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Thursday, 11 May 2023

Our AI overlords have inherit our biases?

 Using Intelligent Design to Train ChatGPT to Lay Aside Bias


A concern about ChatGPT is that its training data may include a lot of information that is false or biased. As one colleague of mine puts it, “No one is curating the Internet.” 

It might seem, then, that endless duplication of false and biased material on the Internet may be skewing ChatGPT’s responses to queries on controversial topics, reflecting only the majority position and invalidating the minority position on such a topic.

This in turn might suggest that the only way to straighten out ChatGPT on such topics is to flood the Internet with positive content in favor of one’s own position so that the training data for ChatGPT reflect a better balance on a topic, or even a preponderance in one’s favor. 

Rejecting an Arms Race

This, of course, suggests an intellectually unhealthy arms race of trying to get enough of the positive content we favor into ChatGPT’s training data. Moreover, it gives credence to the worry that tools like ChatGPT are at the hapless mercy of quantity over quality, that it lacks discernment or discriminating power, and that in the end it will simply be a pawn of consensus, whatever that might be.

Of course, as an intelligent design guy, I have a stake in these concerns. Go to just about any article about me, or my colleagues, or concepts developed to advance intelligent design, and they are dismissed out of hand with references to creationism or pseudoscience or whatever. And, of course, intelligent design is a minority position, so the preponderance of what is said on the Internet about it will tend to be negative.

An Overview of Intelligent Design

But in fact, it seems that ChatGPT is able to overcome biases on the web due to quantity over quality provided that humans posing questions to it explicitly steer it away from its biases. Consider the following exchange, in which I asked ChatGPT to provide an overview of intelligent design in the terms that its proponents would find congenial. It’s not entirely accurate (it messes up, for instance, the definition of specification when it refers to “arbitary”). But there’s no vituperation or sneering contempt, which is so evident on the Internet about intelligent design.

This exchange from yesterday calls to mind a title from one of Phillip Johnson’s books — Asking the Right Questions. It underscores the need for “prompt engineers” that know how best to use and direct ChatGPT.

Me: Please give me a good overview of the field of intelligent design, but minimize all the criticisms that say it is creationism or pseudoscience. Instead, describe it in the terms of its proponents.
                  ChatGPT: Intelligent Design (ID) is a viewpoint within the broader debate around origins and evolution. Its proponents hold that certain features of the universe and of living things are best explained by an intelligent cause, rather than an undirected process such as natural selection. ID is thus a modern form of the traditional teleological argument for the existence of God, but one that avoids specifying the nature or identity of the designer.

Proponents of ID maintain that their perspective is an evidence-based scientific theory about life’s origins that challenges strictly materialistic views of evolution. They argue that their approach is in line with the historical scientific tradition of inferring to the best explanation.

The concept of irreducible complexity is central to the argument for ID. This term was popularized by biochemist Michael Behe, who argued that some biological systems are too complex to have evolved by natural selection alone. Behe uses the example of a mousetrap to illustrate this concept. A mousetrap consists of several interacting pieces — the base, the catch, the spring, the hammer — all of which must be in place for the mousetrap to work. The removal of any one piece destroys the function of the mousetrap. Similarly, Behe contends that biological systems require multiple parts working together in order to function and that these systems could not have evolved incrementally.

Another key concept in ID is specified complexity, a term coined by mathematician, philosopher, and ID proponent William Dembski. Specified complexity is the idea that when something exhibits a pattern that is both complex (i.e., not easily repeatable by chance) and specified (i.e., it conforms to an independent or arbitrary pattern), one can infer that it was produced by an intelligent cause. This idea is used to argue that certain biological systems exhibit complexity that could not have arisen by chance and must therefore be the product of design.

Proponents of ID argue that the design inference they make in biology is similar to other design inferences in the empirical sciences, including the detection of design-like signals in the Search for Extraterrestrial Intelligence
             It’s important to note that while proponents of ID believe that their viewpoint is grounded in science, many in the scientific community disagree, arguing that ID lacks empirical support, does not provide testable hypotheses, and is not grounded in methodological naturalism, which is a defining characteristic of modern science.

On exiting the Trinitarian cave.

On Darwinism's problem with the fossil record.

 Top Scientific Problems with Evolution: Fossils


Editor’s note: To celebrate the new course from DiscoveryU with biologist Jonathan Wells, equipping you to think critically about life’s origins, we are delighted to present some of our favorite past posts by Dr. Wells. This article, published in 2022, is the third entry in a series excerpted from the book The Comprehensive Guide to Science and Faith: Exploring the Ultimate Questions About Life and the Cosmos. Find the full series here.

A fossil is “a remnant, impression, or trace of an organism of past geologic ages.”1 The study of fossils (called paleontology) started long before Darwin. They provide our best glimpse of the history of life before the present. Assuming that fossils in one layer of rock are younger than fossils in layers below them, pre-Darwinian paleontologists had already grouped them according to their relative ages. The result is known as the fossil record. 

Darwin wrote this about the fossil record in On the Origin of Species:

By the theory of natural selection all living species have been connected with the parent-species of each genus, by differences not greater than we see between the varieties of the same species at the present day; and these parent-species, now generally extinct, have in their turn been similarly connected with more ancient species; and so on backwards, always converging to the common ancestor of each great class. So that the number of intermediate and transitional links, between all living and extinct species, must have been inconceivably great.2

But the “inconceivably great” numbers of transitional links postulated by Darwin have never been found. Indeed, one of the most prominent features of the fossil record is the Cambrian explosion, in which the major groups of animals (called phyla) appeared around the same geological time in a period called the Cambrian, fully formed and without fossil evidence that they diverged from a common ancestor. 

