ID Foundations, 8: Switcheroo — the error of asserting without adequate observational evidence that the design of life (from OOL on) is achievable by small, chance- driven, success- reinforced increments of complexity leading to the iconic tree of life

F/N: I have just now added illustrations and a video on the protein synthesis process (on p. 2), HT BA 77, UD News, UD Web master. KF. kairosfocus

F/N: I have just now added illustrations and a video on the protein synthesis process, HT BA 77, UD News, UD Web master. KF. kairosfocus

F/N 3: EA's discussion on IC and FSCI vs Avida here in response to Dr Liddle is well worth a read. kairosfocus

F/N: I have added comments above, (a) here in response to Dr Bot against Venter as providing proof of concept of the engineering design of cell based life and its components through lab methods, and (b) here in response to Dr Liddle (and KH) on "where are the gaps" and the like. The new layout makes it hard to follow sub threads and spot comments, so we eagerly await the chronological view modification. I also must note that it is just a tad frustrating to see direct evidence of failure to do basic due diligence on reading a post before commenting to object, and on similarly failing to do due diligence on what has been going on in nanotechnology over these 20 and more years, and why it is that Venter's work is so significant. GEM of TKI kairosfocus

Dr Liddle (and KH): It is a little hard to follow sub discussions on the new format, so responses will occasionally lag comments. (JC tells us it will take a while to program the requested viewing options feature. Does someone out there know of a WP plug-in that will do the trick?) On the main matter, the trade secret of paleontology and Cambrian revolution excerpts on p. 2 of the original post should make it clear that there is a major problem of a want of relevant branching in the fossil record; the only actual record of the remote past of life beyond written report, however we may date it. Those are facts, facts based on over 250,000 fossil species, millions of samples in museums, and billions in known fossil beds. The plain record is that the first time we see complex body plans, dozens at phylum and sub phylum levels, there are no credible antecedents and on the usual timeline there is a very narrow window in which they appear. This suddenness was known to Darwin, but he anticipated that extensive investigation would correct the gaps then apparent. The extensive investigations have been carried forth over 150 years, and the net result is that we are back at the same point of sudden appearance, stasis, disappearance and/or continuation into the modern world, with gaps at root, trunk and branch level in the tree of life. What the fossils overwhelmingly tell us about -- headlines, museum exhibits and textbooks with breezily confident declarations notwithstanding -- is what everyone agrees on: twig level minor adaptations. In addition, whether or not you are willing to accept it, the proposed darwinian means of generating variations, chance, is sharply challenged to cross config spaces to reach isolated islands of function. This starts with first life, and continues with major body plan innovations that require many co-ordinated changes to all be in place at once. (Cf no 3 in the series on IC and the co-option problem in light of constraints C1 - 5, as well as the Bartlett paper now linked top of this page). It is highly significant that the standard Darwinist response and tendency is to emphasise NATURAL SELECTION, rather than chance variation as the claimed engine by which innovations of function can happen incrementally. But this is misleading, usually inadvertently so. For, the "selection" part is a matter of destructive culling out, not actual addition of information. The fittest surviving is based on the less fit NOT surviving, i.e. certain variants disappear across time, whether at once or in the Malthusian "struggle for existence" that Darwin highlighted. Subtraction is not addition. So, necessarily, it is the chance variation that darwinian mechanism is relying on as the candidate to create: protein etc codes, regulatory code, co-ordinated development mechanisms that trigger at proper stages from zygote on, and more, all in data structures, and in body plans that must unfold in a precise and specific sequence with fatal error as a highly likely outcome if the precise unfolding for body plan formation [cf. addition on p. 2 of OP] is randomly varied. Chance plus trial and error in short. But we already know that complex and functionally specific configurations are rare and isolated in spaces of all possible configurations, as a general rule. As, your friendly local junkyard will tell you. Thus, there is a definite search-space traversal challenge in a context where isolated islands of function sit in seas of non-function, and the resources of the solar system will be overwhelmed at 500 bits, and those of the observed cosmos at 1,000. So, there is a particular burden of proof on advocates of darwinian mechanisms to demonstrate that he tree of life, at its main nodes, is well demonstrated empirically. The first body plan, i.e OO cell based life, is a particularly important point, as the OP highlights: no root, no shoots, no branches and so no tree. As p. 2 of the OP shows, this confronts us with the need to originate a vNSR, which is massively irreducibly complex and riddled with FSCI well beyond the 500 - 1,000 bit threshold. As the mutual ruin of Orgel and Shapiro, now backed up by Freeman's recent summary on the "mystery," the only reasonable candidate on the table for OOL is design. And, despite Dr BOT's strictures, Venter did provide proof of concept, and indeed, it is now 20 years since the underlying basic technical means and possibilities have been demonstrated. Worse, this is all in an observed cosmos that shows all sorts of signs of being finely tuned and set up for C-chemistry, aqueous medium, cell-based life. That is, we have strong reason to infer to design of the cosmos for life, and strong reason to infer to the design of life from the outset. That sharply shifts the balance of epistemological plausibility on the origin of body plans, and in particular the human body plan and the human mind and conscience. Design -- despite much hostility and many attempts to lock it out a priori, by the likes of Lewontin, Sagan, the US NAS, the US NSTA, the NCSE etc etc etc, and despite the way that politically correct thought police tactics have been resorted to to lock it out -- is a viable explanation, and on OO of cosmos and life, is arguably the best or only viable causal explanation. (Indeed, that is what best explains the a priori tactics being used to try to lock it out.) And, pardon directness: you plainly have not read p. 2 of the OP, BTW -- "I don’t see anything in the OP about “observed gaps”, apart from the well-known OOL gap." Finally, please explain to me what the Gould and Meyer excerpts on p 2 are about, if not observed and major fossil record "gaps." (And,the OOL gap you seem to wish to glide over as if it were insignificant is pivotal, as it drastically shifts the balance of epistemic plausibility in favour of design explanations, especially when joined to the cosmological evidence on fine tuning of our observed cosmos.) So, pardon if you find the above exchanges frustrating, but from my perspective, they do show the reasons for the sort of concerns and issues and gaps in addressing evidence on the table that I have pointed to. GEM of TKI kairosfocus

F/N: It's hard to follow the sub-threads, so when I spot something . . . Above it is claimed in effect that Venter was only rearranging the parts of already existing cell based self-replicating forms, so this cannot be proof of concept for the origin of said cells by engineering methods. This re-statement should be enough to show the fatal defect in the objection. For, we see from Venter that the COMPOSITION of DNA etc can be manipulated by engineering means. As the just linked CSM article summarises:

After almost 15 years of work and $40 million, a team of scientists at the J. Craig Venter Institute says they have succeeded in creating the first living organism with a completely synthetic genome. This advance could be proof that genomes designed in a computer and assembled in a lab can function in a donor cell, eventually reproducing fully functional living creatures, that is, artificial life. As described today in the journal Science, the study scientists constructed the genome of the bacterium Mycoplasma mycoides from more than 1,000 sections of preassembled units of DNA. Researchers then transplanted the artificially assembled genome into a M. capricolum cell that had been emptied of its own genome. Once the DNA "booted up," the bacteria began to function and reproduce in the same manner as naturally occurring M. mycoides. "It's a culmination of a series of impressive steps," Ron Weiss, an associate professor of biological engineering at MIT who was not associated with the study, told LiveScience.com. "If you look over the last few years, at what they've been able to produce, it's definitely impressive. Being able to create genomes of this scale? That's impressive." To boot up, the DNA utilized elements of the M. capricolum recipient cells, according to study team member Carole Lartigue of the Venter Institute. The bacterial cells still contained certain "machinery" that let them carry out the process of expressing a gene, or taking the genetic code and using it to build proteins – called transcription. When the artificial genome entered the cell, the cellular machines that run DNA transcription recognized the DNA, and began doing their job, Lartigue said. "This cell's lineage is the computer, it's not any other genetic code," said Daniel Gibson, lead author of the Science paper, also of Venter Institute.

So, we know that nanotech manipulation and composition methods exist and can be used in a molecular nanotech lab. This should be grounds for seeing that the same general sort of methods extend to the original composition of said components, modules and organised integrated frameworks in a cell. Indeed, we did not strictly NEED Venter -- or his Yeast cut and paste methods -- to see that manipulation of nanotech, atom level components by chemical and mechanical means is possible. It is over 20 years ago that the famous "IBM" made of 35 Xenon atoms on a substrate by means of a scanningt-tunnelling microscope, was published and blazed to the world as a picture. (Cf discussion and image here and timeline of achievements here.) In sum, it has been publicly and generally known for over 20 years, that atomic manipulation nanotechnology is possible, and indeed a field of research and applications has grown up across that time. What Venter has done, is to directly bshow that this new field of science and technology is relevant to the world of life, starting with the creation and modification of individual cells. And -- whatever selectively hyperskeptical objectors may want to declare dismissively -- that is indeed empirical proof of concept for the use of similar technologies as a SUFFICIENT cause of the origin of life. GEM of TKI kairosfocus

Elizabeth,

Starting with a minimally functional population of self-replicators in an environment, replicating with variance, adaptation will tend to occur, as we see both in the field and the lab, and in simulations like AVIDA.

What are these minimally functional self-replicators, and where are their populations? What sort of adaptations have been observed, not counting loss-of-function mutations? Statements such as that cited give the impression that the observation of adaptation beyond meaningless phenotypic changes that come and go have been observed, perhaps more than once. In reality they are more like bigfoot, but only if scientists owned stock in bigfoot and were trying to drive it up. ScottAndrews

Re KH:

how does “design” explain anything at all other then it allows you to say “the explanation for it’s origin is that it was designed”. It was designed because it appears to have been designed. It was designed because it shares features with other things that we know to be designed. But that’s not an “explanation” at all, it’s just changing the label.

1 --> Start from a basic reality: we ourselves are designers, and we produce artifacts that often show characteristic empirical signs of design. And it is patently a good explanation of the cause of a house, a house-fire [--> a highly significant case], a car, a pencil, a computer, a Stonehenge, etc to say: it was designed, per reliable signs manifest from the object and/or its traces itself. (BTW, have you looked up TRIZ, the theory of inventive problem solving, as already pointed to? Try here as a start. This suffices to show that how-to is a world of relevant study. That X was designed on empirically tested reliable signs opens up a world of reverse engineering and onward forward engineering methods. Contrary to ever so many glib and/or barbed talking points, such is a science-starter, not a science stopper. Indeed, historically, the designed world view of science was pivotal to the Scientific revolution from 1543 - 1700+. Cf. discussion here.] 2 --> So, design is a known causal factor, i.e something that initiates and/or sustains something else that had a beginning, in existence. All of this is or should be basic, even common sensical, but when a dominant ideology has been imposed in a community in the teeth of what is common sensical, it becomes necessary to clear the air on even basic points. Even in a world in which we are literally surrounded by designed artifacts, and see their characteristic signs almost every time we turn around. (I recall, this was the same problem in the heyday of Marxism.) 3 --> So, as a preliminary step, in Dembski's summary of design as causal process:

. . . (1) A designer conceives a purpose. (2) To accomplish that purpose, the designer forms a plan. (3) To execute the plan, the designer specifies building materials and assembly instructions. (4) Finally, the designer or some surrogate applies the assembly instructions to the building materials. (No Free Lunch, p. xi.)

4 --> It is also helpful to recall here the common definition of engineering that it [intelligently] uses the forces and materials of nature, through knowledge, skill, experience and imagination, to create desired and specified objects, processes, systems and networks, etc, economically, that are to serve the common good. (That last part is key to the ethical requisites of engineering praxis.) 5 --> We may directly observe engineering and design in action -- the stringing of chains of glyphs serving as digital symbols for meaningful sentences such as in blog comments will do for an example, and we have many other cases that are subject to record or are notorious, e.g. the remains of the works of classical civilisations. 6 --> A common feature of such is evidently purposeful arrangement of parts towards a plausible goal. Aqueducts convey water, computers process information based on symbols and physically implemented logical operators [typically, based on controlled switch circuits expressing NAND logic], and typed sentences communicate. 7 --> In some cases, chance and/or mechanical necessity -- two other known causal factors -- may plausibly give rise to phenomena that look like objects of design. Random production of texts is a case in point, i.e. it is possible to get short words and sentences or the like. 8 --> But, this soon runs into a barrier: want of search resources to plausibly get to sufficiently complex cases. As Wiki summarises on random text generation:

The [infinite monkeys] theorem concerns a thought experiment which cannot be fully carried out in practice, since it is predicted to require prohibitive amounts of time and resources. Nonetheless, it has inspired efforts in finite random text generation. One computer program run by Dan Oliver of Scottsdale, Arizona, according to an article in The New Yorker, came up with a result on August 4, 2004: After the group had worked for 42,162,500,000 billion billion monkey-years, one of the "monkeys" typed, “VALENTINE. Cease toIdor:eFLP0FRjWK78aXzVOwm)-‘;8.t" The first 19 letters of this sequence can be found in "The Two Gentlemen of Verona". Other teams have reproduced 18 characters from "Timon of Athens", 17 from "Troilus and Cressida", and 16 from "Richard II".[21] A website entitled The Monkey Shakespeare Simulator, launched on July 1, 2003, contained a Java applet that simulates a large population of monkeys typing randomly, with the stated intention of seeing how long it takes the virtual monkeys to produce a complete Shakespearean play from beginning to end. For example, it produced this partial line from Henry IV, Part 2, reporting that it took "2,737,850 million billion billion billion monkey-years" to reach 24 matching characters: RUMOUR. Open your ears; 9r"5j5&?OWTY Z0d...

9 --> This also shows that even when such cases occur, they have to be detected by a wider system, or they would be lost in a sea of gibberish, the TYPICAL product of random stringing of bits or ASCII characters. In short, we see here the point about the deep isolation in the space of possible configurations, of functional clusters. 10 --> In addition, we can see that spaces of order 10^50 have been successfully searched, but that underscores how the maximum reasonable Planck time, quantum state resources of the 10^57 atoms of our solar system are about 10^102, where even the fastest chemical reactions [ionic ones] take about 10^30 such P-times. Just 500 bits of binary digital places in a string structure, would have 3 * 10^150 possibilities, so the dedication of our solar system to search such a space, would be equivalent to drawing a 1- straw sized sample from a hay bale 3 1/2 light days across. A solar system could be lurking in there, but sampling theory would tell us that, overwhelmingly we would only detect a straw. 11 --> Extending to our observed cosmos -- what we are empirically warranted to discuss -- we have 10^80 or so atoms, and 1,000 bits of info carrying capacity would swamp the 10^150 PTQS resources, to 1 in 10^150. A one straw sized sample from such a haystack could have millions of universes the scope of our observed universe in it, and would still be only likely to pick up a straw. Reasonable sized, but small relative to population samples overwhelmingly tend to pick up the typical, not the atypical. 12 --> Just so, we now can see why one key sign of design is empirically reliable: complex specified information, especially in the form of functionally specific, complex information [and in particular, digitally coded information]. Once we pass a reasonable threshold of complexity, 500 - 1,000 bits, a blind chance and necessity search on the gamut of the observed solar system or cosmos, would overwhelmingly be likely to pick up gibberish or non-functional arrangements of components. (Using meshes of nodes and arcs and/or exploded views, we can convert a complex functionally organised structure into a wiring diagram, thence a structured set of yes-no questions, hence a specified number of bits adequate to give a functional specification. e.g. we could so reduce Mt Rushmore, noting that by contrast with say the former Old Man of the Mountain, the requirements of portraiture impose a tight specification that sharply constrains the number of acceptable configs.) 13 --> We also see here where the island of function in a sea of non-function imagery comes from: complexity and specificity sharply constrain the acceptable subset of the overall space of possibilities. When that complexity passes a threshold -- the solar system is our practical universe -- if a complex object is functionally specific or otherwise confined to a narrow zone of interest, we can be confident that an object with FSCI is designed, not just apparently designed. Statistical miracles of that order are operationally impossible. Indeed, that is the statistical foundation of the second law of thermodynamics. (Note Wiki's infinite monkeys discussion.) 14 --> This can be quantified, as was done here as a summary:

Chi_500 = I*S - 500, bits beyond the solar system threshold, where I is information measured in bits per the well known expression I = - log p or the like, and S is a dummy variable identifying whether or not the circumstance is specific. 73 ASCII characters in English is specific, a string of 500 coins that are tossed at random is not.

15 --> This criterion may be tested in a great many instances, and it will be shown reliable, Indeed the whole Internet, or just the above thread, are enough to show how well it works, and why. 16 --> In short, we have candidate causal explanations, and we have a criterion to objectively distinguish reliably, when chance and or necessity are not plausible relative to design. 17 --> Such a conclusion can then be reasonably extended to cases where we may only see the traces of the actual deep past cause, i.e effects that have endured to the present. 18 --> When that is done, it plainly indicates that C-chemistry, cell based life shows strong signs of design, e.g. just from DNA, which starts out at 100,000 - 1 mn and upwards of billions of bits of information. 19 --> That is itself highly significant, as it potentially revolutionises the institutional status quo on origins science. And, that explains easily the sort of controversies and selectively hyperskeptical objections and strawman objections such as has been cited in the clip being responded to. 20 --> It should be noted to KH, that inference to best, empirically and analytically anchored explanation is not a mere easily dismissed simplistic analogy. And, to set up and knock over such a strawman in the teeth of easily accessible evidence and reasoning to the contrary hardly commends the view being so advanced. (Cf. for instance, the ongoing UD ID Foundations series linked at the head of this post [link to be added as a line], and the IOSE summary page, here as well. Many other sources, including the weak argument correctives at the head of this and every UD page under the resources tab, etc, could and should have been properly consulted before tossing off the clipped argument.) GEM of TKI kairosfocus

Re Dr Liddle:

It is certainly true that we do not yet have a working model of how DNA-based life came to be, although there are plenty of theories, some of which are looking promising. But so far, not supported by persuasive empirical evidence. But then, nor is ID . . .

Actually, Venter's recent work provides proof of concept that shows that intelligent design of life is a sufficient cause of what we see in the living cell. Similarly, given the mutual ruin by Orgel and Shapiro as documented in the OP, blind chance and mechanical necessity, on genes first or metabolism first approaches, is definitely not "promising." (Given the political climate, any promising result would have been awarded a Nobel Prize and would certainly be blazed all across our headlines.) As UD News reminds us, Freeman Dyson has aptly summed up the dilemma for advocates of spontaneous abiogenesis in plausible pre-life contexts:

The origin of life is the deepest mystery in the whole of science. Many books and learned papers have been written about it, but it remains a mystery. There is an enormous gap between the simplest living cell and the most complicated naturally occurring mixture of nonliving chemicals. We have no idea when and how and where this gap was crossed. We only know that it was crossed somehow, either on Earth or on Mars or in some other place from which the ancestors of life on Earth might have come. - Freeman J. Dyson, A Many-Colored Glass: Reflections on the Place of Life in the Universe (Charlotteseville, VA: University of Virginia Press, 2010), 104.

