedure works, and it has 100% specificity. All your “doubts” cannot change that simple fact.

  215. 215
    Mark Frank says:

    GP #214 Your response covers the whole of how you infer design.
    Although, as you know, I disagree with your design inference, that is not the specific issue I was addressing. All I want to establish is that you cannot rationally reject the random variation hypothesis without having an H1 in mind. The proof is easy. You say beta lactamase has a functional specification of 336 bits and therefore the probability of reaching that string exceeds the probabilistic resources of the system.  But so does every other possible string of that length. If a string of that length is generated by a random system than the resulting string must be a string  “exceeds the probabilistic resources of the system.” We would not reject the random explanation if it were any string of that length. Why do we use it to reject H0 just because it is functional? Or to put it another way – on what basis do you ascribe a tiny p value to this string and not to all the others of that length? In the case of Fisherian hypothesis testing you did it on the basis of being at least as extreme – I don’t agree with this – but this example doesn’t even satisfy that criterion.

  216. 216
    REC says:

    gpucio, congrats on still quantifying design, where others here have casted doubt on quantification of information.

    We could discuss how you determine the functional percentage of sequence space, when it is impossible to construct anything but a scant portion of all possible constructs.

    We could also consider the “necessity” of evolving any given activity.

    But I’ll focus on one issue here: “expresses the probability of getting one functional string by a single variation event, in a random search/random walk, starting from an unrelated state” is precisely nobody’s model of how life works.

    B-lactamases, which you conclude have 2^336 (of whatever metric you’re using today) are related in form and function to the peptidases that penicillin and related drugs inhibit. They carry out virtually the same reaction, except that the peptidases get stuck (dead bacteria) and the beta-lactamases recruit a water molecule to break the bond with the drug, destroying it.

    How many mutations does this refinement of function take? Looks like a minimum of 3. How many bits is that?

    Does your procedure have 100% specificity, and no risk of false positives?

    http://www.cell.comchemistry-b.....96)90182-9

    http://www.ncbi.nlm.nih.gov/pm.....393100.pdf

    http://peds.oxfordjournals.org...../1/27.long

  217. 217
    gpuccio says:

    Mark:

    My7 reasoning is simple and explicit. You don’t accept it, but I cannot do anything about that.

    The functional specification is the number of bits necessary to implement an explicitly defined function. There are a lot of functions which are simple, and could be implemented by many types of strings. Other functions are complex, and they require a lot of specific bits to be implemented.

    Those functions are observably, always the result of conscious intentional design. That’s what observed facts tell us. Only a conscious designer can achieve the intentional configuration of a high number of specific bits to implement a function.

    The simple fact is that all complex functions are designed. That’s why my procedure works.

    So, the effect we observe in the scenario I have proposed is “a protein which can implement this complex function”. And we compute the probability for that protein to arise as a result of random variation.

    The same procedure works for any complex function.

  218. 218
    gpuccio says:

    REC:

    Thank you for the congrats.

    As you may know, my argument about design inference for proteins has always been about new protein superfamilies, exactly to avoid the problem of proteins which share part of the sequence and/or the structure and function.

    The paper you refer to (the third one) is an example of èprotein engineering at the active site level to “evolve” an activity which is already potentially present in the superfamily. You can check that beta lactamases and D-Ala carboxy peptidases are part not only of the same superfamily, but also of the same family, in SCOP classification.

    As I have said many times, transitions which imply a limited number of mutations at the active site in a same family/superfamily are perfectly possible, and some of them could in principle be in the theoretical range of what random variation can achieve. That has always been a clear point in my discussions.

    That said, the artificial transition realized in that paper required a lot of complex protein engineering anyway.

    The fact cremains that when I discuss new superfamilies, I discuss the appearance of new superfamilies, and not the minor transitions inside a superfamily or family.

    So, when I say that beta lactamase has 336 bits of functional information, I am referring to the protein family, not to an individual member of it. The functional information implies the general fold and the general structure, and not only the active site, where we know well that transitions of a few aminoacids can shift the affinity for specific substrates, always in the context of that functional superfamily.

    So, while I don’t think that the artificial transition illustrated in the paper is proof of a real transition which happened in natural history (although I remain open to the possibility), it is in no way a case of a new superfamily (of the 2000 we know of) arising through some gradual pathway.

    So yes, my procedure has 100% specificity.

  219. 219
    Dionisio says:

    216 REC

    Please, can you double check the first link? thanks.

    http://www.cell.comchemistry-b.....96)90182-9

  220. 220
    REC says:

    Dioniso-slash between the .com and chemistry:

    http://www.cell.com/chemistry-.....96)90182-9

    How does that get lost during a cut and paste?

  221. 221
    REC says:

    Gpuccio,

    I think the point is made: if “b-lactamase activity” was your chosen specification, then you’d get a big number, which you say indicates design. This specification also happens to be a 3-amino acid change from another pre-existing specification. This gap, I think everyone would admit, seems evolvable. You have stated: “The same procedure works for any complex function.” Any complex function. Whatever specification. 100% specificity in detecting design.

    So, we arrive at a new specification: Post 218 is the first use of “superfamily” as a functional specification in this thread.

    In Durston’s paper “super” doesn’t appear. They are analyzing families, and hoping to correlating sequence information to a given function: “The functionality of the protein can be known and is consistent with the whole protein family.” Although function is loosely defined, their examples hint at biochemical or cellular activity.