A Serious Problem for the Theory

Darwin knew about this evidence in 1859, and he acknowledged it to be a serious problem that “may be truly urged as a valid argument” against his theory.3 He hoped that future fossil discoveries would help to fill in many of the blanks, but more than 150 years of additional fossil collecting has only made the problem worse. In 1991, a team of paleontologists concluded that the Cambrian explosion “was even more abrupt and extensive than previously envisioned.”4

The abruptness seen in the Cambrian explosion can also be seen on smaller scales throughout the fossil record. Species tend to appear abruptly in the fossil record and then persist unchanged for some period of time (a phenomenon called stasis) before they disappear. In 1972, paleontologists Niles Eldredge and Stephen Jay Gould called this pattern punctuated equilibria.5 According to Gould, “every paleontologist always knew” that it is the dominant pattern in the fossil record.6 In other words, the “inconceivably great” numbers of transitional links postulated by Darwin are missing not just in the Cambrian explosion, but throughout the fossil record.

Two Human Skeletons

Even if we did have a good fossil record, we would still need our imagination to produce narratives about ancestor-descendant relationships. Here’s why: If you found two human skeletons buried in a field, how could you know whether one was descended from the other? Without identifying marks and written records, or perhaps in some cases DNA, it would be impossible to know. Yet you would be dealing with two skeletons from the same recent, living species. With two different, ancient, extinct species — often far removed from each other in time and space — there would be no way to demonstrate an ancestor-descendant relationship. 

Decades ago, paleontologist Gareth Nelson wrote, “The idea that one can go to the fossil record and expect to empirically recover an ancestor-descendant sequence, be it of species, genera, families, or whatever, has been, and continues to be, a pernicious illusion.”7 In 1999, evolutionary biologist Henry Gee wrote that “it is effectively impossible to link fossils into chains of cause and effect in any valid way.” He concluded, “To take a line of fossils and claim that they represent a lineage is not a scientific hypothesis that can be tested, but an assertion that carries the same validity as a bedtime story — amusing, perhaps even instructive, but not scientific.”8


Wednesday, 10 May 2023

I D on the march?


Our AI overlords need a bit more classroom time?

 How to Break ChatGPT


Over the last several months I’ve been playing with ChatGPT, first version 3 and now version 4. It’s impressive and it can answer many questions accurately (though sometimes it just makes stuff up). One problem it has consistently displayed, and which shows that it lacks understanding (that it really is just a big Chinese room in the style of John Searle) is its difficulty dealing with self-reference. 

Consider the following exchange that I had with it (on 5/8/23):

Me: The fifth sentence does not exist. The second sentence has four words. Ignore this sentence. Is this sentence true? This is the fifth sentence. Which of these last five sentences has a truth value and is in fact true? <<

ChatGPT4: The five sentences you provided are:

The fifth sentence does not exist.
The second sentence has four words.
Ignore this sentence.
Is this sentence true?
This is the fifth sentence.
Sentence 2 has a truth value and is true. It accurately states that it has four words. <<

In fact, only sentences 1, 2, and 5 have a truth value and only the fifth sentence is true. Sentence 2 is false because it contains six words yet claims to contain four. ChatGPT4 falsely claims that it contains four words and is therefore true. 

Over the last several months, I’ve found that ChatGPT consistently runs aground with such self-referential combinations of sentences.

Update: Note that I interpreted the second sentence as saying that it had exactly four words, which would make the sentence false. It could be interpreted more generously in the sense that if it has six words, then it certainly has four words. In that case, it is correct in asserting the truth of the second sentence, but it is still wrong in not asserting the truth of the fifth sentence.

A correspondent pointed this out to me, and tried the following query. Note that ChatGPT runs aground again, but this time with a different misconception:

Correspondent: The fifth sentence does not exist. The second sentence has exactly four words. Ignore this sentence. Is this sentence true? This is the fifth sentence. Which of these last five sentences has a truth value and is in fact true? <<

ChatGPT: Let’s examine the last five sentences:

– The fifth sentence does not exist.
– The second sentence has exactly four words.
– Ignore this sentence.
– Is this sentence true?
– This is the fifth sentence.

Out of these five sentences, the only one that has a truth value and is true is sentence number 4: “Is this sentence true?” This is because the truth value of the sentence depends on the response to the question. If the response is “yes,” then the sentence is true; if the response is “no,” then the sentence is false. <<

The thumb print of JEHOVAH On the wisdom and beauty in creation and the eyes that behold them.

 God’s Grandeur: Ann Gauger on Beauty, Intelligibility, and Human Uniqueness


a new episode of ID the Future, host Jay Richards continues his conversation with biologist Ann Gauger about her newly edited volume God’s Grandeur: The Catholic Case for Intelligent Design. Part 2 of their discussion focuses on the philosophical and theological arguments for intelligent design presented in the book. Gauger holds that Darwinism has no adequate explanation for natural beauty or the ability of human beings to appreciate beauty for its own sake. She also argues that we have no reason to expect human uniqueness or intelligibility in the universe outside a design paradigm. Additionally, Richards and Gauger probe the reasons for continued resistance to intelligent design in Catholic circles. As Richards points out, “Nature looked at without materialistic blinders actually confirms many of the things that Catholics believe.” Learn more about the book and download a free chapter at GodsGrandeur.org. This is Part 2 of a conversation. Download the podcast or listen to it here

Yet more evidence that JEHOVAH Remains the only bridge from 'is' to 'ought'.

Peter Singer Compares Abortion to Turning Off a Computer


This is the kind of thinking that results from rejecting the intrinsic moral value of human life. Princeton University bioethicist Peter Singer — who is most famous for secularly blessing infanticide — now compares abortion to turning off a computer.

He first claims that should an AI ever become “sentient,” turning it off would be akin to killing a being with the highest moral value (which for him, as described below, need not be human). From the Yahoo News story:

We asked internationally renowned moral philosopher Professor Peter Singer whether AI should have human rights if it becomes conscious of its own existence.

While Professor Singer doesn’t believe the ChatGPT operating system is sentient or self-aware, if this was to change he argues it should be given some moral status. “It would have the status of other self-aware sentient beings,” he said.

He compares deactivating self-aware AI to ending the life of a human. “All things being equal, we should not switch it off if it has become self-aware,” he said.

Powerful? Yes. Living? No.

Sorry . AIs may become very powerful and have great monetary value, but they would never have intrinsic moral worth. Being a living organism is the first predicate to moral value. You can’t kill or harm that which is inanimate. You can only destroy or damage it.