In short, what is known is that once there was no cell based life, and now there is, but there is no credible naturalistic mechanism for OOL. And, yet, thanks to Venter et al, we have proof of concept in hand that intelligent design of the cell is a doable project. Beyond that, the cell is riddled with phenomena and objects that manifest signs that in our observation and on the infinite monkeys type analysis, reliably point to design. Phenomena like digitally coded, functionally specific info beyond the plausible reach of chance and/or necessity on the gamut of the observed cosmos, the presence of coded algorithms and data structures with executing machines, and the like, including a von Neumann self-replicating, code based mechanism. But, design of cell based life is so alien to the mindset of dominant scientific elites today that they will do almost anything rather than seriously discuss such a prospect. As the OP clip from Lewontin shows, and further links highlight that this sort of thinking dominates the US NAS, NSTA, etc. That -- usually implicit -- a priori commitment to materialism and so also to naturalistic explanation by the relevant elites is a part of why it is increasingly obvious that the real issue is not the status of evidence and reasoning on it, but, sadly, prior worldview level ideological commitment and, frankly, indoctrination, by the said elites and their promoters. When it comes to the scientific or epistemic warrant status of the design inference, the start point is that we ourselves are designers, and we have a world full of artifacts that manifest the signs of design. Once such signs show themselves empirically reliable in cases we know directly, we have every reason to trust their reliability until shown otherwise in cases we do not have the opportunity to observe directly. Indeed, this is the premise of many serious areas of praxis, in origins science and studies of the deep past, in forensics, and in day to day life. So strong is this that it is patently selective hyperskepticism -- a fallacy -- to impose a sudden dispute when the results of an inference to best explanation on traces in the present and known causal forces sufficient to cause said patterns, do not lead where elites are willing to go. To infer that life is the product of design and manifests strong signs of being designed, after all, would be no more than the basic view of the co-founder of the modern theory of evolution took, Wallace. For, he titled his book on the subject:

The World of Life: a manifestation of Creative Power, Directive Mind and Ultimate Purpose

On what sound grounds is it to be regarded as unscientific, or "giving up" on science, to use scientific methods to infer inductively by abduction that, per reliable sign, a known sufficient causal factor is responsible for an object, process or phenomenon that shows characteristic signs of said factor? GEM of TKI kairosfocus

Well, not in my view, Eugene :) Elizabeth Liddle

"It was designed because it shares features with other things that we know to be designed." Well, it is something already. Also, it depends what features we talk about. Some of them may be pretty convincing unless one wishes to remain prejudiced. To me, it has a lot more weight than simply asserting that complexity can emerge by itself and that everything came about by fluke. Eugene S

14.1.1.2.34 "Please don’t be so quick to assume that the logical fallacies are on the other side :)" One does not have to assume that, Elizabeth. It is, in fact, the case. Eugene S

Yes, always. ScottAndrews

OK, well, we'll leave it at that. It is certainly true that we do not yet have a working model of how DNA-based life came to be, although there are plenty of theories, some of which are looking promising. But so far, not supported by persuasive empirical evidence. But then, nor is ID :) In fact I'm not sure what it's supposed to be "supported" by, at all. But that seems a reasonable place to leave things - nice to talk to you! Cheers Lizzie Elizabeth Liddle

Elizabeth,

True, I don’t know that it wasn’t, Scott. But can you provide me with one iota of evidence that it was?

I'm reasonable about the weight of the ID inference. But if it's anything, it's an iota. Nonetheless, to trace such a remarkable, self-replicating entity as a cell back to a manufacturing process which in turn traces back to what sure resembles symbolic codes - that bears a remarkable resemblance to the processes long employed by intelligent agents who have never even heard of DNA. I'm not even mentioning the functions within those cells, or all the other cool stuff you can make out of them. So let's call that two iotas. That makes it the most well-supported theory by two iotas. ScottAndrews

Oh, it probably was arbitrary, Scott. I am sure that a different set of tRNA molecules would have worked just as well - the important thing is that there is only one type per codon, which having a reproductive advantage, would tend to evolve. The relevant part of my sentence, oddly, which was the part about "agreed by the community of code-sharers". True, I don't know that it wasn't, Scott. But can you provide me with one iota of evidence that it was? It's not me who is "question-begging" here! You can't infer intelligent input by hypothesising intelligent input! Please don't be so quick to assume that the logical fallacies are on the other side :) Elizabeth Liddle

Elizabeth, But this is just one more.

Once you drop the requirement that the assignment of symbol to referent is an arbitrary one agreed by the community of code-sharers, which you have to do to include DNA

First you are assuming that the assignment of symbol was not arbitrary. How do you know this? Us ID folks are constantly reminded that neither OOL nor evolution searches for a specific target. But now you are saying the very opposite, that if it were designed then only these precise symbols could be used. The integrated circuits within my Pentium processor will only accept highly specified combinations of symbols as instructions. You could argue then that the symbols are not arbitrary, because only certain ones will initiate the right reaction. But in reality the symbols, the medium, and the processor were all designed to function together. That is precisely what makes their arrangement so intelligent. You are asserting that this could not be the case with DNA. Support it. If these symbols could not be arbitrary then what other elements of life would you like to identify which necessarily conform to the exact pattern we observe and could not have occurred any other way, and what impact does that have on the probability of life arising by chance?

agreed by the community of code-sharers

And this is blatant question-begging. DNA is not a symbol because it was not agreed to by a community of code-sharers. And you know this how? You have contradicted your own logic, made assumptions without supporting them, and begged the question. Blow - poof! ScottAndrews

I’ve lost count of how many arguments you’ve made attempting to distinguish DNA from symbolic code, and each disintegrates if you blow on it.

Well, not in my view, Scott. You seem to be missing my point every time! That's why I've tried presenting you with the consequences of your (in my view metaphorical) use of the word code. In order to define "code" or "symbol" in a way that includes DNA, you have to drop the very property gives you the inference you want! Once you drop the requirement that the assignment of symbol to referent is an arbitrary one agreed by the community of code-sharers, which you have to do to include DNA, then you no longer have any case for saying that therefore the code must have been designed! I am using the words in the standard semiotic senses. If we drop the semiotics, you also lose your inference. Take your pick :) Elizabeth Liddle

Darn. Let me repost this part:

Moreover, the DNA molecule itself, or its sequence, without the cell it normally inhabits, does not represent the organism it belongs to, in any sense.

The code to Windows 7 tapped out in morse code doesn’t do me any good without a computer. Again, what distinction are you making? ScottAndrews

Elizabeth,

Without an actual DNA molecule, nothing will happen. Writing “CAG” on a piece of paper won’t give you a glutamine molecule, no matter how many molecules of ink you use. Writing "horse" on a piece of paper doesn't give me horse, either. What distinction are you making?

All jackasses have long ears. He is a jackass. Therefore, he has long ears. In other words, it’s fallacious.

The code to Windows 7 tapped out in morse code doesn't do me any good without a computer. Again, what distinction are you making?

All jackasses have long ears. He is a jackass. Therefore, he has long ears. In other words, it’s fallacious.

It wouldn't be fallacious if every available definition of jackass was "a thing with long ears." And if someone picked a thing with long ears and started making up arbitrary, meaningless reasons why it wasn't a jackass, one would have to wonder what they have invested in it not being a jackass.

human codes involve the agreed assignations of symbols to referents by a group of code users, as well as the fact that those symbols are not themselves instrumental in rendering their meaning.

You're begging the question. (It was only a matter of time.) How do you know whether a group of code users didn't do just that?

the fact that those symbols are not themselves instrumental in rendering their meaning.

My Pentium interprets a certain set of symbols as a specific instruction. Those symbols initiate electronic reactions. One could make the exact same case that those symbols are instrumental in rendering their meaning. I've lost count of how many arguments you've made attempting to distinguish DNA from symbolic code, and each disintegrates if you blow on it. I haven't even pointed out anything you didn't already know. You're repeatedly making arguments that contradict your own knowledge. You do not appear to be reasoning on these things, applying what you already know. That it why I say it is irrational.

ScottAndrews

He = a human being. Sorry that wasn't clear! (Though it's an old chestnut). The point being that taking a generalisation about something that is true, then concluding that when you use that something as a metaphor the generalisation also applies, is fallacious. My favorite is the politician's one that goes: Something must be done This is something Therefore this must be done. All too true, unfortunately. Elizabeth Liddle

Just a comment on board mechanics. UD now has threaded comments, so it makes no sense to edit someone else's post in order to reply. I assume this is a habit left over from the previous board software. Petrushka

All jackasses have long ears. He is a jackass. Therefore, he has long ears. In other words, it’s fallacious.

Shouldn't that be: All jackasses have long ears. He has long ears. Therefore, he is a jackass. Perhaps you have an inability to commit fallacy. Petrushka

Yes, you can represent codons symbolically. That doesn't make codons symbols though! And, when rendered as alphabetic letters, they are incapable of making proteins or RNA molecules. Moreover, the DNA molecule itself, or its sequence, without the cell it normally inhabits, does not represent the organism it belongs to, in any sense. Did you watch that wonderful Denis Noble lecture? And you are completely missing my point about the molecules. Most symbols are made of molecules. Some aren't - some are patterns of energy, for instance auditory symbols like words. But that's beside the point - the point is that it isn't at the molecule level that the meaning is carried. This is not the case with DNA. Without an actual DNA molecule, nothing will happen. Writing "CAG" on a piece of paper won't give you a glutamine molecule, no matter how many molecules of ink you use. But nonetheless, you can call it a "code" or a "symbol" if you want to. But in that case, don't go saying - see, it's a code! And we know that codes (in the normal usage) are made by minds! Therefore DNA was made by a mind! That's equivocation! It's tantamount to saying: All jackasses have long ears. He is a jackass. Therefore, he has long ears. In other words, it's fallacious. Yes, the DNA sequence has something in common with human codes. It also has a great deal that is different, not least being the fact that human codes involve the agreed assignations of symbols to referents by a group of code users, as well as the fact that those symbols are not themselves instrumental in rendering their meaning. Elizabeth Liddle

Elizabeth, I'll expand on this:

But again, those symbols are assigned by minds, then read off by minds

Do you know how many messages and signals encoded in symbols are being passed back and forth within your computer right now? Or how many are traded back and forth between your computer and various servers on the internet? There are components between your computer and those servers that are sending each other messages to help them send and receive your messages. What mind is reading these off? Yes, the origin is a mind. That is why we infer that other such meaningful arrangements of symbols likely also are. But what mind is reading them? None. They are set in motion to communicate with one another. Factoring out the unknown origin, what is the logical inconsistency between such processes and the what occurs when cells reproduce? If the information in DNA were deliberately arranged and the processes for transcribing them designed, this would be entirely consistent with the known intelligent pattern of designing systems that use symbols for internal communication. (And, as previously stated, if they were not arranged and designed then they would be consistent with absolutely nothing.) Why would you even suggest that symbols must be processed by a mind? ScottAndrews

Elizabeth,

Well, I’m just using it as usually used – some kind of representation, that can be in any medium

You make this distinction as if the contents of DNA cannot be in any other medium. They already are. A, G, C, and T are popular. When biologists map genes, how do they store the data? In more DNA molecules? They use a computer. They could write it on paper. They could use morse code if they wanted to.

That doesn’t seem to me to include molecules at all.

I don't know of any medium that doesn't include molecules. You're making an arbitrary determination about what can be a medium. Bytes, yes. Symbols on paper, yes. Hand-clapping modulated as morse code, yes. A specific facial expression, yes. A sequence of molecules, no. I'm sorry but you're just making that up. The point is that symbols and language are known implements of intelligence. The ability to use language is sometimes used as an indicator of intelligence. In contrast, there are no known instances of languages or symbols arising apart from intelligent purpose. I'll posit that it is unimaginable. Prove me wrong. Show that you or anyone else can even imagine it in any amount of detail without using the word "somehow." The arrangements of DNA are clearly not random, as the results of their transcription are not random. That such a code of unknown origin was also purposefully designed is a valid inference. And it's the only conclusion with any connection whatsoever to observed reality. Given that, I'd guess in this order: 1) It was designed 2) Its origin is an absolute mystery 3) Yes is no and true is false 3) It emerged naturally from something which had no use for it because inanimate things have no use for anything. (The last two are neck-in-neck.) ScottAndrews

Well, I'm just using it as usually used - some kind of representation, that can be in any medium, that has a referent agreed by all the people who use it. That doesn't seem to me to include molecules at all. But as I said, let's nonetheless accept your usage: what point are you making? Elizabeth Liddle

Elizabeth,

I think it’s a huge stretch, because a molecule takes part in the in the process of “translation”

Then we're back to the demarcation problem (or, rather, you are.) Define "symbols" in a manner which includes all known means of information processing but excludes this specific means of processing. The definition cannot include an assumption regarding whether it was designed. ScottAndrews

OK (well, as I say, I think it's a huge stretch, because a molecule takes part in the in the process of "translation" - acts as a template for instance, while a picture of a dog doesn't, which seems to me to be rather an important difference) - that's fine as far as it goes, but I meant, what part of your ID argument does your identification of codons as symbols form? Or are we just arguing nomenclature because we are both pedants :)? Elizabeth Liddle

Elizabeth,

What exactly are you inferring from your identification of codons as symbols?

I am inferring that rather than storing miniature representations of finished products, the needed data has altered and compressed to a form that better suits the purpose of both storage and transcription, but which no longer bears a resemblance to what it represents. That is the essence of language. I can say "dog," which is easy, instead of drawing a picture of a dog or producing an actual dog. I can also produce a fully detailed description of a dog in the form of its DNA, which again is easier to transport and transcribe than an actual dog, and does not even resemble one. Compare that to a book about dogs and a book about ships. How do you tell which is which? By which one looks more like a book and which one smells like a dog? No, the books look more like each other. If you don't read the language, you cannot even distinguish them. The same could be said of spoken words. You would have a point if the medium and elements for representing a dog were different than those for tulips. But the same medium and processes are used in both cases. Like it or not, that's a language. Whether we are writing about dogs or tulips we use the same letters and most of the same words. It's not the reactions that make them symbols. It's their consistent reuse to describe varying things. ScottAndrews

For the sake of honesty, let me add that both D and E may also be coupled with a desire for them to be true or such an ingrained belief. A person may possess the reason, the desire, the belief, or any combination of them. But, unlike A, B, and C, there is the option of relating back to some observed realities. Perhaps that relation is tenuous. You may feel that it is weak. But is something to logic can be anchored, whether or not the conclusion is correct. There is neither logic nor reason to which one can anchor A, B, or C. You may reason that A, B, and C are strawman arguments. They are not. They are summaries of actual arguments. If the summaries seem non-specific, it is exactly because they correspond to what they summarize. ScottAndrews

Scott, you keep missing my point. Let't try another tack: What exactly are you inferring from your identification of codons as symbols? Elizabeth Liddle

Elizabeth, This sums up the disconnect.

If you regard as a “symbol” the molecular output of a cascade of chemical reactions triggered by a molecular input,

The symbols are the inputs, first, and then the outputs. Unless you can explain how a system can output symbols that somehow can be used as inputs to recreate itself.

in response to the chemical environment in which the cell is placed, are synthesised in a sequence and manner that generates, maintains, and causes to function, a self-replicating organism.

What an amazing coincidence! There is no "meaining" in DNA, it just so happens that under the right circumstance it becomes an integral component in the manufacture of a living cell. If there is no meaning in DNA, then how did it come to be in a sequence that just happens to be transcribable into components of a living cell? Ever explanation you offer boils down to, 'how convenient.' That brings us back to the central issue. You're focused on the chemical reactions that depend on these sequences of molecules to output life. You ignore the question of how those molecules came to be so arranged. I propose intent. You propose that they simply came to be arranged. My explanation is rather non-specific. Yours is rather non-existent. I am not stretching the meaning of "symbol" to include DNA molecules. You are contracting and contorting it to exclude them. You now face a demarcation problem. Figure out how to exclude DNA while including half of computer science without begging the question. (For anyone unfamiliar with a demarcation problem, it's this: How do I define music to exclude "rap" without unintentionally excluding something I really do think is music, like a drum solo? I can't. Sometimes using words as placeholders for concepts works. Sometimes is doesn't. And sometimes it reveals that our thoughts are subjective, not objective. We have decided in advance what should or should not fit, and we are working backwards from it. It amounts to, 'Rap isn't music because I don't want it to be,' which in my case is true. Or, 'DNA molecules are not symbols because I do not want them to be.') We don't have a videotape of what happened. We must conclude: A) The egg 'somehow' arranged itself from nothing, not having any foreknowledge of a chicken but somehow producing one anyway. B) The chicken 'somehow' arranged itself from nothing, not having any foreknowledge of its own need to reproduce or knowledge of molecular biology, but somehow quickly invented eggs. C) A and B happened in one step. D) The egg was deliberately arranged with the intent of producing a chicken. E) Both the chicken and its ability to reproduce were deliberately arranged with the intent of producing and reproducing chickens. To avoid offending you, I will use less rhetorical language. Given the sum total of human observation and current accumulation of scientific knowledge, A, B, and C are irrational. There is no logic or reason that leads to those conclusions. There is, at most, a desire for them to be true, or perhaps an ingrained belief that they must be true. D and E require further explanation. But they are the very least not inconsistent with the current state of knowledge. They do correlate to observed realities. They are rational and reasonable. In the context of A, B, and C, DNA molecules are not symbols, according to your definition. In the context of D and E, they are, according to most any definition. ScottAndrews

Already answered, above. Onlookers, note as well the remarks of Gould (cf. p. 2 of OP) on the state of the fossil evidence -- the only direct evidence of the world in the past. Also, Meyer on the Cambrian Revolution. it is obviously not very politically correct to says such, but it is evident that the proposed Darwinian mechanisms -- chance variation and culling out on trial and error and success in niches, etc -- are grossly inadequate to account for major body plans. Mechanisms that can address micro-level adaptation within a body plan [e.g. dogs and wolves, red deer vs North American Elks, interbreeding finch varieties in the Galapagos that have different beaks etc], have been extrapolated on a priorism that imposes non-design answers before the evidence can speak. And yet the FSCI in life, from OOL on, is telling us strongly that the only known source of such is design. The whole scheme of origins science needs to be rethought. kairosfocus

I agree with KF that failure to see objective signs of design in one particular type of objects as opposed to others where design inference is accepted, is exposing a huge ideological bias. This has nothing to do with science. Eugene S

Genetic Algorithms are not hill climbing algorithms. Saying that you are using it in a particular context is a poor excuse for using incorrect terminology. Start by using the correct terminology, then you won't have a problem!

The key take-home lesson is that there simply is no solid empirical foundation for the claim of Darwinian incrementalism on chance variation plus success based domination of eco-niches, as accounting for body plans and the grand branching tree of life.

LOL, apart from all the evidence of course ;) DrBot

Elizabeth, I repeat, not all symbols are intended for human interpretation. We also use them to make machines and computer do what we want them to.

At which point they are not serving as symbols, unless you stretch the meaning of "symbol" so far as to render it unable to take the weight of the argument placed on it. If you regard as a "symbol" the molecular output of a cascade of chemical reactions triggered by a molecular input, then there is no difficulty in accounting for this in terms of simple chemistry, therefore no problem for a materialist account of such a process.

By saying that these particular symbols (or whatever you wish to call them) were not arranged by minds is begging the question. I will beat the poor, dead horse. You can choose to view DNA molecules and proteins as different ends of a chemical reaction. But as I said, there are plenty of automated systems in which electrical impulses are passed back and forth that in turn produce specific reactions.

OK. In that case, what is your point?

To say that just any chain of reactions is necessarily deliberate would be absurd. But when that chain of reactions begins with a fixed set of molecules which can be transcribed to produce and assemble functional components, they evidently do have meaning.

Well, they evidently do result in an assembly that effectively reproduces itself. Calling that "meaning" is, as with "symbol" to stretch the term beyond its capacity to bear your argument. That the cascade results in an entity capable of effective self-replication is not in dispute, and is precisely the reason we have to hand an explanation, namely Darwin's, for the cascade - because cascades that tend to result in a self-replicatively efficient entity will be reproduced, by definition, more often than those that don't.

Here’s a really simple way of looking at it. DNA nucleotides are small, and, by themselves, completely useless. And yet they contain patterns that correspond, somehow, to entire functional living things. (For the sake of argument I struggle not to employ the obvious teleological language.)

No, the patterns don't "correspond, somehow, to entire functional living things". I suggest you listen to this fascinating lecture: http://videolectures.net/eccs07_noble_psb/ Denis Noble has also written a book, but the content of the book is contained in the lecture, so that will save you the trouble of getting the book! A DNA molecule is just a molecule. However, in the context of a cell, it forms a database, which evolutionary biologists would argue has been accumulated over billions of years of evolution, of proteins and other molecules that, in response to the chemical environment in which the cell is placed, are synthesised in a sequence and manner that generates, maintains, and causes to function, a self-replicating organism. The molecule doesn't "represent" a human being, nor yet "correspond" to one, and it certainly can't "create" one. Nor would an alien who came across a notated genome, even if they understood the nucleotides represented by each symbol, be able to retrieve the organism from which it was sequenced.

But when you examine these elements closely, you do not see a miniature version of the corresponding person or animal. Instead, you see patterns consisting of a limited set of molecules. And it doesn’t just mirror the physical elements of the person or thing. It corresponds to all of the states through which it will pass from conception onward and all of the processes which will execute within it.

Well, no, it doesn't. From the DNA molecule you simply cannot read off, not even in principle, "all the states through which [an organism] will pass from conception onwards". Those states depend on a huge amount of additional inputs that are not specified in the DNA.

You can call that series of molecules whatever you want. You can call the process that leads from those molecules to the finished product whatever you want. You can say that a thing only has the appearance of being designed. But to say that patterns of molecules that function like a symbols in a code only appear to be symbols in a code, and then come up with new definitions of “code” and “symbol” that exclude them?

