Smoke and Mirrors, Whales and Lampreys: A Guest Post by Ken Miller

By Carl Zimmer | January 2, 2009 6:33 pm

miller-220.jpgIn September 2005, Ken Miller, a Brown University biologist, took the witness stand during a lawsuit known as Kitzmiller v. Dover Area School District. The plaintiffs, a group of parents in Dover, Pennsylvania, objected to “intelligent design” being required to be presented as an scientific alternative to evolution. Miller, the first expert witness called by the plaintiffs, showed that the key claims made by advocates of intelligent design are false. The plaintiffs won the case, and the people of Dover voted out the members of the Dover board of education who had pushed through the intelligent design requirements.

Over three years later, advocates of intelligent design are still trying to relive the case.  In late December, the Discovery Institute unleashed a three-part attack on Miller’s testimony, focusing on the evolution of proteins that make blood clot. I pointed out the absurdity of their arguments with the case of the one-wheeled bike.

But there’s much more to this story, as Miller noted in an email he sent to me the other day–more science and more clues to the strategies intelligent design advocates will be using in the years to come.

While Miller is the author of a number of books and a frequent lecturer, he has not yet been absorbed into the blogosphere. And so I’ve invited him to share his thoughts in three posts. The first appears here; I’ll post the next two over the weekend. [Update: Here’s part two and part three.]

One of the enduring fantasies of the intelligent design (ID) movement is the notion that it might have won the Kitzmiller v. Dover trial if it hadn’t been consistently “misrepresented” in testimony by witnesses from the scientific establishment.  Even worse, they point out, when their own heroes like Scott Minnich and Michael Behe attempted to correct those Darwinist distortions, Judge Jones, that liberal, ACLU-friendly activist, paid no attention.

More than three years after Kitzmiller v. Dover, Discovery Institute spokesman Casey Luskin is still trying to win the case.  During the trial itself, from which Discovery stalwarts William Dembski and Steven Meyer conspicuously withdrew, Luskin stood just outside the courtroom, spinning the day’s testimony for any reporter willing to listen.  Casey’s still spinning, and now he’s doing his manful best to resurrect one of Behe’s favorite arguments for “irreducible complexity” (IC), the vertebrate blood clotting cascade.  The culprit in its demise at the Dover trial, of course, was me.  But according to Casey, my testimony was nothing more than “Smoke-and-Mirrors.”

Here’s what he says:

1) The Mirror:  According to Luskin, I misrepresented Behe’s arguments (from Darwin’s Black Box) by pretending that they were “essentially identical” to those found in the ID textbook Of Pandas and People.  They aren’t, according to Luskin.

2) The Smoke:  Luskin claims that I then used that misrepresentation of Behe’s position to state that ID requires the entire blood clotting cascade to be irreducibly complex. Since Behe, according to Luskin, had actually limited his argument for irreducible complexity to a “particular segment” of the cascade, that’s simply “wrong.”

3) Then, another Mirror: Therefore, according to Luskin, any claim that the absence of three components of the cascade in the puffer fish refutes ID is absolutely false.

4) Finally, the Rehabilitation:  Behe’s actual ideas, according to Luskin, center around an “irreducible core” of components essential for the clotting reaction.  Luskin argues that the core idea, which supports the intelligent design of the system, has stood up brilliantly under scientific scrutiny.

The scientific reality, of course, is entirely different.  First, there’s a perfectly good reason why I compared the clotting treatment in Pandas to Darwin’s Black Box (DBB).  They are indeed nearly identical, and that’s because Behe himself wrote both of them.  Second, Behe actually did state that the entire pathway is irreducibly complex in DBB.  Casey might have skipped over those pages, but I didn’t.  Third, as a result, the absence of any components of the cascade in any organism is indeed a direct contradiction of Behe’s formulation of ID.  And finally, even Luskin’s “irreducible core” has fallen apart as the result of the most recent research findings on the system.

Casey seems to forget — or to ignore — the fact that Behe has never even attempted to do any scientific research to show that he is right. He ignores the fact that ID’s critics have produced a boatload of research showing Behe to be wrong while Behe himself has done no research on the system that might support Luskin. As a result, his attempts at rehabilitating the clotting cascade as an “icon” of ID are a complete failure.  So, for the umpteenth time, let’s go through this again.

Here are the details, one at a time.

1) The Mirror?  The essence of Luskin’s argument is that my testimony on the opening days of the Dover trial misrepresented Michael Behe’s position on the irreducible complexity of blood clotting.  I supposedly did this by falsely conflating Behe’s arguments with those in the ID textbook, Of Pandas and People.  According to Luskin, Behe’s actual arguments (from DBB) are “much more precise.”  To be specific, in DBB, according to Luskin, Behe limited “his argument for irreducible complexity to a particular segment of the blood-clotting cascade.”

The interested reader might begin by comparing pages 141-146 of Pandas to pages 81-97 of DBB (click here for both clotting diagrams).  As you will see, the books show the system in identical diagrams (p. 143 and 82, respectively), clearly indicating that both were derived from a common source.  That source, of course, was the author of both passages, Michael Behe.