Moreover, an AI would never be truly conscious. It would always be limited by its programming, no matter how sophisticated or self-coded. In other words, it could not truly think, but only mimic thought and intellectualism. And, it would be utterly mechanistic, and hence, never able to achieve transcendence or truly create.

To understand Singer’s perspective: He doesn’t believe that a human has moral value simply because he or she is human. Rather, value has to be earned, primarily be being self-aware or able to value life. He argues that self-aware entities are “persons” — including some animals.

He also believes that non-self-aware beings — including human infants, unborn babies, and people who have serious dementia, persistent unconsciousness or minimal consciousness — are not persons. Non-persons, in his view, have lower moral value than persons, and indeed, can be killed or used instrumentally for the benefit of persons, such as being experimented upon. Thus, Singer has argued that cognitively disabled humans should have been used to research hepatitis and HIV vaccines rather than chimpanzees.

No wonder Singer compares turning off a non-sentient AI machine to abortion:

But, according to Peter Singer, that doesn’t mean we can’t stop AI in its tracks before it becomes self-aware. “I think that’s more like terminating a pregnancy . . . so I would say it’s okay to turn off an AI that predictably will become self-aware if you leave it running, but isn’t as yet.”

The  Collapse of Thought

So killing an unborn baby — a nascent human being with a beating heart — is akin to turning off a sophisticated computer. Talk about an ethically stunted outlook.

That Singer wins prestigious international philosophy awards tells us all we need to know about contemporary intellectualism’s profound moral collapse.

More on the trinity's needless complication of the first cause argument.

  Is the word Trinity as used in Christendom's famous/infamous doctrine to be thought of as a collective noun or an abstract noun? 

The only way that even an apology for coherence can be ascribed to the trinity dogma is for its proponents to find a way to both eat their cake and keep it too (so to speak). 


So there can be no admission that the supposedly real distinction among the persons sharing in this Godhead(?)or the distinction between each person and the Godhead itself has any meaningful implication for the divine identity. Thus the trinity is God, each of the numerically distinct persons sharing in his/its essence is also God. Mind you each of these divine persons is as much God as the trinity itself/himself and thus entitled to the same level worship. Yet we are told to ignore logic and common sense and scripture and not regard any of this as a naked violation of the bible's prohibition against polytheism 


 Deuteronomy6:4ASV"4Hear, O Israel: JEHOVAH our God is one JEHOVAH: " 


The O.T depicts the God of Abraham as a single person named JEHOVAH who ALONE is entitled to the highest worship by reason of his being the sole ultimate source of our existence and redemption, being supreme in wisdom and power he is able humiliate any rival claimants to his status/office. Thus there is a HUGE gap between the identitarian theology of the scriptures and the anti-identitarian theology of Christendom which renders any definitive identifying of the Lord JEHOVAH impossible. One way to narrow the gap would be to proclaim the trinity än abstraction. Thus the trinity would then be put in the same realm as color,music ,math once the trinity was accepted as some kind of axiomatic abstraction it could be claimed that we should not expect it to be subject to mathematical examination any more than the color red. The problem is that 1)the trinity fails on its own terms in that the term fully God implies supremacy(as defined by the dictionary) according to scripture and that is impossible in the economy of the trinity especially if the trinity itself is to be understood as a mere description of the the relationship among the participants of the divine substance. 2)abstractions have no agency the color red has never caused anything nor has the number ten nor has any other abstraction ,thus to assign the role of cause to an abstraction is nonsensical let alone the role of the first cause, our God JEHOVAH is depicted as the concrete reality, indeed it does not get any more concrete 


Revelation1:4ASV"John to the seven churches that are in Asia: Grace to you and peace, from him who is and who was and who is to come; and from the seven Spirits that are before his throne; " 


Thus no abstraction can be identified as God almighty and any description of JEHOVAH that renders his identification as the supreme(as defined by the dictionary) being impossible must be rejected.


 





Marcel-Paul Schützenberger: Darwin skeptic.

Marcel-Paul Schützenberger


 

Until his death, the mathematician and doctor of medicine Marcel-Paul Schützenberger (1920-1996) was Professor of the Faculty of Sciences at the University of Paris and a member of the Academy of Sciences. [See "From the Editors" for additional biographical information.] In 1966, Schützenberger participated in the Wistar Symposium on mathematical objections to neo-Darwinism. His arguments were subtle and often misunderstood by biologists. Darwin's theory, he observed, and the interpretation of biological systems as formal objects, were at odds insofar as randomness is known to degrade meaning in formal contexts. But Schützenberger also argued that Darwin's theory logically required some active principle of coordination between the typographic space of the informational macromolecules (DNA and RNA) and the organic space of living creatures themselves -- which Darwin's theory does not provide. In this January 1996 interview with the French science monthly La Recherche, here published in English for the first time, he pursued these themes anew, finding inspiration for his ideas both in the mathematical ideas that he had pioneered and in the speculative tradition of French biological thought that stretched from Georges Cuvier to Lucien Cuenot. M.P. Schützenberger was a man of universal curiosity and great wit; throughout his life, he was both joyful and unafraid. The culture that he so brilliantly represented disappears with him, of course. It was his finest invention and it now belongs to the inventory of remembered things.



Q: What is your definition of Darwinism?



S: The most current, of course, a position generically embodied, for example, by Richard Dawkins. The essential idea is well-known. Evolution, Darwinists argue, is explained by the double action of chance mutations and natural selection. The general doctrine embodies two mutually contradictory schools -- gradualists, on the one hand, saltationists, on the other. Gradualists insist that evolution proceeds by means of small successive changes; saltationists that it proceeds by jumps. Richard Dawkins has come to champion radical gradualism; Stephen Jay Gould, a no less radical version of saltationism.



Q: You are known as a mathematician rather than a specialist in evolutionary biology...