    You should then, inform us that the function you are interested in is not B-lactamase activity, but what I assume is merely the fold? of the superfamily (as the superfamily itself appears to have maybe 20 different functions from transpeptidase to nuclease to esterase).

    You also then need to stop using Durston’s fits for the b-lactamase function, which from the number of sequences used in the paper, must reflects b-lactamase eznymes, not the whole superfamily. Redo the analysis with all 20,000+ member sequences of less than 20% identity and see what you get.

    Also, a warning from Durston et al: “For example, if many sequences that do not share the same function f, are mistakenly included within an aligned set representing some particular function, we should expect the measure of FSC of that set to be degraded, possibly even to a very small value. However, when the specified functionality is chosen meaningfully (even in part), then FSC can be interpreted.”

    As biochemists reveal the simple molecular pathways that give new functions, retreating to the origins of superfamilies (of which there are very few, and which infrequently arise) seems natural. But I’m not sure this will last for you:

    http://www.nature.com/nchembio......1579.html

  222. 222
    Dionisio says:

    220 REC

    Yes, that was it. I did not notice the missing slash 🙂
    Thanks.

    No idea how that slash could have disappeared during a copy&paste operation. As you can see, there are few things we still don’t understand. 🙂

    BTW, your discussion with gpuccio is above my pay grade. All I can do is check if the links work. Nothing else. 🙂

  223. 223
    Dionisio says:

    220 REC

    How does that get lost during a cut and paste?

    Is there some cut&paste* going on in cellular/molecular biology?
    Do ‘slash’ characters get lost in those cases too? 🙂
    Is that biological cut&paste functionality part of an open source app or proprietary software? 🙂

    (*) splicing and that stuff

  224. 224
    Dionisio says:

    221 REC

    As biochemists reveal the simple molecular pathways that give new functions,…

    Since we got into this cut&paste thing a few posts ago, what is the simple molecular pathway that lead to the cut&paste functionality?

  225. 225
    Mark Frank says:

    Gpuccio

    We seem to be passing each other by. I really did not want to revise the whole functional spec debate. I was only interested in the notion that you can dismiss H0 without having any idea what H1 is.

    Mark

  226. 226
    gpuccio says:

    REC:

    You are really trying your best, but you are wrong.

    I have always used the term superfamily in all my discussion on this blog for years. Go and check.

    The functional information in beta lactamase, the 336 bits measured by Durston, refer to the whole functional information in the molecule: its folding, structure and active site.

    In the paper they have engineered a new substrate specificity starting from an existing protein with the appropriate fold and structure (same family). That is protein engineering starting from a lot of functional information (the existing proteins) and and adding the new specificity to the active site by a lot of engineering.

    In my procedure, you have obviously to consider the information that already is in the system. Even Durston’s paper deals with the case of measuring functional information in a transition, which is a completely different scenario. In my discussions here I have always specified that we were measuring a random walk from an unrelated state. Can you read?

    It is typical of those who have no real argument to try to play tricks. Either you don’t understand the concept of functional information, or you don’t want to understand it.

    Let’s say that I have a Shakespeare sonnet and I change by a random search only one word, changing a little the meaning. The transition is simple. I am using most of the information which is already there.

    So, stop paying tricks, and discuss seriously and with respect for what others say.

    Regarding the family/superfamily problem, I have always discussed superfamilies as the best tradeoff which guarantees that the functional islands are unrelated. There are 2000 superfamilies and 4000 families. The choice of what grouping one uses can differ, but the concept remains. Basic foldings are about 1000.

    Durston uses families, but in SCOP classification beta lactamases and D-Ala peptidases are part of the same family, not only of the same superfamily.

    I don’t know if Durston has included only forms of beta lactamase in his computation. Maybe if he had included D-Ala peptidases, the computation would have been lower, but it is also true that the shift in substrate affinity needs functional information too. However you put it, the computation of functional specification is an approximation, and it is perfectly normal that there are technical problems that must be faced. In no way that invalidates the concept and the procedure.

    There is more. According to the big bang theory of protein evolution, new superfamilies appear at some time, and after that they traverse their functional space, by neutral variation and negative selection. So, the diversity that we observe in a superfamily or family at sequence level if generated after the appearance of the functional molecule. That’s how the fold and structure can be retained even in front of big sequence deviations.

    There is more. In many proteins (probably not all) part of the diversity in a protein family can be functional, and not only due to neutral variation. In different species the same molecule can certainly adapt to different context, of localization, of protein interaction, of regulation. That kind of functional variation will be read by the Durston method as non functional diversity. Therefore, it is very likely that the Durston method, in general, uderestimates the true functional complexity.

    By the way, if you want some stronger example, let’s go back to the alpha and beta subunits of ATP synthase, with its hundreds of AA identities from LUCA to humans, through 4 billion years. Or to dynein, with its highly conserved 4000 plus AAs. Or to the Photosystem 2 in cyanobacteria, already there and functioning before the integration in the plant plastids, and highly conserved too? Must I go on with the examples?

    Can you please show the simple molecular pathways that lead to those molecules?

  227. 227
    Dionisio says:

    221 REC

    As biochemists reveal the simple molecular pathways that give new functions,…

    What are the simple molecular pathways that give the functionality seen in the few research examples posted in the thread pointed to by this link?
    http://www.uncommondescent.com.....ent-519017
    Thank you.

  228. 228
    gpuccio says:

    Mark:

    I understand that. And, as I have said, I maintain that in design detection we can dismiss H0 (the hypothesis that the functional information can be explained by random variance) even if we have no idea of how to explain the functional information in other ways.

