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A Darwinist responds to KF’s challenge

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It has been more than a year since kairosfocus posted his now-famous challenge on Uncommon Descent, inviting Darwinists to submit an essay defending their views. A Darwinist named Petrushka has recently responded, over at The Skeptical Zone. (Petrushka describes himself as a Darwinist in a fairly broad sense of the term: he accepts common descent as a result of gradual, unguided change, which includes not only changes occurring as a result of natural selection but also neutral change.)

The terms of the original challenge issued by kairosfocus were as follows:

Compose your summary case for darwinism (or any preferred variant that has at least some significant support in the professional literature, such as punctuated equilibria etc) in a fashion that is accessible to the non-technical reader — based on empirical evidence that warrants the inference to body plan level macroevolution — in up to say 6,000 words [a chapter in a serious paper is often about that long]. Outgoing links are welcome so long as they do not become the main point. That is, there must be a coherent essay, with

(i) an intro,
(ii) a thesis,
(iii) a structure of exposition,
(iv) presentation of empirical warrant that meets the inference to best current empirically grounded explanation [–> IBCE] test for scientific reconstructions of the remote past,
(v) a discussion and from that
(vi) a warranted conclusion.

Your primary objective should be to show in this way, per IBCE, why there is no need to infer to design from the root of the Darwinian tree of life — cf. Smithsonian discussion here – on up (BTW, it will help to find a way to resolve the various divergent trees), on grounds that the Darwinist explanation, as extended to include OOL, is adequate to explain origin and diversification of the tree of life. A second objective of like level is to show how your thesis is further supported by such evidence as suffices to warrant the onward claim that is is credibly the true or approximately true explanation of origin and body-plan level diversification of life; on blind watchmaker style chance variation plus differential reproductive success, starting with some plausible pre-life circumstance.

It would be helpful if in that essay you would outline why alternatives such as design, are inferior on the evidence we face.

Here is Petrushka’s reply:

Evolution is the better model because it can be right or wrong, and its rightness or wrongness can be tested by observation and experiment.

For evolution to be true, molecular evolution must be possible. The islands of function must not be separated by gaps greater than what we observe in the various kinds of mutation. This is a testable proposition.

For evolution to be true, the fossil record must reflect sequential change. This is a testable proposition.

For evolution to be true, the earth must be old enough to have allowed time for these sequential changes. This is a testable proposition.

Evolution has entailments. It is the only model that has entailments. It is either right or wrong, and that is a necessary attribute of any theory or hypothesis.

Evolution is a better model for a second reason. It seeks regularities.

Regularity is the set of physical causes that includes uniform processes, chaos, complexity, stochastic events, and contingency. Regularity can include physical laws, mathematical expressions that predict relationships among phenomena. Regularity can include unpredictable phenomena, such as earthquakes, volcanoes, turbulence, and the single toss of dice.

Regularity can include unknown causes, as it did when the effects of radiation were first observed. It includes currently mysterious phenomena such as dark matter and energy. The principle has been applied to the study of psychic phenomena.

Regularity can include design, so long as one can talk about the methods and capabilities of the designer. One can study spider webs and bird nests and crime scenes and ancient pottery, because one can observe the agents producing the designed objects.

The common threads in all of science are the search for regularities and the insistence that models must have entailments, testable implications. Evolution is the only theory meeting these criteria.

One could assert that evolution is true, but it is more important to say it is a testable model. That is the minimum requirement to be science.

PS:

My references are the peer-reviewed literature. We can take them one by one, if kairosfocus deems it necessary to claim the publishing journals have overlooked errors of fact or interpretation.

PPS:

To make Dembski’s explanatory filter relevant, one must demonstrate that natural history is insufficient. So I will entertain ID arguments that can cite the actual history of the origin of life and point out the place where intervention was required or where some deviation from regular process occurred.

Same for complex structures such as flagella. Cite the actual history and point out where a saltation event occurred.

Or cite any specific reproductive event in the history of life and point out the discontinuity between generations.

PPPS:

If CSI or any of its variants are to be cited, please discuss whether different living things have different quantities of CSI. For example, does a human have more CSI than a mouse? Than an insect? Than an onion? Please show your calculation.

Alternatively, discuss whether a variant within a species can be shown to have more or less CSI than another variant. Perhaps a calculation of the CSI in Lenski’s bacteria before and after adaptation.

