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UD Commenters Win One for the Gipper

Below the fold I have reproduced an interesting comment thread in which ribczynski attacks ID proponents’ criticisms of macroevolution through NDE, and two ID proponents convincingly refute the Darwinist line.

 

DARWINIST’S ATTACK

 

ribczynski writes:

 

The following comments and questions are for those of you who acknowledge that natural selection and common descent are real (with the usual caveats about horizontal gene transfer), but believe that natural selection does not and cannot explain large-scale evolutionary changes (i.e. “macroevolution”).

 

[Note: In this discussion I will be using "natural selection" to encompass both heritable variation and selection, as is commonly done.]

 

1. When ID supporters ask for evidence of macroevolution, biologists point to the fossil record, molecular biology and comparative anatomy to make their case.  The more enlightened IDers accept these as evidence of evolution, but question whether such evolution can be explained as the result of unguided natural selection.  They ask for evidence that unguided macroevolution has been directly observed.

 

The problem is that macroevolution doesn’t happen on a short human timescale. Why demand a demonstration of rapid macroevolution when evolutionary biologists don’t even believe that it occurs? It doesn’t make sense.

 

Some, like jerry, will argue that Darwinians are just using time as an excuse:

 

Since there are no examples of macro evolution happening, Darwinists resort to all sorts of crutches, the most important of which is deep time.  They will say that don’t you see what can happen over millions of years and that is where they stop.

 

The question for jerry is this:  Is he prepared to provide a real-time demonstration of guided macroevolution? If not, why the double standard?

 

2. If a direct demonstration of macroevolution is not possible, then what about the indirect evidence of the fossil record, comparative anatomy and molecular biology?

 

No good, say ID supporters, because you can’t show that the evidence was produced by unguided changes.  They might have been guided.

 

I have three responses:

 

a. In making this complaint, IDers are undermining their own demand for a direct demonstration of unguided macroevolution.  Suppose that such a demonstration could be arranged.  How would we know that it was unguided?  After all, it’s possible that the Designer has his fingers in our demonstrations.  (This, by the way, is what critics mean when they say that ID is unfalsifiable).

 

b. If evolution is guided, why are there no saltations?  Why does the designer always happen to choose the small changes that we would expect to see if natural selection were operating — the same small changes that allow us to deduce the nested hierarchy?

 

c. Apart from their YEC brethren, IDers tend to accept the evidence for geologic processes operating over vast timescales, and they don’t dispute it when geologists contend that these processes were unguided.  Why don’t they demand proof that these processes were unguided?  Could it have anything to do with the fact that their religious beliefs conflict with unguided macroevolution, but not with unguided geology?

 

3. Mathematical or computer modeling of Darwinian processes could demonstrate the plausibility of unguided macroevolution, but as the reaction to Avida indicates, IDers can always insist that a particular model is unrealistic in some crucial way that invalidates the results.

 

IDers demand empirical evidence of unguided macroevolution, but it’s not clear to me what sort of evidence they would actually accept, short of an authentic handwritten note from God.

 

I ask them: In your view, what would count as sufficient empirical evidence for unguided macroevolution?

 

 

ID PROPONENTS’ REBUTTAL:

 

gpuccio writes:

 

ribczynski:

 

When you make specific points, I am always ready to answer.

 

1) is not really a point.  I agree that the supposed unguided macroevoution operates at large time scales:  nobody is asking that it should be “directly” observed.  But we do ask that it may be “indirectly” inferred form observed facts according to a credible model, which is what we can and must ask of all scientific theories.

 

2)

 

a) Wrong. If you can arrange a demonstration, be it direct or indirect, where macroevolution happens in an understandable way, according to a credible model, without any apparent intervention of a designer, that would be falsification of ID.  The objection you suggest, that a designer could still be acting “behind the scenes” is imply unacceptable.  I would never make it, and the same is true for any serious IDist.  Maybe some theistic evolutionists…

 

b) First of all there are saltations. Have you ever heard of “punctuated equilibrium”? That’s not an ID theory.

 

Anyway, I don’t see why a designer should not act gradually.  That’s the usual way of working of designers. Obviously the time scale depends on the nature of the designer.

 

And by the way, we do not observe “the small changes that we would expect to see if natural selection were operating.”  If that were the case, we should see an almost infinite number of “small changes,” not only at the fossil level, but also at the molecular level.  And a credible and detailed model for macroevolution could be inferred.  And that has never happened.  Rather, what we do observe are “the small changes that we would expect to see if intelligent variation and selection were operating.”  I refer you again to the example of intelligent protein engineering.

 

c) About geological processes: personally, I am not completely sure that they are absolutely unguided:  I just don’t know.  The fact is that, as far as we know, geological processes, and other similar processes (evolution of the universe, and so on) do not explicitly exhibit CSI (the fine tuning argument is about the whole universe, and not specific internal processes of it).  So, the ID theory is not at present applicable to them.  They can apparently be explained by laws of necessity, usually with only a few random components.  The model is credible, and we can well accept it.  Religious beliefs have nothing to do with that.

 

3) Existing computer models have in no way demonstrated either the “plausibility of unguided macroevolution” or the emergence of any CSI from unguided processes.  Avida and similar are intellectual frauds.  In case you have not noticed, all the recent work by Dembski and Marks is dedicated to that problem.

 

But it is possible, in principle, to give a demonstration that would falsify ID (and that again shows that ID is falsifiable).  We are eagerly waiting to be falsified!  But Avida?  Please, be serious.

 

Show me a computer model where unplanned and unexpected CSI emerges from random noise on the basis of “spontaneous” self-selection, without the system having been planned in any way to select anything specifically, and we can discuss. After all, that’s what the Darwinist affirm has happened.

 

Jerry then writes:

 

[quoting Rib] “The question for jerry is this: Is he prepared to provide a real-time demonstration of guided macroevolution? If not, why the double standard?”

 

What a silly question.  You are saying that we do not have a video tape of the designer in his/her lab preparing the new species that we have a double standard?  ribczynski, you need to get a reality check.  ID says that the formation of new species with novel complex functions is a mystery.  We are not saying that there is proof that there is a designer but only that it is a very likely explanation for what happened.  Come on; the double standard comment means you are really flailing.

 

Is such a thing as a designer possible.  Certainly, no one doubts that within 50-100 years, engineering genomes to do completely novel things may be possible in labs such as those that exist at MIT.  That my friend will be an example of intelligent design in action.  If such a thing is possible in today’s world what is to say it was not possible in the past.

 

[quoting Rib] “If evolution is guided, why are there no saltations? Why does the designer always happen to choose the small changes that we would expect to see if natural selection were operating — the same small changes that allow us to deduce the nested hierarchy?”

 

Gould said the whole history of the fossil record was one of apparent saltations. That was why he developed his absurd fix for Darwinian processes called punctuated equilibrium.  I suggest you read Gould and as suggested by other, his ideas on punctuated equilibrium.  Everybody immediately just lapped up his ideas and it is now part of the evolutionary canon.

 

[quoting Rib] “If a direct demonstration of macroevolution is not possible, then what about the indirect evidence of the fossil record, comparative anatomy and molecular biology?”

 

The indirect evidence refutes a gradualistic approach which is why Gould proposed his theory.  Comparative anatomy and molecular biology could have been the result of micro evolution once a population gene pool arose.  ID believes and supports micro evolution.  See my comment #88.  The question is where did the original gene pool come from.

 

[quoting Rib] “Apart from their YEC brethren, IDers tend to accept the evidence for geologic processes operating over vast timescales, and they don’t dispute it when geologists contend that these processes were unguided. Why don’t they demand proof that these processes were unguided? Could it have anything to do with the fact that their religious beliefs conflict with unguided macroevolution, but not with unguided geology?”

 

You should study geology. There is evidence of both gradual and catastrophic forces having occurred in the past and operating today in the world.  We can witness massive earth quakes, volcanos, tsunamis and rock slides, sedimentation and erosion before our eyes as well as plate tectonic movements, plate formation at the mid ocean ridges.  All the pieces fit together and I am sure there will be adjustments in it over time.  So all holds together but one thing geology has never done is form any complex specified information.

 

Now biology has nothing similar except for micro biology which we all accept and yet life has complex specified information forming over time and no known process that can do it.  Nothing in the current world shows this tendency to form complex specified information.  Geology produces complexity but it is not specified.  That is why we can accept geology and not biology.  One process leaves a host of forensic evidence on how the non specified complexity has formed, the other leaves no information on how the complex specified information has formed.  In fact the geological evidence is extremely persuasive for ID.  There are gradual processes working over time that can be observed in the current world for geology but none in biology except for micro evolution which does not produce complex specified information.  There is no forensic evidence that micro evolution leads anywhere but to devolution which is the opposite of macro evolution.

 

[quoting Rib] “I ask them: In your view, what would count as sufficient empirical evidence for unguided macroevolution?”

 

How about some examples either in the fossil record or in the current world.  None exist.  Macro evolution has no empirical evidence behind it.  It is not science, but an ideology.  Why don’t you start presenting empirical evidence for macro evolution.  If you could, you would be a Nobel prize winner.

 

Please, provide some evidence, not just the tired old clichés we see all the time.

 

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60 Responses to UD Commenters Win One for the Gipper

  1. Barry,

    Your declaration of victory is a bit premature, given that I haven’t yet responded to my interlocutors.

    Readers,

    The comments that Barry quotes above come from this thread. There are some 25 later comments at the end of that thread, so if you’re interested in following the discussion, you may want to read them first.

    I’ve posted a comment there asking that we move the discussion to this new thread.

  2. 2

    OK Rib. If you’ve got something better than what you’ve given us so far, I hope you’ll stop holding us all in suspense and dish it.

  3. Ok my last post was lost, so I’ll try again.

    It’d be helpful here to clarify terms. ‘Macroevolution’ has been used in several ways, so ppl are often talking at cross purposes in discussions on it.

