The Altenberg Sixteen

[...] the way, Pigliucci was the organizer of the Altenberg 16, so he is no stranger to [...] Uncommon Descent | Could this phrase be a tee shirt?

[...] the way, Pigliucci was the organizer of the Altenberg 16, so he is no stranger to [...] God's iPod - Uncommon Descent - Intelligent Design

That is not just intelligent design; it is personalised, intelligent design. Go figure. Axel

"For the very same reason, I consider any ID argument based on analogy (e.g. “it looks designed, ergo it must designed) to be entirely without logical foundation." To consider logic, Dr McNeill, to be co-terminous with empirical science, is surely the acme of illogicality. The vast body of empirical science, although ultimately derived from the free-ranging discursions of the great paradigm-changers, is proximately the product of minuscule, incremental steps. This is possible since it relates to the basest of all the dimensions of our human existence, namely, the material world - Mr McGoo's specialism, if you like, so to cast it as the sovereign form of knowledge, which seems to be the norm among secular fundamentalists, is folly. The great paradigm-changers of the last century, Einstein, Planck, Bohr and Godel were all, at the very least, not pantheists, but panentheists, ipso facto, convinced of Intelligent Design. Godel was a devout Lutheran. This conviction was primordial, fundamental to their thinking, your perspective on empirical science as being 'the tops', being dubbed by Einstein as 'naive realism.' Physics today has come up against a wall of paradoxes, not counter-intuitive, but counter-rational, and the only way to make progress is to incorporate them - which they duly do, the 'naive realists' no less than those with an, at minimum, panentheistic world-view. Yet the narrative-upholders of empirical science steadfastly refuse to countenance the fact that physicists are facing mysteries which fly in the face of logic as arbitrarily as any Christian or any other religious mystery. No paradox is less opaque and imponderable than any other. They all defy our reason absolutely. If you could travel through time and speak to each one of those great paradigm-changers, individually, what would you say to them, in order to convince them that they had 'got the boot on the wrong foot'? That they were illogical not to consider empirical science as the ultimate form of knowledge? What reason do you have for contending that our universe was not designed, and by an awesome intelligence at that, since you expect the application of our intelligence to fathom its secrets. Planck pointed out that there are no eternal and immutable laws of nature. We have no evidence, can have no evidence, to suggest that what was true concerning the so-called, laws of nature, in the past, governing the physical world, would remain so in the future. So, straight away, the so-called, Christian Fundamentalists, have at least a fifty-fifty chance of being correct. But tell me, is it not the case that only an omniscient, omnipotent, personal God could cause light to hit an observer, travelling at a constant speed in the same direction, at its own absolute speed, irrespective of the speed at which that traveller is moving? What other agency could effect such a phenomenon? Axel

[...] Designers are apparently some of the most vigorous bloggers on evo, and Paul Nelson’s column on the Altenberg story for Uncommon Descent generated 206 [...] Suzan Mazur » Theory Of Form To Evolution Center Stage

Dave Scott at 112, 129, 133, 145 and Allen MacNeill at 102, 114, 143 bFast at 118, 121, 136 Here is a response from John Sanford:

"Regarding Allen's comments: 1. The estimates of mutation rates in the literature are AFTER repair enzyme activity (without repair enzmes, we would all be dead!). Repair enymes can only fix mutations "while the paint is still wet". Beyond that - repair enzymes can not discern which nucleotides are mutant and which are not. The reality of high mutation rates (after repair) is not really contestible. We can only see and measure those mutations that did not get repaired. Furthermore, the hypothetical divergence of the chimp/human genomes requires mutation rates (after repair) of at least 50-100 mutations per individual per generation. Without high mutation rates evolutionary theory does not work. Repair enzymes do not impact our results. 2. My modeling allows for recombination. When we stop recombination - extinction is much faster. We in no way overlooked recombination. 3. We do not require that the genome is the sole source of biological information - we are simply testing the neo-Darwinian model in terms of how the genome arose and how it can (not) be preserved. We show that neo-Darwinian theory is easily falsifiable. 4. If Allen feels I have "massaged the numbers", I am happy to run the program with any numbers he honestly feels reflect biological reality. The modeling program we are developing is entirely adjustable, and has no built-in bias. It is purely an accounting system! We even can do runs with zero mutations, or use only beneficial mutations - whatever Allen feels is biologically realistic. 5. My models have no relation to my religious views on the age of the earth. We are ONLY examining the mechanics of mutation-selection."

DLH

For further discussion on how the Origin Of Life (OOL) is the "Achilles heel" of neo-Darwinism, see: Does neo-Darwinian theory include the origin Of Life?, particularly DLH #88

Some consider OOL “part of” neo-Darwinian “modern” evolution, others insist that it is separate. . .

DLH

Off Topic gpuccio at 200

Anyway, “wicked” has some fascination, hasn’t it?