These are just proposed examples. Any specific calculation would be acceptable, provided it can provide a direct demonstration of different quantities of CSI in different organisms.

In his original challenge, kairosfocus promised:

I will give you two full days of comments before I post any full post level response; though others at UD will be free to respond in their own right.

So let’s hear it from viewers. What do readers think?

Comments
SalC: Let me clip and highlight the Wiki article, Design:
design has been defined as follows.
(noun) a specification of an object, manifested by an agent, intended to accomplish goals, in a particular environment, using a set of primitive components, satisfying a set of requirements, subject to constraints; (verb, transitive) to create a design, in an environment (where the designer operates)[2 Ralph, P. and Wand, Y. (2009). A proposal for a formal definition of the design concept. In Lyytinen, K., Loucopoulos, P., Mylopoulos, J., and (Robinson, W.,) editors, Design Requirements Workshop (LNBIP 14), pp. 103–136. Springer-Verlag, p. 109 doi:10.1007/978-3-540-92966-6_6.]
Another definition for design is a roadmap or a strategic approach for someone to achieve a unique expectation. It defines the specifications, plans, parameters, costs, activities, processes and how and what to do within legal, political, social, environmental, safety and economic constraints in achieving that objective.[3] Here, a "specification" can be manifested as either a plan or a finished product, and "primitives" are the elements from which the design object is composed . . .
In short, design is intelligently directed contingency, constrained to particular clusters of configurations by purpose. The use of "intelligent" therefore is a case of emphasis, meant to highlight agency involvement in the face of the "designoid" concept of things that only appear to be actually designed. (Similarly, in Newton's laws of motion L1 is F = 0 => a = 0, and is entailed by L2: F = dP/dt. But, for conceptual clarity, L1 is very important, identifying what inertia is.) ISCID . . . nope not THAT one . . . International Council on Societies of Industrial Design:
Design is a creative activity whose aim is to establish the multi-faceted qualities of objects, processes, services and their systems in whole life cycles. Therefore, design is the central factor of innovative humanisation of technologies and the crucial factor of cultural and economic exchange . . .
In short, intelligence can be taken as an empirically established phenomenon as common and familiar as writers making posts in blogs, even those objecting to the concepts of intelligence and design due to the fallacy of selective, double-standard based hyperskepticism. The point of design theory is that design leads to configs that often manifest empirically reliable signs of design. So in cases of origins science where we see such signs the vera causa principle allows us to reasonably infer the presence of designing as causal process. That design points onwards to intelligence in designers is a secondary though important question for the scientific causal inference. I do think that there is a place for refusing to grant to the double-standard-using objector manifesting selective hyperskepticism, a veto over that which is plainly cogent. KFkairosfocus
March 15, 2014
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F/N: Gauger on her work with Axe, with onward context: ___________ >>The Real Barrier to Unguided Human Evolution By Ann Gauger [Biologic Institute] Comparing DNA sequences and estimating by how many nucleotides we differ from chimps doesn’t tell us much about what makes us human. Many of those nucleotide differences have no effect, because they are the product of neutral mutation and genetic drift. While these neutral mutations may affect the over-all mutation count, they don’t answer how many mutations are required for the transition from chimp-like to human. This problem is analogous to one we examined concerning protein evolution last year in the BIO-Complexity journal (Gauger and Axe 2011). Converting one protein to another’s function can be viewed as a mini version of converting one species to another. But it is much easier to convert proteins than species. [two proteins pic] We began by identifying two proteins that are close together in structure, but that have distinct functions. We examined what the minimal number of mutations to convert one protein to the other were. If all the places where they differed had to be changed, that would mean we would have to switch 70 % of one protein to achieve conversion to the other’s function. It’s unlikely that all those mutations are required, however, since many if not most of those changes are due to neutral mutation and drift, just like in the chimp-like to human case. So to estimate the minimal number of mutations required for conversion to a new function, we identified and tested the most likely amino acid candidates using structural and sequence comparisons, one by one and in combination. We ended up changing nearly the entire active site to look like the target protein, but failed to achieve conversion. Based on the number of groups we changed, we made a minimum estimate that seven specific mutations would be required for a functional shift to be observed. To get seven coordinated mutations takes way too long, even for bacteria, with their high mutation rate and large population sizes. 