    1. Events that are sudden on an *ecological* timescale. I.e. where there is a significant genetically based phenotypic change within a *single* generation. Richard Goldschmidt’s hopeless monster theory would fall under this definition. As would Gould’s heterochrony ideas (i.e. a change in the timing of an organisms developmental program).

    2. Events that are sudden on a *geological* timescale. As a palaeontologist Gould also used the term macroevolution in this way too, to refer to large scale phenomena in the fossil record, such as the rapid diversification of a certain clade.

  4. Which type of macroevolution are you referring to? And if its the second, does this need any special explanation?

  5. Which type of macroevolution are you referring to?

    And if its the second, does this need any special explanation? (Considering that geologically rapid events translate into 100′s of thousands of years in ecological time).

  6. [off-topic] Barry, the thread on Professor Olofsson’s article is highly remarkable, and at 325 or so comments, is loading slowly. My not post the highlights in a new thread?

  7. This is for Khan since I said I would post it on the 60 minutes thread which turned partially into a thread on macro evolution which has no good definition. So if Green wants to comment also maybe we can come up with a good definition or at least a working definition of macro evolution or maybe some new definitions that have to be made.

    I am posting this in two parts because it is quite long and the second part is much longer than the first.

    In order to understand the ID position, one has to understand first the complexity of life and how difficult it would have been to have formed in the first place and secondly the changes in life forms that have happened since life first appeared on earth about 3.5 million years ago and what was required for all these life forms in terms of changes in the DNA or other genetic elements. ID’s efforts are two fold. One is detailing the failure of the current paradigm, neo Darwinism/Modern Synthesis or whatever you want to call it, to explain many of evolutionary facts and second to examine what processes could possibly account for the immense complexity of even the simplest life forms and the changes that took place over time and which could have happened by naturalistic processes and which seem unlikely to have happened that way.

    A lot of evolutionary biology thinking, is based on the strategy of using negative information to exclude other possible options. Certainly, intelligence could account for the complexity of life. No one real doubts that. Richard Dawkins admitted that in Expelled. Modern biology in the 21st century is probably less than a 100 years away from constructing similar systems to life so the possibility of life having an intelligent origin certainly appears feasible. It cannot be ruled out. Those supporting naturalistic solutions essentially use negative arguments implying no intelligence would construct the life as it is found in our world. Arguments from imperfection or theological arguments (used ironically by atheists) based on the evil and cruelty in the world are the basis for their arguments. The main process used to defend a naturalistic approach to evolution, natural selection, has failed to produce anything but trivial changes in biological organisms mainly because it is never presented with anything meaningful to select. And if it has been presented with meaningful changes, then where did these changes come from.

    The next part is a long analysis of the evolution issues and hopefully we can come up with an accepted definition of macro evolution as a result

  8. The following is an analysis of the changes in life forms and where ID has interests.

    Evolution is essentially a multi-tiered theory.

    The first tier is the origin of life or how did a cell and DNA, RNA and proteins arise. Quite a sticky issue with no sensible answer by science. Lots of speculation and wishful thinking but nothing that makes sense. The problem is enormous yet few admit its size. The solution is always just around the corner and things like the Miller Urey experiments are still used as illustrations of what works. Just imagine how you construct a ribosome by chance or atp synthase. A high percentage of ID concerns are in this tier and zero concerns by neo Darwinism which essentially starts with the first cell. However, a discussion in a Robert Shapiro’s article in Scientific American over a year ago was about this and it is interesting that he invoked Darwinian processes to bolster his claims. I believe Dawkins has used natural selection as a factor in OOL. Usually, evolutionary biology stays away from origin of life issues but nearly every biology book deals with it. The complexity of the origin of life issues is one studied extensively by ID proponents and their conclusion is that only an intelligence could have produced such complex systems.

    The next tier I will call the evolution of single celled organisms. There is really quite a lot of development of significant capabilities here, including Khan’s example of eukaryotes and such things as photosynthesis and of course the favorite, the origin of the flagellum. There are lots of changes in single celled organisms and Khan’s examples are new to us but should be examined. The question is whether the changes can be explained by naturalistic means or not. For most of this I don’t pretend to be very knowledgeable so I shy away from discussing it other than to ask questions about how much change took place and what could have caused this change and to discuss whether current answers are satisfactory or not. For example, Behe listed the flagellum as an irreducible complex system with extraordinary capabilities. Several people have said they have answered Behe’s arguments and it is not irreducibly complex but after reading them, I find them wanting and not convincing and this topic is frequently debated here.

    The third tier is how did a single cell organism form multi-cell organisms and this include how did such complex organisms as the eye arise as these multi-cell organisms arose. How, did brains, limbs, digestive systems, neurological systems arise and all the complex signaling systems between cells and organs. These are immensely complicated but get little discussion except it all happened over time. We have all seen the “it must have evolved” or “it was selected” comment in journal articles and books which is the “begging the question fallacy.” This is also an important area for ID but not as much so for Darwinists. Irreducible complexity operates extensively in this tier. Also most of these systems must have developed before the Cambrian Explosion so there is relatively little geological time for these complexities to have developed and no fossil record of such a predecessor.

    This means that the organisms that appeared during the Cambrian Explosion and their relationship to each other is important. Nothing in the organisms of the Cambrian Explosion is consistent with a gradualist approach to species. It is definitely top down, not bottom up. There is little or no diversity within the various phyla, only isolated instances of various phyla. The diversity came later. A complete contradiction to Darwinian processes. James Valentine, the most knowledgeable of all paleontologists on the Cambrian Explosion, hypothesizes some unknown mechanism that accounted for the uniqueness of each of the phyla. Nothing but speculation but something had to happen because it had to happen without an intelligent input. He begs the question. It is the begging the question fallacy applied continually through out modern evolutionary reasoning.

    The next tier is the one that gets the most debate in the popular press and that is how did one species arise from another species when there are substantial functional differences between them. This is the majors of macro evolution even though the Cambrian Explosion represents the true epitome of the macro evolution problem. How did insects, birds and bats get wings to fly, how did land creatures develop oxygen breathing systems or how did man get such a big brain and why such a long time for children to develop and where did consciousness come from. How did 4 chamber hearts and warm vs. cold blooded arise. How did birds develop their unique oxygen transport system. How did giraffes develop their unique blood pressure system. There is lots of speculation but no evidence, only a series of “just so” stories. An occasional fossil is brought up to show the progression ignoring the fact that there had to be tens of thousands of other steps for these progressions of which only a handful have been found. I believe the forest animal to whale is now neo Darwinism’s best example here and one that Khan presented and even this has millions of years between slightly similar fossils. Are these occasional fossil example of gradualism in action or do they just represent various examples of different organisms whose origin is at best a mystery. In this tier the ID and the Darwinist are sometimes on common turf fighting it out. But ID is relatively less interested in the issues here but still very interested and annoyingly point out the lack of evidence to back up any “just so stories”.

    There is another part of this tier which I call macro-evolution light or the minors. This is how did a lot of the orders and families develop? For example, within Carnivora how did all the families arise? ID seldom cares about this area but evolutionary biology does. I don’t think ID would care much if someone showed how all the family canidae or felidae arose by gradualistic approaches but yet the evolutionary biologists would claim that would be a major verification of their theory. ID would ask what truly novel functional complex capabilities arose during this process or could all just be explained by micro evolutionary processes working on an original gene pool. In other words is this process just a trivial outcome once an original gene pool was available and basic processes which ID does not dispute are the driving forces. This area is a bridge between the third tier and the final tier.

    The final tier is what Darwin observed on his trip on the Beagle and what most of evolutionist are talking about when they think evolution, namely micro-evolution and can be explained by basic genetics, occasional mutations, environmental pressures and of course, natural selection. Few disagree on this fifth tier including those who call themselves Intelligent Design proponents yet this is where all the evidence is that is used to persuade everyone that Darwinism is a valid theory. And even here the evidence is thin with a lot of the evidence coming from changes in single celled organisms. The evidence in this tier is used to justify the first four tiers because the materialist needs all five tiers to justify their philosophy of life but the relevance of the evidence in this last tier for the other tiers is scant at best. It should be understood that Intelligent Design assumes the basic neo Darwinism micro evolutionary process and does not dispute its power to perform minor changes to the genome which is so important in areas of medicine and genetic diseases. It would be interesting to see if Khan’s examples that he proposed end up in this final tier or are there more substantial changes to the genomes that would require more than normal micro evolutionary processes. What changes happened to the organisms in Khan’s examples.

    So to sum up, my experience is that ID concentrates on tier 1, 2 and 3, a fair bit on the novelties that show up in tier 4 and are not concerned at all with tier 5 which is what Darwin observed and supplies nearly all the evidence for neo Darwinism.

    This is a framework under which I look at the evolution problems and it has proved useful in understanding objections to ID and how they are usually misplaced.

    Maybe out of this we can come up with a working definition of macro evolution. One thing that has to be considered is that micro evolution is a process while macro evolution is a result. Macro evolution is not a process so they can not be defined similarly.

  9. Certainly, no one doubts that within 50-100 years, engineering genomes to do completely novel things may be possible in labs such as those that exist at MIT. That my friend will be an example of intelligent design in action. If such a thing is possible in today’s world what is to say it was not possible in the past.

    Gee, this has me thinking of Men in Black, and not 2001. There’s a galaxy enclosed in a spherical bauble hanging from the cat Orion’s “belt” (collar). Obviously this is by design. I wonder if the galaxy has inhabitants that have hidden an even teenier galaxy in the chew-toy of a teeny dog.

    The notion that one entity can construct the reality of another cannot be ruled out logically. But what is the explanatory advantage of a designer regress? It seems purely anti-explanatory to me.