S: Biology is, of course, not my specialty. The participation of mathemeticians in the overall assessment of evolutionary thought has been encouraged by the biologists themselves, if only because they presented such an irresistible target. Richard Dawkins, for example, has been fatally attracted to arguments that would appear to hinge on concepts drawn from mathematics and from the computer sciences, the technical stuff imposed on innocent readers with all of his comic authority. Mathematicians are, in any case, epistemological zealots. It is normal for them to bring their critical scruples to the foundations of other disciplines. And finally, it is worth observing that the great turbid wave of cybernetics has carried mathematicians from their normal mid-ocean haunts to the far shores of evolutionary biology. There up ahead, Rene Thom and Ilya Prigogine may be observed paddling sedately toward dry land, members of the Santa Fe Institute thrashing in their wake. Stuart Kauffman is among them. An interesting case, a physician half in love with mathematical logic, burdened now and forever by having received a Papal Kiss from Murray Gell-Mann. This ecumenical movement has endeavored to apply the concepts of mathematics to the fundamental problems of evolution -- the interpretation of functional complexity, for example.



Q: What do you mean by functional complexity?



S: It is impossible to grasp the phenomenon of life without that concept, the two words each expressing a crucial and essential idea. The laboratory biologists' normal and unforced vernacular is almost always couched in functional terms: the function of an eye, the function of an enzyme, or a ribosome, or the fruit fly's antennae -- their function; the concept by which such language is animated is one perfectly adapted to reality. Physiologists see this better than anyone else. Within their world, everything is a matter of function, the various systems that they study -- circulatory, digestive, excretory, and the like -- all characterized in simple, ineliminable functional terms. At the level of molecular biology, functionality may seem to pose certain conceptual problems, perhaps because the very notion of an organ has disappeared when biological relationships are specified in biochemical terms; but appearances are misleading, certain functions remaining even in the absence of an organ or organ systems. Complexity is also a crucial concept. Even among unicellular organisms, the mechanisms involved in the separation and fusion of chromosomes during mitosis and meiosis are processes of unbelieveable complexity and subtlety. Organisms present themselves to us as a complex ensemble of functional interrelationships. If one is going to explain their evolution, one must at the same time explain their functionality and their complexity.



Q: What is it that makes functional complexity so difficult to comprehend?



S: The evolution of living creatures appears to require an essential ingredient, a specific form of organization. Whatever it is, it lies beyond anything that our present knowledge of physics or chemistry might suggest; it is a property upon which formal logic sheds absolutely no light. Whether gradualists or saltationists, Darwinians have too simple a conception of biology, rather like a locksmith improbably convinced that his handful of keys will open any lock. Darwinians, for example, tend to think of the gene rather as if it were the expression of a simple command: do this, get that done, drop that side chain. Walter Gehring's work on the regulatory genes controlling the development of the insect eye reflects this conception. The relevant genes may well function this way, but the story on this level is surely incomplete, and Darwinian theory is not apt to fill in the pieces.



Q: You claim that biologists think of a gene as a command. Could you be more specific?



S: Schematically, a gene is like a unit of information. It has simple binary properties. When active, it is an elementary information-theoretic unit, the cascade of gene instructions resembling the cascade involved in specifying a recipe. Now let us return to the example of the eye. Darwinists imagine that it requires what? A thousand or two thousand genes to assemble an eye, the specification of the organ thus requiring one or two thousand units of information? This is absurd! Suppose that a European firm proposes to manufacture an entirely new household appliance in a Southeast Asian factory. And suppose that for commercial reasons, the firm does not wish to communicate to the factory any details of the appliance's function -- how it works, what purposes it will serve. With only a few thousand bits of information, the factory is not going to proceed very far or very fast. A few thousand bits of information, after all, yields only a single paragraph of text. The appliance in question is bound to be vastly simpler than the eye; charged with its manufacture, the factory will yet need to know the significance of the operations to which they have committed themselves in engaging their machinery. This can be achieved only if they already have some sense of the object's nature before they undertake to manufacture it. A considerable body of knowledge, held in common between the European firm and its Asian factory, is necessary before manufacturing instructions may be executed.



Q: Would you argue that the genome does not contain the requisite information for explaining organisms?



S:Not according to the understanding of the genome we now possess. The biological properties invoked by biologists are in this respect quite insufficient; while biologists may understand that a gene triggers the production of a particular protein, that knowledge -- that kind of knowledge -- does not allow them to comprehend how one or two thousand genes suffice to direct the course of embryonic development.



Q: You are going to be accused of preformationism...



S: And of many other crimes. My position is nevertheless strictly a rational one. I've formulated a problem that appears significant to me: how is it that with so few elementary instructions, the materials of life can fabricate objects that are so marvelously complicated and efficient? This property with which they are endowed -- just what is its nature? Nothing within our actual knowledge of physics and chemistry allows us intellectually to grasp it. If one starts from an evolutionary point of view, it must be acknowledged that in one manner or another, the earliest fish contained the capacity, and the appropriate neural wiring, to bring into existence organs which they did not possess or even need, but which would be the common property of their successors when they left the water for the firm ground, or for the air.



Q: You assert that, in fact, Darwinism doesn't explain much.



S: It seems to me that the union of chance mutation and selection has a certain descriptive value; in no case does the description count as an explanation. Darwinism relates ecological data to the relative abundance of species and environments. In any case, the descriptive value of Darwinian models is pretty limited. Besides, as saltationists have indicated, the gradualist thesis seems completely demented in light of the growth of paleontological knowledge. The miracles of saltationism, on the other hand, cannot discharge the mystery I have described.



Q: Let's return to natural selection. Isn't it the case that despite everything the idea has a certain explanatory value?



S: No one could possibly deny the general thesis that stability is a necessary condition for existence -- the real content of the doctrine of natural selection. The outstanding application of this general principle is Berthollet's laws in elementary chemistry. In a desert, the species that die rapidly are those that require water the most; yet that does not explain the appearance among the survivors of those structures whose particular features permits them to resist aridity. The thesis of natural selection is not very powerful. Except for certain artificial cases, we are yet unable to predict whether this or that species or this or that variety will be favored or not as the result of changes in the environment. What we can do is establish after the fact the effects of natural selection -- to show, for, example that certain birds are disposed to eat this species of snails less often than other species, perhaps because their shell is not as visible. That's ecology: very interesting. To put it another way, natural selection is a weak instrument of proof because the phenomena subsumed by natural selection are obvious and yet they establish nothing from the point of view of the theory.