A deadly fascination - frequently entrapping and destroying those who venture close - especially those without authority over it. Be warned. DLH

Okay: First, GP, a brilliant job in 194, in response to nos. 188 – 189. On a few points of note: 1] Science is . . . Science is indeed in large part about inference to best current explanation, and retroductive, unifying explanation of diverse phenomena is as important and often at least as powerful as prediction. Some would indeed argue that prediction is a subset of such empirical explanation, i.e providing a unifying construct that points to as yet non-instantiated empirical data. That is, the logic in basic form has structure, where T – theory, O – observation of fact, P – prediction of not yet observed fact: T --> {O1, O2, . . . On} AND {P1, P2, . . . Pm}, where the marker between O's and P's is set temporally and sometimes financially. [Recall here the unbuilt super-collider that was going to be the lifetime employment programme for a lot of physicists . . . pardon my hints of cynicism.] However, there is a further factor, as -- as GP hints at -- domains in science interact. Namely, there are also points where theories have bridges (B) to other domains in science and associated bodies of accepted theory. Thus, we extend the basic model: T --> {O1, O2, . . . On} AND {P1, P2, . . . Pm} AND {B1, B2, . . . Bk} The classic current a case in point would be quantum physics which unifies across a very large cluster of domains across several entire fields of science and associated technologies, brilliantly. Never mind its own gaping inner challenges. Now, too, let us observe: when a bridge to another established domain in science opens up, all at once there is the major potential for cross-checks across entire domains. Thus, the opening of a bridge is fraught with potential for confirmation and disconfirmation, as all at once whole new domains of fact and associated theories are exposed to mutual cross-examination. If there is mutual coherence and support, then it lends our confidence in the underlying constructs in both domains a greatly enhanced weight of credence. [For instance, think here on the import of key bridging concepts such as atoms, energy, particles such as electrons, the wave concept, and now information.] But, on the other hand, where there is incoherence, we then have to look at the weights of the relevant alternative explanations and come to conclusions on where the changes need to be made. That is a major reason why I take the design inference seriously, as the progress of molecular scale biology over the past 60 or so years has revealed elements of a complex, in part digitally based information system at the core of cell based life. Onward, that bridges to an even more established domain of science, thermodynamics. One may deny the bridges but they plainly are there and it boils down to this: the current dominant chance + necessity only paradigm in biology is deeply challenged to account coherently for the information systems and content at the core of cell based life. Now, there is an alternative paradigm, design, that can. But it is controversial as it cuts across major worldview level commitments of many leading practitioners in the sciences. So, we now see a major political dust-up taking place, across entire domains of science and also in the education system and wider culture, where key dominant elites have embedded in key elements of the evolutionary materialist paradigm in their worldviews and life/culture agendas. Also, while I would not go so far as to say that life inherently and inevitably has such a digital information system at its core, it certainly is relevant to observed bio-physical, cell-based life. That brings up my own thoughts on the issue of life . . . 2] On Life I agree with those who point out that we do not know necessary and sufficient conditions to define life, nor can we find an agreed genus and differentia framework that absorbs all accepted cases without serious exception. That leaves us with family resemblance to commonly accepted cases, and notes on oddities that stick out. I even seem to recall a Sci Am article from about 15 years ago on how there is some sort of seaweed that does not seem to have cells in the conventional sense. And of course, I am not convinced that we may properly restrict the phenomena or expressions of life to the strictly biophysical. For instance, is mind an expression of life? If so, it has very unusual properties and may point beyond the simply biophysical. Recall too that attempts to account for mind on biophysically based chance + necessity only founder on the shoals of self-referential incoherence. Having noted that, GP has raised several key considerations that have interesting bridges: life as observed embeds serious energy-flow constraints and associated information systems and structures that exploit some very clever chemistry, polymer science and physics, etc. 3] The bridge from life to information and thermodynamics . . . The above brings to bear all that we know about information and communication systems and associated issues on information generation and the implications of noise and , onward thermodynamics considerations as they affect information issues. It also explains why so many information science and/or technology practitioners are engaged on the ID side at this blog, as they are practically experienced in what is now opening up: a bridge from biology to information and even [statistical] thermodynamics issues. That poses a major empirical test of the soundness of biology theories, i.e. coherence across such a bridge to other domains of science, and the classical NDT-based thought on origins (including extensions to OOL) is not faring well at it. So, the bioscience establishment now finds itself seriously challenged to effectively address links from their major biological models to information science and associated onward links to thermodynamics considerations. (BTW, “negentropy” is due to Brillouin, who defined a form of information metric by observing that – k ln w, i.e. negative Boltzmann entropy [s = k ln w], has the properties of a measure of information. Since the underlying metric is logarithmic, taking the negative has the effect of being the mathematical reciprocal, as opposed to a negative value of entropy as such; fractional numbers have negative logarithms. He was building on earlier work on Maxwell's Demon. Thaxton et al use this in their foundational ID discussion, TMLO chs 7 – 9. This can be found in excerpt in my always linked, appendix 1. I link TMLO ch 8 here.) Okay again . . . GEM of TKI kairosfocus

Allen_MacNeill at 189 and 190 Stephen C. Meyer compiled an excellent review of the data and models in: Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories Proceedings of the Biological Society of Washington, May 18, 2007 (which by the way was peer reviewed by four credentialed reviewers) From his specialty of history of science, Meyer addresses the issues of what is / is not science in: The Scientific Status of Intelligent Design: The Methodological Equivalence of Naturalistic and Non-Naturalistic Origins Theories; Science and Evidence for Design in the Universe (Ignatius Press) November 13, 2005. If you wish to comment on definitions of science and whether evolution and/or ID is science, please address Meyer's arguments. DLH

on "life" Life appears to be regulated and that regulation is critically important. Regulation in turn requires sensing, feedback, control and amplification. Regulation is a central factor in engineering and consequentially a natural expectation from ID theory. DLH

If one is trying to define life, then one is in good company of those who have failed. In Noam Lahav's book titled "Biogenesis" he lists 48 different definitions by experts in the field and none are consistent with each other. Robert Hazen who is active in OOL research has assessed them all and has essentially said there is no good definition of life. A biology book may offer a definition of life but then again it may not. Here are a few: Purves et al 2004 - an organized genetic unit capable of metabolism, reproduction and evolution. Miller and Levine - no definition but characteristics; made of cell, grows, obtain and uses energy, responds to environment, can reproduce Campbell and Reece - 6 edition - refuses to give a definition. John Maynard Smith said life was "any population of entities which has the properties of multiplication, heredity and variation" Nasa defines it as "a self sustained chemical system capable of under going Darwinian evolution" Wikipedia defines it as "Life is a condition that distinguishes organisms from inorganic objects, i.e. non-life, and dead organisms, being manifested by growth through metabolism, reproduction, and the power of adaptation to environment through changes originating internally." Be the first to define life. What are the necessary conditions to define life? jerry