    I anticipate a response along the lines of, “Well, if it’s the truth, science should be open to it.” I disagree. Empirical science gains its power in obtaining certain sorts of explanations by ruling out other sorts. Want the truth? Turn to religion and/or spiritual practice. Want a utilitarian account of how things work in the material universe? Do empirical science, excluding all explanations that invoke the non-material.

    Empirical science does not get you to ultimate truth. Improved understanding of nature can be demonstrated operationally, perhaps, but there is certainly no arrival a point of complete understanding. It boggles my mind that IDists, when it serves their arguments, will invoke Popper and falsification, but just don’t catch on to the fact that inductive inference gives only fallible explanations of empirical observations.

    So, again, what is the utility of changing empirical science to permit a designer regress? That is, what does it profit scientists to contemplate that our universe might be hanging from the collar of a cat, even if it is true?

  10. jerry, as I read your explanation of “tiers,” ID is most interested in areas where we have the least data. Where we have more data, naturalistic explanations seem to provide satisfactory answers. Where the answers are less satisfactory — which of course tends to be where there’s less data — ID steps in and says “design”!

    How is this not a “gaps” argument? (I won’t use the other G word here.)

  11. RoyK,

    It is a gaps argument, namely a gaps in the science argument. There is a lack of evidence that micro evolutionary processes or any other naturalistic processes has ever produced even one example of the necessary functional complexity that exists in abundance in nature.

    You will note that I never say that there may not be some fruitful theory in the future but as of this moment, gradualism fails miserably as does every other naturalistic theory. For gradualism to be an explanation it would have leave all sorts of forensic evidence that it was operating today, or had operated in the past. We see none. So why accept a theory that has no empirical evidence to support it.

    ID says design is an option and one that would explain the evidence. It does not say naturalistic processes are not working, only that none have been described that would explain all the facts of evolution. The more this get investigated, the more design becomes a more viable option. As we said last week, it is a black swan issue but admit there could be a black swan but as of the present all swans are white and we have looked almost everywhere.

    Most of us would be quite happy with a declaration in science courses and textbooks that says that science currently does not have an explanation for the origin of many of the capabilities of species that have arisen over time and Darwin at this moment appears to be wrong on this issue. If the science community made such a declaration, I personally would be happy and would never insist that intelligence be a part of the science curriculum.

    You could also look at the argument as one where a certain process is observed and understood but one then took this process and extrapolated it to areas where they have no information as to its applicability. Such a process is not good science and at least a minimal success rate would be the justification for such a leap of a gap.

  12. jerry, I didn’t say I agree with your assessment of the evidence, or with the tiers picture. I don’t. For example, I think there’s very good support for the relatedness of all life and for universal common descent. UCD goes across all the “tiers” of your model. Of course we can’t observe them: but we can observe some things an extrapolate. Consider Darwin’s last book, on the worm. By observing the humble earthworm in his own lifetime, he was able to explain the formation of the topsoil of England. We only observe incremental evolutionary processes. But we don’t observe direction or intelligence there, so why should we presume that it must operate at the larger scale?

    Here’s my observation: Every time we get a full science explanation, it’s a naturalistic one.

    I’m wondering: has there been a time in the history of science (outside of ID’s hope for the demise of Darwinism) when a naturalistic causal explanation has been replaced by an explanation based on intelligence? Science seems to explain by moving in the other directiion.

  13. correction: for “full science” above, read “fully scientific.”

  14. Jerry,

    You wrote a lot here, and I can’t respond to it all. There are a lot of mistakes and omissions there. For example, OOL has moved well beyond the Miller-Urey expts. google “montmorillonite” and see what you find. it’s still far from a complete picture but you should at least acknowledge that a lot of work has been done on the topic since the 1950′s.

    Second, the Cambrian Explosion (never understood why 8 million yrs is an “explosion”) was nothing like what you describe. Here is a paper by the same James Valentine showing that it was very “bottom up”:

    http://www.pubmedcentral.nih.g.....rtid=44279

    Beyond all that, you still didn’t provide your definition of macroevolution. I have no interest in working towards defining it again, as it has already been done. why don’t we just use the standard def provided by Futuyma (evolution of major new characters that make organisms recognizable as new taxa above the species level)? This seems most fair, since I am still perplexed why you exclude single-celled organisms from your definition and apparently think that even changes significant enough to cause a Family level “speciation” (Family-ation?) might not count as macroevolution. I have never seen those conditions laid out in any scientific work and therefore think it would be invalid to use them in a scientific discussion. Your argument that most discussion of macroevolution concerns multi-cellular organisms does not change the definition of the term.

    So, to get back to my original question, by the standard definition, would you agree that the endosymbiotic origin of mitochondria (evolution of complex novel features and a Kingdom-level change) and the evolution of specialized cells to house symbiotic bacteria in aphids are (again, a complex feature and high taxonomic order change) are examples of macroevolution?

    Here are some sites to brief you on the details:

    http://users.rcn.com/jkimball......iosis.html

    http://biology.plosjournals.or.....&ct=1

  15. gpuccio wrote:

    I agree that the supposed unguided macroevoution operates at large time scales: nobody is asking that it should be “directly” observed. But we do ask that it may be “indirectly” inferred form observed facts according to a credible model, which is what we can and must ask of all scientific theories.

    The evidence (fossil, biochemical, anatomical) is there, but you presumably don’t find natural selection to be a “credible model”. If so, read my later comments in the 60 minutes thread. There I deal with various alleged theoretical limitations of natural selection.

    If you can arrange a demonstration, be it direct or indirect, where macroevolution happens in an understandable way, according to a credible model, without any apparent intervention of a designer, that would be falsification of ID.

    Not unless you stipulate that the designer will not interfere with the demonstration. But if you allow that the designer might be God, how can you know this?


    First of all there are saltations. Have you ever heard of “punctuated equilibrium”?

    Sure, but those aren’t the kind of saltations I’m talking about. I’m talking about changes, instigated by a designer, that happen much faster than they possibly could if natural selection were responsible. Why don’t we see these? Why does the designer always choose to behave in a way that happens to conform to what natural selection would do?

    Anyway, I don’t see why a designer should not act gradually. That’s the usual way of working of designers.

    No it isn’t. Designers will make incremental changes to a design for a while, then abandon it and start fresh when further tweaking becomes unwieldy.

    They definitely do not derive all of their designs from a common predecessor, forming a single continuous nested hierarchy that can be deduced from a careful analysis.

    Your Designer is the odd man out.

    About geological processes: personally, I am not completely sure that they are absolutely unguided: I just don’t know.

    The geological community has no such qualms. Nor do most ID supporters. As I said, I suspect that this is because unguided geological processes pose no particular challenge to their religious beliefs.

    Avida and similar are intellectual frauds.

    Hardly. Avida showed how so-called “irreducible complexity” could be produced by a Darwinian process.

    Show me a computer model where unplanned and unexpected CSI emerges from random noise on the basis of “spontaneous” self-selection, without the system having been planned in any way to select anything specifically, and we can discuss. After all, that’s what the Darwinist affirm has happened.

    “Spontaneous self-selection”?? What are you talking about? That’s not a Darwinian concept.

  16. “Here’s my observation: Every time we get a full science explanation, it’s a naturalistic one.”

    I am not sure this is true. Just watch you favorite version or least objectionable version of CSI. In several cases the story has come down to whether it was an intelligent cause or a naturalistic one.

    This is not a unique case since we do the same in archaeology but so far you are right for SETI.

    But suppose the cause is intelligence and we suppose a naturalistic one, then we by assumption will probably miss the real cause. For the naturalistic world including biology, there seems to be an endless series of dead ends when it come to producing CSI (note same abbreviation for two completely different things.). Nature has not done it in non biological areas and we have no cases where we observed it happening in biological areas so why assume that it must have done it in life forms in the past. You have no precedent for it. It seems illogical too.

    That’s why I say it is ideologically based.

  17. Can you come up with a real, actual example (not a TV show) in the history of science, where a developed naturalistic explanation was replaced by one attributed to agency?

  18. Khan,

    I have Valentine on video saying Darwinian processes cannot explain it and I believe he used the term top down. Valentine also uses the term Explosion since the time period is relatively small for this much disparity to appear. Especially when there was little accompanying diversity.

    We will have to find another definition to suit you. ID does not deny evolutionary processes, only the extent to which they can form novel complex functional capabilities. So call that what you want and we can go from there. If you want to call some small trivial changes, macro evolution, fine but that is not what the debate is about. The debate is not using definitions and then filling up boxes with examples of that definition when the particular examples may not represent anything being debated.

    So tell me what would you call the appearance of novel complex functionality in a species. Give it a name and we can go from there to see if your examples meet the criteria. I would be interested in just what happened in your examples and what changes happened in each species and see where they fit.

  19. RoyK,

    Does the TV show bother you because all the examples were made up or does it bother you that it they are true examples and not made up that they are only an isolated incidents. Are you asking for a theory or are you asking for specific instances? Or would either suit you.

    You really come across as looking to use the God of the Gaps argument which is only valid if you assume all phenomena in nature have a naturalistic cause. The God of the Gaps argument only works for phenomena with naturalistic causes. If the explanation is not naturalistic then invoking a God of the Gaps argument does not work. You can not continue by saying that science has never found anything but naturalistic causes when science may not be capable of finding all causes.

    If we continue to investigate something and continue to come up empty then we may want to ask if this is a case where science may not have the answer.

    Good night.

  20. The TV show bothers me both because it’s not real and because it’s not science.

    Here’s what I’m saying: in the history of science, even screwed-up, only halfway decent naturalistic explanations are not replaced with non-naturalistic explanations. Think about it: Planetary motion. Geologic processes. Human reproduction. I could go on. Does it ever happen? Or would ID, should it succeed, be the first?

  21. Avida showed how so-called “irreducible complexity” could be produced by a Darwinian process.

    That is a lie. The Avida program is just thjat- a program written by humans.