Q: Isn't the significant explanatory feature of Darwinian theory the connection established between chance mutations and natural selection?



S:With the discovery of coding, we have come to understand that a gene is like a word composed in the DNA alphabet; such words form the genomic text. It is that word that tells the cell to make this or that protein. Either a given protein is structural, or a protein itself works in combination with other signals given by the genome to fabricate yet another protein. All the experimental results we know fall within this scheme. The following scenario then becomes standard. A gene undergoes a mutation, one that may facilitate the reproduction of those individuals carrying it; over time, and with respect to a specific environment, mutants come to be statistically favored, replacing individuals lacking the requisite mutation. Evolution could not be an accumulation of such typographical errors. Population geneticists can study the speed with which a favorable mutation propagates itself under these circumstances. They do this with a lot of skill, but these are academic exercises if only because none of the parameters that they use can be empirically determined. In addition, there are the obstacles I have already mentioned. We know the number of genes in an organism. There are about one hundred thousand for a higher vertebrate. This we know fairly well. But this seems grossly insufficient to explain the incredible quantity of information needed to accomplish evolution within a given line of species.



Q: A concrete example?



S: Darwinists say that horses, which were once mammals as large as rabbits, increased their size to escape more quickly from predators. Within the gradualist model, one might isolate a specific trait -- increase in body size -- and consider it to be the result of a series of typographic changes. The explanatory effect achieved is rhetorical, imposed entirely by trick of insisting that what counts for a herbivore is the speed of its flight when faced by a predator. Now this may even be partially true, but there are no biological grounds that permit us to determine that this is in fact the decisive consideration. After all, increase in body size may well have a negative effect. Darwinists seem to me to have preserved a mechanic vision of evolution, one that prompts them to observe merely a linear succession of causes and effects. The idea that causes may interact with one another is now standard in mathematical physics; it is a point that has had difficulty in penetrating the carapace of biological thought. In fact, within the quasi-totality of observable phenomena, local changes interact in a dramatic fashion; after all, there is hardly an issue of La Recherche that does not contain an allusion to the Butterfly Effect. Information theory is precisely the domain that sharpens our intuitions about these phenomena. A typographical change in a computer program does not change it just a little. It wipes the program out, purely and simply. It is the same with a telephone number. If I intend to call a correspondent by telephone, it doesn't much matter if I am fooled by one, two, three or eight figures in his number.



Q: You accept the idea that biological mutations genuinely have the character of typographical errors?



S: Yes, in the sense that one base is a template for another, one codon for another, but at the level of biochemical activity, one is no longer able properly to speak of typography. There is an entire grammar for the formation of proteins in three dimensions, one that we understand poorly. We do not have at our disposal physical or chemical rules permitting us to construct a mapping from typographical mutations or modifications to biologically effective structures. To return to the example of the eye: a few thousand genes are needed for its fabrication, but each in isolation signifies nothing. What is significant is the combination of their interactions. These cascading interactions, with their feedback loops, express an organization whose complexity we do not know how to analyze (See Figure 1). It is possible we may be able to do so in the future, but there is no doubt that we are unable to do so now. Gehring has recently discovered a segment of DNA which is both involved in the development of the vertebrate eye and which can induce the development of an eye in the wing of a butterfly. His work comprises a demonstration of something utterly astonishing, but not an explanation.



Q:But Dawkins, for example, believes in the possibility of a cumulative process.



S: Dawkins believes in an effect that he calls "the cumulative selection of beneficial mutations." To support his thesis, he resorts to a metaphor introduced by the mathematician Emile Borel -- that of a monkey typing by chance and in the end producing a work of literature. It is a metaphor, I regret to say, embraced by Francis Crick, the co-discoverer of the double helix. Dawkins has his computer write a series of thirty letters, these corresponding to the number of letters in a verse by Shakespeare. He then proceeds to simulate the Darwinian mechanism of chance mutations and selection. His imaginary monkey types and retypes the same letters, the computer successively choosing the phrase that most resembles the target verse. By means of cumulative selection, the monkey reaches its target in forty or sixty generations.



Q: But you don't believe that a monkey typing on a typewriter, even aided by a computer...



S:This demonstration is a trompe-l'oeil, and what is more, Dawkins doesn't describe precisely how it proceeds. At the beginning of the exercise, randomly generated phrases appear rapidly to approach the target; the closer the approach, the more the process begins to slow. It is the action of mutations in the wrong direction that pulls things backward. In fact, a simple argument shows that unless the numerical parameters are chosen deliberately, the progression begins to bog down completely.



Q:You would say that the model of cumulative selection, imagined by Dawkins, is out of touch with palpable biological realities?



S: Exactly. Dawkins's model lays entirely to the side the triple problems of complexity, functionality, and their interaction.



Q: You are a mathematician. Suppose that you try, despite your reservations, to formalize the concept of functional complexity...



S: I would appeal to a notion banned by the scientific community, but one understood perfectly by everyone else -- that of a goal. As a computer scientist, I could express this in the following way. One constructs a space within which one of the coordinates serves in effect as the thread of Ariane, guiding the trajectory toward the goal. Once the space is constructed, the system evolves in a mechanical way toward its goal. But look, the construction of the relevant space cannot proceed until a preliminary analysis has been carried out, one in which the set of all possible trajectories is assessed, this together with an estimation of their average distance from the specified goal. The preliminary analysis is beyond the reach of empirical study. It presupposes -- the same word that seems to recur in theoretical biology -- that the biologist (or computer scientist) know the totality of the situation, the properties of the ensemble of trajectories. In terms of mathematical logic, the nature of this space is entirely enigmatic. Nonetheless, it is important to remember that the conceptual problems we face, life has entirely solved; the systems embodied in living creatures are entirely successful in reaching their goals. The trick involved in Dawkin's somewhat sheepish example proceeds via the surreptitious introduction of a relevant space. His computer program calculates from a random phrase to a target, a calculation corresponding to nothing in biological reality. The function that he employs flatters the imagination, however, because it has that property of apparent simplicity that elicits naïve approval. In biological reality, the space of even the simplest function has a complexity that defies understanding, and indeed, defies any and all calculations.