    Once we have rejected H0 (intrinsic probabilistic variation) as an explanation of the functional organization we observe, we are left, as far as I can judge, with two alternatives:

    a) Some explanation based on necessity, IOWs non conscious laws and regularities.

    b) The intervention of a conscious purposeful agent (design).

    As I have explained many times, I don’t say that because I believe a priori that design is the complement of chance and necessity. My point of view is entirely empirical, not logical. If a random explanation is rejected, I really am not aware of other possible explanations except necessity or design. If you know of other alternatives, I am ready to consider them.

  229. 229
    gpuccio says:

    Mark:

    By the way, as you can see REC is already there trying the card of necessity (NS, intermediates, and so on). That is significant.

    The truth is, neo darwinists always try to play the card of random variation as far as they can. When they are in a position where the cannot do that any more, they try to play the card of necessity and NS. And they stick to the few pitiful papers that they think can support a position which is supported by no facts at all.

    Obviously, when they can do that no more, they are ready to play again the card of random variation.

    In the same way, some of our interlocutors are all neutral variation as far as they can. When reminded that neutral variation is completely useless to explain functional information, they “awaken” for a moment and go back to the old reassuring NS. Not for long. When NS remains unsupported by facts, the neutral theory is there again, to lend credibility to a theory which has none.

  230. 230
    Dionisio says:

    #224 grammatical error correction:
    Here I want to correct a grammar mistake I made in post #224:

    221 REC

    As biochemists reveal the simple molecular pathways that give new functions,…

    Since we got into this cut&paste* thing a few posts ago, what are the simple molecular pathways that lead to the cut&paste* functionality?

    (*) splicing and that stuff

  231. 231
    Dionisio says:

    #223 grammatical error correction

    Here I want to correct a grammar mistake I made in post #223:

    220 REC

    How does that get lost during a cut and paste?

    Is there any cut&paste* going on in cellular/molecular biology?
    Do ‘slash’ characters get lost in those cases too? 🙂
    Is that biological cut&paste functionality part of an open source app or proprietary software? 🙂

    (*) splicing and that stuff

  232. 232
    gpuccio says:

    Dionisio:

    I really like your love for precision of language! 🙂

    By the way, always thanks for your references in the “third way” thread. I am using them a lot!

  233. 233
    Dionisio says:

    gpuccio,

    I’m glad to know you can use some of the references in the “third way” thread.
    It’s a pleasure to serve you, amico mio!
    BTW, I still encounter difficulties while trying to understand the reports, but see some gradual progress in my learning. 🙂

  234. 234
    Mung says:

    REC:

    gpucio, congrats on still quantifying design, where others here have casted doubt on quantification of information.

    lol.

  235. 235
    Mark Frank says:

    GP #228

    So let’s agree to concentrate on whether you can dismiss H0 without any assumptions about H1. As far as I can see this is your core argument:

    Now, my point is, any time that any specific functional definition (you can define all the functions you like) requires a sufficiently high number of bits to be implemented (has a sufficiently high functional specification), IOWs exhibits dFSCI, so that the value of its dFSI is so big that it is vastly greater than the probabilistic resources of the system, and the p value computed in the way I have described is extremely small (1e-62 certainly qualifies), then we can safely reject random generation as an explanation, and, if no other credible explanation based on reasonable necessity “contributions” is available, we can safely infer design.
    I know your objection. You say that we should consider “all possible functions” or “all possible specifications”, and that my procedure does not work.

    Actually that is not my objection on this occasion. To simplify the argument let us imagine that beta lactamase is a bit string 336 bits in length. My problem is that all bit strings 336 bits in length are equally improbable and so creating any one of them is vastly greater than the probabilistic resources of the system. Yet you would not reject H0 because it happened to generate a bit string 336 bits in length.  It is invalid to reject H0 simply because the observed result is vastly improbably given H0. You must define a rejection region and give a rationale for that region. I have shown that in Fisherian hypothesis testing the rejection region can differ depending on your H1 (e.g. one-tail or two-tail) but  typically it is defined as “more extreme” than the observation. However, in your example you have rejected H0 not because it is extreme (which would presumably be a very high proportion of one particular base pair) but because it happens to fulfil a specific function.  How does that justify rejecting H0? (Hint – there is a reason but it requires assuming H1).

  236. 236
    gpuccio says:

    Mark:

    I think that your mistake is in saying: “all strings 336 bits in length are equally improbable”.

    You certainly understand that when we compute the probability of something, we are dealing with events, and the events must be clearly defined.

    If I throw a die, I can say that each of the six individual outcomes has the same probability. But I can well define the probability of different events: for example, the probability of getting an even number will be 1/2. The probability of getting a number lower than 3 will be 1/3. And so on.

    Now, let’s go to our example, and to simplify it let’s say that we are discussing binary strings of 336 bits length, and that only one of all strings has the functionality I have defined. So, the target space/search space ratio is 1:2^336, and therefore the functional complexity of the (only) functional string (according to my explicit definition) is of 336 bits. OK?

    Now, the search space is 2^336 strings. Each of them has the same probability of being found in a single random attempt (we assume a uniform probability distribution).

    The point is: what is the event whose probability we want to compute? Let’s see.

    1) What is the probability of getting a string 336 bit long in a single random “extraction” from the search space?

    2) What is the probability of getting a string which has not the defined functionality? 1-(1:2^336). Extremely high.

    3) What is the probability of getting the string with the defined functionality? 1:2^336. Extremely low.