    And the ONLY way to simulate living organisms is to understand everything about their development and sustaining mechanisms. We do not and therefore we cannot sim ulate living organisms.

    You keep on claiming things about the fossil record and keep ignoring the facts about it.

    SZo here it is again:

    Over 90% of the fossil record is of marine invertebrates, which is to be expected from what we know about fossilization.

    Yet in that vast majority we don’t find any evidence for macro-evolution.

    Next Khan claimed the mammals ear evolved from reptiles via bone movement and shrikage.

    That should be easy to confirm except we don’t understand the development of our ears.

    What I mean is we should be able to tinker with reptilian embryos to get the bone movement and shrinkage.

    Yet I doubt anyone is trying that.

    So the bottom-line is all evos have is circumstantial evidence. And circumstantial evidebnce can lead to differing conclusions depending on one’s pre-suppositions.

    “Change te way you look at things and the things you look at will change” unknown

  22. 22
    William J. Murray

    The obvious reason why science has never come up with an intelligent-design answer is because inteligent-design answers are not allowed by science. All hypothesis, theory and explanations are required to be materialistic constructs, and so the entire explanatory process must lead to non-intelligent conclusions.

    There are examples where intelligent design was presumed, and an intelligently-designed conclusion was reached: Newton and Principia Mathematica. Only, his result of intelligently-designed, meticulously arranged natural laws was later co-opted … without explanation … by materialists as “natural” (I’m not sure how natural materialism accounts for the formation of the very “laws” that creates both nature and a material universe).

    When all apparent, even obvious non-materialism (mind) and intelligent design (anthropic principle) is simply asserted and natural, and no intelligence is allowed into the process, how exactly does one expect science to reach a design conclusion?

    You can’t reach conclusion X if the entire process any inclusion of X whatsoever.

  23. 23
    William J. Murray

    Edits:

    is simply asserted as natural,

    and:

    You can’t reach conclusion X if X is specifically excluded.

  24. To all anti-IDists,

    The “evidence” for the evolution of the eye/ vision system is the same now as it was in Darwin’s day:

    The only evidence for the evolution of the vision system is that we have observed varying degrees of complexity in living organisms, from simple light sensitive spots on unicellular organisms to the vision system of more complex metazoans, and we “know” that the first population(s) of living organisms didn’t have either. Therefore the vision system “evolved”.

    Isn’t evolutionary “science” great!

  25. They definitely do not derive all of their designs from a common predecessor, forming a single continuous nested hierarchy that can be deduced from a careful analysis.

    1- Nested Hierarchy is not to be expected
    from evolutionary processes for the simple fact that evolutionary processes do not have a direction. Nested Hierarchies demans a direction.

    For example the animal kingdom is defined by several criteria. The phylums under that kingdom obey those criteria PLUS at least one more.

    Then the class would include the phylum’s criteria (which includes the kingdom’s) PLUS at least one more.

    And it goes on.

    Whereas descent with modification does NOT follow those rules because traits can be lost as well as gained- that is acording to the theory.

  26. To Kahn (again),

    The “evidence” for endosymbiosis can also be used to deduce that m itochondria and chloroplasts arose via devolution from eukaryotes.

    And if you want to use endosymbiosis as evidence for evolution you had bhetter be prepared to provide a demonstration.

  27. Talk origins on macroevolution:

    In evolutionary biology today, macroevolution is used to refer to any evolutionary change at or above the level of species.

    This is useless because we don’t have a concrete definition of species.

    Not only that but even YECs accept that changes can occur at or above the species level.

    The following makes more sense in light of the debate:

    scroll down to evolution:

    evolution, biological n.
    1) “microevolution”—the name used by many evolutionists to describe genetic variation, the empirically observed phenomenon in which exisiting potential variations within the gene pool of a population of organisms are manifested or suppressed among members of that population over a series of generations. Often simplistically (and erroneously) invoked as “proof” of “macro evolution”;

    2) macroevolution—the theory/belief that biological population changes take (and have taken) place (typically via mutations and natural selection) on a large enough scale to produce entirely new structural features and organs, resulting in entirely new species, genera, families, orders, classes, and phyla within the biological world, by generating the requisite (new) genetic information. Many evolutionists have used “macro-evolution” and “Neo-Darwinism” as synonymous for the past 150 years.

  28. Jerry,

    “I have Valentine on video saying Darwinian processes cannot explain it and I believe he used the term top down.”

    I don’t doubt he did since he says the same thing in the first sentence of the paper I linked. It is important to keep both his comments and the Cambrian explosion in their proper context, though. Further in the paper he points out that in fact most diversity appeared in the long Precambrian buildup and that very few truly novel forms actually appear in the “explosion.” Are you familiar with the Ediacara fauna that appear 55 million years before the Cambrian? Or the “little shellies” that dominated the first 25 million years of the Cambrian?

    “The debate is not using definitions and then filling up boxes with examples of that definition when the particular examples may not represent anything being debated.”

    THe basic rules of debate require an agreed-upon definition of terms. so the debate will be about definitions until one is agreed upon. I see no reason why we can’t use Futuyma’s definition, and I have given some examples that I think we can both agree represent macroevolution:

    1) endosymbiotic origin of mitochondria
    2) evolution of bacteriocytes in aphids
    3) evolution of ear bones from jaw bones during synapsid-mammal transition
    4) evolution of whales from land verts
    5) Evolution of horns in Titanotheres (see figure 21.10 in Futuyma)
    6) Increasing brain case size in humans

    I will eliminate the vole example since it just deals w species-level changes. If you think that 6) is just microevolution as well, that is fine. But then you must also consider the evolution of the human brain itself to also be microevolution since it just represents an increase in volume (# synapses, neurons, etc.) with no novel functional parts added.

    I am most interested in what you think of 1) and 2) and I hope you will read some of the info I linked so we can discuss them.

  29. Joseph and Rib,

    Avida showed how so-called “irreducible complexity” could be produced by a Darwinian process.

    That is a lie. The Avida program is just thjat- a program written by humans.

    I just have to comment on this because both you and rib are wrong in your assertions.

    Both the computer simulation AVIDA and biological evolution are instances of Darwinian processes. The only ingredients required for a Darwinian process are replication, heritable variation, and fitness selection. In both, organisms are able to reproduce and pass their characteristics to their offspring. In both, random mutations arise which affect the organisms’ ability to survive and produce offspring. In both, selection pressures favor some varieties and penalize others.

    You must be certain your understanding of the definition of “irreducible complexity” is not faulty. While it’s true that AVIDA does not mimic real-life biology (and the authors do not deny that), it does show that an IC system can evolve via indirect stepwise pathways in tightly constrained environments under certain conditions of replication, variation, and (artificial) selection. This is important, as some ID supporters seem to regard “irreducibly complex” as tantamount to “unevolvable in principle”. This is not a problem since IC primarily deals with DIRECT Darwinian Pathways and always has. Behe has always stated that INDIRECT Darwinian pathways are another matter.

    We must also consider the level of complexity: the number of components involved. Behe has long noted that IC structures with a small number of components (2-4) may form depending on the conditions. But what about IC structures that are composed of tens or hundreds of interlocking components? That is the real problem ignored by Darwinists. They cannot even conceive of potential pathways…and it’s not like the flagellum is all that complex. It’s actually fairly simple in comparison to many other systems.

    When it comes to AVIDA, in the “The Evolutionary Origin of Complex Features,” published in Nature in 2003 by Lenski, the selective forces that have 100% probability affixed are those for various simple binary arithmetic functions, which are ultimately used to build the “equals” (EQU) function, and for the EQU function itself. What’s more, the more complex the function, the greater the reward given to the digital organisms for it. There is no analogy for such selective forces in nature. Nature doesn’t care whether something is more or less functionally complex; it only cares whether it can survive in a particular environment. And what happens when no step-by-step rewards are given for functional complexity? An article on AVIDA in Discover magazine (Feb. 2005) stated, “When the researchers took away rewards for simpler operations, the organisms never evolved an equals program.” By building rewards into the system — i.e. incorporating active information by providing a highly constrained fitness function — the programmers gave the system a purpose. Hence its creative power:

    dynamics.org/Altenberg/FILES/LeeEEGP.pdf

    “Both the regression and the search bias terms require the transmission function to have ‘knowledge’ about the fitness function. Under random search, the expected value of both these terms would be zero. Some knowledge of the fitness function must be incorporated in the transmission function for the expected value of these terms to be positive. It is this knowledge — whether incorporated explicitly or implicitly — that is the source of power in genetic algorithms.”

    The key point is that simulations like AVIDA are set up precisely so they can produce results…NOT necessarily that they strictly follow nature as a guideline. The question is what can Darwinian mechanisms do under the much broader constraints of nature without intelligence (active information) being involved.

    Now I’m back to lurking since I have work to do.

  30. Roy,

    “Here’s what I’m saying: in the history of science, even screwed-up, only halfway decent naturalistic explanations are not replaced with non-naturalistic explanations.”

    In the history of Science, nothing that I know of that has been originally held as a non-materialist explanation has been subsequently explained by a materialist one, save for the one in question.

    “Think about it: Planetary motion. Geologic processes. Human reproduction. I could go on. Does it ever happen? Or would ID, should it succeed, be the first?”

    Please do go on, because all of these examples were understood to be natural processes even in the time of Aristotle.

  31. Lord Timothy [30], just one example: human reproduction. In Aristotle, the material contribution of reproduction comes from the female, while the male seems to contribute an immaterial soul or intellect. From On the Generation of Animals:

    Now the reason why it is not all males that have a generative secretion, while all females do, is that the animal is a body with Soul or life; the female always provides the material, the male that which fashions it, for this is the power that we say they each possess, and this is what is meant by calling them male and female. Thus while it is necessary for the female to provide a body and a material mass, it is not necessary for the male, because it is not within the work of art or the embryo that the tools or the maker must exist.