10^27 years is our estimate, based on Doug Axe’s population genetics model, also published in BIO-Complexity. Personally, I think the chimp-like to human conversion would have to have taken many more years than any protein conversion, if it happened at all. A few years back Durrett and Schmidt published two papers where they estimated how long it would take to get a single mutation, and then a second mutation to produce an eight base DNA binding site somewhere within a thousand base region near a gene. They stipulated that within the thousand base region there already was a sequence with six out of eight bases matching the target. The reason they chose to examine DNA binding sites? Many evolutionists think that evolution happens by changing gene expression, and changing gene expression most often requires changes to the regulatory regions around genes. Their results? They calculated it would take six million years for a single base change to match the target and spread throughout the population, and 216 million years to get both base changes necessary to complete the eight base binding site. Note that the entire time span for our evolution from last common ancestor with chimps to estimated to be about six million years. Time enough for one mutation to occur and be fixed, by their account. To be sure, they did say that since there are some 20,000 genes that could be evolving simultaneously, the problem is not impossible. But they overlooked this point. Mutations occur at random and most of the time independently, but their effects are not independent. Mutations that benefit one trait may inhibit another. In addition, many if not all these traits are complex adaptations. Each trait requires multiple mutations to achieve a beneficial change. And many of the traits must occur together to be of any benefit. Take for example the changes required for upright bipedalism. Hips, legs, feet, spine, ribcage, and skull all need to work together to allow free and efficient motion. All must be changed. But changing the hips before changing the angle of the legs would not be helpful. Changing to upright posture without lengthening the neck and setting the skull atop the spine would not work. The point is this. There are hundreds of traits that distinguish us from chimps, probably requiring tens of thousands of mutations in total. But even if it takes only 30 or 40 specific trait changes to move from primate to human, and hundred of mutations, the time required would be astronomical. Longer than the age of the universe, actually. Like Sternberg’s argument about whales, the argument from what is required to what is possible shows there just isn’t time enough for it to have happened by unguided means. >> __________ Sobering. And, demanding a sober answer. KFkairosfocus
March 15, 2014
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specification, irreducible complexity,
Those are D theories. We can say something is specified without reference to intelligence. We did that when we asked Nick Matzke about 500 coins, not once did we mention intelligence. We can do the same for IC. The importance of this is we can then critique whether a proposed mechanism (like Darwinian evolution) can create artifacts that are specified. IC systems are a subset of specified systems. D inferences (Design Inferences) are formal, mathematical and unassailable. The only way to assail a D inference is with a Chewbacca defense as illustrated in A Statistics Question for Nick Matzke. ID inferences are circumstantial. Though circumstantial, I believe them to be correct. A fence sitter or someone sympathetic but willing to be persuaded toward ID will find D theory arguments adequately convincing of ID for the simple fact if something looks designed, it must have a designer. People who will insist vehemently otherwise will never be persuaded, and we only argue with them to make them look stupid in front of the fence sitters as we did in A Statistics Question for Nick Matzke. Unfortunately the Darwinists figured out our strategy and Nick and others wised up and didn't even show up for the next simple question: Another question for Matzke
If “seeing” by eyes is the conditio sine qua non of knowledge, then half of modern science is not knowledge and is not believable. Have you ever seen, say, an electron, a black hole, a quark, a multiverse…?
Electrons may not be directly observed, but we can state their properties and predict their behaviors (i.e. mass, charge, spin). Not so with intelligent agencies because they are capricious. It's not exactly right to say that one unobserved entity (intelligence that created life) is in the same class as another unobserved entity (electron). Intelligence is capricious, electrons are predictable or at least predictable in their capriciousness (i.e. Heisenberg uncertainty). Science can make lab experiments with unobserved, but predictable entities. Science will be hard pressed to deal with unobserved, unpredictable, or historical entities. One can still call it science if they insist, but it is not in the same class of verification, even if ultimately true. It's a mistake to equate operational science with historical or circumstantial claims. Evolutionary biologists like Coyne do that, but ID proponents invite unnecessary arguments if they don't recognize the difference.scordova
March 15, 2014