    In my definition of specification, I have said very clearly that specification is any explicit rule which generates a binary partition in the search space. What we are interested in is the probability of the target space, not of any specific string. In functional specification, the partition is generated by an explicit definition of a function. Given the definition, each string can be classified as having the functionality, or not.

    So, what do you mean when you say: “”all strings 336 bits in length are equally improbable”? What is the event you define whose probability we should compute?

    You can say: I define as success the random generation of this particular string: and then give each single bit of your specification.

    Well, that is called: pre-specification. It works only if you give the sequence in advance. Then, if you really get that sequence in a random attempt, I will gladly admit that ID is wrong, or simply that you are either a splendid fraud or a splendid magician.

    But if you get a random string, and then define the event as: getting exactly this string (and here you give the bits), and then you state that you have got an event extremely improbable, than you are cheating, or simply misunderstanding.

    There is nothing improbable in the event you got: you got exactly one of the many strings without any special specification, whose only individual specification can come from enumerating its bits after you have got the string. IOWs, you cannot use the random complexity that you have already got, and use it to build a “specification”, and then use that definition to say that the previous event was improbable. The previous event was not improbable at all. If you get that string after you have specified it, then that would be something.

    But with true specifications, based on function, or meaning, or simply on ordered states, it’s all another matter.

    A string of 336 1s will never be seen as an outcome of a random system. Why? Because it is part of an extremely tiny subset of the search space, the subset of very ordered sequences (which, as you certainly understand, can be defined in different ways, while remaining extremely tiny). In this case, the general definition generates an objective partition, even if I don’t use the individual bits of the string in my definition. So, I can certainly compute the probability of the following event:

    4) What is the probability of getting a string where all the 336 bits have the same value? 2:2^336. Extremely low.

    So, if I get that type of string, I will reject the null hypothesis: “This is the result of the random variance in the system” (the system could well be the throwing of a fair coin 336 times).

    As you can see, I need no explicit H1 to reject H0. I just reject it. Then I can inquire on possible alternative explanations. The simplest one is that the coin is not fair. Another one is that there is some fraud in the system. As you can see, there are many possible explanations of what we observe, and they are based either on necessity or on design, or a mix of the two. But they have no relevance in our rejection of the null hypothesis. And, to decide which is the best explanation, we really need other types of cognitive considerations, and not statistics.

    The same is true for design detection. The event we observe is a functional string. We define the function. We compute how many bits are essential to implement the function. We compute the probability of the following event, well defined:

    “How likely is it that a string which implements this function is generated by the random variation in the system?”

    We compute the probability. And, if it is really low, we reject H0. We need no explicit H1. If you want, we can say that we have a generic H1, the logical opposite of H0, in the form:

    “This string was not generated by the random variation in the system, but by something else”.

    But again, that is simply the negation of H0, and not an explicit alternative explanation.

    Regarding the rejection region, as I have said I use the binomial distribution. I simply compute the upper tail of “getting at least one success (as defined) in n attempts, when the individual probability of success in each attempt is p”. Or, if necessary, we can compute the probability for at least n successes. But, in our discussion, “at least one” is appropriate.

  237. 237
    Mark Frank says:

    GP
    When I write:

    all strings 336 bits in length are equally improbable

    I mean just that – no more. Each individual possible string from all 1s through to all 0s has the same probability given H0.

    However, it is clear you are talking about the probability of the string being in a specified subset of the set of all possible strings. Your specification is  “fulfils the function of beta lactamase”. My question is how does that act as a justification for rejecting H0?  We don’t normally dismiss H0 because the test statistic happens to have a value which performs a function (or meets any other arbitrary specification) however small the probability of meeting that specification. It needs some justification!

    You stress the importance of the function being specified in advance. I take it you don’t literally mean the timing is important. If we happened to discover the function of beta lactamase after the protein was decoded I imagine you would still say it could be used to reject H0. I assume what you are getting at is the specification should not be derived from the string but should be derived independently. But there are an infinite number of such specifications (not necessarily functional – any old specification would do – my Sanskrit poem expressed in binary would be one). For all we know the vast majority of the 2^336 strings meet some such specification – we just don’t know what they are. We should not reject H0 because we discovered the string met a specification even if it were the only string to do so.

    What you are doing is like setting a rejection region for the difference of two sample means because that difference happens to be an interesting number for some other reason (perhaps it is someone’s birthday).  This is a game everyone can play – finding their own interesting number range and rejecting H0 because there is a very small chance of the difference in two means falling into that range. You need to find some justification why a particular small range is grounds for rejecting H0 (and that justification lies in H1).

  238. 238
    gpuccio says:

    Mark:

    No. Again, you do not understand.

    My point is, as explained, that any specification which generates a binary partition in the search space so that the probability of the target space is extremely low is a reason to reject H0, if we observe exactly a string which is part of that tiny subset.

    I have given the example of a highly ordered state: all binary strings whose bits have the same value.

    I have given the example of specifications based on meaning (Shakespeare’s sonnet), and on function (software, machines, proteins).

    The concept is the same.

    The error you make is that you consider only the specification. That is really wrong, and I don’t understand how you, who have been discussing ID for years, can still make that error.

    The point is: complex specifications.

    You are right. There are a lot of possible specifications. Almost any string can be specified in some way. And there are a lot of potential functions. Almost any object can be used for some purpose.

    But the point is: there are not exactly a lot of complex specifications, of complex functions. IOWs, of specifications or functions that generate an extremely small target space.