I'm not coming up with a "new definition" of "symbol" (I'm happy to use the word "code" although according to some definitons of "code" DNA is not a "code"). I'm balking at stretching the word to cover something that it does not normally cover, and, if it is stretched to cover it, no longer makes the point you seem to want to make. But for the sake of argument, let's call any molecular entity that forms part of a chemical cascade in which the output molecule is more than one step away from the input molecule a "symbol", if, and only if, the resulting output molecule serves some "function". Right. What do we mean by "function" in the case of a living thing? Well, we seem to mean: causes the entity of which it forms a part to persist over time and/or cause it to self-replicate. OK? So why does such a thing have to have been "designed"? Now we've stretched the meaning of "symbol" so far as to cover a self-perpetuating system, where is the Intelligent Design argument?

Find a definition of “code” that includes the word “mind.” Even the crazy Wikipedia people see it. This is DNA which contains units named genes that can produce proteins through a code (genetic code) in which a series of triplets {codons} of four possible nucleotides are translated into one of twenty possible amino acids. A sequence of codons results in a corresponding sequence of amino acids that form a protein. A symbol is something which represents an idea, a physical entity or a process but is distinct from it. This is DNA which contains units named genes that can produce proteins through a code (genetic code) in which a series of triplets {codons} of four possible nucleotides are translated into one of twenty possible amino acids. A sequence of codons results in a corresponding sequence of amino acids that form a protein. In the genetic code, a stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.

As I said, I'm happy to use the word code in regard to DNA, as long as there is then no equivocation with uses of the word in contexts where it is defined in such a way that excludes DNA (and there are). But the word symbol, as you define it above, does not seem to me to cover either DNA or codons, at least not without gross stretching.

They are a symbols forming a code which is translated, and signals to distinguish between messaging units. “atg act cac cga gcg cga agc tga tac tga gtg gct cgc gct tcg act…” in, sand dollars and tulips out. It takes layer upon layer of insulation to protect oneself from knowing it.

Your final sentence is uncivil and unwarranted. Scott: you may use the words as you like; what you may not do, in a rational argument, is use a stretched definition in one part of your argument, then equivocate with that definition in another part. If you want to use the words "code" and "symbol" and "meaning" and "represent" and "correspond" to describe biochemical cascades, fine. But you are not then entitled to use the hoary old chestnut of an argument that "only minds produce codes, therefore DNA was produced by a mind". Right? Elizabeth Liddle

F/N: One of the real problems withthe new format at UD is the lack of a chronological sequence view. That has been requested but we have been informed that will take a fair bit of programming and will not be here in a hurry. So, let us be patient, we are not going to spot comments buried deep in long threads, unless there is a comment at the end that it is there above. (I saw the above comment by accident as I was about to close this tab.) kairosfocus

Dr Bot: Did you see my remark above on context, rooted in Dawkins' Mt Improbable etc and going back over years of discussion? The general context of discussion on GA's etc is that they climb upwards in value on fitness functions. there may be glitches along the way and getting stuck at local but not global maxima or run into saddles, etc etc, but that does not change the material point or context. Please note, that context was set from the opening paragraph of the OP. All of this side tracking is simply distractive. The key take-home lesson is that there simply is no solid empirical foundation for the claim of Darwinian incrementalism on chance variation plus success based domination of eco-niches, as accounting for body plans and the grand branching tree of life. That has been clear for several days now, and well past both 1,000 views and 100 comments. The Darwinian Tree of Life model is groundless, and -- taking in OOL -- rootless. GEM of TKI kairosfocus

Judge not, that ye be not judged. For with what judgment ye judge, ye shall be judged: and with what measure ye mete, it shall be measured to you again. And why beholdest thou the mote that is in thy brother's eye, but considerest not the beam that is in thine own eye? Or how wilt thou say to thy brother, Let me pull out the mote out of thine eye; and, behold, a beam is in thine own eye? Thou hypocrite, first cast out the beam out of thine own eye; and then shalt thou see clearly to cast out the mote out of thy brother's eye. ED: Dr BOT, do you want me to cite Shakespeare on who often quotes scripture? In the context where one has a responsible position -- start with parents and their children, one must and is responsible to judge. In short, again, there is an issue of context here. And, yes, you have now crossed the same threshold KH did. Please take some time to think again. DrBot

Dr BOT: Pardon, but you need to pause and rethink both substance and tone just above. In particular, I have made no personal attacks, though I did use a correct descriptive term for the sort of remarks that tried to put in my mouth a rejection of "continental drift" and the like. Corrective description is not personal attack, and has never been. KH reached a point of snideness, where -- in my considered judgement -- I found it appropriate to respond by making my comments directly beneath his/hers; including by referring him to a post at UD and what is in effect a course unit elsewhere that anticipates his/her objections. (It is quite clear where his/her comment ends and mine in response begins.) That is not "defacement." (In particular, I have made no changes to his/her actual remarks, I simply put my responses directly below, once s/he had refused to heed a corrective.) You may not like it, but it is well-merited correction. Your own “shame on you” is out of order, sir. You will further see that I have addressed his and other arguments on the merits, right from the OP on; though in this case hampered by the exigencies of travel and its aftermath. I do not find your remarks just above in much better tone at this point. Please, think again. Good day GEM of TKI kairosfocus

I do not appreciate the distraction and piling on tactic. This is something that is simple and that is easy to understand. At least, until it was turned into a neat talking point to strawmannise. I am decidedly not amused.

KF WHY do you keep launching personal attacks against people asking you for clarification or evidence on the topic under discussion? WHY can't you just respond to arguments on their merits? Cultivating offense at people who disagree with you just makes it look like you have nothing substantial to say in response to the point under discussion, it just serves to poison the atmosphere. The fact that people are disagreeing with your arguments is not because they want to attack you personally, and disagreeing with you is not a personal attack, despite what you have said in the past about this! People like me, EL etc are disagreeing with you because your arguments are unconvincing. Get over yourself and deal with it! DrBot

This is why I have been quite annoyed at the rhetorical talking point that GA’s do not use hill-climbing that appears above in this thread.

Why don't you start with the wikipedia page on hill climbing algorithms. This is not a rhetorical distinction - it is an important distinction that defines what the algorithm does, and does not, as compared to a GA. I'm afraid you cannot just re-write these distinctions to suit yourself. You need to acquire a proper understanding of these algorithms and the technical language that scientists use to distinguish them if you want to engage in a rational debate about them with me. I have taught aspects of this at University and if a student used terminology the same way you do I would correct them - because it is wrong! GA's don't just climb hills, they navigate very complex multidimensional fitness surfaces. They go up and down, traverse valleys and neutral plains. All things that hill climbing algorithms find hard. DrBot

KF, Please, lay off the dismissive, grossly exaggerated generalities that play off strawman dismissals and address the substantial issues on the table. You are now even editing other peoples comments to add in your own personal attacks. You are the one having problems with their tone. Please address peoples arguments on their merits rather than just dismissing them with rhetoric and defacing their posts. Shame on you. DrBot

F/N; Updates added on p1 -- a "typical" fitness function illustrated as a mesh, and on p 2 -- the Hox genes in body plan development at Sci Daily. kairosfocus

KH: Please, lay off the dismissive, grossly exaggerated generalities that play off strawman dismissals and address the substantial issues on the table. (And that is again a big slice of your tone problem.) The just above in light of the OP should be a good start, if you need a fresh start. GEM of TKI kairosfocus

F/N: On Climbing "Mt Improbable," Dawkinsian hill climbing and GA's Wiki notes on Dawkins' 1996 book:

Climbing Mount Improbable is a 1996 popular science book by Richard Dawkins. The book is about probability and how it applies to the theory of evolution, and specifically is designed to debunk claims by creationists about the probability of naturalistic mechanisms like natural selection. The main metaphorical treatment is of a geographical landscape, upon which evolution can only ascend in a gradual way, not being able to climb cliffs (this is known as an adaptive landscape). In the book he gives various ideas about a seemingly complex mechanism coming about from many different gradual steps, that were previously unseen . . .

This of course builds on his infamous Weasel, of 1986 that introduced the notion of "cumulative selection." It is also closely related to the way GA's are designed and are presented as mimics of "evolution." Namely, per Wiki again:

In a genetic algorithm, a population of strings (called chromosomes or the genotype of the genome), which encode candidate solutions (called individuals, creatures, or phenotypes) to an optimization problem, evolves toward better solutions. Traditionally, solutions are represented in binary as strings of 0s and 1s, but other encodings are also possible. The evolution usually starts from a population of randomly generated individuals and happens in generations. In each generation, the fitness of every individual in the population is evaluated, multiple individuals are stochastically selected from the current population (based on their fitness), and modified (recombined and possibly randomly mutated) to form a new population. The new population is then used in the next iteration of the algorithm. Commonly, the algorithm terminates when either a maximum number of generations has been produced, or a satisfactory fitness level has been reached for the population.

In that light, we should also note the way Wiki describes varieties of the more specific, narrow-sense computer Science Hill-Climbing algorithms (as linked from the Original Post, 1st paragraph):

In computer science, hill climbing is a mathematical optimization technique which belongs to the family of local search. It is an iterative algorithm that starts with an arbitrary solution to a problem, then attempts to find a better solution by incrementally changing a single element of the solution. If the change produces a better solution, an incremental change is made to the new solution, repeating until no further improvements can be found . . . . In simple hill climbing, the first closer node is chosen, whereas in steepest ascent hill climbing all successors are compared and the closest to the solution is chosen. Both forms fail if there is no closer node, which may happen if there are local maxima in the search space which are not solutions. Steepest ascent hill climbing is similar to best-first search, which tries all possible extensions of the current path instead of only one. Stochastic hill climbing does not examine all neighbors before deciding how to move. Rather, it selects a neighbor at random, and decides (based on the amount of improvement in that neighbor) whether to move to that neighbor or to examine another. Random-restart hill climbing is a meta-algorithm built on top of the hill climbing algorithm. It is also known as Shotgun hill climbing. It iteratively does hill-climbing, each time with a random initial condition x0. The best xm is kept: if a new run of hill climbing produces a better xm than the stored state, it replaces the stored state. Random-restart hill climbing is a surprisingly effective algorithm in many cases. It turns out that it is often better to spend CPU time exploring the space, than carefully optimizing from an initial condition. [ --> This is of course connected to the novelty search idea in the OP]

In this light -- given the context of the OP that begins:

Ever since Dawkins’ Mt Improbable analogy, a common argument of design objectors has been that such complex designs as we see in life forms can “easily” be achieved incrementally, by steps within plausible reach of chance processes, that are then stamped in by success, i.e. by hill-climbing. Success, measured by reproductive advantage and what used to be called “survival of the fittest.” Weasel’s “cumulative selection” algorithm was the classic — and deeply flawed, even outright misleading — illustration . . .

-- it should have been quite clear from the outset just what context of "hill Climbing" was being used; a quite broad one that includes but is not limited tot he more narrow sense. This is why I have been quite annoyed at the rhetorical talking point that GA's do not use hill-climbing that appears above in this thread. The plain answer is that hey are ascending the slopes of a fitness landscape, using methods that do climb hills, similar to Dawkins' general notions presented in his 1986 and 1996 works under the themes "Weasel" and Mt Improbable." So, simple reading in context with a reasonable attitude would have shown that he issue is a mole-hill not a mountain. I trust that further discussions by objectors will now cease from the distractive strawman and piling on tactics that appear above. The further key point, is that the crucial issue is not adaptation within islands of function, but the arrival at the shorelines of islands of function. The objectors above have acknowledged explicitly -- indeed,they seem to say they were in effect insisting on it all along -- that GA's operate within continuous, trendy hill-range like domains. The current biggie objections are, first, that evolution is not about origin of life. To which, I reply: tell that to the zoo and museum staff, the artists and scientists preparing tree of life diagrams, the textbook [including college textbook] writers, and Darwin's ghost with his letter on the warm little pond (by then he full well knew he would be the subject of major biographies and his correspondence would play a key role in that) tabled in evidence. I further point out that the OOL problem is pivotal to the whole scheme so the hiving off of the fact that the Darwinist tree of life has no root seems a very convenient way to dodge a crucial issue. The origin of the reproductive capacity that is the basis for the claimed power to evolve novel body plans by so-called natural so-called selection. (These terms are pretty slippery when we ask for empirically anchored, well-warranted clarification, with questions on circularity coming tot the fore, connected to a raft of other issues.) So, the OOL issue is about the origin of cell based life body plan no 1. It turns out that this needs a metabolic mechanism joined to a symbolic, nanomachine driven self replicator under the von Neumann self-replicator [vNSR] architecture. Such a vNSR, in turn is irreducibly complex, rooted in codes and algorithms, and is dependent on the prior existence of symbolism, language and the like; also being well beyond the 500 - 1,000 bit FSCI threshold. These strongly point to the living cell being a work of ART, i.e design. When we look at the creation of other, more complex body plans, we are looking at the embryological development process, with the sort of hox algorithm just described being implicated, in the context of a wider step by step preprogrammed process that leads from a generalised initial cell to a structured and viable body plan, where random chance variations expressed early enough in development to affect body plans are strongly likely to be fatal. This process is FSCI rich and is full of candidate irreducibly complex features. That is, we are looking at credible islands of specific function deeply isolated in vast seas of non-function. Protein fold domains and the 1 in 10^70 or thereabouts estimates on recent investigations can stand in, as can the identified irreducible complexity of the bacterial flagellum as tested by Minnich and co. So, the reasonable -- not Lewontinian a priori materialist -- view is that the living cell is designed, and the major body plans are likewise designed and made to be adaptable within islands of function. Which makes sense for robustness and sustainability in the face of a variable environment, within a given time, and over the long haul of time. So, the ball is back int eh court of the Darweinist objectors: show us evidence in its own right that we are not dealing with islands of function [this would for instance include providing empirically anchored refutations of Gould's remarks on the trade secret of paleontology] but a continent of life with smoothly cumulative evolution at macro level leading to an empirically observed tree of life. This last will require a sound answer to the Cambrian life revolution challenge. GEM of TKI kairosfocus

Elizabeth, A further note, and I will try not to post repeating Wikipedia quotes. It goes beyond the ability to translate a series of repeating molecules into a functional physical entity which in no way resembles the molecules that represent it. If we could understand the meaning of every single gene, know which ones were functional and which were not, and exactly how they are processed, we could create that same entity in the abstract sense. We could write down alphabetic representations of those molecules on lots and lots of paper, read them back, and then write down on another every detail of the organism it represents. You could draw a picture of the organism or make a sculpture from that information. You could do the converse and write your own genetic code to express a living thing, and then choose whether to implement it or just imagine it. The information can exist separately from the molecules that contain it. The use of a code, in turn, means forward thinking. A code can be likened to a tool. Having a hammer when you need to hammer a nail is never a happy coincidence. You foresaw the need for one and purchased or borrowed it. Or stole it. Someone else foresaw that need and manufactured it. Were it not for awareness of that need, there would be no hammers, period. Similarly, a code is useless without a need to represent or communicate something. An inanimate object can never have that need. It just is, and then eventually it isn't. It is not somehow gifted with an ability to abstract anything, including itself. It's always the same story in the end. Either someone made the hammers and the nails to fulfill a purpose, or the hammers and nails just decided to start hammering and getting hammered for no apparent reason. I can't imagine how much effort it must take to maintain a worldview in which houses build themselves. ScottAndrews

KF, Can you give an example of what specifically would satisfy you with regard to the evolution of "bodyplans"? I.E would organism A evolving into a slightly bigger form satisfy you? Or would it be something more significant? A new ability? A new appendage? What *exactly* is the minimum difference from one “bodyplan” to another that needs to be demonstrated here that you would accept as evidence? And what timescale would that evidence be generated over? Given you know exactly how slow evolution usually is when compared to the human lifespan? As presumably new evidence would need to be generated as you've written off all existing evidence in favor of "bodyplan" evolution already. So I'm hoping you are not asking for evidence of "bodyplan to bodyplan" evolution that could only be generated long after we're both dead and buried. If you in fact are asking for such, then I guess you don't believe in continental drift either. ED: This note, especially in the last paragraph, aptly illustrates the tone problem KH has. Evidently s/he is not cognizant of the significance of empirical observation in moving from speculative philosophy to empirically warranted science, including origins science. It is suggested that s/he read here and here in the IOSE before making further snide remarks on scientific methodology and things like plate tectonics -- which is based on significant direct observation of subduction and spreading zones, volcanism and earthquakes etc. On the body plan origin challenge, had KH read p. 2 of the OP, it would have made it clear that the exhibit no 1 for 150 years has been the Cambrian life Revolution, at phylum and sub-phylum levels; OOL i.e. of cell based body plan 1, is exhibit 2. For a lower end example the origin of the bird's wings and flight mechanism, or the whale and the bat's echolocation mechanism [including the close resemblance], and the origin of the human verbal linguistic capacity would be examples. kellyhomes

Can you give an example of what form such evidence would take? I.E would organism A evolving into a slightly bigger form satisfy you? Or would it be something more significant? A new ability? A new appendage? What exactly is the minimum difference from one "bodyplan" to another that needs to be demonstrated here? kellyhomes

Elizabeth, I repeat, not all symbols are intended for human interpretation. We also use them to make machines and computer do what we want them to. By saying that these particular symbols (or whatever you wish to call them) were not arranged by minds is begging the question. I will beat the poor, dead horse. You can choose to view DNA molecules and proteins as different ends of a chemical reaction. But as I said, there are plenty of automated systems in which electrical impulses are passed back and forth that in turn produce specific reactions. To say that just any chain of reactions is necessarily deliberate would be absurd. But when that chain of reactions begins with a fixed set of molecules which can be transcribed to produce and assemble functional components, they evidently do have meaning. Here's a really simple way of looking at it. DNA nucleotides are small, and, by themselves, completely useless. And yet they contain patterns that correspond, somehow, to entire functional living things. (For the sake of argument I struggle not to employ the obvious teleological language.) But when you examine these elements closely, you do not see a miniature version of the corresponding person or animal. Instead, you see patterns consisting of a limited set of molecules. And it doesn't just mirror the physical elements of the person or thing. It corresponds to all of the states through which it will pass from conception onward and all of the processes which will execute within it. You can call that series of molecules whatever you want. You can call the process that leads from those molecules to the finished product whatever you want. You can say that a thing only has the appearance of being designed. But to say that patterns of molecules that function like a symbols in a code only appear to be symbols in a code, and then come up with new definitions of "code" and "symbol" that exclude them? Find a definition of "code" that includes the word "mind." Even the crazy Wikipedia people see it.

This is DNA which contains units named genes that can produce proteins through a code (genetic code) in which a series of triplets {codons} of four possible nucleotides are translated into one of twenty possible amino acids. A sequence of codons results in a corresponding sequence of amino acids that form a protein.

A symbol is something which represents an idea, a physical entity or a process but is distinct from it.

This is DNA which contains units named genes that can produce proteins through a code (genetic code) in which a series of triplets {codons} of four possible nucleotides are translated into one of twenty possible amino acids. A sequence of codons results in a corresponding sequence of amino acids that form a protein.

In the genetic code, a stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.

They are a symbols forming a code which is translated, and signals to distinguish between messaging units. "atg act cac cga gcg cga agc tga tac tga gtg gct cgc gct tcg act..." in, sand dollars and tulips out. It takes layer upon layer of insulation to protect oneself from knowing it. ScottAndrews

KF,

There is a reason why from the FSCI involved, we know credibly that symbolic, algorithmic systems point to their source in a mind like a compass to the north pole.

So if I give you a 'symbolic, algorithmic system' can you put a specific value on the FSCI contained within it and explain how you obtained that figure? Presumably you have a worked example to hand, otherwise on what basis are you making that claim? Care to provide it? ED: KH would profit by considering the UD post here and onward discussions over the past 6 months or so. In addition, s/he should take time to work through say Abel's peer-reviewed paper on the universal plausibility bound, here. kellyhomes

KF,

Please, adjust tone.

I saw notihing approching "tone" in any of the post you are complaining about. What I saw was a cogent point by point dismantling of all your primary claims which you obviously are unwilling or more likely unable to rebut. In fact the only person I see here doing anything approximating "tone" is you, by dismissing well argued points by pretending to take offense but then continuing to argue as if no counter arguments had in fact been made, as if no counter points had in fact been made you are not fooling anyone. You are simply looking more and more foolish. More and more panicked.