DLH: "Without evidence of conscious moral failure, lets be charitable and suggest they are “uninformed” or “deluded” rather than “lying” or “wicked”" OK, you're right, I apologize. I got carried away. Maybe it's the bad influence Dawkins has on my personality! Anyway, "wicked" has some fascination, hasn't it? :-) gpuccio

Dr. MacNeill, you said "Science is entirely about the formulation of testable hypotheses, followed by the formulation of testable predictions on the basis of those hypotheses, followed by experimental tests of those predictions, followed by statistical analysis of the results of such tests, and the publication of such results and the discussion of their relevance to the original hypothesis. Cite for me one example of this method being applied to an ID hypothesis. Until you can do this, I assert that what you are talking about is not science." I maintain that thousands of ID studies are done every year. They are just not identified as such. For example, much of the work done on malaria is ID research. Lenski's research at Michigan State on bacteria is ID research. All the work that is mapping the genomes of various species is ID research. Of course this may sound absurd but just because a study does not have ID as its stated objectives does not mean that it isn't ID research. Now what is the basis of my claims. It is the work of Behe in his book "The Edge of Evolution." In it he claims that naturalistic methods with large numbers of reproductive events, billions x billions of events, will not produce novelty in the genome. That is an hypothesis that flows from the ID assumption that naturalistic means can not produce novelty. He defines novelty in a couple different ways very conservatively. So far the research for uni-celled organisms has supported this proposition. Studies of prokaryotes, single celled eukaryotes and viruses (not cellular but highly reproductive) have all supported this hypothesis. Each study of a genome of a bird, fish, mammal, insect also has the potential to falsify or support this hypothesis. Thus, each study which is sequencing the various species of an order, family or genera has the potential to support or falsify this hypothesis. These studies also have the potential of supporting or falsifying the viability of your 47 engines of variation. So ID is on the line at this very moment in thousands of research studies all over the world. If genome after genome comes back and does not indicate any additions to the gene pool of any demonstrative change in complexity then one of ID's basic assumption is supported. When all the canine species, chichlid species, feline species etc. have been compared and analyzed for differences then one can make a conclusion as to whether this ID hypothesis is valid or not. This will never be done by researchers with an ID objective because it would never be approved. But ID will have access to the results to see if all this research validates Behe's claims. jerry

Science works via inductive reasoning, not argument by analogy, and therefore until someone publishes empirical results that clearly support a prediction flowing from an ID hypothesis, ID is not science, but speculation.

Does the non-telic position even offer a hypothsis? Can we see it? Has someone published empirical results that clearly demonstrate that non-telic processes can cobble together all the parts required to meet minimal self-reproduction? Has someone published empirical results that clearly demonstrate that non-telic processes can account for the bacterial flagellum? Has someone published empirical results that clearly demonstrate that non-telic processes can account for the physiological and anatomical differences observed between chimps and humans? I would say if the standards are EQUALLY applied something has to give. Joseph

1) A selectively permeable plasma membrane, enclosing a quantity of cytosol that includes all of the materials necessary to assemble and operate the cell; 2) at least one DNA molecule, containing the genetic information by means of which the various subassemblies of the cell are assembled and operated; and 3) several ribosomes, by means of which the genetic information carried in the DNA can be translated into those various subassemblies.--Allen MacNeill

Where do you think that genetic information comes from? How do you think it is encoded onto the DNA? From my ID PoV I see DNA as a disk- that is the coding side of the DNA is encoded with the information much like a computer system's hard-drive is encoded. That data is used as needed and directed both internally and externally. And right before reproducing the information on the coding side is parallel loaded to the template side. Once complete that information is transferred to the newly created coding side. But how does the information get there in the first place? I think that is a universal mystery. One more question- Given what you posted about those requirements what is your position on non-telic abiogenesis? Joseph

gpuccio at 195 Excellent observations on how science has operated in the past in fitting better models to existing facts. gpuccio at 194 Thanks for the input on critical features. Recommend using "Complex Specified Information" rather than "negative entropy". (Entropy increases from zero.)

"That’s why if anybody affirms that he can explain and model deterministically what happens in a living being, he is simply lying."

Without evidence of conscious moral failure, lets be charitable and suggest they are "uninformed" or "deluded" rather than "lying" or "wicked". {DLH PS See kairosfocus at 204 explaining the origin of "negative entropy" and a proper explanation of the "negative." } DLH