    A highly ordered string is an example (if long enough).

    Meaningful and functional strings are another example (if long enough and if the function requires a sufficient number of specific functional bits).

    The point is: that kind of specification is only observed as the outcome of necessity or design. Not of random variation (the probability is too low, and H0 can be safely rejected).

    A highly ordered string can be the outcome of necessity. Complex meaning and function in strings can never be explained by a simple necessity algorithm, and is a certain indicator of design.

    The reason why we do not observe outcomes which are part of extremely improbable special subsets, as often said by KF, is the same why we do not observe ordered states of gas molecules: they are possible, but too unlikely. For the same reason, gas molecules or any other random system do nor generate the characters of a Shakespeare sonnet (not by any possible code). For the same reason functional proteins do not emerge from random mutations.

  239. 239
    Mark Frank says:

    GP

    It is not that I do not understand. It is that I did not explain myself clearly.

    But the point is: there are not exactly a lot of complex specifications, of complex functions. IOWs, of specifications or functions that generate an extremely small target space.

    My point is twofold:

    How do you know there are very few complex specifications? There are infinitely many specifications out there and in general it is not obvious given a string whether it conforms to a specification.

    More importantly – why is this a reason for rejecting H0? I don’t see it in any textbook on hypothesis testing. If your principle were adopted generally then we should reject H0 whenever the results conform to a complex specification. Imagine an RCT of a new drug (double blind with a placebo). The experimenters notice that the difference in means between drug group and control group, while small, is the president’s birthday in seconds since 1900. It meets a complex specification. The p-value is tiny and they can confidentally reject H0. The medicine is clearly effective! The potential for pharma companies wantig to get their drugs to market is enormous.

  240. 240
    gpuccio says:

    Mark:

    a) All the complex specifications we observe are the result of design. Except biological molecules, which are the object of our debate.

    Please, offer any counter-example.

    b) Complex function is not something we find in nature. We find it only in designed things and in biological molecules and structures. Nowhere else.

    Therefore, observing a complex function is a special observation, and it is perfectly normal that we try to explain why we observe it.

    Random variation can generate apparent meaning and function, which is not intentional and is not designed.

    The purpose of design detection is to differentiate between those forms of pseudo function (a true functionality ion an object which was never intended for a function by some designer) and truly designed things.

    Now, we cannot do that if the function is simple. Random variation can generate simple pseudo functionalities.

    But we can do that if the function is complex. Random variation cannot do that.

    Again, that is first of all an empirical observation.

    So, we reject H0 because our question is very specific: “can random variation do that?”. And the answer is simple: “No, because that result is too unlikely, and, while logically possible, it will never be empirically observed”.

    IOWs, we reject H0 as a credible answer to our question. There is no need of any book which legitimates that procedure. The procedure is the same as in classic hypothesis testing, but its application to design detection is specific of ID theory. And, as you know, ID theory bis not exactly popular in our academic world. No book will tell you that you can safely reject the random origin of complex functional information, because that means validating ID theory. I need no book to believe what is evidently true.

    The proof of how true the theory is is that you cannot provide any true example of complex functional information generated in a random system. IOWs, you cannot offer any example of complex language, or functional software, generated randomly.

    So, what can you do? You do your best, and try to “play tricks” (in good faith, in good faith) with the definition of functional information.

    For example, your last example tries to renovate, in different form, the only objection that you made when I met the “challenge” of applying my procedure to any example offered by our friends at TSZ.

    Both are wrong arguments. This last example is even improper methodologically. You continue to treat the rejection of H0 as though it were an absolute. No. In all cases, we reject H0 as an answer to a specific question (which has nothing to do with any need to have an alternative H1).

    So, in the RCT example, H0 is simply that there is no difference between the drug group and the placebo group. So, we reject H0 if no significant difference is observed. We are not interested, here, in peculiarities of the string which measure the difference in means. You seem really confused about that.

    Now, let’s say instead that our experiment has the purpose of answering the question: can a random difference of means be an indirect measure of the president’s birthday in seconds since 1900 (or of any other specified set of data)?

    To that question, it is easy to find a negative answer by an experiment, and so reject the H0. Indeed, what will happen is that you will observe no similarity between the value of the difference of means and the birthdays, except for rare random correspondences, perfectly compatible with random variation of random values.

    But again, if you take any sequence of random digits, and just google it to see if there is any data in the internet which is similar to it, you can probably observe some result. It is simple: again, you are comparing a post-specification with all the available data in a big, very big database.

    That’s the probability you have to check. You get a series of digits, and you compare it to a database which is very huge. The scenario is similar to a search on BLASTp. It is possible to compute a probability for the H0 hypothesis, but you have to compute it well.

    Even so, I think that if you use a long enough series of random digits (let’s say, just to be safe, 500 decimal digits) you will never find a perfect correspondence, not even in the Internet, not even in the universe. 10^500 (about 1600 bits, I believe) is a really a big number. Big enough. Dembski’s UPB for the universe is 500 bits.

    A big number, isn’t it?

    Not so big, after all. 1600 bits is more or less the functional complexity in the alpha subunit of ATP synthase (300-400 perfectly conserved AAs from LUCA to humans)!

    Any comments?

  241. 241
    gpuccio says:

    HeKS:

    This discussion started as an answer to you. Are you following it?

    Your contribution would certainly be very welcome!

  242. 242
    Mark Frank says:

    GP

    In all cases, we reject H0 as an answer to a specific question (which has nothing to do with any need to have an alternative H1).