    Aristotle, like most ancients, thought the male contributed the soul and the female contributed the body. In terms of his theory of causes, the male was the “efficient cause” and the female was the “material cause” of the offspring. In any event, the male contributes something that is not material — soul.

    Science, however, has moved on to explain human reproduction in terms that are entirely material.

  32. Khan,

    Here is the question to Valentine on the video – “Does the fossil record confirm or contradict the bottom to top pattern?”

    Here is Valentine’s answer

    “Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas. Although once we get into the fossil record where we got a complete fossil record we can see the gradual changes within lineages as Darwin predicted.”

    Now Valentine is a believer in a naturalistic approach to evolution so I would assume that the above quote is not biased and thus supports the comments I made about the Cambrian Explosion from the world’s pre-eminent invertebrate paleontologist.
    I have other quotes which express the same sentiment but for the time being this will do. From what I understand his book also is consistent with a non Darwinian explanation for the Cambrian Explosion. For example, one of the chapter sub-headings is “In Sum, the Cambrian Fossils Imply an Explosion of Bodyplans, but the Underlying Causes Remain Uncertain”

    You brought up the Ediacara fauna so I suggest that you outline their significance. I was under the impression that they are insignificant to the Cambrian explosion from what Valentine and others have said.

    For your examples, please outline how the changes you referred to represent the origin of novel complex capabilities that represent new systems in both the host and the single celled organism.

    This is what is under debate and will have to do since we cannot agree on a definition of macro evolution. Maybe we can call it “meaningful macro evolution” where the adjective meaningful refers to the evolution debate and not to whether the changes had any consequence in general.

  33. Roy [31],

    In terms of his Four causes, the male was the efficient cause, not the soul. To say otherwise is taking him out of context: “because it is not within the work of art or the embryo that the tools or the maker must exist.”

    Who contributed the soul is not the point. The point is that reproduction itself was viewed as occurring naturally even by Aristotle.

    If you want to argue the existence of the soul, that is another discussion alltogether, and another in which materialist dogma is being advanced at the expense of reality.

  34. Here’s my observation: Every time we get a full science explanation, it’s a naturalistic one.

    Not at all, not if naturalistic stands as opposed to theistic or designed as most proponents of “Enlightement” and the mythological view of Progress typical to it insist.

    The theory of gravity is an example, note how proponents of a mythological view of Progress said one thing while Newton himself said another:

    One of the first actions of those who proclaimed the ‘Enlightenment’ was the ‘deification of Newton.’ Voltaire set the example by calling him the greatest man who ever lived. Thus began an unexcelled outpouring of worshipful prose and extravagant poetry. David Hume wrote that Newton was ‘the greatest and rarest genius that ever rose for the ornament and instruction of the species.’ As Gay noted, ‘the adjectives ‘divine’ and ‘immortal’ became practically compulsory.’ [...] In 1802 the French philosophe Claude-Henri de Sain-Simon (1760-1825) founded a Godless religion to be led by scientist-priests and called it the Religion of Newton (his pupil Auguste Comte renamed it ’sociology’).
    However, as the ‘Enlightenment’ became more outspokenly atheistic and more determined to establish the incompatibility of science and religion, a pressing matter arose: what was to be done about Newton’s religion? Trouble was that Newton’s religious views were not a matter of hearsay or repute. He had, after all, in 1713 added a concluding section to the second editions of his monumental Principia, the ‘General Scholium’ (or proposition), which was devoted entirely to his ideas about God. In it, Newton undertook to demonstrate the existence of God, concluding that:
    ‘…the true God is a living, intelligent, powerful Being….’
    ‘…he governs all things, and knows all things that are done or can be done.’
    ‘….He endures forever, and is everywhere present.’
    ‘…As a blind man has no ideas of colors, so have we no idea of the manner by which the all-wise God perceives and understands all things.’
    Worse yet, Newton had written four letters during 1692-1693 explaining his theology to Richard Bentley. In the ‘Bentley Letters’ Newton ridiculed the idea that the world could be explained in impersonal, mechanical terms. Above all, having discovered the elegant lawfulness of things, Newton believed that he had, once and for all, demonstrated the certainty that behind all existence there is an intelligent, aware, omnipotent God. Any other assumption is ‘inconsistent with my system.’
    (For the Glory of God: How Monotheism Led to Reformations, Science, Witch Hunts and the End of Slavery by Rodney Stark :167-168)

    Natural explanations rooted in the rational structure of the universe are possible based on theism.

    I’m wondering: has there been a time in the history of science (outside of ID’s hope for the demise of Darwinism) when a naturalistic causal explanation has been replaced by an explanation based on intelligence?

    You are proposing a contradiction based on the mythology of “Enlightenment” which was rooted in a denial of historical facts.

    Science seems to explain by moving in the other directiion.

    If science is moving away from rational explanations and toward “natural” explanations then it will become increasingly irrational and pseudo-scientific. If we use an ignorant view of Progress to shift towards explanations which seem “natural” while maintaining a blindness to rational explanations is to undermine our knowledge as rational beings. If science is constantly moving away from intelligent agency then it is moving towards the view that your own language has more to do with natural selection operating on the mating habits of ancient worm-like creatures than intelligence. Or it could be some other utterly irrational “explanation” devoid of a rational view of intelligence but given the mythology of Progress it will inevitably be a fundamentally unintelligible view. I’ve always wondered why proponents of ID don’t somehow work a mythology of Progress into everything they say. E.g. “Well, there isn’t much evidence now but an explanation of this type will be verified in the future. Our view defines the nature of science itself. It’s inevitable.” It’s not as if they could not because the part of the nature of scientia/knowledge may be that it is intelligible and then there you have it, all Progress will inevitably be associated with or tend towards verifying ID and falsifying “chance”/ignorance based viewpoints. ;-)

  35. The point is that reproduction itself was viewed as occurring naturally even by Aristotle.

    It’s important to note that Aristotle didn’t see a contradiction between natural and rational explanations or the supposed logic of “natural and therefore not designed, specified or set in motion by intelligence.” I’m not sure what he would think of the logic of: “intelligent, therefore just a gap in scientific knowledge which will inevitably be filled with unintelligent mechanisms.” After all, he viewed the ultimate unmoved Mover or unchanged Changer (or unevolved Evolver) as the ground of all scientia/knowledge and the beginning of science because although he thought the Cosmos eternal causal patterns still trace back to something at present.

    Instead of asking, as many modern naturalists do, what past events “cause” the Cosmos as we see it now it is just as relevant to ask what causal patterns are the foundation of everything at present. And after all, if we are always seeking past events to explain the world around us we may begin to imagine things about the past based on naturalism while losing a more rational focus rooted in studying things which can be observed empirically and understood by the intellect at the moment.

  36. ribczynski (#15):

    “If so, read my later comments in the 60 minutes thread. ”

    And you, read my other answers to your posts in the same thread: #122, answering in detail your posts @115 and # 117; and #125, answering in detail your post #123. Hadn’t you eve realized that I had already promptly answered all your posts in that thread?

    “Not unless you stipulate that the designer will not interfere with the demonstration. But if you allow that the designer might be God, how can you know this?”

    Why repeat that? I have already answered. You can find my answer in my point a) above, but I will copy it here for your convenience:

    “The objection you suggest, that a designer could still be acting “behind the scenes” is simply unacceptable. I would never make it, and the same is true for any serious IDist. Maybe some theistic evolutionists…”

    In other words, to be more clear I have never, and never will, gone out of the scientific approach. I I should appeal to a God who might act without any possible inference form the observable, I would be doing philosophy or religion, not science. I have never done that. So you may be reassured, if you give me scientific confutation of ID, I will promptly accept it. And, like me, all serious IDists. ID is science, not religion. And it is scientifically falsifiable. It’s darwinists who, being unable to falsify it, hide behind false religious arguments.

    “Sure, but those aren’t the kind of saltations I’m talking about. I’m talking about changes, instigated by a designer, that happen much faster than they possibly could if natural selection were responsible.”

    Who tells you that those changes are not instigated by a designer? That’s exactly our hypothesis. And they happen fast enough to make classical darwinian theory completely uncomfortable, so much so that Gould had to create a whole new (and vastly unbelievable) approach to try to save what could be saved. And why are you so sure to know how fast a designer would act? What’s your model? Bill Gates?

    “Why does the designer always choose to behave in a way that happens to conform to what natural selection would do?”

    He certainly doesn’t do that. Indeed, nothing in natural history happened according to what “natural selection would do”. If that were the case, we would still have a planet without life (but, of course, we would not be here to know that).

    “Designers will make incremental changes to a design for a while, then abandon it and start fresh when further tweaking becomes unwieldy.”

    Have you ever heard of “object oriented programming”? That’s the most effective modality of software design, and it is based on reutilizaton of software parts (objects) even when you change radically the general structure of the program.

    “They definitely do not derive all of their designs from a common predecessor, forming a single continuous nested hierarchy that can be deduced from a careful analysis.”

    Why not? Because you say that? Just to make a gross example, automobiles do form a nested hierarchy at least as much as living beings, so much so that many times darwinists have taken that as example of how their model of evolution works, momentarily forgetting that automobiles are designed. The same could be said of computer operating systems. And of course, the number and nature of the designers would strongly condition those aspects.

    “The geological community has no such qualms. Nor do most ID supporters.”

    I have nothing to add. I just don’t know, but I’m fine with the current scientific explanations.

    “As I said, I suspect that this is because unguided geological processes pose no particular challenge to their religious beliefs.”

    Your accusing IDists for what they “accept” of current science is just a new culmination of the objective and fair approach of darwinists.

    “Avida showed how so-called “irreducible complexity” could be produced by a Darwinian process. ”

    That’s really news for me. I thought Avida was a software carefully written to show that programmers can obtain what they want, if it is simple enough (and even if they are not that good). Dembski and Marks, and many others, have commented on Avida. See also next point.