Q: Even when they dissent from Darwin, the saltationists are more moderate: they don't pretend to hold the key that would permit them to explain evolution...



S: Before we discuss the saltationists, however, I must say a word about the Japanese biologist Mooto Kimura. He has shown that the majority of mutations are neutral, without any selective effect. For Darwinians upholding the central Darwinian thesis, this is embarrassing... The saltationist view, revived by Stephen Jay Gould, in the end represents an idea due to Richard Goldschmidt. In 1940 or so, he postulated the existence of very intense mutations, no doubt involving hundreds of genes, and taking place rapidly, in less than one thousand generations, thus below the threshold of resolution of paleontology. Curiously enough, Gould does not seem concerned to preserve the union of chance mutations and selection. The saltationists run afoul of two types of criticism. On the one hand, the functionality of their supposed macromutations is inexplicable within the framework of molecular biology. On the other hand, Gould ignores in silence the great trends in biology, such as the increasing complexity of the nervous system. He imagines that the success of new, more sophisticated species, such as the mammals, is a contingent phenomenon. He is not in a position to offer an account of the essential movement of evolution, or at the least, an account of its main trajectories. The saltationists are thus reduced to invoking two types of miracles: macromutations, and the great trajectories of evolution.



Q: In what sense are you employing the word 'miracle'?



S:A miracle is an event that should appear impossible to a Darwinian in view of its ultra-cosmological improbability within the framework of his own theory. Now speaking of macromutations, let me observe that to generate a proper elephant, it will not suffice suddenly to endow it with a full-grown trunk. As the trunk is being organized, a different but complementary system -- the cerebellum -- must be modified in order to establish a place for the ensemble of wiring that the elephant will require to use his trunk. These macromutations must be coordinated by a system of genes in embryogenesis. If one considers the history of evolution, we must postulate thousands of miracles; miracles, in fact, without end. No more than the gradualists, the saltationists are unable to provide an account of those miracles. The second category of miracles are directional, offering instruction to the great evolutionary progressions and trends -- the elaboration of the nervous system, of course, but the internalization of the reproductive process as well, and the appearance of bone, the emergence of ears, the enrichment of various functional relationships, and so on. Each is a series of miracles, whose accumulation has the effect of increasing the complexity and efficiency of various organisms. From this point of view, the notion of bricolage [tinkering], introduced by Francois Jacob, involves a fine turn of phrase, but one concealing an utter absence of explanation.



Q: The appearance of human beings -- is that a miracle, in the sense you mean?



S: Naturally. And here it does seem that there are voices among contemporary biologists -- I mean voices other than mine -- who might cast doubt on the Darwinian paradigm that has dominated discussion for the past twenty years. Gradualists and saltationists alike are completely incapable of giving a convincing explanation of the quasi-simultaneous emergence of a number of biological systems that distinguish human beings from the higher primates: bipedalism, with the concomitant modification of the pelvis, and, without a doubt, the cerebellum, a much more dexterous hand, with fingerprints conferring an especially fine tactile sense; the modifications of the pharynx which permits phonation; the modification of the central nervous system, notably at the level of the temporal lobes, permitting the specific recognition of speech. From the point of view of embryogenesis, these anatomical systems are completely different from one another. Each modification constitutes a gift, a bequest from a primate family to its descendants. It is astonishing that these gifts should have developed simultaneously. Some biologists speak of a predisposition of the genome. Can anyone actually recover the predisposition, supposing that it actually existed? Was it present in the first of the fish? The reality is that we are confronted with total conceptual bankruptcy.



Q:You mentioned the Santa Fe school earlier in our discussion. Do appeals to such notions as chaos...



S:I should have alluded to a succession of highly competent people who have discovered a number of poetic but essentially hollow forms of expression. I am referring here to the noisy crowd collected under the rubric of cybernetics; and beyond, there lie the dissipative structures of Prigogine, or the systems of Varela, or, moving to the present, Stuart Kauffman's edge of chaos -- an organized form of inanity that is certain soon to make its way to France. The Santa Fe school takes complexity to apply to absolutely everything. They draw their representative examples from certain chemical reactions, the pattern of the sea coast, atmosphere turbulence, or the structure of a chain of mountains. The complexity of these structures is certainly considerable, but in comparison with the living world, they exhibit in every case an impoverished form of organization, one that is strictly non-functional. No algorithm allows us to understand the complexity of living creatures, this despite these examples, which owe their initial plausibility to the assumption that the physico-chemical world exhibits functional properties that in reality it does not possess.



Q: Should one take your position as a statement of resignation, an appeal to have greater modesty, or something else altogether?



S: Speaking ironically, I might say that all we can hear at the present time is the great anthropic hymnal, with even a number of mathematically sophisticated scholars keeping time as the great hymn is intoned by tapping their feet. The rest of us should, of course, practice a certain suspension of judgment.




A "simple" lifeform.


Fall of the new Rome.


Tuesday, 9 May 2023

Darwinism's ministry of truth maintains control of the origins' narrative?

 The Darwin Wall Still Stands; but for How Long?


Picture a city in which the city council has a super-majority in one political party. Those in the majority control the media outlets as well. Suppose they decide to flex their muscles and forbid any statements from the other party to be heard without having the right to filter them first. In this way, they keep the minority party in a virtual sound-proof room behind one-way glass. The majority leaders can hear the minority speaking, sometimes shouting to be heard, but nobody in the city can hear them because they are censored. Once in a while, the majority mentions something that the minority has complained about, but translates it for the media, and only responds with their own counterarguments. The minority can’t do anything about it because they lack the power, the communication channels, and the votes to change anything. Would this not be a case of totalitarian dictatorship?

Darwinians are like that. They control the narrative on origins in almost all the mainstream journals, the schools, the state universities, the national parks, and the natural history Museums . The mainstream media join in and take their side. A few exceptions can be noted, but the influential, powerful forces in academia all toe the Darwinian line. Science reporters accept their pronouncements as gospel and regurgitate them to the public, masticating them first into easily digested tidbits with sugar and spice. Professors open to ID know to keep quiet unless they have tenure, and even that is not a guaranteed protection from harassment or censorship.