    Think about this. It means that given the same data but a different question we might reject H0 in one case and not in another. So the conclusion depends not on the data but on the interests of the experimenter! (This incidentally is one of the acknowledged problems with classical hypothesis testing.)

  243. 243
    gpuccio says:

    Mark:

    I really can’t see what is the problem.

    If you have a set of data, and you ask different questions about them, it’s obvious that the answers will be different. Why is that a problem?

    H0 must be formulated as a specific hypothesis, a specific question. In the case of design detection, the question is: can the functional complexity we observe be explained credibly by random variations in the system?

    Now, let’s say you have a very detailed, unpainted marble sculpture.

    You ask: “Can the form of this object be explained by random variation in a natural system?”

    Well, if the sculpture is complex enough, the answer will be: No. And we will reject H0.

    Now you ask: “Can the colours and patterns on the surface of this object be explained by random variation in a natural system?”

    The answer is: Yes. The marble colours and patterns can certainly be explained that way.

    The data are the same (the sculpture). The questions are different. We have two different H0s: both assume a random origin of what we observe, but they refer to different properties of the same object. The answers are different. In one case H0 is rejected, in the other case it is not.

    What is the problem?

    A “conclusion” is not an absolute, abstract entity, as you seem to assume. A conclusion is a specific process of our mind, a meaning we derive from data, an answer to some specific question. We can have different conclusions about the same data, provided that they are not logically incompatible.

    Again, where is the problem?

  244. 244
    Mark Frank says:

    GP

    But H0 hypotheses are about what happened – not what they explain. Examples of H0 might be:

    A) the two samples are drawn from the same population or
    B) this DNA string was created by random mutation

    Different people can have different interests in what H0 explains. Take example A – one person might be interested in whether H0 explains that sample A has a higher mean than sample B. Another person might be interested in whether H0 explains why sample A’s mean is almost exactly one standard deviation from sample B. One might have a high p value, the other a low p value. So does their different interest mean that one of them can rationally conclude that the two samples are from a different population while the other cannot?

  245. 245
    Mark Frank says:

    GP (cont)

    I should have addressed your example of marble statue.

    The data are the same (the sculpture). The questions are different. We have two different H0s: both assume a random origin of what we observe, but they refer to different properties of the same object. The answers are different. In one case H0 is rejected, in the other case it is not.

    This is silly. Clearly the colours and the shape of the statue are different data. They may be data about the same object but they are not the same observations.

    There are different possible H0s but they shouldn’t be phrased in terms of what they explain. The H0s might be:

    A) The shape of this statue is the result of natural weathering
    B) The colours in this statue are the result the natural colour of the marble used

    Each of these H0s might be used to explain different things depending on the interests of the person looking at the data. (A ) might be offered as an explanation at to why there is an arm missing or why the face looks very much like president Kennedy. The p-value for an arm missing is quite high. The p-value for looking like President Kennedy is rather low. So does the evidence for the shape being the result of natural processes depend not just on the data but on the interest of the person examining the data?

  246. 246
    Joe says:

    Why is Mark talking about hypothesis testing when his position doesn’t have any testable hypotheses?

  247. 247
    gpuccio says:

    Mark:

    No.

    A) the two samples are drawn from the same population

    This is an hypothesis, not a conclusion. The same term “the same population” can have a lot of meanings. The correct form is “populations in which the variable we are measuring is independent from the variable by which we group the cases”.

    In each case, you have to define very precisely:

    a) H0

    b) The effect that H0 is supposed to explain.

    We always reject H0 as an explanation of something. We are not trying to decide if H0 is absolutely true or not.

    Data are measurements made on objects. So, let’s say that our string is the object. We can measure different things in it. Let’s say that we measure the relative percentage of nucleotides.

    Our H0 will be:

    The relative percentage of nucleotides in this DNA string can be explained by random mutation.

    That is our hypothesis. And, very likely, it cannot be rejected.

    You should certainly understand that, if we do not reject H0, we are not demonstrating that it is true. We are simply stating that H0 remains a good explanation for the observed effect. Our conclusion is about what we can infer about reality, not about absolute reality. That is the nature of empirical science.

    Let’s say, instead, that in the same string we measure the functional information.

    Our H0 will be:

    The functional information for our defined function in this DNA string can be explained by random mutation.

    That is our hypothesis. And, if our measurements allow it, it can be rejected.

    So, we have the same string, and we measure two different properties of it. And we test two different hypotheses, each of which assumes a random origin of the string, but to explain two different measured data.

    What is the problem?

    It’s the same case as the marble sculpture: same object, different aspects of the object, different data, different hypotheses to test.

    There is no contradiction in saying that H0 cannot be rejected as an explanation of the first type of measurement, while it can be rejected as an explanation of the second type of measurement. We are testing our hypotheses, and we have two different hypotheses, regarding two different aspects of the same object.

    Nowhere we are stating: this string was not generated randomly. That would not be science, it would just be prophecy.

    What we are saying is: given this aspect of the string, it is not credible that it was generated randomly. Other aspects of the string are perfectly compatible with a random origin.

    There is absolutely no contradiction in all this process of cognition. The only problem would be if the same aspects (data to be explained) were used to reject or not reject the same hypothesis about them at the same time. That would be a logical contradiction.

    But that is not the case. Not in ID, at least.

  248. 248
    Mark Frank says:

    GP

    I am finding your ideas on hypothesis testing utterly bizarre – but I will make a couple more attempts to communicate.

    This is an hypothesis, not a conclusion.