    ““Spontaneous self-selection”?? What are you talking about? That’s not a Darwinian concept.”

    It’s simple. Natural selection, even if it’s something which is usually conceived as some force coming from the environment, is in reality linked to intrinsic properties of the replicator, and to how those properties can cope with the environment. That’s what I mean with “Spontaneous self-selection”. In a GA we should have selection for the spontaneously emerging properties of the replicators. The environment must not be programmed to select a specific result we have in mind: that’s again design.

    This is an important point, so I will elaborate more on it. The environment must exert the selection in a completely unprogrammed way, because of its inherent rules. A computer environment has some properties, like any natural environment. Those properties must nor be in any way “designed” to select something: they must select in an unguided way, according to the natural constraints inherent in the system.

    the replicators, on their part, must be able to replicate, and must be subjected to random variation. The programmer can try any kind and level of random variation, and any kind of replicator. But then the new information must arise form that random noise, and create some new function, not programmed or anticipated by the programmer, and selected only according to the new properties emerged by random variation and how they interact with the inherent laws of the system. That would be a computer simulation of the darwinian theory.

    In darwinian theory, nobody has ever instructed the system about what has to take place. And nobody instructs the replicators about how they can or cannot change. Most important of all, nobody instructs the system about what should be selected or not: what is selected is totally unexpected by the system, and is selected only because its inherent emerging properties give the replicator true and objective advantages, which work in the system for their own merit, and not because the system “recognizes” them because we have instructed it to recognize them and because that was the purpose we had in mind.

    That’s why no simulation of darwinian theory exists: they are all bad simulations of design.

  37. Just to make a gross example, automobiles do form a nested hierarchy at least as much as living beings, so much so that many times darwinists have taken that as example of how their model of evolution works, momentarily forgetting that automobiles are designed.

    Very good point, GP.

  38. Jerry,
    Re: Valentine. Again, he says the same thing in the paper I linked to. But then he goes on to point out data suggesting that very little truly novel appeared in the Cambrian. do you agree that peer-reviewed papers in top-tier journals are a better source for scientific information than quotations from videos?

    The significance of the Ediacara fauna to the Cambrian explosion is that they are most likely the ancestors to the Cambrian fauna. While the systematics of many of the soft-bodied fauna is unclear (jellyfish-like? sea pen-like? completely unique?), clearly Bilaterian worms (from trace fossil evidence) from this period are most likely the ancestors of the Cambrian fauna. Again, it’s all in the paper I linked to.

    OK, macroevolution examples. Mitochondria: Do I really have to explain how an entirely new organelle capable of performing aerobic respiration is a novel, complex and highly useful feature for the host cell? The guest cell gets so many goodies from the host cell that its genome has degraded and it is no longer capable of living outside of the host. But it still replicates independently and in some cases behaves in a selfish manner.

    Similar story for the aphids- the aphids get essential amino acids from the bacteria and have evolved specialized cells (bacteriocytes) to house them in- kind of like bacteria farms. These bacteriocytes are complex, novel structures as you would see if you read the other paper I linked to (open access, so it’s yours for the taking). Again, the Buchnera bacteria get so much other stuff from the host that their genome has degraded and they can not live outside the host.

    I argue that these two well-understood examples represent strong evidence of macroevolution however you define it. If you disagree, please explain why. And you can talk about how information is lost in one species and gained in another or whatever, but the basic point that new complex structures can arise through natural processes is unchanged.

  39. Khan,

    you said

    “But then he goes on to point out data suggesting that very little truly novel appeared in the Cambrian.”

    I am sorry bit I am bewildered by this. Just that all the phyla with their unique body plans appeared out of no where with no predecessor and you are saying that “very little truly novel appeared.”

    I am sort of stunned by such a comment. I would tend not to take anything else by someone who made such a comment with any seriousness.

    You also mischaracterize the fossils of the pre Cambrian which were mostly trace fossils, that is no organism but disturbances in the sediment that indicate something live caused them. Thus, using the methods of intelligent design Valentine and others have concluded that they were due to non law, non chance origins and probably due to some living fauna. You know what we agree with Valentine’s use of ID methods in this case.

    There is no known predecessor to the Cambrian fauna and all Valentine is doing by hypothesizing what it must be and after assuming there is one, he then uses molecular clocks to estimate its content and appearance. He is again using intelligent design principles, which uses science to estimate what must have happened but he begs three questions, first that such an organism must exist, second that changes in this organism must follow a certain time pattern and third there must be a naturalistic process to explain it. He has to show each is more than just a reasonable assumption, not just beg them.

    All these speculations get into a peer reviewed paper. I wouldn’t mind that they do as long as them admit the questions they are begging.

    My quote from Valentine post dates this paper and still stands. So deal with the content of Valentine’s statement and as you said nothing in this paper is contradictory to Valentine’s video statement from a latter time.

    At least we agree on something.

  40. Jerry,

    “I am sorry bit I am bewildered by this. Just that all the phyla with their unique body plans appeared out of no where with no predecessor and you are saying that “very little truly novel appeared.”

    Actually, I didn’t say this. I said Valentine said this in the paper. and he did: Just look under “tempo and mode of body plans” on page 6755. I also didn’t say that nothing in the quotation contradicts what he says in the paper. I said that he says something similar but then goes on in the rest of the paper to discuss evidence that the statement may not be completely accurate.

    “You also mischaracterize the fossils of the pre Cambrian which were mostly trace fossils, that is no organism but disturbances in the sediment that indicate something live caused them.”

    I never said we had complete fossils of precambrian worms. I used the exact same word you did- trace fossils.

    “There is no known predecessor to the Cambrian fauna and all Valentine is doing by hypothesizing what it must be and after assuming there is one, he then uses molecular clocks to estimate its content and appearance.”

    Yes, he made a hypothesis and tested it.

    In any case, this is all a distraction from the main point. I will ask again: do you think that the evolution of mitochondria by endosymbiosis in primitive cells and the evolution of bacteriocytes for symbiotic bacteria in aphids are examples of macroevolution? I have provided several papers and links. Have you looked at them?

  41. p.s. Jerry, if you’re saying that all Precambrian fauna are known from trace fossils, you’re wrong. look up Ediacara fauna again.

    and when you think about novelty, think about both morphological and genetic novelty. Part of Valentine’s argument is that the novelty of body forms in the Cambrian came about through relatively simple changes in patterns of gene expression. this is because of the modular nature of their body plans. that’s how i interpet it, but I could be wrong.

  42. Khan,

    I said

    “You also mischaracterize the fossils of the pre Cambrian which were mostly trace fossils”

    I believe that is true. There were some others but I believe they were small and hard to determine what they were but maybe there was one small one that may possibly be a predecessor to one of the many phyla. I haven’t time to go an look this up now but I believe that is what the state was. I quickly went to wikipedia and here is what they say

    “The Ediacara, formerly Vendian) biota are ancient lifeforms of the Ediacaran Period, which represent the earliest known complex multicellular organisms. They appeared soon after the Earth thawed from the Cryogenian period’s extensive glaciers, and largely disappeared soon before the rapid appearance of biodiversity known as the Cambrian explosion, which saw the first appearance in the fossil record of the basic patterns and body-plans that would go on to form the basis of modern animals. Little of the diversity of the Ediacara biota would be incorporated in this new scheme, with a distinct Cambrian biota arising and usurping the organisms that dominated the Ediacaran fossil record.

    The organisms of the Ediacaran Period first appeared around 580 million years ago and flourished until the cusp of the Cambrian 542 million years ago, when the characteristic communities of fossils vanished. While rare fossils that may represent survivors have been found as late as the Middle Cambrian (510 to 500 million years ago), the earlier fossil communities disappear from the record at the end of the Ediacaran, leaving only controversial fragments of once-thriving ecosystems, if anything.[1] Multiple hypotheses exist to explain this disappearance, including preservation bias, a changing environment, the advent of predators, and competition from other lifeforms.

    Some Ediacaran organisms might have been closely related to groups that would rise to prominence later; for instance, Kimberella shows some similarity to molluscs, and other organisms have been thought to show bilateral symmetry, though this is controversial. Most microscopic fossils are morphologically distinct from later lifeforms: they resemble discs, mud-filled bags, or quilted mattresses. Classification is difficult, and the assignment of some species even at the level of kingdom — animal, fungus, protist or something else — is uncertain: one paleontologist has even gained support for a separate kingdom Vendozoa (now renamed Vendobionta).[2] Their strange form and apparent disconnectedness from later organisms have led some to consider them a “failed experiment” in multicellular life, with later multicellular life independently re-evolving from unrelated single-celled organisms”

    If all the body plans were the result of relatively simple changes in patterns of gene expression then why is that not true today and can one change a jelly fish into a vertebrate through gene expression. Well we will have to see on that one. I am not sure I would go to the wall on this.

    Also let me explain the debate for you. If you do not like to accept my definition of macro evolution, that is fine but then you cannot use your definition to say that because there is macro evolution under your definition, there is a partial refutation of ID. That is a complete non sequitur.

    On the case of the endosymbiotic origin of mitochondria, it is a non issue. Suppose it did happen. So what. It has nothing to do with the debate. If it did happen, it represents an interesting occurrence and nothing more and ID would not be upset about it because it does not invalidate the ID hypothesis. So it is not something ID is going to care a lot about. Maybe you should explain why ID should care.

    ID is very interested in things like the flagellum because of its complexity and function and its efficiency. But I am not sure I would classify mitchochondria the same way. Maybe they would. I have not seen a discussion on it. Why should ID care about it? Some ID people believe all the necessary information for all of life was front loaded into some original cells so a process that happened 2 billion years after life began is a yawner to them. For those who don’t think all was front loaded, it remains an interesting phenomenon but whether it is true or not is to be seen.