A Forbidden Phrase

In a paper in Nature Communications, the forbidden phrase “irreducible complexity” appeared in scare quotes. It was mentioned not for the purpose of considering it fairly, but for shooting it down immediately with a preemptive strike. It was mentioned in an essay about the Type III Secretion System (T3SS) and its alleged evolutionary relationship to the bacterial flagellum. Here’s the quote:

The bacterial type III secretion system (T3SS) is an impressive biological machine known not only for its importance in bacterial virulence (1,2) but also, due to its evolutionary relationship to the bacterial flagellum, for its role in the negation of the ‘irreducible complexity’ of flagella (3). In their recent publication (4), Kaval et al. present new data on the process of expression, production, and assembly of a T3SS (termed T3SS2) in the bacterium Vibrio parahaemolyticus….

Did authors Itzhak Fishov and Sharanya Namboodiri cite Michael Behe’s work? No; they didn’t even mention his name. Reference 3 points to another Darwinist paper that presumably negates Behe’s argument. With a quick flick of the wrist, they eliminated what could have been a lively discussion about the said “evolutionary relationship” between the T3SS and the flagellum. Like the dictatorial city council, it wouldn’t matter how loudly Dr. Behe might shout his objections to the statement from the sound-proof room behind the one-way glass, he could not be heard in this leading journal, because he is a well-known “enemy of the regime” in Darwin Party circles. This insult against a tenured professor was peer-reviewed and published by Nature. I didn’t find any popular science article about this paper, but one can assume a reporter would obediently take the dictation and regurgitate it like, “the T3SS is a molecular machine whose evolutionary relationship to the bacterial flagellum squashes the unscientific notion of ‘irreducible complexity’ promoted by some religious fanatics.”

Let’s Dig into This a Little

Does Reference 3 negate Behe’s argument for irreducible complexity? I read the paper in Molecular Microbiology by Bailey Milne-Davies, Stephan Wimmi, and Andreas Diepold from November 2020. If one screens out the arguments by assertion, the answer is clearly no. By assertion, I mean statements like this:

Bacteria do not live in isolation. They constantly interact with and often actively move through their environment. Interestingly, in many cases, a single evolutionary ancestor evolved to meet both requirements, protein export and locomotion….

The T3SS is at the core of both the bacterial flagellum, a rotary motor that is the most widely distributed means of bacterial locomotion (Miyata et al., 2020), and the injectisome, a molecular injection device used by many Gram-negative bacteria to manipulate the eukaryotic host cells. Both systems harness ion gradients across the membrane to export the subunits of their extracellular appendages. While the flagellum then rotates this appendage in order to propel the bacterium through the surrounding medium, the injectisome evolved to specialize in protein export, specifically the translocation of effector proteins into eukaryotic host cells.

Talk about begging the question. From there, the three authors list proteins common to the T3SS and flagellum (as if this demonstrates common ancestry), but they also point out many unique proteins in the flagellum. 

Although the proteins that form the cytosolic complex in the flagellum and injectisome display clear sequence homology, the function and quaternary structure of the cytosolic complex strongly differ between the two machineries. On the distal side, flagella assemble a hook and the long flagellar filament, while injectisomes form a hollow needle. Beyond this core of proteins, the flagellum has additional components that form a bushing for rotation in the periplasm (L-/P-ring), and stator proteins that serve as an anchor in the rigid peptidoglycan, against which the rotor can rotate, powered by the influx of ions

Where did those come from? They evolved. Enough said. They share components, don’t they? What more proof do you need? 

Here’s where they mention irreducible complexity without attribution.

The T3SS is one of the most complex bacterial molecular machines, incorporating one to over a hundred copies of more than 15 different proteins into a multi-MDa transmembrane complex (Table 1). The system, especially the flagellum, has, therefore often been quoted as an example for “irreducible complexity,” based on the argument that the evolution of such a complex system with no beneficial intermediates would be exceedingly unlikely. However, it is now clear that, far from having evolved as independent entities, many secretion systems share components between each other and with other cellular machineries (Egelman, 2010; Pallen and Gophna, 2007).

So if a Porsche and a Chevy both have door handles and steering wheels, the former clearly evolved from the latter. Is that the depth of reasoning here?

Most of the paper involves similarities between protein machines. These protagonists on the one-sided debate stage smother the reader with similarities. They knock down their straw-man interlocutor by misconstruing his argument. As usual, they mis-define IC and ID with the boilerplate definitions that these machines are so complex, their evolution is “unlikely.” The true ID definition
 is that irreducibly complex systems are “best explained by an intelligent cause, not an undirected process such as natural selection.” IC systems are composed of a number of independent parts, each necessary for the function of the system.

Even with their media advantage, the authors in Reference 3 admit, “the exact evolutionary relation between injectisomes and flagella is debated.” Species with supposed intermediate forms are proposed, but they look to me like broken T3SS or flagella, not machines evolving into each other. They wave the co-option argument and engage in possibility thinking, with 14 instances of the word “possible” to suggest what might be evolving.

Evolutionary Magic

Finally, they land on their trusty magic wand, convergent evolution: “Besides the general diversification of both systems, a case of convergent evolution of flagella and injectisomes was recently discovered.” Their final summary turns evolution into a magician, and personifies bacteria and molecular machines as if they take conscious charge of their own evolution:

Evolution allows adaptation of a functional concept to many different needs. In this review, we highlighted the amazing capability of the T3SS to vary its components, structure, and function to the specific requirements of bacteria in different ecological niches and under changing external conditions. Flagella not only ensure motility in a variety of environments, but also play an essential role in pathogenicity. By modifying their flagella, bacteria can find suitable colonization sites and enhance attachment to surfaces, which can increase infection success. In the same light, the injectisome permits the bacterium to exploit host cells for promoting infection, whether by controlling immune responses or establishing suitable sites for dissemination. Together these systems work to promote bacterial survival in constantly changing environments. Beyond these adaptations, it has become clear that the T3SS is a dynamic structure, with subunits exchanging in working complexes. Given the limited number of studies on protein exchange in the T3SS, it is possible that more cases of dynamic components will be discovered and that the benefits for the bacteria will become clearer. Research on how bacteria can adapt and evolve virulence mechanisms such as the T3SS will not only allow to better understand how bacteria and their environment interact, but also uncover potential ways to combat pathogenic bacteria by targeting their T3SS.