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RB: I suggest the use of a version on the French quote marks, as using the angle bracket that goes the other way has unfortunate effects in WP. As in SOURCE: >>cited>> (Now you know why I do some of those odd little things. BTW, some at TSZ need to know that END at the end of a text file is not just a book convention but tells that the text has in fact completed. I do not want to use the more cryptic hash marks ### ) KF PS: Post scripts and footnotes (as well as end notes) explain themselves, as do numbered arrow bullet points, which trace ultimately back to a Readak course I did 40 years ago. Lists of works cited would be jut too formal. Square brackets will not get funny interpretations from WP or Word.kairosfocus
March 15, 2014
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kairosfocus, Petrushka et al., are making ignorance-based claims about us and Dr Axe. And I can handle myself but I am not going to let those minions attack Dr Axe. Those ilk don't know anything compared with Axe. petrushka's insipidity is well known. He is just an lower class version of Zachriel.Joe
March 15, 2014
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Reciprocating Bill: I apologize for the misunderstanding. I thought you were addressing Petrushka, and giving your personal ideas. So, all my comments in posts #128 and #129 are meant for Petrushka. Again, I apologize.gpuccio
March 15, 2014
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GP:
As you posted your personal comments too, I will try to answer them.
I should have been more clear in my last post. All of the comments appearing under my name above, including 119, are Petrushka's (and 119 does begin, "Petrushka:").Reciprocating Bill
March 15, 2014
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PPS: SB, GP, while VJT is deservedly getting star headlines, the steady creep up on what is still UD's No 2 most hit post, the WACs (it's not really a normal FAQ), now at 31,718 . . . near enough to where the Dr Tour post took off from . . . are also showing the significance of our joint effort from those several years back.kairosfocus
March 15, 2014
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GP, well said -- as usual. KF PS: Good to see the old troika back pulling together in this thread!kairosfocus
March 15, 2014
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EA, Mapou & RB: Indirect paths dependent on co-optations face Menuge's challenges C1 - 5:
For a working [bacterial] flagellum to be built by exaptation [[--> pulling together diverse parts that work elsewhere, to form a new functional entity], the five following conditions would all have to be met: C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function. C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time. C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed. C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant. C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly. [Agents Under Fire: Materialism and the Rationality of Science (Rowman & Littlefield, 2004), pp. 104-105 . HT: ENV.]
The Apollo 13 rescue after the service module explosion aptly illustrates the sorts of challenges involved and the best solution: high-grade engineering. In short, "adapt the wheel (Don't re-invent it)" is a well known DESIGN strategy, one that often relies on the tendency to standardise components. Indeed, back in 1996, Behe quite cogently observed:
What type of biological system could not be formed by “numerous successive, slight modifications?” Well, for starters, a system that is irreducibly complex. By irreducibly complex I mean a single system composed of several well-matched interacting parts that contribute to the basic function, wherein the removal of any one of the [core] parts causes the system to effectively cease functioning. [[Darwin's Black Box (Free Press, 1996), p. 39, emphases and parenthesis added. Later, he highlights the emergence of such steps by noting: “An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.” (A Response to Critics of Darwin’s Black Box, by Michael Behe, PCID, Volume 1.1, January February March, 2002; iscid.org)] Even if a system is irreducibly complex (and thus cannot [[plausibly] have been produced directly), however, one can not definitively rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows. [[Darwin's Black Box (Free Press, 1996), p. 40 . Parenthesis added.]
In effect, a complex, functionally specific organised system can be described by making a nodes- and- arcs 3-dimensional "drawing" or description of parts and the way they are arranged and coupled together, which in turn can be reduced to strings of bits such as is used in AutoCAD and similar Drawing Packages. This boils the task down to a structured string of Yes/No questions, i.e. as has been repeatedly noted, analysis on strings is WLOG. As the string of Y/N questions -- bits -- for a functionally specific system rises to and then exceeds the threshold of functionally specific complex information and/or organisation of 500 - 1,000, the plausibility of finding such an entity by blind chance and/or mechanical necessity . . . Dawkins' Blind Watchmaker . . . rapidly diminishes to the point of vanishing. Not to mention, the challenge of getting incremental mutations to "set" in populations in reasonable times at reasonable mut rates and with reasonable pop sizes. 200 MY for a couple of co-ordinated muts does not work. And remember actual info and function gain muts as well as stepping beyond the roughness and sub optimisation problems are seriously unsolved. The smooth back-slope up Mt Improbable on Continent of Life [--> Isle Isolated] by blind watchmaker mechanisms is a just so story, not empirically well-substantiated fact. Not, where origin of novel body plans is concerned. No wonder Wells argues:
The origin of Species included only one illustration, showing the branching pattern that would result from this process of descent with modification . . . Darwin thus pictured the history of life as a tree, with the universal common ancestor as its root, and modern species as "its green and budding twigs." He called this the "great Tree of Life." [[--> The echo of the one in Genesis and the Revelation is obvious, and shows the shift in pivotal imagery and how it has affected our civilisation. This is similar to the debate about rationalist "enlightenment" vs. the Medieval "dark ages" vs. Johannine light and darkness imagery, which provides significantly unwarranted plausibility for the concept of a war of enlightening rationalistic science with benighted and oppressive religion. Cf. Pearcey's evaluation of this ill-founded metaphor.] Of all the Icons of Evolution, the Tree of Life is the most pervasive, because descent from a common ancestor is the foundation of Darwin's theory. Neo-Darwinist Ernst Mayr boldly proclaimed in 1991 that "there is probably no biologist left today who would question that all organisms now found on the earth have descended from a single origin of life." Yet Darwin knew -- and scientists have recently confirmed -- that the early fossil record turns the evolutionary tree of life upside down. Ten years ago [[-->i.e. in the 1990's] it was hoped that molecular evidence might save the tree, but recent discoveries [[--> of sharply divergent molecular "trees"] have dashed that hope. Although you would not learn it from reading biology textbooks, Darwin's Tree of Life has been uprooted . . . . Darwin believed that if we could have been there to observe the process, we would have seen the ancestral species [[--> e.g. of humans and fruit flies] split into several species only slightly different from each other. These species would then have evolved in different directions under the influence of natural selection. More and more distinct species would have appeared; and eventually at least one of them would have become so different from the others that it could be considered a different genus . . . differences would have continued to accumulate, eventually giving rise to separate families . . . . Thus the large differences separating orders and classes would emerge only after a very long history of small differences: "As natural selection acts only by accumulating slight, successive, favourable variations, it can produce no great or sudden modifications; it can act only by short and slow steps." These "short and slow steps" give Darwin's illustration its characteristic branching-tree pattern . . . . But in Darwin's theory, there is no way Phylum-level differences could have appeared right at the start. Yet that is what [[--> understood on the conventional timeline] the fossil record shows. [[Icons of Evolution, 2000, pp. 29 - 35.]
In the end, the facts will out, and the dynamics of reality will break in on fantasy worlds. So, rhetorical "victories" and manipulation of the public, the media, courtrooms and legislatures may prop up a system that is quite evidently an ideological shadow show for a time. But one day, reality will come a-knocking. For instance, the above thread and the obvious problems Darwinists of whatever stripe are having with grounding their case on evidence in light of the vera causa principle, shows the problem more starkly than critics of blind watchmaker thesis hydrogen to humans via cosmological, chemical, and biological evolutions in train, can put in words that are liable to be drowned out by those who hold power and influence. But, I think a lot of people are waking up and wising up. That's why the current count on VJT's Dr Tour post is 155,170 and rising fast enough that I cannot post in time for that to still be true when I hit post. Soon, the awake and alert are going to act up, and they will not forget just who were ever so busily manipulating them with shadow shows. (BTW, I have put the animation of the parable in the RH column of my personal blog. It also appears in the post I put up in SC's new CEU, in the thread on threadjacking tactics.) KF PS: EA, GP, Timaeus, looking forward to posts. SB and UB, we need to hear a lot more from you folks. UB, launch mon, LAUNCH !!!!!kairosfocus
March 15, 2014
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To Petrushka: I invite you to read my previous post to RB. I will go on from that.
The number of states being tested is always limited to those in the immediate vicinity. That is not an astronomical number. Once a duplication occurs — as in the Lensky experiment — negative selection is pretty much irrelevant. Most mutations in the duplicate are going to be neutral. Again, Lensky.
So, we have two different scenarios here. Please, be simple and do not equivocate between the two: 1) A functional gene can test new states, but only in the "immediate vicinity". Negative NS prevent, here, any traversing of the protein space in the direction of new, different functional islands. The result? The big bang theory of protein evolution: sequences change, while maintaining structure and function. With a bit of luck, we can accept some optimization here of what already exists. Never a new complex functional structure. 2) A duplicated, inactivated gene can test any new state. Negative NS does not apply here. Well, and here the probabilistic barriers apply completely. Mutations are neutral by definition, unless and until a new functional state is reached by mere RV (and it must also in some way be transcripted and translated to have any effect on reproductive fitness, and you must explain how that can happen to a duplicated, non functional gene!). Please, remember that genetic drift is part of RV, and does not change the probabilistic barriers in any way. So, what is your argument? Functional genes can only remain the same, or sometimes be slightly optimized. And non functional genes can go anywhere, but have no reasonable probability of finding a new functional island. What do you think?