    And if it is  rejected then the conclusion is that it is not true.Right?

    The same term “the same population” can have a lot of meanings. The correct form is “populations in which the variable we are measuring is independent from the variable by which we group the cases”.

    No problem with that. I was using a shorthand.

    We always reject H0 as an explanation of something. We are not trying to decide if H0 is absolutely true or not.

    Well that is where we disagree. Suppose I am a psychologist investigating the correlation between gender and reading speed age 10. I take a sample of 10 year old boys and a sample of 10 year old girls and measure reading speed. My H0 is that reading speed is independent from the variable gender. What is this H0 meant to be explaining? All I want to do is find out if it is true!

    Our H0 will be:
    The relative percentage of nucleotides in this DNA string can be explained by random mutation.

    Well of course you are free to believe this but it flies in the face of everything I have ever learned about hypothesis testing. As I have been taught (and I think rather well taught) there is a difference between the hypothesis – which is simply something that may be true or false – and the range of test statistics that may be used to confirm or reject it. So if the hypothesis is that the DNA string was created by random mutation then that could be tested by measuring the relative percentage of nucleotides – but that is quite crude – it would fail to reject the hypothesis if the nucleotides were in the equal proportions but all in a regular pattern. A better test might be something based on compression. In statistical terms that test would be more powerful. But there is nothing here about testing the hypothesis as an explanation of the KC complexity. The process is to decide on the hypothesis and then select the test.
    It may help to realise that tests for medical conditions are a form of hypothesis testing. The hypothesis is the condition. The test statistic is the result of whatever test you use. Suppose the hypothesis were – this woman has breast cancer. There are a number of tests you could use with varying sensitivity and specificity (and costs). If you choose a mammogram and get a negative result that will have one p-value, if you choose a biopsy you will get another. Are you going to say to her “you have breast cancer as an explanation of the mammogram, but not as an explanation of the biopsy”.

    You should certainly understand that, if we do not reject H0, we are not demonstrating that it is true. We are simply stating that H0 remains a good explanation for the observed effect. Our conclusion is about what we can infer about reality, not about absolute reality. That is the nature of empirical science.

    Well of course the conclusion is not certain. And I understand very well that classical hypothesis testing can only rule out H0 – it can never confirm H0 – that is one of its weaknesses. But we are still talking about a real thing that might be true or false. The woman has breast cancer or she does not.

    There is no contradiction in saying that H0 cannot be rejected as an explanation of the first type of measurement, while it can be rejected as an explanation of the second type of measurement.

    Of course – and that is why we choose the measurement that gives us the best combination of sensitivity and specificity.

    We are testing our hypotheses, and we have two different hypotheses, regarding two different aspects of the same object.

    In the previous sentence you had one H0 and two measurements. In this sentence you have two H0s. I understand the first sentence but not this one.

    Nowhere we are stating: this string was not generated randomly. That would not be science, it would just be prophecy.

    Why? Are you not prepared to reject the hypothesis that beta lactamase was generated randomly? Will you tell the woman that to come to a conclusion about her breast cancer would not be science. it would just be prophecy?

    What we are saying is: given this aspect of the string, it is not credible that it was generated randomly. Other aspects of the string are perfectly compatible with a random origin.

    If one aspect is incompatible with random origin then it doesn’t have a random origin – period. It doesn’t matter that other aspects are compatible.

  249. 249
    gpuccio says:

    Mark:

    “Well that is where we disagree. Suppose I am a psychologist investigating the correlation between gender and reading speed age 10. I take a sample of 10 year old boys and a sample of 10 year old girls and measure reading speed. My H0 is that reading speed is independent from the variable gender. What is this H0 meant to be explaining? All I want to do is find out if it is true!”

    If I observe no difference which is relevant, indeed I need no H0. I have just observed no effect. (Please, note that the concept of “relevant” is completely different from the concept of “significant”. A difference will always be there. But a researcher is always interested only on effects of a minimum size).

    If I observe an effect, I want to know if that effect can be generalized to a general population (IOWs, if it has predictive power in another set of cases) or if it is just a random fluctuation due to the sampling. That’s why I need H0. To decide if the observed effect can be explained by the null hypothesis, and therefore if I have credible reasons to reject it, and suggest an alternative explanation. So, I try to explain the observed effect by H0, and compute its probability under the null hypothesis.

    “Are you going to say to her “you have breast cancer as an explanation of the mammogram, but not as an explanation of the biopsy”

    I simply don’t think you have been well taught (just my humble opinion).

    Diagnostic tests can have different predictive value, sensitivity and specificity. Those parameters are usually measured in controlled conditions, and then applied in practice.

    A diagnosis is only the empirical application of the testing tools available, with awareness of their sensitivity and specificity, and then a personal judgement that must be communicated to the patient in the most realistic way. You don’t give a patient a p value. At most, you give him or her a reasonable assessment of the probabilities of a disease, or of a healing. That’s another thing.

    If you have a diagnosis by some test with very high specificity, your diagnosis is rather certain. Otherwise, you have to use other tools.

    But you never compute a p value in an individual case. You do that when you are researching, and trying to establish the sensitivity and specificity of your diagnostic tools.

    A thing is certainly true or false. Our conviction about its truth is anyway a theory, more or less based on facts. If I conclude that a string was designed, I must do that because I reject the H0 for some appropriate observed effect, and not for others. As some effects measure in the object can be compatible with a random origin, while other are not, even a single effect which is strongly incompatible with a random explanation will be enough to reject a random of the object. That is not in contradiction with the fact that other observed aspects of the object are compatible with a random explanation. Really, I don’t see your problems.