Next, the issue of a narrow island of function is a direct matter of the nature of coded algorithms vs the set of possibilities for strings of digits of the same length not so constrained.

This illustrates your fundamental misunderstanding. Except you have been corrected on it so many times it cannot possibly be due to ignorance any more. So, these rare "islands of function" you claim provide the "evidence" for ID don't in fact exist at all. You know nothing of the fitness landscapes of early, first or in fact any living organism or component thereof. Your definition of "landscape" is on the same order as your definition of FSCI, simply a comparison of one string against a randomly generated string of the same length. One arrangement of proteins against all possible arrangements. The only person talking about a tornado in a junkyard is you.

the a priori materialism that has driven the demand that we see algorithmic programming like this as a product of blind chance and mechanical necessity

Nobody is forcing *you* to see anything any way other then you want to. So why don't you stop wasting your time here making the same TLDR arguments over and over with Darwinists who never seem to be convinced by them and see where seeing algorithmic programming like in life as something other then a product of blind chance and mechanical necessity? Perhaps you could get some paper published, I understand there are some active ID journals desperately looking for papers to publish. I'd not worry too much about their peer review process. Go for it! ED: The just above, regrettably, is a capital example of the snide dismissiveness I have pointed out above. There is a case to be addressed on the merits, not simply brushed aside on strawamannish dismissals embedding a supercilious sneering tone [such as asserting that I am panicking, of all things!], cf. my onward remark below for just one example on the merits issues. FYI, KH, matters of warrant are not decided on strawman tactic rhetorical objections such as are too common in general and are all too evident above from defenders of Darwin. Instead, each view has to be justified on the relevant observational facts and on cogent reasoning; so the issue is that we need to see the root for the tree of life and for the claimed major body plan level branching justified on Darwinian Incrementalism; which justification -- after two to three days and well past 1,000 views and over 100 comments [including by NCSE's former PR person] -- is still conspicuously absent. (The absence of Nobel prizes on the OOL and the explanation of the Cambrian Life Revolution, etc, should provide clues to the actual state on the merits. Cf the mutually ruinous exchange between Orgel and Shapiro as cited in the OP and the critical remarks on the Cambrian revolution by Meyer. Gould's deathbed counsel to the fields of paleontology and evolutionary biology -- also cited -- should also be reckoned with.) As for fitness landscapes, it is by now notorious that GA's operate within islands of function, i.e carefully designed zones where trends of fitness leading to at least local peaks can be picked up by varying a so-called genome. In addition, it should be quite plain that cell based, C-Chemistry metabolising life using DNA and associated mechanisms uses proteins that come from deeply isolated fold domains [ 1 in 10^70 or thereabouts of the AA sequence space], that the vNSR-based replicator mechanism is irreducibly complex and dependent on algorithms and language, thus moves us to very specific zones in the space for strings of symbols of the relevant length, and that functionally specific, complex information, in general, cannot be had on the cheap by chance variation of strings that create languages, codes, algorithms and executing machinery by trial and error on the gamut of our observed cosmos. We hardly need to stress that the only empirically known source of codes, algorithms, symbolic communication systems and machinery that executes such is intelligence; other than to highlight that this inductively warrants the strong inference that such are empirically reliable signs of intelligent action. To date, we find many dismissive and strawmannish objections, but no provision of actual empirical warrant for the notion that a warm little pond of plausible chemistry or the equivalent can spontaneously lead to C-chemistry, aqueous medium, metabolic, von Neuman self replicator, life. Nor, for the further notion that such life would spontaneously evolve major novel body plans, on observation of cases X, Y, Z. Instead we see the "always on the attack" default to Darwin question-begging approach that is ever so familiar. KH should also read the onward comments on further posts s/he has made, and the main response on Mt Improbable below. kellyhomes

No, I am not "begging the question" kf. I am making no inferences about the "source" of the sequence. I am talking about what reads the sequence, and, in the case of a self-replicating molecule, it isn't a thing with a mind, and which therefore can only "read" it (scare quotes deliberate) in the medium in which it is cast. It cannot "read" it if it is instead printed in ink or moulded in playdough. That's because it isn't a symbol, it's just a polymeric molecule with a particular sequence of bases. Elizabeth Liddle

Dr Liddle, from memory on the defn of engg: using the forces and materials of nature, in light of skill, knowledge and economic considerations, to produce designs -- objects, processed, etc -- for the benefit of humanity. Of course, chemistry is used in engineering, as is physics, as is electricity as is materials science -- semiconductors especially -- etc. That is a component of engineering. If you object that "straightforward" chemical forces and processes are at work, you might as well object to how a car engine works off simple combustion under controlled circumstances as thought hat disproves the design of a car engine. GEM of TKI kairosfocus

Dr Liddle, you are simply begging the question. There is a reason why from the FSCI involved, we know credibly that symbolic, algorithmic systems point to their source in a mind like a compass to the north pole. Please think about the significance of a tested, reliable sign and what it credibly points to. GEM of TKI kairosfocus

Okay, there is no symbolic layer in a computer either. It’s just electricity being conducted according to natural laws.

Scott, computers are full of symbolic layers! We would not be able to use them if they weren't! But again, those symbols are assigned by minds, then read off by minds. That's the sense in which they are symbols. Not only that, but you could run exactly the same computation in any medium, including black and white stones, if you had worlds enough and time. The same is not true of the chemical reaction that is in a molecule. Elizabeth Liddle

Well, no, I must disagree that they are "utterly irrelevant to biology". Although of course I quite agree that they are designed. My point was simply that they reproduce through straightforward chemistry. Elizabeth Liddle

Elizabeth,

But symbols in Ink, paper fibers etc are read by things with minds!

Symbols in electronic impulses are not. We make things that talk to each other. Computers and switches and routers keep on going even when people aren't paying attention. The microprocessor in my computer can only read instructions fed to in a very specific medium. But you could write those same instructions on paper or even memorize them.

In other words there is simply no symbolic layer in either translation or transcription processes in the cell.

Okay, there is no symbolic layer in a computer either. It's just electricity being conducted according to natural laws. Why would that be true of one and not of the other? And don't answer because one is designed or there is no mind, etc. That's begging the question. ScottAndrews

It isn't a distraction, kf, and nor is it "piling on". I just wanted to make sure that point was established. As long as by "hill-climbing algorithm" you include evolutionary algorithms that can go down hill as well as up, we are on the same page. I didn't mean to offend you, I was just trying to establish common ground. Elizabeth Liddle

Dr Liddle the molecules you speak of are set up in environments that are utterly irrelevant to biology. Indeed, they are manifestations of how self-replication -- templating actually -- is produced by careful and skilled design. GEM of TKI PS: The attempt just above to claim that the digital processing using discrete symbols in the cell is not that because it uses smart polymer chains, is inadvertently so revealing that it backfires via reductio ad absurdum. The genetic code is a code and that one has to distract from that is telling. The genetic code is plainly a code, accept that and come to terms with it. Just as with the algorithmic clockwork like assembly of body plans. Paley wins this one. kairosfocus

Dr Liddle, I have repeatedly explained what hill climbing in the wider sense is about; I used this descriptively long before I noted on the specific set of algors called hill climbing, some of which are in fact highly relevant to GAs and evolutionary claims, just follow the link in the OP and read the part on varieties. I do not appreciate the distraction and piling on tactic. This is something that is simple and that is easy to understand. At least, until it was turned into a neat talking point to strawmannise. I am decidedly not amused. Please do better next time. GEM of TKI kairosfocus

Dr BOT: Pardon, but there is a tone problem again, sufficiently serious that I note first of all. Please, adjust tone. On substance, the term hill climbing has a more narrow sense of a particular class of optimisation algorithms, and a broader sense that would capture algors that move uphill to a target, including by tossing our a spray of samples and moving uphill. On the expectation built into the algor that that is where the hot zones lie. This was thrashed out in gory details months ago with MG et al over Ev. Next, the issue of a narrow island of function is a direct matter of the nature of coded algorithms vs the set of possibilities for strings of digits of the same length not so constrained. If you want to see just how precise and narrow this is, why not look at the UD post today on body plan unfolding stepwise on Hox Genes and the onward article in the science daily site? notice especially these SD clips, that I will soon add to the OP:

Why don't our arms grow from the middle of our bodies? The question isn't as trivial as it appears. Vertebrae, limbs, ribs, tailbone ... in only two days, all these elements take their place in the embryo, in the right spot and with the precision of a Swiss watch. Intrigued by the extraordinary reliability of this mechanism, biologists have long wondered how it works. Now, researchers at EPFL (Ecole Polytechnique Fédérale de Lausanne) and the University of Geneva (Unige) have solved the mystery . . . . During the development of an embryo, everything happens at a specific moment. In about 48 hours, it will grow from the top to the bottom, one slice at a time -- scientists call this the embryo's segmentation. "We're made up of thirty-odd horizontal slices," explains Denis Duboule, a professor at EPFL and Unige. "These slices correspond more or less to the number of vertebrae we have." Every hour and a half, a new segment is built. The genes corresponding to the cervical vertebrae, the thoracic vertebrae, the lumbar vertebrae and the tailbone become activated at exactly the right moment one after another. "If the timing is not followed to the letter, you'll end up with ribs coming off your lumbar vertebrae," jokes Duboule. How do the genes know how to launch themselves into action in such a perfectly synchronized manner? "We assumed that the DNA played the role of a kind of clock. But we didn't understand how." . . . . Very specific genes, known as "Hox," are involved in this process. Responsible for the formation of limbs and the spinal column, they have a remarkable characteristic. "Hox genes are situated one exactly after the other on the DNA strand, in four groups. First the neck, then the thorax, then the lumbar, and so on," explains Duboule. "This unique arrangement inevitably had to play a role." The process is astonishingly simple. In the embryo's first moments, the Hox genes are dormant, packaged like a spool of wound yarn on the DNA. When the time is right, the strand begins to unwind. When the embryo begins to form the upper levels, the genes encoding the formation of cervical vertebrae come off the spool and become activated. Then it is the thoracic vertebrae's turn, and so on down to the tailbone. The DNA strand acts a bit like an old-fashioned computer punchcard, delivering specific instructions as it progressively goes through the machine. "A new gene comes out of the spool every ninety minutes, which corresponds to the time needed for a new layer of the embryo to be built," explains Duboule. "It takes two days for the strand to completely unwind; this is the same time that's needed for all the layers of the embryo to be completed." This system is the first "mechanical" clock ever discovered in genetics. And it explains why the system is so remarkably precise . . . . The process discovered at EPFL is shared by numerous living beings, from humans to some kinds of worms, from blue whales to insects. The structure of all these animals -- the distribution of their vertebrae, limbs and other appendices along their bodies -- is programmed like a sheet of player-piano music by the sequence of Hox genes along the DNA strand.

Now, compose such by chance variations and survival of the fittest. Ouch, Paley's watch is a bear to stumble over -- including his self-replicating watch. (Yup, Paley has been routinely strawmannised.) Finally, you know or should know that Lewontin documents, in a way that reflects the views of a dominant sector of the science and sci edu elites [cf. here on], the a priori materialism that has driven the demand that we see algorithmic programming like this as a product of blind chance and mechanical necessity. GEM of TKI kairosfocus

Well, there are self-replicating peptides and self-replicating RNA molecules as well. But they are still all molecules, just as DNA is a molecule.

Ink, paper fibers, and stone don’t have minds either. You’re making an arbitrary distinction. If you know the source of the symbols, they are symbols, because symbols originate with minds. But if they look like symbols and function like symbols but you don’t know the source, then they aren’t symbols.

But symbols in Ink, paper fibers etc are read by things with minds! Indeed they are read by the same kinds of minds that assigned symbol to referent, and without a shared knowledge of the assignment, the symbol cannot be read. The analogy with the reaction between molecules completely breaks down. DNA and RNA sequences are not "read" by things with minds, and, moreover, the "reader" would be totally unable to "read" the sequence were it to be rendered in any other medium. In other words there is simply no symbolic layer in either translation or transcription processes in the cell. Argument-by-analogy is unsound anyway, but when the analogy is stretched to breaking point at the exact point that bears the weight of the argument, then it becomes seriously fallacious! Elizabeth Liddle

Elizabeth, Are you talking about your hypothetical self-replicator again?

When it comes to a self-replicating molecule, we are not talking about some abstraction at the level of a “system”.

All the ones we know of that exist have DNA.

In contrast, a symbol transcends the material it is rendered in, because it is interpreted by a mind, and that mind doesn’t care whether the thing is printed in ink or etched in stone. A molecule has no mind.

Ink, paper fibers, and stone don't have minds either. You're making an arbitrary distinction. If you know the source of the symbols, they are symbols, because symbols originate with minds. But if they look like symbols and function like symbols but you don't know the source, then they aren't symbols. What sounds like logic often ends up as arbitrary and preferential. ScottAndrews

kairosfocus, can we just establish one point and get it out of the way: Do you agree that evolution is not a hill-climbing algorithm? Elizabeth Liddle

Petrushka, pardon but you are just repeating yourself in the teeth of having already being corrected. All this shows is that when targetting is implicit many people won't see it for what it is, hence the success of switcheroo. And, months ago we had to dissect Ev and the targetting for that notorious case was not even implicit, so soon as you read the details. GA's start within target zones and walk in to hot spots by using trends, while being fine tuned to do just that. GEM of TKI kairosfocus

Scott:

Whether it’s bits and bytes or ink molecules interacting with paper fibers, everything is chemical or electrical. By your reasoning, what isn’t “chemistry?”

A thought isn't "chemistry", Scott, nor is "reading" and "speaking" and writing. Chemical interactions underlie the processes, but the symbol use, the representatations, the abstraction are only explicable at the the level of the system not at the level of specific chemical reactions. That's why we talk about "systems neuroscience" btw. When it comes to a self-replicating molecule, we are not talking about some abstraction at the level of a "system". We are talking about lock-and-key type interactions that can be perfectly well understood at the level of chemical bonds. You do not need to model the process at some higher "systems" level ot understand it, and there is no "symbolic" process going on. The clearest indication of this is that the alleged "symbols" cannot be rendered in any other material and still "represent" what it is supposed to represent. In contrast, a symbol transcends the material it is rendered in, because it is interpreted by a mind, and that mind doesn't care whether the thing is printed in ink or etched in stone. A molecule has no mind.

Apparently the only way you can reason around “representations and protocols” in biology is to negate all of them everywhere and render the very words meaningless. I call it reading, responding, and typing a post. What do you call it, “electronics?”

On the contrary, Scott, my objection to UBP's use of the word representation is that it is far too broad, and renders the word meaningless. I am aiming for a precision that I find lacking in UBP's post, a lack of precision that I think is fatal to his argument. A molecule is not a symbol. Elizabeth Liddle

Elizabeth, Whether it's bits and bytes or ink molecules interacting with paper fibers, everything is chemical or electrical. By your reasoning, what isn't "chemistry?" Apparently the only way you can reason around "representations and protocols" in biology is to negate all of them everywhere and render the very words meaningless. I call it reading, responding, and typing a post. What do you call it, "electronics?" ScottAndrews

a system of representations and protocols

This, as always, UBP, is question-begging. There are already in existence some self-replicating molecules. Whether you call what they do a "representation" or a "protocol" is up to you. The fact is that they do it, and what they do when they do it is called by most people "chemistry". Elizabeth Liddle

Pardon, but have you considered the implications of starting in a narrow island of specific function in a large space of possible configurations, and then proceeding within that island by hill-climbing, and contrasted that with the claimed mechanisms of origin of life and of body plans?

No, you are not pardoned. Yes, I've considered the implications. A GA is not a hill climbing algorithm. What claimed mechanisms of OOL? Can you try and be clear about exactly what you are talking about - Evolution OR Origin of Life - they are not the same thing. Now you make a claim there - 'starting in a narrow island of specific function in a large space of possible configurations' - I agree that the space of possible configurations is large but how do you know that it is starting on a narrow island of function - by making this statement you imply that you know what the topology of the landscape for a proto-replicator is. If you do know, as you constantly imply, then publish your data because the entire field of biology would like to know!

That is why “acknowledgement” is so important, as the beginning within such an island of function in a space of vastly more configs that are non-functional is a matter of being targetted from the outset.

Another claim without evidence. And again - what acknowledgement? To me this reads like this: I have made an aeroplane Can it fly to the moon? No, it is an aeroplane. Ha! you admit then that it is not actually capable of spaceflight! No, I said it was an aero plane, I never said it was a rocket. Try and be clear about the topic being discussed: Evolution OR Origin of Life. They are not the same thing.

Hill climbing is then moving by successive increments to hot spots within the island. (Think about what proportion of strings of ASCII characters of the same length will be GA algorithms, and what fraction will be non-functional gibberish>)

Yes, but a GA is not a hill climbing algorithm - get your facts straight - and then you suddenly switch mid paragraph to talking about what fraction of possible code configurations would be a GA. Replication is what we are talking about.

In short GA’s — properly addressed — are about what is not in dispute, not even by Young Earth Creationists.

The problem is you have never properly addressed them, I'm not even sure you really understand them, if you did you wouldn't keep confusing genetic algorithms with hill climbing algorithms.

And, specifically, GA’s therefore tell us nothing about how we get to islands of function with nice trendy uphill slopes pointing the way to peaks of function.

No, they don't, as we keep saying again and again and again. How many times will we have to repeat to you - Evolution, and GA's are not ever proposed as explanations for the origin of evolution or GA's. GA's are not hill climbing algorithms - they can deal with much more rugged landscapes than hill climbing algorithms, that is why they are not called hill climbing algorithms, that is why they are called Genetic Algorithms!

So, the use of GAs and related algorithms as icons of evolution, since Dawkins’ Weasel, is yet another fundamentally misleading icon that makes unwarranted extrapolation driven by Lewontinian a priori materialism in the dominant sectors of science education, popular education and the school room.

Why do you keep on about WEASEL - it is a toy example from a pop-sci book, it is only an 'Icon' to you. If you want to talk about GA's to scientists (like me) then please referr to published science, not coffee table books because it just reinforces the already strong impression that your understanding of GA's is entirely based on pop-science and not real academic literature. Try starting with Holland's work and look at the vast body of other actual science that has been done in this area (to which Dawkins has contributed almost nothing!). What has this guy Lewontin got to do with anything (apart from feeding your paranoid conspiracy theories). GA's are based on observed phenomena - reproduction with variety leading to differential survival rates of members of a population in an environment. DrBot

evolutionary search is usually driven by measuring how close the current candidate solution is to the objective.

Well no. Biological evolution, like the traveling salesman problem, does not have a goal or target. It has a way of comparing variants with each other, but not a way of measuring them against a goal. That is not a trivial difference. It is why the probability argument is irrelevant. There is nothing about biological evolution that knows whether it is making progress. There is nothing to calculate the probability against. The population survives or it doesn't. Populations do not see hills and do not attempt to climb them. If they happen to take a route that seems unlikely, it is only so in retrospect. It did not intend to take any particular route, and each is is likely as the next. Petrushka

Dr BOT: Pardon, but have you considered the implications of starting in a narrow island of specific function in a large space of possible configurations, and then proceeding within that island by hill-climbing, and contrasted that with the claimed mechanisms of origin of life and of body plans? That is why "acknowledgement" is so important, as the beginning within such an island of function in a space of vastly more configs that are non-functional is a matter of being targetted from the outset. Hill climbing is then moving by successive increments to hot spots within the island. (Think about what proportion of strings of ASCII characters of the same length will be GA algorithms, and what fraction will be non-functional gibberish>) In short, GA's if they can be said to mimic anything evolutionary, mimic adaptations of an existing body plan, under actually artificial selection based on a defined trend and a well-tuned algorithm. In short GA's -- properly addressed -- are about what is not in dispute, not even by Young Earth Creationists. And, specifically, GA's therefore tell us nothing about how we get to islands of function with nice trendy uphill slopes pointing the way to peaks of function. So, the use of GAs and related algorithms as icons of evolution, since Dawkins' Weasel, is yet another fundamentally misleading icon that makes unwarranted extrapolation driven by Lewontinian a priori materialism in the dominant sectors of science education, popular education and the school room. GEM of TKI kairosfocus

Thanks for your acknowledgement that a GA works within an island of function; which has been highlighted from the beginning of the discussion, by the design side:

Good grief KF: evolution, and GA's require systems that replicate and are therefore already have those functions - this is not an admission, this is what we have always said! I don't understand why you keep harping on about it, we have always made this crystal clear, along with the distinction between evolution and OOL, one which you insist on equivocating over. DrBot

Petrushka, Thanks for your acknowledgement that a GA works within an island of function; which has been highlighted from the beginning of the discussion, by the design side:

It’s central to understanding that a GA requires a connected landscape in order to navigate incrementally . . .