Allen_MacNeill: "Science is entirely about the formulation of testable hypotheses, followed by the formulation of testable predictions on the basis of those hypotheses, followed by experimental tests of those predictions, followed by statistical analysis of the results of such tests, and the publication of such results and the discussion of their relevance to the original hypothesis. Cite for me one example of this method being applied to an ID hypothesis. Until you can do this, I assert that what you are talking about is not science." Again, I have to disagree about your epistemological views. Very briefly: The first, and main, activity of science is to create models which can explain the known facts. Obviously, another important activity is to gather facts so that models can be proposed for them. Finally, a third important activity is to gather new facts whic may support or not support existing models. In other words, experimental science gathers facts, either generically (any new fact is useful), or specifically with the intent to test a model. On the contrary, theoretical science is busy working with models: creating them, adapting them, refuting them. Theoretical science utilizes facts, but utilizes them creatively. All the pertinent facts were known when Einstein created his theory of relativity, but nobody had yet interpreted them the way he did. The predictions, so much and so often extolled as if they were the only mark of science, are indeed a corollary, important and useful, but not always available. The theory of relativity shook the scientific world "before" the first experiment could support it. Why? Because it explained known facts better than the classical theories. Quantum mechanincs was created because scientists had to explain the black body radiation, which was a fact well known in advance, and not a prediction. Predictions are very important when experimental confirmation is available. Einstein and Bohr debated for years about what had to become an experiment decades after. What I mean is: Darwinian theory and ID are two theoretical paradigms which try to explain known facts: the emergence of life and its "evolution". Both make predictions, but maby of those predictions cannot be confirmed directly by experiments, because they refer to facts which happened in the distant past. Anyway, as our knowledge of the present world improves, it is likely that new facts may confirm or disconfirm both theories. Indeed, as we have often affirmed here, many of the new knowledge in biology definitely supports the ID scenario, starting from all the new acquisitions about the genome (non coding DNA, etc.) and passing through each new layer of complexity which is dicovered, and which cannot be explained by the darwinian theory. About experimentation, I will repeat here what I have often said on this blog: there is no reason that experiments have to be realized by ID biologists (they are so few, and they have no resources). Experiments can well be realized by evolutionary biologists, and still support ID, even if the researchers who performed them think differently. Experiments, as I have already said, give us facts, and facts belong to everybody. Scientific works give us both facts and interpretations. We can take the first, and refute the second. Darwinism and ID are general theories, general scenarios. They are, indeed, alternative scenarios. Therefore, any new fact is, inevitably, in favour of one or the other. The great superiority of ID as a general scenario becomes ever more obvious with each new biological discovery. But, if you are not available to really discuss the ID arguments for their intrinsic value, we can have no real confrontation on the things that really matter. gpuccio

DLH: "What other features of self reproducing cells do you see as essential?" Here is my input: For life to be present, a lot of extraordinarily unlikely features have to be present, at the same time, and perfectly associated in any living structure. I would like to strees that, in my opinion, we should bring again the emphasis on the concept of "life", however difficult it may be, and not only on the concept of "self-reproduction". The absolute dominance of self-reproduction against life is one of the sad consequences of darwinist ideology. Computer programs can self-reproduce, but they are nor alive. Life id the real deal. Self-reproduction is important because it maintains life. The same concept of evolution is less important. Life is important in itself, independently of its potentiality to evolve. Even if life had remained limited to bacteria and archea, still it would be astonishing, and would deserve to be understood and admired. But let's get back to the "essentials": 1) The membrane. I agree, that's fundamental. But ir is important to consider that the membrane is not important in itself, as a physical structure. The membrane, in living beings, is essentially a very complex, dynamic and functional separation. Its purpose is to separate the outside from the inside, so that the inside can be different from the ouside. It is an active organ, which builds incredible difference between the microcosm of the cytoplasm and the macrocosm of the external environment, usually a fluid. One of the main activities of the cell membrane, in most living cells, is to extrude Na exchanging it with K (the sodium pump). That creates a stunning diversity bewteen intracellular fluid and extracellular fluid, using a lot of the cell's energy to that purpose. So, the inner life of the cytoplasm can go on in a completely "artificial" environment, intelligently created with great expense of energy (see after). 2) The negative entropy. However one thinks about the second law and biology (one of the hottest topics here at UD, it seems), it cannot be denied that living cells are concentrated islands of extreme negative entropy. Indeed, they are so improbable that it is really a miracle that they exist. Without addressing here the fundamental problem of information in relation to the second law, recently discussed here at UD, it is important to remember that anyway such a high state of negative entropy is achieved only through a huge expenditure of energy, which takes us to the next point. 3) The energy production. All living cells have to produce and utilize an incredible and continuous quantity of energy to ensure the maintanance of the negative entropy, of which the difference between inside and outside is a very good example. Although I am no expert of comparative biology, I believe that most living beings derive such energy by one of two basci methods: a) Photosynthesis (energy from the sun) b) Degradation of organic molecules from other living beings (chemical energy) It is important to notice that the flow of energy has to be constant: living systems cannot tolerate even momentary interruptions of that flow, which has often to be maintained through storage systems (glycogen, fats). Moreovere, the almost ubiquitous ATP synthase, well known here at UD, provides an elegant way to transform and transfer energy through the various systems. 4) Systems far from equilibrium. Living beings are the most extreme systems far from equilibrium. Those systems are extremely difficult to model from a mathemathical point of view. That’s why if anybody affirms that he can explain and model deterministically what happens in a living being, he is simply lying. That’s why any assumption tha living beings strictly obey known physical laws, and only those laws, is, indeed, an assumption, and cannot be verified experimentally. In other words, we don’t really know how living systems work from a physical perspective. Almost everything is still to be discovered. Biophysics is still in its cradle, and a better understanding and modeling of systems far from equilibrium is the first step to go beyond the gross approximation of biochemistry. 5) Procedural information. More attention should be given to the problem of how cells manage the static information stored in their genomes. In other words, attention has been given up to now mainly to the gross effector information (protein sequences), and not to the procedures necessary to activate, measure, control, verify and inhibit that information in ordered sequences and models. But those procedures have to be there, because no life is possible without them. Where are they? How are they implemented? gpuccio

PS: This discussion and this one will help us clarify the strengths and limitations of reasoning by analogy. kairosfocus