Regarding your “Experimental Rugged Fitness Landscape in Protein? Sequence Space” You are the proponent of intelligent selection. You have argued it is more powerful than natural selection, and I have argued the opposite. You present evidence that goal directed design is hard. Your conceptual problem is assuming there is a goal. You ignore sideways meandering.
I don't understand your point. Please, read my previous post to RB. The rugged landscape paper is exactly about the failure of RV + natural selection, with all its possible "sideways meandering". On the contrary, the Szostak paper (and all modern protein engineering) and antibody maturation are exactly about the triumphs of design and intelligent selection. Design, with its top down and bottom up strategies, can achieve all that RV + NS never will. Finally, I still don't understand your argument about languages. I certainly agree that natural languages are not designed by a single person, but certainly they are formed and evolve because of the interactions of all the conscious intelligent people who speak them. That is not a "non design system". Understanding and purpose are an integral part of the system. Therefore, the evolution of the system is largely designed, although not in the same sense of a poem or a software, and not by a single designer. Therefore, again, your attempt to derive conclusions about non designed non conscious systems from a system where consciousness, meaning and purpose are an integral part is really misleading.gpuccio
March 15, 2014
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Reciprocating Bill: First of all, I want to really thank you for taking the time to post Petrushka's comments here. I appreciate that very much. As you posted your personal comments too, I will try to answer them. That will answer in part also some of Petrushka's arguments, even if I will try to asses them directly in next post. First of all, I think that you are wrong in seeing the rugged landscape as an obstacle to directed evolution while it would allow non directed evolution. That is completely wrong. I must remind you that the rugged landscape paper I quoted is essentially a good model of NS, not of IS. The reason for that is that the property used for enrichment after each cycle of random mutation was infectivity, which can be considered, for the phage, a good equivalent of reproductive fitness. Therefore, what we are observing and measuring is the ability of RV + NS to reach optimization of an existing function, because the original setting of the experiment, with the introduction of the random peptide as one domain of the g3p protein, reduced infectivity, but did not extinguish it. So, we have two aspects here: a) The initial setting is designed, and the lab procedures are designed, but: b) What is being measured in the evolution of the system is essentially the result of RV and natural selection. With all that, and even with the help of an existing function at the beginning, which should only be optimized (there is nothing like the emergence of a new function here!), still RV and NS cannot achieve real optimization of the function, and fall completely short of the wild type protein. And the authors clearly state that initial population of huge size (of the order of 10^70) would be necessary to overcome the probabilistic obstacles posed by the rugged landscape to this simple optimization process. Therefore, these are the limits of NS, even when using all your beloved "sideways". How could Intelligent Design and Intelligent Selection improve this scenario? It's really simple. ID uses understanding and purpose as its tools. Even if the designer uses bottom up procedures, and therefore a random search, he integrates it with intelligent selection. That makes the procedure much more powerful. That was the case, for example, in the famous Szostak paper, where intelligent selection achieved important results in few passages. The difference is extremely important: a) In the rugged landscape paper, the enrichment is based on infectivity, which is reproductive fitness. So, we are testing NS (or at least a good model of it). b) In the Szostak paper, the enrichment is based on direct measurement of the desired property (the ability to bind ATP), even at very low levels. The important point is that in that way you quickly achieve a molecule which strongly binds ATP (the desired result). However, such a molecule remains completely useless for reproductive fitness (as showed by further studies). Another example of how IS can overcome the difficulties inherent in NS is antibody maturation. Here, a definite intelligent algorithm mutates the existing antibody (in a very targeted and controlled way), and selects for affinity to the epitope (which is available in the system). In that way, high optimization of the existing molecule is achieved in a few months. It is one of the best examples of how an intelligent algorithm, which has a definite purpose and can use information inputted into the system (the epitope) can achieve extraordinary results in a very short time. Just think how the process could work if the selection of each mutated molecule were left to a reproductive advantage of the individual, with each new configuration simply transmitted to the descendants. That would never work. That is the huge difference between NS and IS. IS uses knowledge and understanding, bothin the initial setting of a procedure and in the following stages. It is infinitely more powerful than RV and NS. That is the simple truth.gpuccio