I note that in the case cited at the head of the p. 1 of the OP, I showed how Stanley and Lehman wrote:

. . . evolutionary search is usually driven by measuring how close the current candidate solution is to the objective. That measure then determines whether the candidate is rewarded (i.e. whether it will have offspring) or discarded . . . . surprisingly, sometimes not looking for the goal in this way leads to finding the goal [--> notice, an admission of goal- directedness . . . ] more quickly and consistently. While it may sound strange, in some problems ignoring the goal outperforms looking for it. The reason for this phenomenon is that sometimes the intermediate steps to the goal do not resemble the goal itself. John Stuart Mill termed this source of confusion the “like-causes-like” fallacy. In such situations, rewarding resemblance to the goal does not respect the intermediate steps that lead to the goal, often causing search to fail . . .

In short, there are issues of following a hill climbing trend as implicit goal-seeking based on carefully selected fitness functions and search procedures, as well as the issue of needing several things to be in place at once for function to appear, i.e. an implied case of irreducible complexity. [NB: Did you cross-reference no 3 in the ID founds series (as linked in OP), on this issue, and did you read the J Bartlett paper on analysing IC on a Turing machine? Also, kindly note that the strawman fallacy of caricaturing the other party -- as you have done (how can you act as though we have not addressed the precise problem that GA's work on hill climbing requiring a continuous and well behaved zone with nice not "deceptive" trends, cf. the illustration at the top of the post), is a species of red herring distractor, that works precisely by being a distractive tangent.] Now, too, we have repeatedly put on the table [start with p. 2, OP] and linked relevant information on why we should expect and on evidence do observe such islands of function separated by vast seas of non-function in config spaces. Having provided evidence and citations from the biological world [on the tree of life], kindly explain to us how we are supposedly begging questions by asserting a disconnected landscape of life "axiomatically," which sounds suspiciously like a turnabout argument attempt, given the Lewontinian a prioris noted for evo mat. It seems to us rather that on abundant evidence, we should expect that complex, specific, information-rich function, starting from the joint metabolic systems and vNSR in first cell based life, will be disconnected. We find that: 1 --> the difficulty of elaborating algorithmic digital codes incrementally while preserving function at each step, 2 --> the observed status of the fossil record [note the extensive cite on the Cambrian revolution and the remarks by Gould], 3 --> the evidence that points to discrete protein fold domains, deeply isolated in AA sequence space [of order about 1 in 10^70], 4 --> the evident presence of irreducible complexity tracing to multiple core necessary factors, 5 --> The mutual ruin of genes first and metabolism first OOL models, etc . . . all point to serious and unresolved problems with the evolutionary materialist paradigm that have persisted for decades or even more than a century in some cases. In that context, we think it is time for a paradigm shift to one that does not have an evidently insuperable problem surmounting search challenges in a config space with isolated islands of function in an exponentially growing domain as complexity increases. Namely, design, which is known to routinely produce FSCO/I rich entities, and which in the case of Venter etc. is showing proof of concept of direct applicability to cell based life. Can you -- by way of supplying correction to our implied ignorance (or worse, a la Dawkins et al) -- demonstrate, on observation, why the Darwinian connected continent of viable forms traversed by a tree of life model at OOL, OO body plans etc, is empirically well warranted? Is it not the case that each argument in science must account for all the credible facts, and that it must have such facts on the table? And if you cannot supply unambiguous facts rooted in actual observation, then do we not instead have divergent schools of thought, which should have the right to proceed on their own terms, seeking support? [As in, no censorship in education on strengths and limitations of origins science theories, and no career busting in institutions for practitioners; cf. recent and classic cases in point.] GEM of TKI kairosfocus

Dr Bot: Pardon, I will ignore the patent hostility of tone, simply noting that I have monitored carefully and that our evaluation of comments is plainly very different. If you know comments that in fact demonstrate how, on observation: (a) OOL from plausible prelife circumstances and through mechanisms of chance and/or necessity, and/or (b) OO major body plans or significant body subsystems through incremental chance variations and differential reproductive success . . . have been warranted, kindly identify the specific comments. Note, I am interested in observationally anchored evidence, not speculations, simulations that show instead targetted search algorithms that result in hill-climbing within an island of function [i.e. the novel body plan is already implicitly assumed, and we are dealing with variations within the body plan], etc. In short, where has the proposed darwinian mechanism, and/or where have chem evo mechanisms been shown to be adequate for the major claims being made. As a bonus, kindly explain why to date those who have shown these things have not been awarded say the Nobel Prize. (Prigogine's Prize for far from equilibrium systems does not count, as he admitted; cf. remarks in say Thaxton et al, TMLO, 1984.) GEM of TKI kairosfocus

It's not at all tangential. It's central to understanding that a GA requires a connected landscape in order to navigate incrementally. Without discussing the attributes of actual landscapes there can be no useful discussion of whether evolution is possible or impossible. A (good) cryptogram is specifically designed to defeat incremental attacks. So the argument about hill climbing and such is going to boil down to the empirical question of whether the actual biological sequence landscape can be navigated. It's not something that can be known axiomatically. Petrushka

Have you not read any of the comments in this thread? You are constantly being presented with the evidence you demand, then performing rhetorical back flips to avoid dealing with it. DrBot

Dr Liddle, Grabbing a moment, first, please warrant on observation tracing to plausible prelife circumstances, the concept:

if you are talking about how the first minimal Darwinian-capable self-replicator came about (OOL) – fine. Darwinian mechanisms can’t explain the origins of a Darwinian-capable population.

The only observational evidence of life I am aware of is of cell based organisms that integrate metabolism and vNSR, digital code based self-replication that also codes for the metabolic subsystem. Such an entity is irreducibly complex per having multiple necessary causal factors to account for the two key facilities, and is also well beyond the FSCI threshold, just on the known stored info of at least 100,000 - 1 mn bits or so. If my information is incomplete on this matter, kindly enlighten me. However, if my information is accurate to what we know, it highlights that the only credible explanation of such is design, especially through the use of language, codes, algorithms, and data structures coupled to implementing machinery (expressed in turn based on said coded information). So also, once design is on the table, I have no reason to dismiss the significance of complex, integrated systems, that they normally contain many interacting, causally necessary core components. That starts with the need for heat, fuel and oxidiser to make a fire, and goes on from there to a pervasive phenomenon in the world of multiple component systems. So, I EXPECT to find islands of function as the characteristic pattern for cell based multicellular complex life forms that develop by cell multiplication and specialisation into tissues, structures, organs and an integrated body plan for each organism and individual. In some cases, there are two complementary sexes, both of which are required for reproduction, i.e. the minimum for reproduction is two individuals, of diverse sex. As p 2 of the OP highlights, the actual fossil record -- long since known to be dominated by sudden appearance, stasis and disappearance and/or continuation into the modern world -- reflects a non-gradualistic plan, i.e it supports the expectation. (I first saw that with marine fossils from my grandparents' farm in St Elizabeth, Jamaica, and this continued with the similar pattern of marine fossils in Barbados. So, the remarks by Gould et al are not a great surprise to me.) Complex, functionally specific, integrated systems with many necessary components are a "natural" and expected pattern in designed systems. Multiply, by the informational challenges to get to a viable body plan and implementing embryological development algorithm for a new type of organism, dozens of times over, on earth. Mix in mosaic creatures that look a lot like code reuse through a library. Also, so called convergent evolutions -- echo location with whales and bats jumps up. Think on how large sections of the human genome seem to be just sitting there in kangaroos, where on the usual timeline, the divergence for these types of mammals is said to be about 150 MYA, about the time often suggested for emergence of/dating of early birds and well back in the dinosaur period. All of this points, in my mind, to a pervasive pattern of what we should expect from the activities of designers. Direct molecular manipulation and code writing, use of viri as injectors of novel genetic programs, forms of frontloading, etc, are all possibilities on ways and means. But, we must know there are different ways to skin a catfish, and TRIZ gives a useful framework for thinking about the known challenges of engineering development. But of course, in raising themes like just above, I am widening the scope of reflections. Strictly speaking design theory is about the inference from empirically tested and reliable sign to key causal factors, across chance and/or necessity and/or design. GEM of TKI kairosfocus

Distractively tangential. Please focus on the primary issues in the OP, pp1 & 2. kairosfocus

Joseph, can you tell us more about how you used GAs to find solutions to encryption issues? dmullenix

Onlookers and participants: First, please read p. 2 of the OP. Second, note how: a--> after 1 1/2 days, 1,000+ views and 100+ comments, b--> including from the former PR man for NCSE, c --> we still have yet to see empirical observational data on the origin of FSCO/I by blind chance and necessity, d --> or how on empirical observations we have a C + N pathway from Darwin's pond or a modern equivalent to a cell based, metabolising and vNSR self-replicating, cell based organism. e --> We know that the only empirically known source of FSCO/I is intelligence. f --> Similarly, Venter has given proof of concept that designers can use nanotech techniques to design elements for a living cell. g --> And, we know that designers form holistic systems, crossing vast config spaces to reach islands of function. h --> So, as of now the empirically best warranted account for OOL with such vNSR and metabolism, is design. i --> Where, there is a whole panoply of relevant design techniques and strategies [cf TRIZ], so, that new line of objections is a distractor. j --> With design on the table at OOL, it is on the table all along the rest of the way, and so it is quite significant that objectors from the darwinist side have been unable to show observational basis for the claimed power of chance variations incremented through differential reproductive success. k --> Design is known to be empirically adequate to account for complex functionally specific systems and structures, as can be seen from the world of technology we inhabit. l --> It is being asked, why don't we see designer trash around. Actually, what is more relevant is that we see known strong signs of design, fingerprints if you will: digital, coded algorithmic info in the heart of cell based life stands out as a case in point. m --> In any less ideologically loaded context, to suggest that such info, in the millions of bits, wrote itself out of accumulated lucky noise feeding trial and error, would be dismissed as a patent absurdity, with excellent reason in light of the space of possibilities for complexity of that order. So, let us see if the darwinist objectors are now able to warrant, on credible observation, why they stick to their model for origin of life and of major body plans. GEM of TKI kairosfocus

You have been with us so long and do not follow the threshold of complexity with functional specificity issue?

kf, I find it a little frustrating that you assume that if I do not agree with something it is because I do not "follow it", despite having been "told". This is not a justified assumption. I have repeatedly said that I do not accept your evidence for these "thresholds" and "islands" that you talk about. It is my position (and the position of standard evolutionary biology) that the "thresholds" and "islands" you allege are illusory, or, at least, can be reached by incremental change.

Have you shown, empirically how darwinian incrementalism can bridge spontaneous info generation challenges?

Yes, many times, not least by AVIDA, but also through the evidence from "microevolution" i.e. evolution that can be observed happening from generation to generation. Each generation passes "information" from itself to the next, and differential reproduction means that that that information that leads to more offspring is selectively reproduced, resulting in the accumulation of information as to how best to build an organism fit for that environment.

By contrast, designers, notoriously, work holistically and by integrating components to achieve overall function. They face no problem in traversing vast config spaces to islands of function.

Exactly. So in human designs we see solutions transferred wholesale from one "lineage" to another. We do not see such transfers in nature, because, as you say, incremental evolutionary processes cannot do this. This is strong evidence that in nature, the "design" processes are incremental and Darwinian, not the results of a far-sighted, holistic designer.

BTW, have you read p 2 of the OP on the observed gaps?

I don't see anything in the OP about "observed gaps", apart from the well-known OOL gap. Can you give an example of a post-OOL "gap" that you think is untraversable by incremental means? Elizabeth Liddle

KH: Once design is on the table, the panoply of methods known or plausible for engineering is also on the table -- just show us that you have looked up TRIZ as one example. The decisive issue, given institutional forces, however, is empirically tested, signs of design. Dr Liddle: You have been with us so long and do not follow the threshold of complexity with functional specificity issue? Have you shown, empirically how darwinian incrementalism can bridge spontaneous info generation challenges? By contrast, designers, notoriously, work holistically and by integrating components to achieve overall function. They face no problem in traversing vast config spaces to islands of function. BTW, have you read p 2 of the OP on the observed gaps? GEM of TKI kairosfocus

My point is easy enough to understand from the quoted text above. Dr Bot states that "real scientist" don't appeal to evolution in explaining OOL issues. My experience is somewhat different than his/hers apparently. Dr Liddle is a brilliant "real scientist", and yet she does it repeatedly, even after being told:

LIDDLE: Yes, my answer does indeed “suggest the source the code”. And if you think that “the simplistic observation that living systems that function will exist longer than ones that don’t” is pointless, then you are missing a very important point!

BIPED: You are saying that the differential survival of a replicating system is the source of the code which causes the system to exist. But the differential survival of a physical system wouldn’t have happened until the code-driven system itself existed. (Alternatively, you can provide plausible evidence of a non-code-driven system providing inheritance, then point to the cause of a code arising within that system). In any case, differential survival is the result of an adaptive system in a variable environment, and it very obviously requires the system. This was already pointed out to you in my previous post. If something requires something else to exist before it can come into being, then it cannot logically be the cause of the thing it requires – because it doesn’t exist yet.

BIPED: The issue now is the same as it was last time. Provide some evidence for a self-replicating molecular entity which provides for its inheritance without a system of representations and protocols, then point to the rise of representations and protocols in that system.

Now, am I suggesting that Dr Liddle isn't clever enough to parse it out if pressed on the issue? No of course not. But then the next time it comes up, she goes right back to it as some fuzzy amorphous mechanism where everything works out anyway. And she is hardly the only "real scientist" who does this. It happens here all the time. ;) Upright BiPed

I did not calculate the FSCI, but I think we can all agree that it is well beyond the universal probability limit. All I did was answer his question. Relating to biology, how can you rule in self-replication w/ heritable variation in reproductive success? No evidence anywhere of this creating FSCI. I didn't know that you had the sources to prove this mechanism to be a "potent source of functional complexity", which we have all been asking of you for months on end now. uoflcard

Within body plans, the argument to improvement over primitive features through differential reproductive success is a hill climbing claim. Again, the challenge is to get to the body plans, i.e. shores of islands of function. kairosfocus

All you have to do is show that body plan evo, per observation, occurs on darwinian methods and that this then best explains what we are seeing in the world of life. BTW, I think the pic of my son next to a canon is the best. But, others have their votes. kairosfocus

I am no biologist. What I know about fish is that it breathes in oxygen dissolved in water, right? If you are a biologist, perhaps you could tell me what happens to fish after it is taken out of water into fresh air. Maybe it is a stupid question, in which case you have to forgive my ignorance, but how come a chance sequence of infinitesimal changes can enable fish to start breathing in the air and decide to become something else, e.g. a pig? How exactly?

It's not a stupid question, and it has been the subject of considerable research. One set of clues is given by extant lobe-limbed fish like lungfish which have primitive lungs as well as gills, and which resemble in many ways the lobe-limbed fossil fish that seem to have been ancestral to early tetrapods. Have you read Neil Shubin's "Your Inner Fish"? Elizabeth Liddle

All the best with the trip! Elizabeth Liddle

kf, if you are talking about how the first minimal Darwinian-capable self-replicator came about (OOL) - fine. Darwinian mechanisms can't explain the origins of a Darwinian-capable population. However, you seem to be saying that there are other islands, and that is what we dispute. Starting with a minimally functional population of self-replicators in an environment, replicating with variance, adaptation will tend to occur, as we see both in the field and the lab, and in simulations like AVIDA. These are not "hill-climbing" algorithms, and, as a result, are able to traverse a "rugged" landscape. So the "islands" argument is no longer relevant, once the Darwinian process has been initiated. Elizabeth Liddle

Why can't Darwinist mechanisms explain body plans? Elizabeth Liddle

Kelly: Please go look at the field of engineering, and ask yourself how important design is, and how important detection of designs on signs could be. Then, go look up key approaches such as TRIZ and reverse engineering. BTW, the conclusion that something was designed on tested reliable signs of design is an inference to best, abductive explanation argument, not a simple analogy. This pattern of reasoning happens to underlie both science and history -- and forensics. Think abouty the case of seeking the truth about the origins of our world of life and our cosmos that seems fine tuned for such life, then ask yourself what significance such could have. Gotta go now -- thankfully not on a ferry over 7 ft seas. Gotta get a son to a photographer so his pic can go on a local artists feature calendar. Later on. Maybe we can tempt StephenB out of hiding to address some of your questions, or VJT might have some interest. But for me, I'm off NOW. GEM of TKI kairosfocus

Caveat: I am no biologist. What I know about fish is that it breathes in oxygen dissolved in water, right? If you are a biologist, perhaps you could tell me what happens to fish after it is taken out of water into fresh air.

It depends on whether the fish has the ability to breath air. Why not Google "air breathing fish" or "amphibious fish"? Petrushka

KH: It is very important to bring out the insufficiency of Darwinist mechanisms to explain body plans, as the notion that blind chance and necessity driven incrementalism is good enough to explain the world of life has been entrenched to the point of being a quasi religious ideology. But, without adequate warrant. (Lewontinian, question-begging redefinitions of science do not count as good warrant; as Johnson pointed out -- cf. OP.) kairosfocus

KF

And once design is on the table, it is also a good candidate to explain body plans for more complex organisms.

But how does "design" explain anything at all other then it allows you to say "the explanation for it's origin is that it was designed". It was designed because it appears to have been designed. It was designed because it shares features with other things that we know to be designed. But that's not an "explanation" at all, it's just changing the label.

is science about the imposition of a priori materialistic ideology a la Lewontin, or is it seriously committed to the exploration of the truth about our world insofar as we may discover it and find warrant, however provisional?

Whatever science is about I doubt it's about saying "the explanation for X is Design as Darwinism has never been observed creating X" and leaving it at that. kellyhomes

5.1.1.1.8 Acipenser "Let's exam." Caveat: I am no biologist. What I know about fish is that it breathes in oxygen dissolved in water, right? If you are a biologist, perhaps you could tell me what happens to fish after it is taken out of water into fresh air. Maybe it is a stupid question, in which case you have to forgive my ignorance, but how come a chance sequence of infinitesimal changes can enable fish to start breathing in the air and decide to become something else, e.g. a pig? How exactly? Eugene S

KF,

We have caught the designer in the act, through empirically tested reliable signs.

Hmm, that sounds more like fortune telling then science to me I'm afraid. What sort of signs? Red sky at night, that sort of thing?

The issue is that there has been a major attempt to deflect the significance of such signs of design, which has now plainly failed.

No, I'd really actually quite like to know what you can tell me about the origin of life. I understand that you are felling oppressed but that's neither here nor there with regard to the question.

It is always possible to move goal posts and demand more and more proofs to arbitrarily high standard — I once saw someone who wanted to demand in effect a direct video or observation of the deep past! — but that is not the material issue.

And I know somebody that even when they were presented with such video evidence they simply refused to believe what they were seeing and constructed an elaborate explanation as to why the video was not showing what it was plainly showing. The person viewing the video never latched on to it's true meaning. So even video evidence would not suffice for that sort of person. But luckily I'm not demanding that sort of evidence! In fact, I'm not asking for evidence at all, as such. Just for what you know about either the process of getting to the shorelines or the process where bodyplans are updated millions of times over millions of years. You don't even have to support it with evidence, not yet anyway! I'm just interested in what ID says rather then what ID says Darwinism is not.

That issue is that we have a field of deep past sciences of origins. Those sciences work by inferring on traces of the past in the present in light of known best-explanation causal factors on cases where we do directly observe the process in the present.

So it really just does boil down to "people design things, life was designed" then? Somewhat disappointing, to say the least! I can't say I've observed somebody designing life from scratch and then developing it gradually for millions of years over an entire planet. So I can't personally say I've directly observed such a case.

So, we start from what we can and should credibly know about the past on such terms, then we can go on to further issues of interest.

Actually, no, I'm interested in the detail and so far nothing has been said approaching any level of detail at all.

You will see that this whole series of posts is about that first stage, as thee is a plainly ideologically driven agenda of refusal to address the issues.