    In general ID is not as interested in single celled changes as they are in multi-celled changes. The flagellum is a particular example of interest and there may be others. What ID is interested in is how novel information can arise that governs systems of new capabilities. Now your other examples may fit this category but I haven’t the time to examine them. Since you are interested, I suggest you bring these examples forth with the relevant data about what new and complex and functional developed in each. That shouldn’t be too hard if you have an interest in them.

  43. Jerry,

    Re: Ediacara. THere are two components to this fauna. 1) preserved impressions of soft-bodied organisms. these are plentiful, but their phylogeny is debated. they are prob not direct ancestors of the Cambrian fauna bc they are not bilaterally symmetrical. 2) trace fossils of bilateral worms. These worms increase in complexity through time and are prob the direct ancestors of the Cambrian fauna. Valentine suggests that most of the major diversification in metazoans occured before the explosion, and that the explosion just represented further branching within already existing diversity. the bilateral symmetry, modularity and presence of the same developmental gene clusters common to almost all living things suggests that this branching could have occurred through relatively simple changes in gene expression. but that is an ongoing (and very hot) area of research right now and no one claims to have it all figured out.

    the point of the mitochondria is a simple one. you have claimed in numerous posts that there is no evidence for macroevolution. You have still not defined what you mean by macroevolution, but from piecing things together it seems to be something like “not a process but something else, involves large changes in phenotypes leading to changes in taxonomic classification sometimes at the genus and family level but not always and not in single-celled organisms except when talking about the flagellum.” i don’t know how to respond to this definition, except to say that it seems somewhat, um, personal and arbitrary. closer to art than science. my definition, while admittedly also vague is at least consistent and would definitely include the origin of the flagellum. I am even willing to say that we don’t know how the flagellum evolved. we do, however, have a very good idea of how the mitochondria evolved and it is a very complex structure and is one of the defining characters of an entire Kingdom. If that is not macroevolution I don’t know what is. so, with that in mind, I bring us back to my original point: there is evidence for macroevolution. maybe it’s not exactly what you had in mind, but by anyone’s definition except your own it is true. so please, you can say that there is no evidence for the gradual evolution of the flagellum or the eye or whatever but you can not say there is no evidence for macroevolution in general. It is simply false. I would never say that the mitochondria falsifies ID, and likewise you should not say that our ignorance about flagella falsifies evolution. Agreed?

    p.s. Margulis also hypothesized that the flagellum arose through endosymbiosis- you should check it out sometime! unfortunately, the evidence isn’t v good :(

  44. Khan:

    I don’t want to join your discussion with Jerry about macroevolution, because I too have problems with a clear definition. But, as the important point for me (and, I think, for ID) is the generation of CSI, would you agree that the model about origin of mitochondria (if it is acceptable, which I am not debating here) is not necessarily an example of generation of new CSI? After all, if I understand the essence of the model (and may be I don’t), it is essentially one of adaptation by loss of information.

  45. My comments are still being held up in the moderation queue, but I’ll take a chance on responding here.

    gpuccio wrote:

    Just to make a gross example, automobiles do form a nested hierarchy at least as much as living beings… The same could be said of computer operating systems. And of course, the number and nature of the designers would strongly condition those aspects.

    I hear this from ID supporters all the time, but it’s not true.

    Sure, you can form a nested hierarchy of cars based on, say, engines. But the hierarchy you derive by examining engines won’t match hierarchies based on radios or air conditioners or hub caps. Each characteristic yields a different nested hierarchy — unless the designer goes out of his way to make them match. There is no single “true” nested hierarchy for designed objects.

    For a group of living species, by contrast, there is just one true nested hierarchy (otherwise known as the phylogenetic tree). Within a certain small margin of error, you get the same phylogenetic tree regardless of which characteristic you look at, whether it is phenotypic or genetic.

    This is enormously powerful evidence for common descent with gradual change.

  46. gpuccio
    I won’t use the language of ID bc it is unclear to me (return the favor with bio terminology, please?), but I will say that the genome and metabolic abilities of the guest cell degraded as it became the mitochondria. However, massive lateral gene transfer from the guest to the host occurred and the host acquired some completely novel abilities and structures. so there is both loss and gain from genetic, metabolic and morphological perspectives. neat stuff, huh?

  47. Khan,

    What you’re missing is that evidence for potential/speculative generalized macro-evolutionary events–which many ID proponents might agree with–is very, very different from evidence that Darwinian mechanisms are capable of producing said macro-evolution in a uniform manner. I don’t care how macro-evolution is defined but personally I believe that given the prior existence of CSI (OOL) in an intelligently designed system that Darwinian mechanisms “should” be capable of producing a limited set of macro-evolutionary events. I haven’t seen evidence for this yet but I will not be surprised if we do.

    and when you think about novelty, think about both morphological and genetic novelty. Part of Valentine’s argument is that the novelty of body forms in the Cambrian came about through relatively simple changes in patterns of gene expression. this is because of the modular nature of their body plans.

    Heh. Sounds like you’re describing a common ID-compatible hypothesis. Whence came the modularity? And foresighted mechanisms? Why should ID proponents reject the capabilities of LGT if the system is designed to take advantage of it? (Although I will add that so far evidence for the extent of the capabilities of LGT is fairly limited yet it is assumed to be very active regardless.)

    #45,

    Nice assertions.

    Bushes in the Tree of Life

    “recent analyses of some key clades in life’s history have produced bushes and not resolved trees.”

    “The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.”

    “Wolf and colleagues omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom”

    “The evidence presented here suggests that large amounts of conventional characters will not always suffice, even if analyzed by state-of-the-art methodology.”

    ID proponents typically interpret homology as compatible with universal common descent, common descent from multiple LUCAs, or Designer Information Reuse (which is itself compatible with multiple scenarios). Instead of resolving a tree we’re getting bushes since we cannot find the gradual informational links that would be expected of Darwinian Common Descent. Continuing the theme of “islands of functional information”, these bushes could also be called “archipelagos of functional information” which must be bridged by informational leaps. Designed mechanisms could bridge (or traverse) these informational leap, thus producing Designed Common Descent.

    EDIT:

    I’d also like to add that there probably should be made a distinction between Undirected/Non-Foresighted LGT and Active/Foresighted LGT. Now it’s possible that a Designer could build a system in expectation of undirected processes, but at least one ID-compatible hypothesis would expect A-LGT. For example, viruses as a whole could have once contained the functionality of networking all organisms and triggering macro-evolutionary events.

    The problem with such functionality is that it would be expected to be highly susceptible to deleterious mutations since it’s not necessary for survival and thus this particular biosphere system for evolving would degrade with time. Eventually we’d be left with simple replicators totally focused on self-survival as we see today. BUT since they’re such fast replicators we might hope that some remnant of this functionality might survive.

  48. Patrick

    “What you’re missing is that evidence for potential/speculative generalized macro-evolutionary events–which many ID proponents might agree with–is very, very different from evidence that Darwinian mechanisms are capable of producing said macro-evolution in a uniform manner.”

    we have good evidence both that endosymbiotic events occured and that they proceeded through standard processes of evolution by natural selection- I don’t know if you’d define it as “uniform” but whatever. some of the nicest evidence is that we have observed cases of similar processes occurring in real time:

    Okamoto, N. & Inouye, I. (2005), “A Secondary Symbiosis in Progress?”, Science, 310, p. 287

    Jeon, K. W. 2004. Genetic and physiological interactions in the amoeba-bacteria symbiosis. J Eukaryot Microbiol 51:502-8

    p.s. and if you won’t define macroevolution and don’t care how it’s defined then why do you keep using it? It is very confusing. words need to have specific meanings or we can never have meaningful dialogues.

  49. What I meant is I don’t care to argue over definitions, not whether it is or should be defined. As in, I’m ignoring the recent argument in my discussion.

  50. ribczynski:

    “Within a certain small margin of error, you get the same phylogenetic tree regardless of which characteristic you look at, whether it is phenotypic or genetic.”

    You must be kidding. “One” phylogenetic tree? What kind of scientific literature do you read? Unless, when you say “within a certain margin of error”, you are thinking of that “margin” as very, very large!

  51. Khan:

    ID has no problems with horizontal gene transfer, in any form. It’s obviously “exchange” of information, and not “creation” of information, whatever language you are using. And if you want to debate ID, anyway, you have to understand its language.

    Moreover, you must admit that in the theory about mitochondria a lot remains to be explained: even if it were true that mitochondria originated that way, still you have to explain how that really happened: in other ways, either make it happen again in the lab, or give a detailed enough, and credible, molecular model of how it happened. And I do believe that such a model would still have huge gaps from a deterministic point of view, and would need to be explained in terms of design, or at least of active, intelligent, programmed adaptation.

    As far as I can see, that kind of model is still at the level of “natural history hypothesis”, and nowhere near to a true “causal theory”. In other words, darwinists, in all parts of their “theory”, still have to make the shift (and probably never will) from “it happened that way” to “it happened that way because these causal factors can and did accomplish it”. In other words, from myth to scientific explanatory models.

  52. Khan:

    By the way, if you want to call lateral gene transfer, even in massive form, or symbiosis, “macroevolution”, I have no problem with that. I usually don’t fight about words, I just try to define them in a context, to avoid ambiguities.

    And I think there is no doubt that we do observe lateral gene transfer (although usually not massive) and symbiosis in nature. You have still to prove that those processes were the real and sufficient cause of the emergence of mitochondria in eukaryotes.

  53. gpuccio,
    if you’d read the sources I’ve cited above, you’d see that we have observed the same processes occurring in the lab. there is a vast body of literature on the mitochondria endosymbiosis. please read up on it and tell me if you remain unconvinced.