March 15, 2014
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Stephen and Optimus: Thank you the kind words! And my congratulations to Eric and Timaeus. It's great to have such friends in our group :)gpuccio
March 15, 2014
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Barry: I just saw your post #117. Thank you, I am really honored. This is strong motivation to work more :) Thank you ahain!gpuccio
March 15, 2014
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Eric Anderson @116:
It is therefore supremely unhelpful for anyone who is hoping to advance the debate or bring clarity to the discussion to conflate the two and claim that ID somehow includes or “merges” these second-order questions with the purely objective and scientific inquiry about whether design is detectable. It is extremely unhelpful for public perception, and it is wrong logically.
Questions about the identity or methods of the designers may be second order to the design inference but, in the greater scheme of things, they are the first order questions that need to be asked. The problem with the ID side of the debate is that they have allowed the opposition to dictate how the debate should be conducted. This is weak, in my opinion, and it's probably the main reason that you are not winning. In fact, I would say that, politically, you are losing and may have already lost. But I would not worry too much about all of this. Those who designed life on earth are certainly aware of what's going on and I'm sure events are transpiring just as they should. But then again, this is just one man's my opinion.Mapou
March 14, 2014
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Reciprocating Bill:
I would argue that straight line paths up Mount Improbable are very improbable. This makes goal directed design very hard and very unlikely. But it doesn’t impede evolution, because evolution is not goal directed. Evolution wanders sideways more than upward.
I'm trying to make sure I understand this. It sounds like the claim is that evolution is more likely to arrive at a functional island because it wanders aimlessly and has no goal or direction?Eric Anderson
March 14, 2014
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Upright Biped has made a very good point.
Yeah, he has a habit of doing that. :)Chance Ratcliff
March 14, 2014
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Congrats, EA, GP and Timaeus! I greatly look forward to reading your OPs.Optimus
March 14, 2014
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Eric, just click on new post above and type in your post. Pretty intuitive.Barry Arrington
March 14, 2014
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Eric, You're certainly worthy of being an author. Salscordova
March 14, 2014
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Petrushka: Friday nights are generally rather slow, and I may not be available to post much for the next 24 to 36 hours. So I’m going to summarize where I think the discussion has been. The most convincing argument I see is against any straight path from minimal functionality to optimal functionality. Call it the problem of local maxima. To this I would respond that this is an argument against design. In particular it is an argument against gpuccio’s concept of directed or intelligent selection. I would argue that straight line paths up Mount Improbable are very improbable. This makes goal directed design very hard and very unlikely. But it doesn’t impede evolution, because evolution is not goal directed. Evolution wanders sideways more than upward. It does not “need” to leap out of local maxima, because populations are always alive and functional, or they would be extinct. When something in the environment changes and makes adaptation necessary, the most likely result is extinction. Intelligent selection is not likely to come to the rescue. The Lensky experiment directly addresses this problem and illustrates how evolution can work sideways and sometimes find a path around a barrier. But it is important to note that the populations in Lensky’s experiment were not goal directed and did not need to change. Nor was there any way for an intelligent selector/designer to know which neutral mutation would be the enabler. This is the fatal flaw in Axe’s approach. He does not consider sideways evolution.Reciprocating Bill
March 14, 2014
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StephenB, thank you for the kind comments. Barry, I can't promise to generate many new threads or to spend a lot of time, but I would be honored if it is a simple process to get it set up. I can be reached at my email address on file at UD. Thanks,Eric Anderson
March 14, 2014
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GPuccio, Eric Anderson, and Timaeus should be given posting privileges.
Agreed. They now have them.Barry Arrington
March 14, 2014