Dr McNeill: First, I appreciate your willingness to acknowledge that there is a major empirical data gap relative to the usual evolutionary materialist origins scenarios. Second, in re your: I consider any ID argument based on analogy (e.g. “it looks designed, ergo it must designed) to be entirely without logical foundation. Science works via inductive reasoning, not argument by analogy I have just a moment. I note to you that I like many others here at UD, work on a routine basis with digital data strings of enormous complexity, isolated in configuration spaces. When I observe that e.g. DNA is such a digital string of isolated functional information, I am observing an empirical fact. [That one may code digitally using monomers is not in principle different from using alphanumeric symbols, or magnetic states or currents or voltages etc. Indeed, in my always linked, for purposes of illustration, I suggest a digital system based on the pips on the faces of strings of dice.] This is a fact long since noted, for instance by Sir Francis Crick in his March 19, 1953 letter to his son, Michael:

"Now we believe that the DNA is a code. That is, the order of bases (the letters) makes one gene different from another gene (just as one page of print is different from another)."

When I therefore apply basic analyses of phase/configuration space to DNA, I am not reasoning by mere analogy [which BTW is a form of inductive reasoning . . . which category of reasoning, per Lord Russell's Inductive Turkey (who made a bad mistake about being fed every morning at 9 am one certain Christmas Eve . . . the issue being how many material points of comparison obtain) is always in principle defeatable], I am addressing a known observed characteristic of digital data. And, I am highly confident that a config space corresponding to 300 - 500,000 much less 3 - 4 bn cells, will incredibly isolate islands of functionality relative to the power of random walk based state space searches, however reinforced by hill climbing algorithms. I know that intelligent agents routinely go to such islands of functionality based on understanding of functional requisites; but that is a wholly different order of causation from chance + necessity only. That is why the OOL issue is so important, and it is why the origin of major body plans is so important, as they are in material part characterised by increments of functionally specified, complex digital information that on the gamut of our observable cosmos are comfortably well beyond the reach of chance + necessity only. GEM of TKI kairosfocus

DLH asked: “What other features of self reproducing cells do you see as essential?” As I tell my students (usually during the first week of lectures of introductory biology), a living cell needs a bare minimum of three structural/functional features: 1) A selectively permeable plasma membrane, enclosing a quantity of cytosol that includes all of the materials necessary to assemble and operate the cell; 2) at least one DNA molecule, containing the genetic information by means of which the various subassemblies of the cell are assembled and operated; and 3) several ribosomes, by means of which the genetic information carried in the DNA can be translated into those various subassemblies. Allen_MacNeill

DLH wrote: “In keeping with the initial thread, I would like to learn more about the hard data of what modern biology/ biochemistry/ genomics/ proteomics etc have been finding that would be the reasons for gathering the Altenburg 16 together to formulate the next “modern synthesis” equivalent.” I have already suggested reading Jablonka and Lamb’s new book Evolution in Four Dimensions, to which I would add Elliot Sober and David Sloan Wilson’s book Unto Others: The Evolutionary Psychology of Unselfish Behavior and Lynn Margulis’s book Acquiring Genomes (coauthored with her son, Dorion Sagan). I am myself writing a new evolutionary biology textbook on the subject (now tentatively entitled Evolution: The Continuing Revolution, but that won’t be out for at least two years. Until then, you will have to follow up on what’s happening in the field, which means perusing the pages of such journals as Evolution and Quarterly Review of Biology, available at any college or university library (or online, but usually for an exorbitant fee). Allen_MacNeill

kairosfocus wrote: “I was speaking in the main to phylum and sub-phylum level differentiation in the context of the fossil record’s Cambrian life revolution.” Once again we are discussing subjects about which there is not (and almost certainly will never be) empirical evidence: that is, the genetic regulation of the body plans exhibited in the Burgess shale and other Cambrian fossils. Homeotic genes do not fossilize, ergo we will never have direct empirical evidence of what genetic regulatory processes may have led to the appearance of the various body plans that appear in the fossil record. The best we can do is to argue by analogy to those processes we can investigate today using empirical methods. Evolutionary developmental biologists have discovered an immense amount about how homeotic gene regulatory mechanisms produce both the body plans we observe, and changes in those body plans as the result of the 47 mechanisms of phenotypic variation that I have listed at my blog. ID “scientists” have produced no empirically verifiable alternative explanations. Until they do, their speculation is not science, as it is not based on observable empirical evidence, but rather metaphysical speculation. Science is entirely about the formulation of testable hypotheses, followed by the formulation of testable predictions on the basis of those hypotheses, followed by experimental tests of those predictions, followed by statistical analysis of the results of such tests, and the publication of such results and the discussion of their relevance to the original hypothesis. Cite for me one example of this method being applied to an ID hypothesis. Until you can do this, I assert that what you are talking about is not science. Allen_MacNeill

kairosfocus asked: "...where does the biofunctional information in DNA and associated systems and structures come from at origin?" The answer is simple: nobody knows. There is no direct or indirect empirical evidence either way, and as I have argued above, there seems to be little or no prospect of such evidence becoming available. The best we will ever have is (perhaps) some laboratory models that suggest how it might have happened. To me, this isn’t empirical science, according to the standards that I have learned and to which most scientists adhere. For the very same reason, I consider any ID argument based on analogy (e.g. “it looks designed, ergo it must designed) to be entirely without logical foundation. Science works via inductive reasoning, not argument by analogy, and therefore until someone publishes empirical results that clearly support a prediction flowing from an ID hypothesis, ID is not science, but speculation. And, to anticipate the usual objections, check out any recent issue of any of the myriad journals on evolutionary biology for examples of precisely the kind of empirical research to which I am referring. None of the articles published on ID in refereed journals contains original empirical research. Not one. Ergo, they are not science, but speculation, no different in logical force from the various hypotheses for the spontaneous origin of life from non-living material. Allen_MacNeill