  54. Khan:

    I have read both references you give. They are interesting papers, but they are about naturally occurring processes of symbiosis, the first between two eukaryotes, the second between an eukaryote and a prokaryote. Both exemples seem to interestingly show that there is very active interaction between host and symbiont, and different forms of adaptation. Frankly, nothing of that seems to have the characteristics of random variation. And, after all, I am still unconvinced that those kinds of observation prove anything about the origin of mithochondria, even if thet may rightly be the basis for a model.

    But, as I have told before, I would not call those things “macroevolution”, or, if we want to call them that way, they are examples of a kind of “macroevolution” which is very different from the classical form, based on RV and NS. Here we onserve active adaptation between existing species, and the biologic information for the expressed functions is already there, it is rather actively mixed, shared, and in some way readjusted. The process, although more complex, seems similar to lateral gene transfer bewteen bacteria. Shall I remember that LGT is a common procedure, and that it is in some way part of the natural functions of bacteria? Symbiosis too is a common event in nature. It is a form of cooperation, not of generation of new functions from random events.

    And again, the details of how the various kinds of symbiosis are realized are usually missing. The fact that we see it happen does not mean that we understand how it happens.

  55. gpuccio,

    “Both exemples seem to interestingly show that there is very active interaction between host and symbiont, and different forms of adaptation. Frankly, nothing of that seems to have the characteristics of random variation.”

    You’re right, but why does it have to be random mutation/recombination? THat’s what Darwin proposed, but we’ve progressed a lot since Darwin. In fact, as you probably know, Margulis’ ideas were not readily accepted bc they seemed to be opposed to the classic Darwinian paradigm. But she and her coworkers eventually compiled enough evidence to make a convincing case (not “prove” it bc no one ever “proves” anything in science), and the endosymbiosis theory is now widely accepted. As you note, symbiosis is a powerful force in evolution and can clearly contribute to the evolution of complex systems. mutation and recombination may build simpler systems and then symbiosis combines them to form more complex systems. the human body has tons of symbioses- we have more bacterial cells than eukaryotic cells in our bodies! so ID folks should not overlook symbiosis when they think about how complex systems could evolve. there’s more to evolution than RV and NS- This is one of the reason most evolutionary biologists don’t call themselves “Darwinists” anymore.

  56. Obviously, Darwin didn’t explicitly propose mutation/recombo.. just variation.

  57. Khan:

    I may agree on some of your points, but some clarifications are due:

    It’s OK for me to consider exchanhe of information and symbiosis as important elements in the modeling of living beings. They are, from bacteria to humans. But that changes nothing in the fundamental problem of the genesis of information.

    Biological information must exist before it can be exchanged or remixed. All biological information, at its fundamental level, cannot just be the product of “exchange”. Proteins with their functions, the DNA code, regulation networks, complex molecular machines, body plans, transcriptome regulations, and so on, all must exist and work, and then they can sometimes be exchanged and/or shared between different living beings. So, arguments such as symbiosis and similar mechanisms are of no help to explain the origin of information.

    You say:

    “mutation and recombination may build simpler systems and then symbiosis combines them to form more complex systems”

    No, that’s exactly the wrong way to look at it. Mutation and recomlbination cannot even build a single functional protein. Moreover, symbiosis does not combine simpler systems to form more complex systems; symbiosis is rather an adaptive phenomenon where two complex systems share existing functions, probably according to modalities partially or totally inherent in their complexity. There is no evidence that symbiosis may happen randomly. In other words, sharing complexity is a complex issue. It happens, but we don’t know well how, or why.

    In the end, RV and NS are the only “non design” mechanisms for the generation of biological information for which some model, although unsatisfying, exists. In that sense, I don’t agree that “we’ve progressed a lot since Darwin”. That’s not true. It’s still RV + NS, and practically nothing else, whatever McNeill and others may think in their “lists” of engines which are not engines, of causes which are not causes.

    At present, the only structured alternative to RV and NS is design.

  58. gpuccio,
    would you consider a eukaryotic cell with organelles to be more complex than a eukaryotic cell without organelles? that organelle got there by symbiosis. so symbiosis can lead to increased complexity. and the mitochondria is radically different then its progenitor cell, so it’s not simply a combination of two existing life forms- a lot changed in both the guest and host cell after they combined- the “information” is v different. you could even say it evolved.
    and your assertions on mutation not being able to generate a single functional protein are incorrect:

    Keefe and Szostak, 2001: functional proteins from a random-sequence library. Nature 410, 715-18

    Davidson and Sauer 1994. Folded proteins occur frequently in libraries of random amino acid sequences PNAS 91, 2146-50

    CHen et al. 1997. evolution of antifreeze glycoproteins in Antarctic notothenoid fish PNAS 94, 3811-16

  59. Khan,

    Margulis’ ideas were not readily accepted bc they seemed to be opposed to the classic Darwinian paradigm. But she and her coworkers eventually compiled enough evidence to make a convincing case (not “prove” it bc no one ever “proves” anything in science), and the endosymbiosis theory is now widely accepted.

    Really? Last time I read up on this subject I was under the impression her ideas were still fairly controversial. I guess it depends on what circles you travel in… *shrugs* Personally I considered the evidence “potentially convincing” and I don’t hold a preference. Whether widely accepted or not I already made my opinion on this issue in the first paragraph of #47.

    And gpuccio makes a good point that we should probably not consider symbiosis to be a subset of Darwinian mechanisms. But if you insist that we define it as such I have no problem with conceding that under your definitions that a subset of Darwinian mechanisms is “apparently” capable of producing macro-evolution. But it’s not like you can define ID away…

  60. Khan:

    Very interesting discussion, thank you!

    “would you consider a eukaryotic cell with organelles to be more complex than a eukaryotic cell without organelles?”

    Yes: it has gained the complexitu of the organelles. But id the organelles pre-existed, then there is no real gain in information. I can agree, anyway, that some information is necessary to effectively realize the symbiosis, but as I told in my previous post, I assume that such information comes from active adaptive processes, and that it depends on previous abilities inherent in the two cells. I have no reason to believe that an effective symbiosis process may happen randomly.

    “that organelle got there by symbiosis. so symbiosis can lead to increased complexity.”

    Again, if you consider the union of set A and set B, it is obviously greater than A and B. That’s almost trivial. Regarding any possible new function deriving from the interaction of the two cells, see previous point. Anyway, cooperation in nature is a general rule, beginning with the cooperating behaviour of bacteria (see Shapiro) up to the organized patterns of flight in migrating birds. Cooperation does not even require symbiosis. And it is generally a very organized, active and intelligent (and highly mysterious) process.

    “and the mitochondria is radically different then its progenitor cell, so it’s not simply a combination of two existing life forms- a lot changed in both the guest and host cell after they combined- the “information” is v different.”

    That’s why I am not sure we really understand the origin of mytochondria. A simple loss of no more necessary genes is still in some way explainable, but what about all the other differences?

    “you could even say it evolved.”

    You could even say it was designed. Again, natural history is not a causal explanation.

    “and your assertions on mutation not being able to generate a single functional protein are incorrect”

    I really thank you for bringing the debate on technical knowledge about proteins. That’s exactly the kind of discussion which can let us understand more about the real problems, even if experimental data are still not abundant. I have always affirmed that data from protein engineering will let us know more precisely what is reasonable and what is not in our respective models.

    But I must say that I don’t share your enthusiasm that the papers you cite falsify in any way my affirmation. Let us see:

    1) I could not access the full text of the Keefe and Szostak paper, which is probably the most interesting of the three. So, I had to use a comment by Rachel Brem on Genome Biology, which I found on the Internet. I paste here part of it:

    “Keefe and Szostak began with a library of 1012 80-mers. Following eight rounds of selection and amplification, 6.2% of the library bound the ATP column. After mutagenesis and further selection, 34% of the library bound the ATP column. From the final generation, eight clones were purified in milligram quantities and characterized as free proteins. All shared about 80% sequence identity among themselves but are not related to any other known sequence.”

    Well that looks very much as protein engineering here. There is vast use of intelligent selection. And the final function is just ATP binding, which in itself seems scarcely selectable in a natural context.

    Here is one final note from the above commenter (who is in no way an IDists):

    “As a protein design study, this paper hits the mark expertly. As a study of sequence evolution rates, there are some gray areas. For example, proteins from Keefe and Szostak’s first eight rounds of selection appear to use their tethered mRNA in binding ATP; thus, strictly speaking, 10^11 80-mers alone may not yield one functional protein.”

    2) I could reqad, instead, the full text of the paper by Davidson and Sauer, and I must say that I am not very impressed by it. The study is about very artificial random proteins, made of 3 aminoacids only, and the authors could only demonstrate some secondary alpha helix structure, and indirectly argue for some unknown tertiary structure and oligomeric organization. Obviously, no function at all.
    The question of how many proteins can fold is obviously a fundamental question, but its true form is: how many truly random proteins (made of all 20 aminoacids) can fold stably enough in one of the known folding patterns which are associated with function in biology? That’s the right question, and I don’t believe that this study helps much to answer it.
    And, as you know, folding is not function, but only a prerequisite for it.

    3) I will not comment in detail about that, because Behe has already done that in TEOE. Behe concludes that this example is in the range of what unguided evolution can do. But I will cite here the last words in the abstract of the paper, which are indeed revealing:

    “The notothenioid trypsinogen to AFGP conversion is the first clear example of how an old protein gene
    spawned a new gene for an entirely new protein with a new function. It also represents a rare instance in which protein evolution, organismal adaptation, and environmental conditions can be linked directly.”

    Interesting, isn’t it? I would add “the first ‘and only’ clear example”. And Behe shows the reasons why it is not a real example of emergenge of complexity (in the sense of CSI). The first example: how does that ring for a theory which, in the minds of most, is considered “a fact”?

    Anyway, again I must say that I appreciate your line of discussion. Science is done by reasoning openmindedly on known facts, and not by sticking to dogmatism.

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