Ok, I get it, you won't spill the beans as that would spoil a later post you've got planned where you go into more detail on the OOL. kellyhomes

Drs BOT & Liddle: Kindly observe the location of OOL in the TOL diagram just put up. Note from the OP, too that the pivotal issue in getting the observed vNSR based replicating cell, is an irreducibly complex, functionally specific, complex organised, code based info rich entity. Such plainly sits on an island of very specific function in a vast config space, relative to warm little ponds or whatnot. How you get from warm little ponds to the living cell, on observational evidence, without intelligence is a challenge. We know that intelligence can do the job, as Venter has given us proof of concept. On best explanation, in light of those observations and the analysis of config spaces and related statistical thermodynamics etc, the only plausible explanation -- hyperskeptical objectors notwithstanding -- is design. And once design is on the table, it is also a good candidate to explain body plans for more complex organisms. Which require even bigger increments of FSCI, dozens of times over, on earth. As to methods, designers have ever so many possible ways, which are secondary to the main input: smarts that allows bridging seas of non-functional configs, to reach islands of function. (An exploration of possible methods may be interesting and perhaps profitable, as in genetic engineering and nanomolecular engineering are significant possible fields.) But underneath all of this, is something even more important: is science about the imposition of a priori materialistic ideology a la Lewontin, or is it seriously committed to the exploration of the truth about our world insofar as we may discover it and find warrant, however provisional? If truth and integrity are key values to science, then the above is very, very important. (Just ask those who are beginning to feel the full impact of the climate-gate revelations.) If it is not, science is dead. Science as a branch of ideological politics and agendas, is simply yet another means of manipulation. (That is part of why I keep coming down so hard on Lewontin. Science, for the sake of civilisaitonal survival, has to break out of ideological, a priori materialism, etc.) And so, given how important science is, this stuff is important indeed. GEM of TKI kairosfocus

I'm sure Upright will be happy to explain. He seems like a nice, pleasant chap to me! kellyhomes

KH: We have caught the designer in the act, through empirically tested reliable signs. The issue is that there has been a major attempt to deflect the significance of such signs of design, which has now plainly failed. It is always possible to move goal posts and demand more and more proofs to arbitrarily high standard -- I once saw someone who wanted to demand in effect a direct video or observation of the deep past! -- but that is not the material issue. That issue is that we have a field of deep past sciences of origins. Those sciences work by inferring on traces of the past in the present in light of known best-explanation causal factors on cases where we do directly observe the process in the present. So, we start from what we can and should credibly know about the past on such terms, then we can go on to further issues of interest. You will see that this whole series of posts is about that first stage, as there is a plainly ideologically driven agenda of refusal to address the issues. Note what has been clipped from Lewontin -- and that can be multiplied. First things first, and not merely on a "for the sake of argument" basis. GEM of TKI kairosfocus

Kairosfocus

In short, intelligent design is an empirically observed, known sufficient cause for systems with the characteristics of biological systems.

You say "in short" but is there actually any more to it then that? I'm very interested to hear what else you/ID have to say about how we got to the "shores of information". I read all the time about how people are doing research on self catalyzing systems, lipid membranes and so on and so forth. But here you are plainly stating that the biggest mystery of all has been solved, and for some time by the casual way you state it! So, if I may ask you to expand on that, what does ID tell us specifically about the origin of life? Presumably there is more to it then "it was designed" and that's what I want to hear! What can you tell me about this ultimate, first "cause"? Was it physical, as we'd understand it, or other? Any small detail would be more then I've managed to find so far here. kellyhomes

Kellyholmes, "Yes you can" (have a fossil record of incremental genetic changes.) Okay, in Petrushka's example of mammalian inner ear evolution, what are the incremental genetic changes recorded in this record of incremental genetic changes? Produce the record, or do not call it a record of incremental changes. ScottAndrews

Well, I'm certainly not sure what it was. Elizabeth Liddle

Added a Darwinian TOL pic to show nodal root importance of OOL, whatever the rhetorical deflections may try to say. There is a Zoo shot, but not a good enough resolution. kairosfocus

Thank you kairosfocus.

In computer science, hill climbing is a mathematical optimization technique which belongs to the family of local search. It is an iterative algorithm that starts with an arbitrary solution to a problem, then attempts to find a better solution by incrementally changing a single element of the solution. If the change produces a better solution, an incremental change is made to the new solution, repeating until no further improvements can be found . . . . Hill climbing is good for finding a local optimum (a solution that cannot be improved by considering a neighboring configuration) but it is not guaranteed to find the best possible solution (the global optimum) out of all possible solutions (the search space).

If this is what you mean by a "hill climbing algorithm" it is not the same thing as an evolutionary algorithm. Evolutionary algorithms are not restricted to upward steps. This means that they are far less likely to be trapped on a local optimum. Moreover, if there are multiple dimensions to the "landscape", as there are in many evolutionary algorithms, as indeed there are in nature, a population is far less likely to get stuck on a local optimum. Indeed, in any case, the population may split, with one part staying put, and another part crossing a valley to another peak. This is especially true if some kind of cross-over algorithm is implemented, as in sexual reproduction, so that bits of genome can propagate independently through the population. This is a really important point, because the criticisms leveled at hill-climbing algorithms simply do not apply to Darwinian algorithms, as we see from the AVIDA results, in which the function EQU repeatedly evolved via a path that traversed a deep fitness "valley". Elizabeth Liddle

Yes Bot, the point went over your head. Don't sweat it. Upright BiPed

ScottAndrews

You cannot have a fossil record of incremental genetic changes.

Yes, you can.

That, and the idea that evolution supposedly resulted in the exact same change numerous times convergently despite the fact that you try to mitigate the vast probability issues by reminding everyone that it has no specific target, should be enough to set everyone’s BS meters buzzing.

Perhaps something was common to all of the situations where these changes arose? Begins with an E? And there are only so many solutions available. And only 1 set of laws of physics. Joseph believes that there is a specific target to evolution, one that is programmed in. Programmed responses (targets) to environmental triggers (more targets). So given that it's understandable, even expected, that you'd get the 'exact same change numerous times convergently'. So, I think that Joseph's point answers your question neatly. kellyhomes

They keep pulling me back in! Petrushka,

And yet we have a well preserved example of incremental changes leading to a major new function

No, no, no! In evolutionary terms, incremental changes are genetic. You cannot have a fossil record of incremental genetic changes. It I've said this before. If the hypothesis is change through incremental genetic changes, the test cannot be a series of possibly transitional fossils in which every step may consist of an unknown number of unidentified genetic changes, except that you don't even know whether they are part of a single transition and even if you did it's still beside the point. Please stop saying that the fossil record shows incremental changes. That, and the idea that evolution supposedly resulted in the exact same change numerous times convergently despite the fact that you try to mitigate the vast probability issues by reminding everyone that it has no specific target, should be enough to set everyone's BS meters buzzing. ScottAndrews

KF

The issue primarily addressed by ID is getting to the shorelines of islands of complex, specific function.

Fascinating! And what does ID tell us about nothing less then the origin of life itself?

That Darwinian theory seems to crucially pivot on the opposite, incrementalism to create great complexity

So, let's take that as a given. Let's rule out Darwinian theory as an explanation for the diversity of life that we see around us both at the micro and macro level. A constantly changing diversity reflected in the fossil record everywhere on the planet for many millions of years. Billions, more, individual organisms. Trillions. So, even if we're only considering 'bodyplan level' and above it seems to me that a very large amount of near-constant changes are required to be made, given the insufficiently of Darwinian processes, in order to generate the observed diversity in the observed timescales. Given that I find it very odd that we've never 'caught the designer in the act'. A mistake, an early version of something too early in the fossil record. A tool mark. An empty gestation bottle, who knows. Given the number of interventions required once you rule out Darwin and his processes it's a remarkable state of affairs. So, anyway, if the issue primarily addressed by ID is getting to the shorelines of islands of complex, specific function then could you tell me about that explanation please, as all I've read so far is explanations of why Darwinism is insufficient. kellyhomes

Venter et al have given proof of concept of design of biological self replicating systems by intelligent designers.

No he hasn't. Did he create a self replicating entity from the ground up? Nope, he re-engineered an existing one. You ask for direct observations of evolution, I ask for direct observations of the designer behind life designing - not of humans designing. Remember:

Advocates of such universal common descent by chance variation and fixation of new varieties by differential reproductive success, can make their case by simply showing how such Darwinian macroevolution at body plan level has actually been observed, rather than inferred ...

The same rules apply to you - I don't want an inference that life was designed because humans can design things, I want a direct observation of life being designed by the designer - because we can be pretty certain that Humans didn't design Humans. DrBot

PS: I should note that I do not mean specific methods too precisely, but am describing the pattern of tossing out a bubble of fairly nearby variants -- per Darwinian approaches, through chance-driven, blind variation -- then cumulatively going uphill until a peak is reached. kairosfocus

Dr Bot on ‘applying evolutionary thought to OOL’:

in which DrBot explains how evolution only applies to self replicators...

Dr Liddle on ‘OOL’:

In which Dr Liddle talks about self replicators ... Did you have a point? DrBot

Joseph,

Yes I have programmed and used GAs to find solutions to encryption issues.

I find this very interesting. You mention that GAs have targets programmed in but I've never heard of a GA being used in relation to encryption, could you elaborate a little more? Have you published anything on this that you could refer me to perhaps? I know a little (a little little) about both fields, but obviously I'm missing something central. kellyhomes

What are the mechanisms for air-breathing in fish? Do they require ‘huge changes’ or increments of tiny modifications?

Why not just look at modern amphibians? Or at modern fish that can survive out of water? I would say they illustrate the possibility of incremental adaptation. Petrushka

What encryption issues exactly?

I repaired encryption devices in the Army. It strikes me that encryption would be a poster child for a landscape that wouldn't support cracking via GAs. Aside from simple substitution ciphers. Certainly no commercial or military ciphers. Petrushka

"For example, I can’t see how from the classical Darwinist perspective sea creepy-crawlies could allegedly venture out without a major reorganisation as biosystems as a prerequisite to being fit for such a drastic change of habitat in the first place. Explaining such huge changes using incremental tiny modifications fixed by natural selection is simply not credible, nor, to my knowledge, is actually observed anywhere." Let's exam your presumptions a bit to see if they hold water. What are the mechanisms for air-breathing in fish? Do they require 'huge changes' or increments of tiny modifications? Acipenser

Explaining such huge changes using incremental tiny modifications fixed by natural selection is simply not credible, nor, to my knowledge, is actually observed anywhere.

And yet we have a well preserved example of incremental changes leading to a major new function, the bones of the middle ear, adapting from sound transmitted through water to sound transmitted through air. Are you arguing that because we don't have videotape, it isn't observed? This is accomplished not by inventing new proteins or new genes, but by changes in gene expression. No different in principle from the changes from wolf to teacup poodle. Petrushka

Dr Bot on 'applying evolutionary thought to OOL':

Yes, as we keep saying, and as every real scientist knows, evolution is a theory of what happens when you already function as a replicator ... When scientists study evolution they are studying the behavior of successive populations of replicators, they are NOT studying the origin of those replicators.

Dr Liddle on 'OOL':

And we don’t know, exactly, but what we do know is that any sequence that enhances the whole thing’s chances of self-replication will become more frequently represented in the population of self-replicators (logic dictates this), and so while we do not know the exact historical pathway by which these sequences came about, we can infer that in the proto-cell’s ancestry, certain sequences produced reproductively advantageous results.

Upright BiPed

Yes I have programmed and used GAs to find solutions to encryption issues.

What encryption issues exactly? It sounds like an interesting project, I'm not aware of GA's being used in encryption at all. Can you tell us more? DrBot

Dr BOT Design of functionally specific complex entities is a commonplace observation. Second, Venter et al have given proof of concept of design of biological self replicating systems by intelligent designers. In short, intelligent design is an empirically observed, known sufficient cause for systems with the characteristics of biological systems. By contrast, chance variation and natural selection simply has not met this criterion. This has been repeatedly pointed out to you. GEM of TKI kairosfocus

Dr Liddle: This is a common enough illustration of optimisation by incremental/cumulative improvement in a space characterised by an objective function. Cf e.g. Wiki as linked in the first paragraph of the original post, here. We may clip:

In computer science, hill climbing is a mathematical optimization technique which belongs to the family of local search. It is an iterative algorithm that starts with an arbitrary solution to a problem, then attempts to find a better solution by incrementally changing a single element of the solution. If the change produces a better solution, an incremental change is made to the new solution, repeating until no further improvements can be found . . . . Hill climbing is good for finding a local optimum (a solution that cannot be improved by considering a neighboring configuration) but it is not guaranteed to find the best possible solution (the global optimum) out of all possible solutions (the search space).

This of course precisely describes moving about, uphill, within an island of function. The issue primarily addressed by ID is getting to the shorelines of islands of complex, specific function. UD contributor Bartlet's paper, here, gives some useful onward thoughts in terms of Turing Machines. It is simply not the case that in general, o4r even in a plausibly large subset of reasonable cases, that incremental solutions will lead to growing complexity. For the same reason why "See Spot run," cannot plausibly be incrementally adjusted into say the original post for this thread, or a similarly complex document, one or a few letters at a time, while always being functional as a grammatically correct and meaningful English Language expression. That Darwinian theory seems to crucially pivot on the opposite, incrementalism to create great complexity [including irreducible complexity in life systems in the face of the C1 - 5 factors discussed in Post 3 of this series, cf 9.1.1.2 above, here], is telling. GEM of TKI kairosfocus

Advocates of such design, can make their case by simply showing how such design has actually been observed, rather than inferred or extrapolated ...

The biggest begged question problem on fitness landscapes is that they are all working within islands of existing function.

Yes, as we keep saying, and as every real scientist knows, evolution is a theory of what happens when you already function as a replicator. It is your own switcheroo tactic that is the problem - every time we try and debate evolution you start trying to switch the issue to OOL. When scientists study evolution they are studying the behavior of successive populations of replicators, they are NOT studying the origin of those replicators. Some other scientists are doing actual real research into the origin of life, and are trying to answer that question. You say it is begged, they are working on answers. Personally, when an ID'ist says design I say it begs the question 'By what'. Now are any ID'ists researching that question? DrBot

This explanation is also supported by a great deal of evidence, such as the existence of the Windows 7 designers. (And by the way, how did you calculate the FSCO/I?) More to the point, we know that Windows does not design itself by self-replication with heritable variance in reproductive success, so we can rule out another potent source of functional complexity. So we have two reasons for inferring an ID: 1) We have corroborative evidence that it was designed by a human being 2) We can rule out self-replication with heritable variance in reproductive success as an alternative explanation. Neither of these are the case when it comes to biological organisms. Elizabeth Liddle

So you’re saying the biological evolution happens due to a functional mechanism. How the heck does that not violate TOE?

Well, in what sense does it? Darwinian mechanisms can and do work at population level as well as individual level. Mutation rates themselves optimise, as populations with optimal mutation rates persist longer than ones with less optimal (greater, lesser) mutation rates. Elizabeth Liddle

Could you give an empirical example of a manifestation of FSCO/I that exceeds the universal probability bound, that is adequately explained only by design?

The computer code to Windows 7. If you disagree, name one other possible explanation of this other than design. Do that successfully and start writing your Noble Prize speech. uoflcard

Petrushka

What Shapiro does is compare evolution to the immune system, which steps up the rate of production for variants when challenged. ... I challenge you to find anything in it that requires intervention or non-mainstream processes.

I'm not saying it must be an interventionist supernatural force that creates all biological change. Just as Joseph says:

The immune system does what it does due to its design.

...the immune system is engineered to produce useful antibodies is this manner. You say that biological evolution follows a similar process and that this is mainstream and requires no change to TOE. The immune system is a functional mechanism. So you're saying the biological evolution happens due to a functional mechanism. How the heck does that not violate TOE? As I said in my original post:

These changes are clearly non-Darwinian, yet they are dogmatically tucked under the Darwinian cloak by saying “whatever mechanism caused this was itself formed by a Darwinian process”.

Even if there does turn out to be an autonomous, naturally-behaving mechanism that "intelligently" guides genomic change due to environmental stress, that only begs the question of where that mechanism came from. Your explanation would be a Darwinian process, again begging the question since all complex biological innovations we witness do not arise from pure Darwinian processes. uoflcard

kf: can you explain exactly what you mean by "hill-climbing"? Yes of course all Darwinian evolution starts from the base of existing minimal functionality, namely, the ability to self-replicate in the current environment. And we know that works, and that extremely complex and novel functions can evolve from there onwards. Elizabeth Liddle

Joseph: The biggest begged question problem on fitness landscapes is that they are all working within islands of existing function. That is, not only do they look for bull's-eyes, but they start from within a wider target, and use hill-climbing to walk in to the bull's-eye zones. And, it takes considerable algorithm design and usually a fair bit of tuning -- as we saw with Ev months ago -- to get to the islands of function. Targetting within targetting. But also, it is plain from especially the nature of junkyards [parts scattered together every which way] and of the possibilities for scrambling text strings, that there are many, many possible configs for a set of components, that are non-functional, actually it should be easy to see that they vastly outnumber the functional states. So, it is reasonable to accept that functionality sits on islands of function in vast seas of non-function. ID (in that light) is about how do we navigate to such islands of function, in light of the only directly observed adequate causal path: design. Once we are on such an island, we can happily hand over movement to niches to built in adaptation mechanisms, set up for robustness. (It is no accident that the actual observed cases of evolution are of such minor adaptations.) And, without the functionality that starts with integrated metabolism and replication in unicellular organisms, and goes on to embryologically, environmentally and reproductively viable complex organisms, we have no empirical basis for the tree of life model of Darwinian Macro evo. Advocates of such universal common descent by chance variation and fixation of new varieties by differential reproductive success, can make their case by simply showing how such Darwinian macroevolution at body plan level has actually been observed, rather than inferred or extrapolated on the cumulative steps assumption addressed in the OP. Since such Darwinian macroevo is commonly stated to be a FACT, even comparable to gravity, that is a reasonable expectation. The point that after a full day we are approaching 100 comments and 1,000 views -- including comments from the former publicity officer for NCSE -- but have not got a citation or a link to such a clear demonstration, should give us all pause. GEM of TKI kairosfocus

It's as directed as a GA, Joseph. Evolution in both is constrained by the fitness landscape. If you call that "directed" in a GA, then call it "directed" in nature. Or in neither. But don't use the word for one and not for the other, and then claim they are different. The crucial point is that in neither is are any solutions designed in advance, and in both each step is "blind" i.e. may be neutral, deleterious, or advantageous. Elizabeth Liddle

I though you said that GAs were your field, Joseph? Do I need to explain the concept of a fitness landscape? Of course the GA is programmed to find a solution to a problem. And the way it is programmed is to use the power of evolution, which also finds solutions to problems. What is not programmed in is a solution. That evolves, which is why you use a GA in the first place - to evolve a solution to a problem you want to solve. Elizabeth Liddle

Elizabeth:

In the sense that a GA does have a target/goal (the population has to adapt to a fitness landscape), so does evolution.

Nice bald assertion. "Fitness landscape"?

In the sense that a GA doesn’t (you don’t know the solution in advance, and it is not set as a goal), nor does evolution. GAs have a goal. The solution is not fixed but the solution is part of the DESIGN. As in the solution wouldn't have been found if the GA was not programmed to do so.

Joseph

Elizabeth:

A GA is “blind” Joseph.

Nio, it isn't. GAs have targets/ goals that they seek to achieve.

As for “undirected” – it is “directed” in the sense that evolution is also “directed” – by the environment.