Allen Once again, virtually none of the theories of evolutionary biology depend in any way on the resolution to the question of the origin of life. Alrighty then. So you don't have a problem with the first life being the created forms Adam and Eve and every other living thing in the Garden of Eden then evolution proceeding from there mostly as devolution from originally perfect forms. If you do have a problem with that then obviously you have some commitment to some other OOL story and thus your statement about biology having no vested interest in OOL is false. The entire neo-Darwinian story is built around simpler forms becoming increasingly complex over time. To draw a line of demarcation at the point where the basic machinery of life that enables free living cells to exist and say the story has no commitments before that point is absurd and is handily demonstrated by the fact that any hypothesis wherein the first cells contained all the complexity that exists today and evolution is the story of how that complexity unfolded in a prescribed sequence is roundly rejected because it doesn't fit the simple to complex model that underpins neo-Darwinism. DaveScot

Allen et al. In keeping with the initial thread, I would like to learn more about the hard data of what modern biology/ biochemistry/ genomics/ proteomics etc have been finding that would be the reasons for gathering the Altenburg 16 together to formulate the next "modern synthesis" equivalent. Similarly Allen stated:

Rather, they absolutely require the presence of membranes for their function, and so until such membranes are constructed (either spontaneously in the OOL, or artificially in the laboratory), the “creation” of life that relies on such assemblies for their energy is quite literally impossible.

What other features of self reproducing cells do you see as essential? Then we can examine how successful various theories are in explaining the data on origin of self reproducing life and subsequent development of observed biochemical complexity, and where they need to be altered or extended as the Altenberg 16 are apparently considering. DLH

H'mm: Some very interesting and revealing comments overnight. On a few select points: 1] Jerry, 166: this discussion is about the modern synthesis and what may replace it and has nothing to do with OOL. We all understand the OOL problem more or less but the issue here in this thread is the mechanism for change of multicellular life. I must respectfully beg to disagree. The critical issue that underpins both is the mechanism that most cogently explains the origin of bio-functionally specified, complex information. And, the failure of he evolutionary materialist cascade at OOL, as DLH pointed out in 167, is a major crack in the foundation of NDT and other similar materialistic [non-agent, chance + necessity only] theories of origins:

OOL is Darwinism’s Achilles heel . . . Without abiogenesis, Darwinism has no foundation to stand on.

2] this is not a site for Evangelicals to press their religious views as science. Excuse me, but that sounds rather strawmannish. There is, first, an issue of genetic entropy on the table that (including discussion of credible mutation rates) is about deterioration of the genome through corruption by noise. Someone has noted that one may put the deterioration of lifespan reported in biblical accounts on a plot that does in fact fit that pattern. Interesting but not primary. Perhaps, you mean to speak to my PS -- and observe that this means that this is not a major point but it is relevant enough to note -- at 165, on how evolutionary materialistic and rationalist, secularist assumptions and assertions have distorted the process of much of theology and archeology in recent decades. That is an unfortunate fact, as you could easily see by following up the link. Indeed, the article on the discovery of David's palace, linked by an earlier commenter, underscores the point. So, an informed reader should beware of such biases in reading the assertions of those who rely on that scholarship. 3] Where I live fundamentalist Christians especially YEC’s are very suspect. And I am being kind with that description of people’s attitudes toward their beliefs. Now they have the right to say “we don’t care” but I am talking about decent religious people who hold these views Let's see some of why, citing a recent Moderator for the United Church of Jamaica and Grand Cayman, written but a few short weeks after the 9/11 terrorist attacks:

The human tragedy in USA has also served to bring into sharp focus the use of terror by religious fanatics/fundamentalists. Fundamentalism or fundamentalists are terms that are applicable to every extreme conservative in every religious system . . . . During the twentieth century in particular we have seen the rise of militant expression of these faiths by extreme conservatives who have sought to respond to what they identify as 'liberal' revisions that have weakened the fundamentals of their faith . . . They opt for a belligerent, militant and separatist posture in their public discourse that can easily employ violence to achieve their goals. [Gleaner, Sept. 26, 2001]

One does not pander to such prejudice that would tar rationalism- and evolutionary materialism- rejecting, Bible-believing Christians with a smear-word that then allows them to draw out utterly unwarranted and even slanderous inferences and dismiss all they have to say. On the contrary, one identifies, exposes and corrects such bigotry and slander. 4] what about "Evangelicals . . . press[ing] their religious views as science"? Sometimes that happens and it is a category confusion to put theology as science. So, while some may argue that we have sufficient evidence to hold say Genesis as record of history to be explained rather than dismissed by science, that is sufficiently in dispute that one would be begging the question at stake to try that. [Cf how say Paul reasoned when he came to Athens in Ac 17, relative to the ideas and facts that were a common-place to that culture. he then pointed out the critical instability int he foundation of the worldview of the day, and from that argued for a fair-minded consideration of alternatives. For too many, he only got a closed-minded dismissal.] But equally category confusion goes the other way, and in much more damaging ways: for instance, consider the attempt to redefine science as in effect the best materialistic explanation of the cosmos from hydrogen to humans. That is philosophical question-begging, not science. 5] Allen, 172: Kairosfocus wrote: “…mutations of the kind that macroevolution doesn’t need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don’t occur.” First and foremost, this is an interesting mis-perception of the status of the CITED remarks. For, it in fact excerpts Meyer's peer-reviewed, closing summary of the comments by McDonald, a researcher writing in the peer-reviewed literature:

McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.