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Mapou @109: Intelligent design has been defined by the primary proponents of ID (Dembski, Behe, Meyer, et al.) as the idea that "certain features of the universe and of living things are best explained by an intelligent cause rather than an undirected process." Period. That's it. Yes, that inference includes -- by definition if something is designed -- a reference to the existence of a designer, but it does not get into questions about the designer's intent, identity, purposes, desires, motives, methods or otherwise. These second-order questions may be interesting in their own right. And an affirmative answer to the design question may have implications for some of these second-order questions, but they are logically distinct and separate and must be recognized as such. The fact that a forum like UD hosts various threads and contains comments and tangents, including from those who desire to delve into these second-order questions, has nothing to do with whether or not these issues should be kept carefully separate. I will be the first to acknowledge that the second-order questions are interesting, but they must not be conflated with the fundamental questions that intelligent design asks. A tremendous amount of effort, time, energy, and spilled ink has been spent by the primary proponents of intelligent design to make sure everyone is clear on this point. Unfortunately, as anyone familiar with the debate knows, and as UB has aptly pointed out, one of the primary ploys of anti-ID rhetoric is to conflate the question of design detection with secondary questions about the identity, intent, methods, motives, etc. of this or that putative designer. It is therefore supremely unhelpful for anyone who is hoping to advance the debate or bring clarity to the discussion to conflate the two and claim that ID somehow includes or "merges" these second-order questions with the purely objective and scientific inquiry about whether design is detectable. It is extremely unhelpful for public perception, and it is wrong logically.Eric Anderson
March 14, 2014
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By the way, he would make an excellent UD author
Stephen, UB has posting privileges here. Like someone else I could mention, he prefers to do most of his writing in the comboxes.Barry Arrington
March 14, 2014
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Upright Biped has made a very good point. (By the way, he would make an excellent UD author). In my judgment, ID supporters worry far too much about how unfair readers will interpret and characterize their arguments. They should design their message for fair readers and let the chips fall where they may. One thing they should not do is try to anticipate irrelevant objections about the designer's capacities or worse, answer those objections in a way that makes them appear legitimate. Another thing they should not do is split the ID argument into two pieces (intelligence arguments vs design arguments) as if Stephen Meyer's historical approach was incompatible with William Dembski's mathematical approach. As UB points out, we need to get back to basics, which is best characterized by ID's definition of itself: "The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection." At the same time, I insist that ID proponents should also be familiar with the philosophical arguments that support their theories. If our adversaries cannot reason properly, a fallout from an anti-intellectual culture, we should attend to these deficiencies as well. Scientific arguments alone cannot address that defect. Still, we should not contaminate the scientific arguments by injecting philosophical arguments into their substance. The two points should be used individually and in concert, not as part if the same argument.StephenB
March 14, 2014
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Upright BiPed @111:
To anyone consisdering the idea of relaxing ID standards at this critical time, may I suggest you revisit SunTzu, or Boyd, or even Ries. It is absolutely not the thing to do.
I think this is a strawman because nobody here is asking for a relaxation of ID standards. There is, however, a dire need to bring additional theories or complementary hypotheses into the fight.Mapou
March 14, 2014
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SB: I agree. KFkairosfocus
March 14, 2014
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To anyone consisdering the idea of relaxing ID standards at this critical time, may I suggest you revisit SunTzu, or Boyd, or even Ries. It is absolutely not the thing to do.Upright BiPed
March 14, 2014
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egads! Just now revisiting my 4:00am post from earlier this week, I was awfully snarky. My apologies to Dr Torley for my tone. That was not my intention, and I regret my wording. No one at UD need question my respect for Vincent, or the service he provides to UD on a regular basis - I believe I have been more than just casually vocal about my great appreciation of Dr Torley for years here. He knows this himself. While I regret my wording, I must stand by the underlying conviction. ID has a formidible challenge. A major part of that challenge is a constant will on the part of ID critics to misrepresent what ID actually is. This is the very heart of the ID critic's very successful social, politial, and legal defense against ID. It stands in the place of their not having a truly science-based response to ID's core claims of specification, irreducible complexity, and the actual fossil record (to which I would like to add semiosis as well). The challenge for ID is therefore not lessened by being less disciplined than our critics about those core claims. There is just simply no room for it. So again, my apologies to Dr Torley, but for myself, I cannot and will not follow in that direction.Upright BiPed
March 14, 2014
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