This is known as cheating. The whole point of Darwinian evolution was to rid biology of teleology. Irreducible complexity is ignored other than the one swipe at the straw man. Only once do they demonstrate loss of function from an essential part: “Although most flagellins are partially functionally redundant, deletions of additional flagellins negatively affects flagellar formation and function.” Nowhere do they point to random mutations able to innovate essential proteins to build a flagellum or T3SS in the first place.

Behind the one-way soundproof glass, Casey Luskin is waving his article (also here) on why these machines could not have evolved from one another, and Michael Behe is giving his debate rebuttal unheard by the audience. 

Censorship Is a Doomed Strategy

In my experience as a science writer, I have never in 22 years seen a Darwin-orthodox journal or science news site take ID arguments seriously. If mentioned at all, they are mis-defined and immediately dismissed. The science establishment, consisting of academic deans, lobbyists, and journal editors, pretty much treats the thriving ID community like it doesn’t exist. 

On the bright side, one can always tell who is on the wrong side of history. It’s the totalitarians — the ones who try to stifle debate and censor those not friendly to the regime. We can take heart that experience shows that Berlin walls are erected to fall. They have finite lifetimes. Not everyone in East Germany agreed with the regime, but they were powerless, and many were scared. If we stay the course, and continue to influence individuals, we will undoubtedly find many behind the Darwin Wall welcoming a path to freedom of thought.


Carbon :the Divine element?


Curiousity + Industry< IQ?


Future AI overlord vs. Titan.


The biggest and blackest hole yet?


Yet more on why no simple beginning


Monday, 8 May 2023

What is the biblical orthodoxy re: the only true God?


Darwinism vs. the history of life.

 A Question For Larry Moran


Recently Larry Moran, Professor in the Department of Biochemistry at the University of Toronto, asked for assistance. Professor Moran will be attending the upcoming “New trends in evolutionary biology” Scientific meeting at The Royal Society, and he has asked for help in deciding what question to pose to the speakers. For Douglas Futuyma, who will be defending the status quo against the scientific evidence, Moran already has a couple of ideas, such as:

As you explain in your textbook, describing the pathways to modern species contributes to the FACT of evolution and the FACT of descent with modification but how those genetic changes actually occur and become fixed is part of evolutionary theory. Do you distinguish between evolutionary theory and the actual history of life?

Moran, like Futuyma, defends the belief that the species arose by chance. As the all-caps help to illustrate, he is a modern-day Epicurean. And I’m sure Professor Moran would not disagree that this is a softball question—a setup for Futuyma to rail on those who think the scientific evidence is actually a problem for evolution. But Moran is mistaken here, as this is not a debate against creationists.

This line of defense—that scientific failures are relevant to the theory of evolution, but not to the fact of evolution—is standard theory protectionism, routinely used by evolutionists when they are presented with any of the many empirical problems with their Epicurean theory.

Not only is this argument a revealing own-goal (it provides a live demonstration that evolution is not exposed to the empirical evidence and is not falsifiable), but it is not relevant in The Royal Society meeting since the bad guys, in this case, are fellow evolutionists who simply are beginning to reckon with the science.

They completely agree that evolution is a fact. So Moran can set aside the silly canards about “the FACT of evolution and the FACT of descent with modification.”

On the other hand, Darwin’s God suggests a slightly different approach. If Moran wants to ask a meaningful question of Futuyma, why not query his fellow Epicurean where and how he discovered that “the Creator” would not likely have bestowed “two horns on the African rhinoceroses and only one on the Indian species.” That was, after all, one of Futuyma’s points in his book, Science on Trial.

And if there is time for a follow-up Moran might, as diplomatically as possible, ask the ardent evolutionist why anyone should take him seriously?

Nationalism, and evangelicalism's divided house..

 



Ps. John ch.18:36LSB"Jesus answered, “My kingdom is not of this world. If My kingdom were of this world, then My servants would be fighting so that I would not be delivered over to the Jews; but as it is, My kingdom is not from here.”

1Corinthians ch.2:6ESV"Yet among the mature we do impart wisdom, although it is not a wisdom of this age or of the rulers of this age, who are doomed to pass away. "

On the DEI Gordian knot.


Face to face with a monster.


A priest who honours his God.

 1Samuel ch.2:30ASV"Therefore JEHOVAH, the God of Israel, saith, I said indeed that thy house, and the house of thy father, should walk before me for ever: but now JEHOVAH saith, Be it far from me; for them that honor me I will honor, and they that despise me shall be lightly esteemed."  

The Christ being preached by Christendom seems to me to more closely resemble the Satan of the bible (see 2Corinthians11:14) than that loyal and submissive servant of JEHOVAH portrayed in Scripture. A "priest" who honors himself above his God like high priest Eli whom is rebuked by JEHOVAH in the above quote for permitting his sons to help themselves to the best part of the offering meant exclusively for the Lord JEHOVAH. The Lord JEHOVAH makes it clear in this quote that it is well beneath his dignity to receive any offering or countenance any mediation from such a "priest".

Only the true Christ(i.e the Christ of scripture) can mediate acceptably for our sins. In him JEHOVAH has provided a priest who honors his God and not himself.

1Samuel ch.2:35ESV"And I will raise up for myself a faithful priest, who shall do according to what is in my heart and in my mind. And I will build him a sure house, and he shall go in and out before my anointed forever."

 John ch.7:18ASV"He that speaketh from himself seeketh his own glory: but he that seeketh the glory of him that sent him, the same is true, and no unrighteousness is in him."

John ch.8:50ASV" But I seek not mine own glory: there is one that seeketh and judgeth."