Other commenters have already addressed the basic on-the-merits problem with the attempted rebuttal. I excerpt, for instance, GP at 184:

the abstract you [Allen] posted shows the typical methodology of evo-devo: homologies and sequence changes are “observed” (I have no problems with that, indeed that’s a very useful gathering of facts); and then, the most surprising theoretical models are hypothesized, and often the only substance in the hypothesis is that it fits the preexisting theory.

I will note in addition that my [and Meyer's] context also clearly identifies that by body plan divergences I was speaking in the main to phylum and sub-phylum level differentiation in the context of the fossil record's Cambrian life revolution. What is the mechanism capable of accounting for the hundreds of megabytes of additional DNA , dozens of times over within 5 – 10 MY on the usual timeline and on this one small planet, to move to these phyla and sub-phyla by chance + necessity only without exhausting probabilistic resopurces? Of that – the issue in the main – we find nowhere the faintest trace. 6] 173, Sean Carroll’s book, Endless Forms Most Beautiful contains a concise and lucid description of precisely this process, supported by a growing mountain of empirical data. Again, a poorly founded dismissal of the underlying issue: where does the biofunctional information in DNA and associated systems and structures come from at origin? I note for instance Jerry at 181:

. . . what are the documented cases of variation creation by these 47 methods and the species creation they led to. I realize all may have happened but what has been the pay out. Have there been any instances of novelty creation by any of these processes? Which of these processes would lead to bats and their sonar, birds and their wings, giraffes and their special blood pressure system, birds and their special oxygen delivery system, mammals and their four chambered hearts and warm bloodiness, humans and their long childhood development. I have read Sean Carroll’s book and did not find anything that pointed to any source of variation that would lead to the complexity we see.

Absent specific well-documented dynamical cause-effect chain specifying evidence [preferably mathematical but logical will do] we remain for good reason skeptical on claimed mountains of evidence. And, remember I am principally asking on the difference between say a starfish and a trilobite or a turtle, not the relatively minor differences between say humans vs chimps. [Even those differences run into probabilistic resources problems so we need to see sufficient details that we can see, dynamically -- not in a just-so ad hoc story, how chance + necessity account for the scale of difference. 2% or whatever estimate you wish of 3 bn base pairs is 60 mns, or about 120 Mbits, which would have to be accounted for within 10 MY, and on earth.] 7] My own position on this problem [OOL] is that, given the immensely long period of time that has elapsed since the origin of life, the rocks that were formed during this period no longer exist at the Earth’s surface (they are either buried so deeply as to be inaccessible, or have been destroyed by tectonic subduction). Furthermore, molecules do not fossilize, and so speculation about the chemical origins of life will always remain precisely that: speculation, unsupported by direct empirical evidence. That is tantamount to saying that yours is not a scientific, evidence-controlled view but a faith-commitment. Such is your right, but you and others do not have a just right to then pass this or similar views off as the only credible and “scientific” view. By sharpest contrast, that FSCI is in all cases where we do know the causal story directly is the product of agency IS an empirical observation. I am thus well-warranted to hold that in all cases, absent a convincing reason to see other wise, FSCI is the product of agency given the principles of statistical thermodynamics issues attaching to finding intricate functional configurations in config spaces well beyond 10^300 cells. Given the complexity of life at cellular level, inference to design is an empirically anchored alternative, and thus a superior and credibly scioentific explanation of OOL. The same basic point obtains for things that DO find themselves int eh fossil record, i.e. body-plan level biodiversity. 8] the question of the origin of life has virtually no bearing on the origin of phenotypic variation or mechanisms of descent with modification, both of which are the core of evolutionary biology That is a matter of how the debate has been framed. Once we look a the underlying crucial issue, origin of functionally specified complex information, there is a very direct relevance as the two are instances of the same problem. Indeed, GP is tellingly apt in 183:

I understand that your position about the OOL question is the only possible if one wants not to address the question of design. That’s formally acceptable, but totally wrong in the wider context of trying to understand if our scientific models of reality are supported by reality itself, which after all is the main purpose of science. So, your position is tenable if you restrict your aim to what you call “evolutionary biology”, but that means only that you are artificially separating evolutionary biology from science itself . . . . where is the relevance of all that to darwinism? It’s very simple. Even if the majority of the scientific community insists to remain obstinately blind to that fact, it is a fact that there exists a model which can offer a perfectly rational and scientifically sound scenario to start explaining both OOL and evolution (and, probably, many other things). That model is called ID, it has been proposed and carried on by perfectly serious, intelligent and reliable scientists like Dembski, Behe and others, and is there for anyone unprejudiced to consider . . . . OOL “is” absolutely relevant to darwinism, unless one tries to artificailly restrict the scientific thought to categories which do not communicate. It is relevant, because we have one theory, and only one, which can in principle explain both, and no single other theory which can explain each of them, even separately.