Darwinian evolution isn't directed by anything. Joseph

Yes, it evolves within the confines of the favourable parameter settings (made possible initially via intelligent intervention). Call this evolution, I have no objection. I prefer calling it adaptation to always varying environments. This adaptation is within the boundaries where a fitness lanscape is defined, not evolution in the sense of bionovelty emerging spontaneously and incrementally by small amounts which are then fixed by natural selection. A classical example is the shapes of finch beaks. What about more significant changes (tissue/organ/body plan levels)? Highly constrained complex systems, which biosystems are indeed, are typically brittle i.e. they are highly sensitive to parameter tuning. In other words, even a small amount of "novelty" i.e. a small deviation from the tuned parameter values may prove fatal to the system. For example, I can't see how from the classical Darwinist perspective sea creepy-crawlies could allegedly venture out without a major reorganisation as biosystems as a prerequisite to being fit for such a drastic change of habitat in the first place. Explaining such huge changes using incremental tiny modifications fixed by natural selection is simply not credible, nor, to my knowledge, is actually observed anywhere. Eugene S

One more note, and then I really am off. I hope. I am not dismissing the fact that someone can eyeball these various causes and suspect that they might be related. I'm not so blind that I can't see what you see and understand why you want them together. That is not where I am finding fault. But when something seems to make sense, when a causes and effects appear to be connected, that is when you determine whether you can formulate it into a specific, testable hypothesis. If you can't do that, it never goes beyond speculation. If you can do that, then you must test the hypothesis. You cannot skip these steps and proclaim that you have identified the causes of an effect. It's a shortcut around science. It's the leap from speculation to [provisional] certainty. You can't go that way, even if lots of people, even scientists, say otherwise. ScottAndrews

A GA is "blind" Joseph. As for "undirected" - it is "directed" in the sense that evolution is also "directed" - by the environment. There is no other direction in either case. Elizabeth Liddle

In the sense that a GA does have a target/goal (the population has to adapt to a fitness landscape), so does evolution. In the sense that a GA doesn't (you don't know the solution in advance, and it is not set as a goal), nor does evolution. Elizabeth Liddle

Petrushka, You're still not bringing it all together. You're talking about small variations in bones but leaving out the underlying genetic or regulatory changes and omitting the specific reasons for the selection of each step. As I've said repeatedly, I know that it is unrealistic to ask for such detail in every single case of proposed evolution. A few detailed examples would suffice. That is what separates science from assuming that correlation indicates causation. You cannot toss together a bunch of causes and attribute an effect to them. In this case there are good reasons to doubt that the causes are sufficient. But that doesn't even matter. You have to put all the pieces together and make sure they do what you think they do. There is no way to move that burden to someone else. It's yours. Or Nick's. Whoever. You claim that a series of causes correlate to form a process of accumulating function. Then you show us evidence of the individual causes, which are already well known, and accuse us of ignorance or ignoring evidence. We know about variation. We know about selection. Relate variation at the incremental genetic level to specific instances of selection, fit in the population genetics, and chain a bunch of them together. Otherwise you're extrapolating, which in this case means an supported guess. I need to drop off this for while. Too much to do. ScottAndrews

Why did you need to use a GA to find your solution? Elizabeth Liddle

Yes I have programmed and used GAs to find solutions to encryption issues.

As for the antenna GA – sure it has a goal, which is to maximise the gain. That’s the fitness function. It’s not the design of the antenna.

the goal was to find an antenna that fit the specifcations. The program reached the goal. The current theory of evolutuion- NO GOALS AVIDA does NOT mimic Darwinism, that is why it is bogus. Joseph

Elizabeth, There is a target/ goal, period, end of story. How the GA reaches that goal is not specified, nor does it need to be. And BTW ID is NOT anti-evolution- designed to evolve/ evolved by design. And design is a natural process. ID argues against blind, undirected processes Joseph

Yes, as expressed in the fitness function. Just as in nature, it found naturally in the environment. What is not a "goal" in either case is a specific solution. That has to evolve, aka "found". There may be many, and, of course, in life, there are. That's why, in your wiki quote, it describes a GA as "a search heuristic that mimics the process of natural evolution". Elizabeth Liddle

GAs are your field? Can you give me an example? As for the antenna GA - sure it has a goal, which is to maximise the gain. That's the fitness function. It's not the design of the antenna. If the evolved design of the antenna was programmed in as a "goal" then there would be no point in running the GA. AVIDA is not "bogus", because, as with the antenna GA, the evolved solution is not "programmed in". Only the fitness function (and the starting population of course). Elizabeth Liddle

wikipedia on GAs:

A genetic algorithm (GA) is a search heuristic that mimics the process of natural evolution. This heuristic is routinely used to generate useful solutions to optimization and search problems. Genetic algorithms belong to the larger class of evolutionary algorithms (EA), which generate solutions to optimization problems using techniques inspired by natural evolution, such as inheritance, mutation, selection, and crossover.

There you have it- GAs have a goal/ target.... Joseph

Elizabeth, GAs are MY fiel and they do have tarhets/ goals. The antenna GA is one such GA with a target/ goal. AVIDA OTOH is bogus for all the reasons provided. Joseph

Not in the sense you are interpreting the words. The "Target" of a GA is the evolution of a virtual organism that can solve a problem. That is identical to the "Target" of a biological population in an environment - to evolve a solution that maximises its fitness within that environment. The "Target" in a GA, therefore, is set up as the "environment" that the "virtual organisms" have to evolve to survive well in. But the solution to that problem, or set of problems, is not "programmed in". It evolves, just as in nature. And different runs will often give you different solutions, again, as in nature. Elizabeth Liddle

GAs have targets. GAs have goals. That is why they were designed- to solve a problem. Joseph

Petrushka:

Or in the Lenski experiment or the Thornton work, three steps, including one that would, on its own, be detrimental.

The Lenski experiment supports baraminology and Thorton's doesn't support your position.

Not to mention the fact that the entire vertebrate lineage does not require any new proteins. (There are some, but their novelties are not critical to any function.)

Reference please.

Vertebrate evolution is mostly a succession of small changes in the quantity and timing of events. This includes the evolution of the middle ear bones.

Nice unsupportable bald assertion.

So when Behe discusses the difficulty of evolving new proteins, he is discussing something that happened for the most part billions of years before multi-celled organisms, in populations large enough to try every possible variation.

Behe discusses the difficulty of blind and undirected chemical processeproducing proteins, and so far he remains unrefuted. Joseph

Petrushka:

That is why you can trace a person’s lineage by the nested hierarchy of alleles.

Descent with modification does not predict/ expect a nested hierarchy. Joseph

DrREC:

My genome is enormous, but I doubt it contains more than the universal probability bound of information MORE than that of my parents.

Question-begging. Joseph

There still isn't any way to test the premise of universal common descent so no one knows if the tools are in place or not. As for mutations other than point mutations, well there still isn't any justification with calling them blind, undirected processes. The immune system does what it does due to its design. I challenge evos to find positive evidence to support their claims. Joseph

Petrushka:

I have noticed that ID argues against a version of evolution that doesn’t correspond to anything used to guide biological research.

I have noticed that ID argues against the version of evolution promoted by evolutionary biologists. OTOH all Petrushka has is a bald assertion. Go figure... Joseph

Hey I think I'm about to figure this 'projection' thing out. Is it like when neo-Darwinists built an entire missing link, between man and apes, based on a single tooth that was later found to be a pig's tooth?

EVOLUTION FORGERIES EPISODE 3- NEBRASKA MAN - video http://www.youtube.com/watch?v=Fz1kTR_P75A EVOLUTION FORGERIES Excerpt: Many authorities gave Osborn their support. Based on this single tooth, reconstructions of the Nebraska man's head and body were drawn. Moreover, Nebraska man was even pictured along with his wife and children, as a whole family in a natural setting. All of these scenarios were developed from just one tooth. Evolutionist circles placed such faith in this "ghost man" that when a researcher named William Bryan opposed these biased conclusions relying on a single tooth, he was harshly criticised. http://www.harunyahya.com/books/darwinism/atlas_creation/atlas_creation_17.php

Now that has to be getting really close to what you guys mean by projection!?! Shoot, neo-Darwinists 'projected' a entire non-existent species based on a single pig's tooth. bornagain77

Dr Rec, Re: ID uses the irreducible complexity argument without ever demonstrating irreducible complexity–it is an assumption about a complex looking system, not anything proven. Pardon, what are you talking about? (cf. ID founds 3, here.) Gene knockout techniques DEPEND on the reality of IC to identify function of genes. Notice ID researcher Scott Minnich's testimony on his flagellum studies, Day 20 the infamous Dover Trial, as can be seen in the just linked, with onward link:

Scott Minnich has properly tested for irreducible complexity through genetic knock-out experiments he performed in his own laboratory at the University of Idaho. He presented this evidence during the Dover trial, which showed that the bacterial flagellum is irreducibly complex with respect to its complement of thirty-five genes. As Minnich testified: “One mutation, one part knock out, it can’t swim. Put that single gene back in we restore motility. Same thing over here. We put, knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We’ve done that with all 35 components of the flagellum, and we get the same effect.” [Dover Trial, Day 20 PM Testimony, pp. 107-108. Unfortunately, Judge Jones simply ignored this fact reported by the researcher who did the work, in the open court room.]

That should be plain enough, and it is a bonus that Minnich runs a lab that has been doing ID based research for years. But, the media and darwinist spin doctors were so busy twisting what happened at Dover into pretzels that this has somehow not got the headlines it needs. In addition, in complex systems all around us, it is routine to have an irreducible -- all parts in the core are necessary causal factors -- core. Indeed, even a fire is IC: the heat, oxidiser and fuel are necessary components. IC is an empirical fact, not an easily dismissible "assumption." The only question is whether a particular biosystem is IC, and plainly many of them are, or are serious candidates to be such. But, all of this is a switcheroo: in fact the onus is on those who claim common descent through incremental chance occasioned by chance variation and culling out of less successful variations, to demonstrate that this works, not only for microevo but for body plan level macroevo. Until that is done, what is going on is little more than imposition of Lewontinian materialist a prioris on origins science. Which is a key point of the Original Post. GEM of TKI kairosfocus

Homologies run into the problem of evident code libraries as may be seen from mosaic creatures, such as the platypus -- which is so odd that it was at first thought to be a fake by scientists. (So obvious is its mosaic character.) Of this strange creature -- an egg-laying, milk producing, duck-billed, venomous, beaver-tailed and web-footed mammal with some 18,000 genes -- it has been said that its set of genes "contain alive-and-well representatives from mammals, birds and reptiles." It is a mosaic at body-plan and molecular levels. kairosfocus

Projection much? That’s MASTER projectionist to you, sir!,,, Well, exactly what is projection? Is it something like when neo-Darwinists name a ancient fossil, that looks exactly like a modern species, a completely different genus and species name simply because it does not fit their preconceived neo-Darwinian worldview??? i.e. that they 'project' their preconceived bias onto the evidence instead of letting the evidence speak for itself???

Living Fossils - video http://www.youtube.com/user/EvolutionVsCreation#p/u/12/y6PjtmQbP7U

Or is projection something more like when neo-Darwinists pretend that materialism is the ultimate basis of reality, from which to form the foundation of their atheistic worldview, when in fact the 'material' universe is now shown, conclusively, to be neither self-originating nor self-sustaining in the first place??? i.e. when they 'project' their view of reality onto reality even though reality is not anything like what they have apriori 'projected' onto it??? Or is that just plain old fashioned self-deception, 'Denialism', of reality in the face of all contrary evidence? bornagain77

Thanks, took about 2 hrs in 7 ft seas, thankfully running WITH them is much nicer. How I miss the catamarans! kairosfocus

Projection much?

That's MASTER projectionist to you, sir! ;) paragwinn

And a song DrREC; Creed - Six Feet http://www.youtube.com/v/aQ9GrZ3CEyY&fs=1&source=uds&autoplay=1 bornagain77

Petrushka, When I say that there is no hypothesis, you're supposed to say, "Why, yes there is. There are several. Here is one." Or something to that effect. But if you would rather concede, that's fine. ScottAndrews

PS: Seven foot seas. kairosfocus

Distractive and irrelevant. Again, the SOURCE of the variability -- contingency -- is the chance variability of initial and/or intervening circumstances, not the mechanical necessity of the dynamical system. The rhetorical attempt to create the impression that there is a third source of high contingency than chance and/or design fails. Mechanical necessity is not responsible for high contingency, period. kairosfocus

We’re debating against a hypothesis that does not exist.

I have noticed that ID argues against a version of evolution that doesn't correspond to anything used to guide biological research. Petrushka

Inspirational quote for your future experiment DrREC:

GILBERT NEWTON LEWIS: AMERICAN CHEMIST (1875-1946) "I have attempted to give you a glimpse...of what there may be of soul in chemistry. But it may have been in vain. Perchance the chemist is already damned and the guardian the blackest. But if the chemist has lost his soul, he will not have lost his courage and as he descends into the inferno, sees the rows of glowing furnaces and sniffs the homey fumes of brimstone, he will call out-: 'Asmodeus, hand me a test-tube.'"(1) Gilbert Newton Lewis http://www.woodrow.org/teachers/ci/1992/Lewis.html

further notes:

Time dilation Excerpt: Time dilation: special vs. general theories of relativity: In Albert Einstein's theories of relativity, time dilation in these two circumstances can be summarized: 1. --In special relativity (or, hypothetically far from all gravitational mass), clocks that are moving with respect to an inertial system of observation are measured to be running slower. (i.e. For any observer accelerating, hypothetically, to the speed of light, time, as we understand it, will come to a complete stop). 2.--In general relativity, clocks at lower potentials in a gravitational field—such as in closer proximity to a planet—are found to be running slower. http://en.wikipedia.org/wiki/Time_dilation

i.e. As with any observer accelerating to the speed of light, it is found that for any observer falling into the event horizon of a black hole, that time, as we understand it, will come to a complete stop for them.

Albert Einstein - Special Relativity - Insight Into Eternity - 'thought experiment' video http://www.metacafe.com/w/6545941/

bornagain77

Now DrREC, being the helpful guy I am, always trying to help you atheists out when i get a chance, I've been trying to piece together a experiment that would prove once and for all, for everyone to see, that RANDOM variation plus undirected natural selection can produce functional proteins. Now I about got the RANDOM part of the experiment down for you! I've searched for the maximum source of RANDOMNESS I could find in the universe, (since the god of randomness is who who claim for your creator), and I think I've found it; First:

Thermodynamics - 3.1 Entropy Excerpt: Entropy - A measure of the amount of randomness or disorder in a system. http://www.saskschools.ca/curr_content/chem30_05/1_energy/energy3_1.htm

Thus, the more entropy a system has the more randomness it will generate for our experiment to find a RANDOM functional protein. And if we ask, 'what is the maximum source of entropy, i.e. RANDOMNESS, in the universe?', we find this:

Entropy of the Universe - Hugh Ross - May 2010 Excerpt: Egan and Lineweaver found that supermassive black holes are the largest contributor to the observable universe’s entropy. They showed that these supermassive black holes contribute about 30 times more entropy than what the previous research teams estimated. http://www.reasons.org/entropy-universe

Plus DrREC for a added bonus for you guys, being the helpful guy I am, I found that if you find a supermassive blackhole you might just start to overcome your homochirality problem as well:

Homochirality and Darwin: part 2 - Robert Sheldon - May 2010 Excerpt: With regard to the deniers who think homochirality is not much of a problem, I only ask whether a solution requiring multiple massive magnetized black-hole supernovae doesn't imply there is at least a small difficulty to overcome? A difficulty, perhaps, that points to the non-random nature of life in the cosmos? http://procrustes.blogtownhall.com/page3

But of course there is the problem with actually getting you guys to the blackhole to actually do your experiment. So that you may try to RANDOMLY generate a functional protein, not to mention the problem of you guys trying to survive being stretched into as a piece of spaghetti by the extreme warping of space-time near the blackhole. But what the hey, it is just a little sacrifice for 'science' right?!?! At least you guys will have a maximum source of randomness to work with in you experiments!!! But there is another problem I probably need to tell you about before you pack up and go off to the blackhole in order to prove to the world that your 'god of randomness' can create all things,

"Gain in entropy always means loss of information, and nothing more." Gilbert Newton Lewis - Eminent Chemist "Is there a real connection between entropy in physics and the entropy of information? ....The equations of information theory and the second law are the same, suggesting that the idea of entropy is something fundamental..." Tom Siegfried, Dallas Morning News, 5/14/90 - Quotes attributed to Robert W. Lucky, Ex. Director of Research, AT&T, Bell Laboratories & John A. Wheeler, of Princeton & Univ. of TX, Austin in the article http://www.bible.ca/tracks/dp-lawsScience.htm

But what the hey, you don't need no stinking equations anyway do you DrREC!?! bornagain77

I learned well from you guys!!! :) bornagain77

But the completely deterministic system is hugely magnifying some arbitrarily tiny initial variation. Without the deterministic system, you'd have just tiny, unnoticeable variations in your system. I believe this is basically the same thing as the "butterfly effect." NickMatzke_UD

DrREC, Molecular evolution does not explain the relationship between variation, the steps, and differential reproduction. There's not even a consensus within the field on which factors affect it most. This is typical. One person studies molecular differences. Another compares fossils looking for apparent trends. Another observes environmental pressures on living populations. But no one brings it all together. How do molecular changes, the phenotypic or behavioral changes they produce, and a specific selective pressure resulting in differential reproduction all come together and produce significant evolutionary change? (What is significant evolutionary change? For the sake of these discussions we should set some goalposts, because that it admittedly vague.) Before it can be generalized it must be hypothesized and tested in specific cases, and no one has done that. Not even a hypothesis. ScottAndrews

Petrushka, You are saying you have a triangle and showing me three lines. I'm not denying any of the lines. I'm not denying that there is variation. I'm not denying that there is differential reproduction. I'm not denying that some creatures appear to ancestral or related to others. You wonder why we don't see your point because you keep pointing out these three lines. We don't even necessarily disagree with you, so why don't we see it? It's because you have three lines, but there's more to a triangle than three lines. You have to connect them all to form something more than just lines. There is no evidence connecting them all together at the same time. There isn't even a hypothesis. You might correctly state that, triangle or not (I just picked a triangle, I don't mean anything by it) you still have multiple lines of evidence supporting an interpretation. But they do not support that interpretation exclusively, and there is lots of evidence that contradicts even the vague unification of them to explain all diversity. But that's beside the point. There is no hypothesis that combines individual variations, differential reproduction resulting from a specific pressure or need, and common ancestry between functionally different life forms. Darwinists have put us in an impossible position. We're debating against a hypothesis that does not exist. Only if winning is the point is that something to be proud of. ScottAndrews

"You guys need to roll up you sleeves and do the actual experimental work " Projection much? What experimental work have you ever done? DrREC

Quite a trick-call all studies of evolution 'sequence comparisons' and rule out directed evolution as 'designed' experiments, and you get to ignore the data! Well done! Except that you keep using sequence comparisons when you want to, you have no good reason to dismiss them, and directed evolution uses random inputs. DrREC

Matzke's paper has a table of homologies that I think are more legit. http://home.planet.nl/~gkorthof/pdf/Pallen_Matzke.pdf Starbuck

Moreover DrREC, you don't seem to grasp that if you use 'natural genetic engineering', as Shapiro termed it, to try to prove neo-darwinian processes, you still have completely failed to prove that purely neo-Darwinian processes (RANDOM variation and Natural Selection) have done what you have claimed they have done. As far as i'm concerned the variation within 'kind' is the result of 'top down' design, when 'natural genetic engineering' is involved!!!

Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf

You guys need to roll up you sleeves and do the actual experimental work rather than shoehorning your conclusion into evidence that doesn't even belong to you!!! bornagain77

Sure, there is debate over it. Nevertheless, it is a hell of a stretch to say the flagella MUST be irreducibly complex, and its components could have come from no other functional system or subsystem, despite what is known about it. ID uses the irreducible complexity argument without ever demonstrating irreducible complexity--it is an assumption about a complex looking system, not anything proven. DrREC

The homology within these proteins is probably pure artifact (despite being published in PNAS). This view is held by many (if not nearly all) microbial evolution people, including Eugene Koonin, Peter Gogarten, Mark Pallen etc... For a thorough explanation see: http://www.pandasthumb.org/archives/2007/04/flagellum_evolu_3.html Starbuck

Let's see, we have a failure to communicate, i asked for a actual demonstration of neo-Darwinian processes to transform a protein, and you give me sequence comparisons??? bornagain77

"Shoot DrREC, much less than showing me a molecular machine arising by chance (which should be a piece of cake for your darwinian god), how about the much more modest task of actually demonstrating one protein can transform into another?!" Thornton and Benner's groups do exactly that- One example is the duplication and diversifications of aromatases that allowed pigs to have large litters: http://www.ffame.org/pubs/bmcbio2.19.pdf Or the arrival of digestive RNAses from non-digestive ancestors, allowing ruminants to digest the bacteria they cultivate in their stomachs. http://www.nature.com/nature/journal/v374/n6517/abs/374057a0.html Directed evolution approaches convert enzyme specificities routinely. DrREC

BA77@5.5.1.3.6 "Oh goody another sequence similarity study" You do know many of your citations, including the ORFan ones are based on sequence comparison? "And the actual scientific demonstration that neo-Darwinism is capable of building molecular machines, that vastly surpass man-made machines in efficiency and power, is where exactly other than in your blind faith that it did happen by pure accident?" It is in the paper I provided you. I don't see any effort on your part to refute it, just a quote that predates the paper, and some usual links.... DrREC

Shoot DrREC, much less than showing me a molecular machine arising by chance (which should be a piece of cake for your darwinian god), how about the much more modest task of actually demonstrating one protein can transform into another?!? What makes matters much worse for the materialist is that he will try to assert that existing functional proteins of one structure can easily mutate into other functional proteins, of a completely different structure or function, by pure chance. Yet once again the empirical evidence betrays the materialist. The proteins that are found in life are shown to be highly constrained in their ability to evolve into other proteins:

Dollo’s law, the symmetry of time, and the edge of evolution - Michael Behe - Oct 2009 Excerpt: Nature has recently published an interesting paper which places severe limits on Darwinian evolution.,,, A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses. http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim.html Severe Limits to Darwinian Evolution: - Michael Behe - Oct. 2009 Excerpt: The immediate, obvious implication is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on.,,,Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed. http://www.evolutionnews.org/2009/10/severe_limits_to_darwinian_evo.html#more Wheel of Fortune: New Work by Thornton's Group Supports Time-Asymmetric Dollo's Law - Michael Behe - October 5, 2011 Excerpt: Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection. http://www.evolutionnews.org/2011/10/wheel_of_fortune_new_work_by_t051621.html Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, http://www.ncbi.nlm.nih.gov/pubmed/19765975 The Evolutionary Accessibility of New Enzyme Functions: A Case Study from the Biotin Pathway - Ann K. Gauger and Douglas D. Axe - April 2011 Excerpt: We infer from the mutants examined that successful functional conversion would in this case require seven or more nucleotide substitutions. But evolutionary innovations requiring that many changes would be extraordinarily rare, becoming probable only on timescales much longer than the age of life on earth. http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1/BIO-C.2011.1 When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/ Corticosteroid Receptors in Vertebrates: Luck or Design? - Ann Gauger - October 11, 2011 Excerpt: if merely changing binding preferences is hard, even when you start with the right ancestral form, then converting an enzyme to a new function is completely beyond the reach of unguided evolution, no matter where you start. http://www.evolutionnews.org/2011/10/luck_or_design051801.html “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed - along with the organism carrying it.” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) "A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble." Problems in Protein Evolution: http://www.cs.unc.edu/~plaisted/ce/blocked.html Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors - Doug Axe Excerpt: Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. http://nsmserver2.fullerton.edu/departments/chemistry/evolution_creation/web/AxeProteinEvolution.pdf

bornagain77

Oh goody another sequence similarity study that presupposes its conclusion in its analysis:

'Stepwise formation of the bacterial flagellar system'

And the actual scientific demonstration that neo-Darwinism is capable of building molecular machines, that vastly surpass man-made machines in efficiency and power, is where exactly other than in your blind faith that it did happen by pure accident?

Articles and Videos on Molecular Motors http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=en Michael Behe - Life Reeks Of Design - 2010 - video http://www.metacafe.com/watch/5066181

And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.

"There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist

The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,,

‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,,

Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,,

,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology

bornagain77

BA77@5.5.1.3.5 "DrREC, you ask;; Do you think orfans are signs of design? You bet!!!" How did you detect the design? Why don't you use one as an example. DrREC

DrREC, you ask;; Do you think orfans are signs of design? You bet!!!

ORFan Genes Challenge Common Descent - Paul Nelson - video http://vimeo.com/17135166 Estimating the size of the bacterial pan-genome - Pascal Lapierre and J. Peter Gogarten - 2008 Excerpt: We have found >139 000 rare (ORFan) gene families scattered throughout the bacterial genomes included in this study. The finding that the fitted exponential function approaches a plateau indicates an open pan-genome (i.e. the bacterial protein universe is of infinite size); a finding supported through extrapolation using a Kezdy-Swinbourne plot (Figure S3). This does not exclude the possibility that, with many more sampled genomes, the number of novel genes per additional genome might ultimately decline; however, our analyses and those presented in Ref. [11] do not provide any indication for such a decline and confirm earlier observations that many new protein families with few members remain to be discovered. http://www.paulyu.org/wp-content/uploads/2010/02/Estimating-the-size-of-the-bacterial-pan-genome.pdf

bornagain77

Corrected link; https://uncommondesc.wpengine.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-6/#comment-358547 bornagain77

The contingency across runs of such a system comes from the randomness in the initial conditions, not from the mechanical necessity. The chaotic behaviour is due to sensitive dependence on initial -- and sometimes intervening -- conditions, NOT the mechanical necessity. Gotta go. kairosfocus

There is no reproduction in GAs, just a simulation model. The algorithms are optimising or something close to that, and do so precisely by hill climbing up the slope of a so-called fitness function. In life forms, we see varieties, and the usual notion is that the fitter ones survive and dominate pops across time. However, just the very fact of a viable organism with a body plan puts us on an island of function. And, adaptation to niches is about small variations within the body plan. Where the evolutionary materialistic paradigm goes astray, is when they extrapolate from variations and adaptations within a body plan, to the inferred origin of said plans by same means, never mind the problems with incrementalism as outlined in the OP. Gotta go real soon. kairosfocus

Safe travels! DrREC

Ferry from Antigua to Montserrat. Yellow hole is a notoriously rough patch north of the latter, I think a volcanic seamount of yellowish colour. kairosfocus

There is no hill-like function. There is no target. There is the automatic fact that some variants have different reproductive success. In the case of neutral or neutral variation, the difference really is chance, and multiple variants can coexist. We know that multiple variants can coexist because we see it in all populations across all species. Petrushka

bornagain, These references fall shy of a coherent argument. Do you think orfans are signs of design? Orfan genes have no detectable homology with other genomes. Sometimes other genomes get sequenced, and homology is found. Some may be spurious detection of a non-orf The genome annotators aren't hiding anything, just coming up with metrics to detect and catalog human genes. Many approaches are taken. If someone detects transcription, translation, and function within those, they'll be re-annotated for certain. And Howard Ochman may not be the support you're looking for: "Stepwise formation of the bacterial flagellar system" Renyi Liu and Howard Ochman PNAS 2007;104;7116-7121 oops DrREC

Did you get the link wrong? the term ORFans does not occur either at the UD page or in the Douglas Axe paper. You also fail to provide any reason why a non-coding region cannot be dropped from a lineage. Now if the region were coding, and chimpanzees had an equivalent but different region, that could present a problem, but there's no reason why a non-functional region can't be dropped. Petrushka

One, that ducks the observed fact that there are exactly two observed sources of highly contingent outcomes: chance [e.g. what would happen by tossing a tray of dice] and intelligent arrangement [e.g. arranging the same tray of dice in a specific pattern]. Mechanical necessity [e.g. a dropped heavy object reliably falls at 9.8 m/s2 near earth's surface] is not a source of high contingency. So, in the combination of blind chance and mechanical necessity, the highly contingent outcomes would be coming from the chance component.

There is a third possibility -- a completely deterministic system exhibiting chaotic behavior, with just a teeny tiny amount of randomness/uncertainty at the beginning. NickMatzke_UD

"Pardon, gotta go catch a ferry and dance with the notorious Yellow Hole." Colorful, but apparently non-universal idiom. Curious what it means. DrREC

Folks: Thanks for the thoughts. See you all later on. GEM of TKI kairosfocus

Petrushka: Pardon, gotta go catch a ferry and dance with the notorious Yellow Hole. Once you have a hill-like objective function that covers the range of acceptable variation, and a hill-climbing algorithm that5 is tuned to work in that situation -- a bit ticklish, you have targetted search. No ifs, ands or buts. However, so long as things are implicit rather than explicit, or even just lost in code comment lines [as with Schneider's Ev], a great many people will miss the targetting. And BTW, I am not the one suggesting that GA's and EAs more broadly show such targetting behavious, it is the proposers of novelty search as an alternative. GEM of TKI kairosfocus

please carefully note having no homology (and often no structural similarity) to proteins in any other genome. bornagain77

as to this neo-Darwinian claim:

Comparative genomics supports stepwise change and common descent. The more genomes we sequence, the more apparent it becomes that lineages of proteins are ancient, and that even modern proteins have sequences that can be traced back billions of years.

Yet that is not the case at all:

Dr. Howard Ochman - Dept. of Biochemistry at the University of Arizona Excerpt of Proposal: The aims of this proposal are to investigate this enigmatic class of genes by elucidating the source and functions of “ORFans”, i.e., sequences within a genome that encode proteins having no homology (and often no structural similarity) to proteins in any other genome. Moreover, the uniqueness of ORFan genes prohibits use of any of homology-based methods that have traditionally been employed to establish gene function.,,, Although it has been hypothesized that ORFans might represent non-coding regions rather than actual genes, we have recently established that the vast majority that ORFans present in the E. coli genome are under selective constraints and encode functional proteins. https://uncommondesc.wpengine.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-5/#comment-358868

Further note:

Study Reports a Whopping "23% of Our Genome" Contradicts Standard Human-Ape Evolutionary Phylogeny - Casey Luskin - June 2011 Excerpt: For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. (of note; 1/3 of our genes is equal to about 7000 genes that we do not share with chimpanzees) http://www.evolutionnews.org/2011/06/study_reports_a_whopping_23_of047041.html

Moreover it appears that even though functional proteins are astronomically rare in sequence space, that there is some startling evidence that unique protein sequences may reside within, or even be 'tailored' for, each individual person;

New level of genetic diversity in human RNA sequences uncovered Excerpt: A detailed comparison of DNA and RNA in human cells has uncovered a surprising number of cases where the corresponding sequences are not, as has long been assumed, identical. The RNA-DNA differences generate proteins that do not precisely match the genes that encode them.,,, Nearly half of the RDDs uncovered in the new study cannot be explained by the activity of deaminase enzymes, however, indicating that unknown processes must be modifying the RNA sequence, either during or after transcription. ,,, Although all of the individuals analyzed in the study had a large number of RDDs, there was a great deal of variability in the specific RDDs found in each person's genetic material." http://www.physorg.com/news/2011-05-genetic-diversity-human-rna-sequences.html

bornagain77

Perhaps you failed to notice that the lost "genes" have no coding function, and being lost in a cousin lineage has no apparent negative consequences. Petrushka

From your last link:

More broadly, the research reveals that little invention of genes has occurred since mammalian ancestors diverged from the non-mammalian lineage. “There’s no real creativity going on in the mammalian genome,” explained Clamp. That means that the number, structure, and function of protein-coding genes are not expected to differ very much from mammal to mammal, so what makes humans different from mice and dogs likely lies outside this realm of the genome.

Exactly what I said. Petrushka

short refutation of the preceding bunk:

Genomes of similar species - Cornelius Hunter PhD. Excerpt; As one science writer put it, “an astonishing 12 per cent of recently evolved genes in fruit flies appear to have evolved from scratch.” [10] These so-called novel genes would have had to have evolved over a few million years—a time period previously considered to allow only for minor genetic changes. [11,12] ,,, etc.. etc… http://www.darwinspredictions.com/#_4.2_Genomes_of A New Model for Evolution: A Rhizome - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html

but hey I guess if neo-Darwinists are allowed to throw out all unique sequences that don't fit what their Darwinian bias tells them to expect, then you can say pretty much what petrushka said and get away with it:

Human Gene Count Tumbles Again – 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes.,,, Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. (The 1,177 ORFan genes in humans are completely unique to our lineage) http://www.sciencedaily.com/releases/2008/01/080113161406.htm

In fact it turns out that the authors of the preceding ‘kick the ORFans out in the street’ paper actually did know that there was clear and unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore that strong evidence in favor of their preconceived evolutionary bias of forcing the genetic sequences of chimps and humans to be as similar as possible. That is EXACTLY how you ARE NOT suppose to practice science!!!: https://uncommondesc.wpengine.com/intelligent-design/proteins-fold-as-darwin-crumbles/comment-page-4/#comment-358547 bornagain77

You’re stating exactly what we know about evolution. It can reach any point that is one step away.

Or in the Lenski experiment or the Thornton work, three steps, including one that would, on its own, be detrimental. Not to mention the fact that the entire vertebrate lineage does not require any new proteins. (There are some, but their novelties are not critical to any function.) Vertebrate evolution is mostly a succession of small changes in the quantity and timing of events. This includes the evolution of the middle ear bones. So when Behe discusses the difficulty of evolving new proteins, he is discussing something that happened for the most part billions of years before multi-celled organisms, in populations large enough to try every possible variation. Petrushka

One final comment. Comparative genomics supports stepwise change and common descent. The more genomes we sequence, the more apparent it becomes that lineages of proteins are ancient, and that even modern proteins have sequences that can be traced back billions of years. Petrushka

"If you can’t show us a pathway made of steps, you cannot support the theory." That is what the work or Steven Benner, or Joe Thornton, or anyone studying molecular evolution does. They study the molecular steps in evolutionary transitions. DrREC

One, that ducks the observed fact that there are exactly two observed sources of highly contingent outcomes: chance [e.g. what would happen by tossing a tray of dice] and intelligent arrangement [e.g. arranging the same tray of dice in a specific pattern].

One can observe, as in the Lenski experiment, that a relatively small population of bacteria can test or sample every possible one-step change in it's genome in a couple of decades. There is no element of chance required. The population can buy every possible lottery ticket. It makes no difference whether the ticket numbers are sampled randomly or sequentially, they will all be tried. Nearly all proteins have been created by microbes in this way, nearly all of them in the first billion years of life, billions of years before the Cambrian. That's according to Shapiro and Koonin. There are a few new proteins in mammals, but there are no known protein differences separating one mammal from another that are essential or required. Mammal divergence required no new proteins at all. When you consider that there is no element of chance required for microbes to find all possible one-step variants, what is left is reproductive success. One can observe that many variants are synonyms, many are equivalent, and many are nearly equivalent, and an occasional one is an improvement. any of these can survive in a population and form the basis for further change. Petrushka

Petrushka,

It tests every state that is one step away from the current state.

You're stating exactly what we know about evolution. It can reach any point that is one step away. But you can't use evolution to explain anything beyond that if you don't know what the intermediate steps are and whether they are reachable in one step. Instead you show a series of fossils to demonstrate a small change, but you don't even attempt to say what the individual steps are. The steps are mutations which are selected. We both know that you cannot determine that from fossils. We know what the theory is. It's steps. Show us pathways made of steps. Even if a series of fossils are in fact transitional, they are not steps. If you can't show us a pathway made of steps, you cannot support the theory. Period. ScottAndrews

In such situations, rewarding resemblance to the goal does not respect the intermediate steps that lead to the goal, often causing search to fail . . . .

There is no goal. There is differential reproductive success. Petrushka

The reason for this phenomenon is that sometimes the intermediate steps to the goal do not resemble the goal itself.

There is no goal or target. There is differential reproductive success. Petrushka

Well let's start with this:

evolutionary search is usually driven by measuring how close the current candidate solution is to the objective.

Wrong in almost every possible way. a GA does not have an objective or target (except for some toy versions). A Ga has a measure of whether one variant is better than another. Not at all the same thing. For example, in the traveling salesman problem, there is no way to know what the correct solution is, but one can tell whether one route is shorter than another. This is a critical distinction that determines whether evolution will work in a particular instance. It is certainly possible to have functional spaces that do not support evolution. The key concept in evolution is not direction. It is comparison of currently existing variants. In biological evolution, the comparison is automatic. Individuals differ in the number of descendents. Petrushka

It makes one wonder if they even bothered to read the original post. William J Murray

But I think the most powerful argument of all are the observations of novel biological structures and systems that appear in a few years as opposed to a few hundred millennia, as documented in James Shapiro’s book, among many other places.

Odd that Shapiro argues that evolution has all the tools needed to account for common descent. The fact that there are kinds of mutations that are more sweeping than single point base pair mutations does not change anything about TOE except for the way textbooks need to talk about it. What Shapiro does is compare evolution to the immune system, which steps up the rate of production for variants when challenged. Shapiro argues that cells step up the rate of certain kinds of genomic mutations when confronted by environmental stress. I have the recent book. I challenge you to find anything in it that requires intervention or non-mainstream processes. Petrushka

That's the ID fallacy in a nutshell. Evolution doesn't test or probe every possible state. It tests every state that is one step away from the current state. That is why genomes look like they are related by descent. That is why you can trace a person's lineage by the nested hierarchy of alleles. Petrushka

"So, when we see the manifestation of FSCO/I, we do have a known, adequate mechanism, and ONLY one known, adequate mechanism. Design" Could you give an empirical example of a manifestation of FSCO/I that exceeds the universal probability bound, that is adequately explained only by design? My genome is enormous, but I doubt it contains more than the universal probability bound of information MORE than that of my parents. DrREC

How ironic that Darwinism has become the very thing those who promote it claim to fear most: a publically enforced religion. Interesting that Lewontin's charge that those who can believe in a supernatural god can believe anything is exactly the opposite of what we find; it is actually those who believe in materialism who can believe in anything - justified by appeals to infinite chance. "Anything can happen, and everything does happen, given enough time and resources" provides the proof of the "believe anything" mindset of modern materialists. Mindless matter can organize itself into mind; deterministic processes can produce free will; fantastic machines can be constructed by happenstance. However, those who believe in a supernatural, good, rational god cannot believe in "anything"; what they can believe in is strictly curtailed by their fundamental, ordering and thus limiting premise. Brute, infinite chance is not an ordering or limiting premise of any sort. And so, Darwinists have become exactly what Lewontin's words fear: an army of thugs who can believe anything in service of their ideology, including the idea that forcing others to believe as they do can be a good and moral thing. William J Murray

How did it ever come to this? There is a hypothesis, in a very vague sense. It has not been tested. It is clearly plausible to some people, which is entirely subjective. But in practice, in reality, the burden appears to sit entirely on those who don't find it plausible to quantify their reasoning six ways from Sunday. The point made repeatedly on this forum is that this hypothesis has not "earned" a serious refutation. The focus should be on testing and evidence for the specific hypothesis or the lack thereof, not whether anyone who disagrees has all their ducks in a row. For such a hypothesis to even be noteworthy it must be well-defined and specific. To say that all diversity in biology results from variation and selection (plus this that and the other thing) is neither well-defined nor specific. The trouble, as I see it, is that the concepts are never unified into one hypothesis. It appears that living things are modified over time with descent, although the extent is uncertain. It's also known that living things vary genetically. It's also known that variations may result in differential reproduction. But no attempt has been made to unify these causes to explain an effect. There is no hypothesis that unites them in any specific, testable way. Anyone who doubts their unified effect is repeatedly reminded that each of these components are observed phenomena, suggesting that the doubter is willfully ignoring evidence. I am not ignoring evidence. I am weighing what conclusions it does and does not support. That is what everyone should do. Formulating a hypothesis that would link these combined causes to observable effects would be difficult. Testing it would be harder. But that is no excuse for bypassing this step, assuming its validity, applying it to anything and everything, and laying the burden on doubters to disprove what has never been clearly and specifically asserted. ScottAndrews

I think the immense probabilistic hurdles, the repeatedly observed "canyons" between functional designs, the empirically undeniable veracity of design as an actual causal mechanism and the powerful logic of the design inference are all very strong arguments against natural, bit-by-bit gradual theories of evolution. But I think the most powerful argument of all are the observations of novel biological structures and systems that appear in a few years as opposed to a few hundred millennia, as documented in James Shapiro's book, among many other places. These changes are clearly non-Darwinian, yet they are dogmatically tucked under the Darwinian cloak by saying "whatever mechanism caused this was itself formed by a Darwinian process". This is the very essence of denial, of the desperate cling to a antiquated, worthless theory - no... worldview Unfortunately, billions of dollars and thousands of gifted scientists' careers are still being wasted on this theory, but its utter worthlessness will only become more and more obvious as we dig deeper and deeper into the rabbit hole of complexity in biology. And no matter how dogmatic a worldview is or how iron-fisted and powerful its administrators are, every false worldview/theory will eventually crumble at a certain evidence threshold. To those interested and intelligent enough, yet not indoctrinated, neo-Darwinism is a painfully useless explanation for biological complexity. But it will reach the masses and Darwinism's own kind in due time. uoflcard