    Obviously, it is the task of the researcher to understand what effect can be useful to reject a random origin of the object (if, like in ID, that is the purpose). dFSCI is a tool which has been chosen exactly for that reason: because it is appropriate, it has 100% specificity as a design detection tool. All your “objections” have only one meaning: science is not mere statistics. It requires a correct, reasonable methodology. The methodology of OD is absolutely correct.

    “In the previous sentence you had one H0 and two measurements. In this sentence you have two H0s. I understand the first sentence but not this one.”

    It’s because I mean, as hypothesis, the whole cognitive context: this effect I observe can be explained by a random variation in the system. If you prefer to call hypothesis the simple statement that in the system there is only random variation, then you have one hypothesis with which you try to explain two different observed effects. You choice. I maintain that a correct formulation of H= is only in reference to an observed effect. But what is the difference, in the end? What problems do you find with my definition and procedure, except that it is a little different from what you are accustomed to think?

    “Why? Are you not prepared to reject the hypothesis that beta lactamase was generated randomly? Will you tell the woman that to come to a conclusion about her breast cancer would not be science. it would just be prophecy?”

    I reject the hypothesis that beta lactamase was generated randomly only because of its functional information. So, I am rejecting an H0 connected to a specific effect. I see no cognitive utility in separating the two concepts. I have no scientific independent truths, only scientific theories justified by observed facts and correct interpretation. I try to keep my categories pure.

    A diagnosis to a person is all another matter. It is an operative communication, which has its deontology. It is not a matter of p values, but of honest communication of the degree of certainty that the existing tools can give us, according to existing research and knowledge, in that individual case. IOWs, it is an application of existing predictive models which have already been tested before.

    I am afraid that you confuse scientific principles with their practical application. Medicine is a practical problem, not only an abstract science.

    “If one aspect is incompatible with random origin then it doesn’t have a random origin – period. It doesn’t matter that other aspects are compatible.”

    Or better, it is reasonable to reject the random origin. Because of the single aspect which was not compatible. Again, what is the problem? Have I ever said anything different?

    My point is simple: a correct application of hypothesis testing, with a correct methodology and understanding of what we are doing, generates no special problems, and works very well. In medicine like in ID. I have made very specific examples. I still don’t understand where you believe that my procedure would generate a problem, or bring me to a wrong conclusion.

    I have clearly shown that you can reject a correctly formulated H0 if you observe some well defined effect which cannot be explained by random variation, and that has nothing to do with any detailed formulation of H1 or H2, if not as the simple logical opposite of H0: “This effect cannot be explained by random variation”.

    You started all this by saying that if I have not an explicit H1, I cannot reject H0. And that Fisherian hypothesis testing is a problem. I think you have show mo reasons for any of those statements.

  250. 250
    Mark Frank says:

    Well GP I guess we just have to differ. I find your opinions about this to be quite bizarre but I see no value in pursuing it.

    If you are interested here is a classic paper on the problems with p-values. There are many such papers.

  251. 251
    gpuccio says:

    Mark:

    OK, we just have to differ. 🙂

  252. 252
    Mung says:

    gpuccio,

    Thank you, as always.

    And to gpuccio and Mark, such a gentlemanly exchange. Kudos.

  253. 253
    Mark Frank says:

    GP

    I just noticed something you wrote which worries me because if you really believe it you will be giving wrong diagnoses. This is not an attempt to restart our debate.

    If you have a diagnosis by some test with very high specificity, your diagnosis is rather certain.

    This is just not true. You must also know the specificity and base rate. This is not open to dispute. It is a mathematical certainty. Please reassure me you know this and this was a typo.

  254. 254
    gpuccio says:

    Mark:

    Yes, you are right. I should have said very high PPV. Thank you for the correction. 🙂

  255. 255
    Dionisio says:

    gpuccio

    What does PPV stand for in this case?
    Positive Predictive Value?
    The probability that a person with a positive test result has, or will get, a given disease?
    At least that’s what I found in a dictionary.
    Thank you.

  256. 256
    Dionisio says:

    gpuccio
    Sorry for asking such a dumb question in my previous post, but I don’t recall seeing that term when I worked on engineering design software development for a number of years. Your medical field and biological science have quite a bit of acronyms that make my learning much slower 🙂

  257. 257
    gpuccio says:

    Dionisio:

    Yes, it’s Positive Predictive value, the ratio:

    True Positives / Total test positives.

    Specificity is the ratio:

    True negatives / Condition negatives

    Indeed, the number of parameters that can be derived from the basic 2×2 table is astounding, and to make things worse, many of them have more than one acronym!

    So, we have:

    Sensitivity (also called True Positive Rate)

    Specificity (also called True Negative Rate)

    Precision (also called Positive Predictive Value)

    Negative Predictive Value

    Prevalence

    Accuracy

    False Positive Rate (1-Specificity)

    And so on… (I hope I made no mistakes!) 🙂

  258. 258
    Dionisio says:

    gpuccio:

    Thank you for the explanation!

    If you made a mistake, I won’t tell you about it, because my ignorance won’t allow me to notice it! 🙂

    BTW, now I recall someone telling me a few months ago that I could not learn anything in this site. 🙂

  259. 259
    Mark Frank says:

    GP

    Did you know that the world of information retrieval uses exactly the same concepts with different names?. It drives me crazy.

    Mark

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