Okay, let's discuss onward. GEM of TKI kairosfocus

Allen_MacNeill: About FOXP2. I just comment from what you posted, I am not an expert of the subject. It seems that the abstract you posted shows the typical methodology of evo-devo: homologies and sequence changes are "observed" (I have no problems with that, indeed that's a very useful gathering of facts); and then, the most surprising theoretical models are hypothesized, and often the only substance in the hypothesis is that it fits the preexisting theory. That leap is evident in the last sentences of the abstract, which follows what is just a simple enunciation of very simple facts: "Researchers hypothesized that the gene is responsible for orofacial movements. They hypothesize that the gene may be responsible for the expansion of modern humans". Obviously, I should read the whole article, but I don't know if I can get access. We'll see. In the meantime, I'll tell you what I think about hox genes and similar, which are indeed the only solid piece of evidence evo-devo is based upon. Hox genes are certainly interesting and important. They are final effectors in very important regulation procedures. They probably act as transcription regulators, and it is obvious that the very complex, and still vastly non understood, network of transcription factors is the effector system through which all nuclear regulations are obtained. Still, discovering an effector molecule does not in any way mean that we understand the "regulation" behind it. I cite here a simple sentence from an online article about hox genes, just to start the discussion: "But, one must again ask a question: if all animals utilise this common conserved mechanism with the same or similar genes for development, why don't all animals look exactly alike? The key determining factors are (1) concentration ; (2) location ; (3) timing ; and (4) target gene specificity" (Gareth Brady) Hox genes are effectors involved in spatial control of the body plan. That does not mean that they "realize" spatial control. Rather, the information network which controls body plans very intelligently utilizes hox genes (and probably a lot of other effector tools) to realize its programs, finely tuning their "(1) concentration ; (2) location ; (3) timing ; and (4) target gene specificity" to attain specific results. Again, we don't know where the information is. The simple fact that alterations in the final effectors brings gross alterations in the final result does not imply that the effector is sufficient for the result: it just shows that it is necessary. That logical trick, of implicitly passing necessity for sufficiency, is uniformly widespread in all darwinist thought. It is a logical trick, and nothing else. We don't know how the information controlling body plans works. We just know that tampering with the final pointers obvioulsy determines gross changes in the final result. In the same way, if you change the value of a single important system variable in a complex software (let's say an operating system, let's say windows xp), the results can really be devastating, but you are not authorized to say that, as you understand the role of that single variable, you understand the whole software behind it, or even worse, that such a software does not exist. gpuccio

Allen_MacNeill: I understand that your position about the OOL question is the only possible if one wants not to address the question of design. That's formally acceptable, but totally wrong in the wider context of trying to understand if our scientific models of reality are supported by reality itself, which after all is the main purpose of science. So, your position is tenable if you restrict your aim to what you call "evolutionary biology", but that means only that you are artificially separating evolutionary biology from science itself. My view of the question is as follows: OOL is a scientific problem, one of the biggest problems in science. You correctly point to a series of aspects which could be obstacles to its analysis, and I can partially agree. But science has not to stop in front of obstacles. After all, scientists are every day debating about even more difficult topics (such as the big bang, which after all is the origin of everything), even if their models are certainly, at present, not accurate. The problem with OOL is not that we have no clue, from fossils or anything else, of how it happened among many possible models. The problem is that we have no possible model (unless you accept any of those suggested as possible, but in that case you do have an opinion, and we can discuss it). And science has really a duty to address facts (life exists, after all) for which it has no possible model. That's how great scientific theories, such as relativity and quantum mechanics, have started. So, where is the relevance of all that to darwinism? It's very simple. Even if the majority of the scientific community insists to remain obstinately blind to that fact, it is a fact that there exists a model which can offer a perfectly rational and scientifically sound scenario to start explaining both OOL and evolution (and, probably, many other things). That model is called ID, it has been proposed and carried on by perfectly serious, intelligent and reliable scientists like Dembski, Behe and others, and is there for anyone unprejudiced to consider. The ID model states that both OOL and evolution of biological complexity (and, if we want to widen the perspective, fine tuning of the fundamental constants in the known universe) "cannot" in any way be explained by any known deterministic model. The ID model gives definite reasons for that, and performs a detaile analysis of those reasons. The ID model states that, anyway, we do have one model, derived from empirical experience, which allows to conceive a causal explanation of those facts in a rational context: that model is design. Nothing else can do that. Design is an empirical reality. It is observed in human artifacts. It has specific recognizable characteristics, as Dembski has been arguing for years. CSI is a definite, very important concept. No reasoning individual should easily dismiss it. Design is recognizable, and design is recognizable in the highest degree in biological information. Facts are: 1) Biological information had to appear where no biological information was present (OOL). 2) Biological information had to "increase", to generate the complexity and diversity we can observe today. None of those two points can be explained with any model which does not include ID. Both become perfectly amenable to scientific thought if the ID scenario is assumed. So, in my opinion, OOL "is" absolutely relevant to darwinism, unless one tries to artificailly restrict the scientific thought to categories which do not communicate. It is relevant, because we have one theory, and only one, which can in principle explain both, and no single other theory which can explain each of them, even separately. Indeed, I understand that you and others are trying to affirm, in different ways, that such a theory which can explain evolution does exist. I appreciate your attempts, but cannot agree with them. It is interesting, for instance, that your approach is forced in some way to reduce the "theory of evolution" more to a form of natural history (decription of events) than to a real causal theory (mathematical/logical modeling of the causes of events). Please, note that I have always spoken of mathematical/logical modeling. I agree that some empirical sciences may not have an explicit mathematical model, but I know of no one, even the most rarefied (think of psychoanalisis, for instance), which doesn't have a definite logical causal model. Because that's what science is. It observes facts in nature (natural history) and builds up mathematical/logical models for their possible causes (scientific theories). The theories of evolution which we have, those who refute the ID scenario, all of them, do have logical models behind them, but they are inconsistent and not tenable. The same is valid for OOL theories. ID theory has a definite logical "and" mathematical model behind itself. It is perfectly rational and sound. It is consistent, in accord with data, and allows a scientific scenario to start exploring in the right perspective fundamental unsolved scientific problems. In the light of that, only obstination and prejudice can prevent the scientific community from accepting ID as a perfectly valid and very important scientific theory, to be discussed "and" pursued. gpuccio