More to the point, these matching diagrams show at least 16 different factors in the cascade.  Both books then use these complex diagrams to frame the essence of the clotting argument in nearly identical language in both passages:  All of the parts have to be present simultaneous for the system to work.  Here’s how he put it in the two books:

“When the system is lacking just one of the components, such as anti-hemophilic factor, severe health problems often result.  Only when all the components of the system are present in good working order does the system function properly.” [Pandas, p. 145]

“… none of the cascade proteins is used for anything except controlling the formation of a blood clot.  Yet in the absence of any one of the components, blood does not clot and the system fails.” [DBB, p. 86]

Writing in both books, Behe describes that as problem for evolution.  Although the narrative style differs, the meaning of both passages is identical.  Pandas notes similarities between some of the clotting proteins, which could be interpreted as evidence of common ancestry.  However, it waves away that possibility by stating:  “that even if this were the case, all of the proteins had to be present simultaneously for the blood clotting system to function” [Pandas, p. 146].

In DBB, the same issue is addressed this way: “The bottom line is that clusters of proteins have to be inserted all at once into the cascade.  This can be done only by postulating a ‘hopeful monster’ who luckily gets all of the proteins at once, or by the guidance of an intelligent agent” [p. 96]. [emphasis in the original in both quotations].

In summary, there is at best only one difference between the two treatments, a passage found on page 86 of DBB:

“Leaving aside the system before the fork in the pathway, where details are less well known, the blood clotting system fits the definition of irreducible complexity.   …   The components of the system (beyond the fork in the pathway) are fibrinogen, prothrombin, Stuart factor, and proaccelerin.” [DBB, p. 86]

By ignoring this important difference, according to Luskin, I had misrepresented Behe and misled the Court.  Behe clearly stated that the system contained just those parts past the “fork” in the pathway.  How dare I pretend otherwise?  Oh, the dishonesty!

So, where did I get the idea that Behe’s argument for ID actually included the whole system, just like Pandas’s treatment?  Easy.  Unlike Mr. Luskin, I read Behe’s whole book — including the parts before and after page 86, and I took Michael Behe at his word, as you will see.

2) The Smoke?  The claim that Michael Behe meant to include only a handful of components from the cascade in his “irreducibly complex” system would come as a shock to anyone who has actually read DBB.  Behe describes the system in great detail, asking us to consider the whole system in all its complexity, including each of its 16 different components.  In fact, Behe emphasizes how critical each and every component of the system is, pointing out that the absence of certain factors (VIII and IX) cause potentially fatal human diseases (hemophilia A and B, respectively).  But then, just as Luskin points out, on page 87, he suddenly seems to retreat, limiting the system to just four factors (fibrinogen, prothrombin, Stuart factor, and proaccelerin).  So any suggestion to the contrary is unfair to Behe and ID, right?

Not so fast.  Just keep reading.  He doesn’t actually limit his “irreducible core” at all in the way that Luskin now pretends.  Instead, on the very next page [p. 87] he discusses the hopelessness of evolution being able to change even a “slightly simplified system” gradually into a “complex, intact system.” Why?  Because adding even a single step to the pathway is beyond the range of evolution.  As Behe puts it, “From the beginning, a new step in the cascade would require both a proenzyme and also an activating enzyme to switch on the proenzyme at the correct time and place.”  Then he drops the bombshell that Luskin seems not to have noticed (or, at least he wasn’t willing to tell his readers about):

“Since each step necessarily requires several parts, not only is the entire blood-clotting system irreducibly complex, but so is each step in the pathway.” [DBB, p. 87]

Got that?  The “entire blood-clotting system” is “irreducibly complex,” and “so is each step in the pathway.”  Which Michael Behe should we believe?  The pre-Dover trial one who described the whole magnificent system as an argument for ID?  Or the one who flip-flops to a tiny core of just four proteins? Or the one who flip-flops again a page later, and once again says that the “entire blood-clotting system” and each of its steps are irreducibly complex?

I wasn’t blowing any “smoke” when I characterized Behe’s views as pertaining to the entire clotting pathway in both books.  What I was actually doing, unlike Luskin, was taking Behe’s claims in their totality.  Behe really did argue that the whole system is irreducibly complex, and that it would be impossible for evolution to add so much as a single step to it.  That’s why I testified to the effect those missing clotting factors in the pufferfish were a fatal blow to Behe’s argument.  And so they are.  The only mirror I held up to the Court was the one that reflected Behe’s own written arguments in Pandas and DBB.

3) The Judge?  Luskin seems surprised that the Judge paid no attention to Behe’s attempts to “correct” my testimony on this point.  After all, isn’t the blood-clotting argument in DBB more carefully qualified than the one in Pandas?  Well, it may be.  It certainly is more detailed, since it is intended for readers a bit older than your average 14-year-old.

But there is something very strange, and even distressing, about Luskin’s contention that the obvious failings of the arguments in Pandas are somehow less important than the ones in DBB.  Why is it OK to give high school readers an argument about the irreducible complexity of the entire cascade that you know to be false (as Luskin admits), just as long as you modify that argument in another book?  Luskin seems to have forgotten that the Dover trial was about an issue much more important than the fate of ID…. It was about what should be taught to high school science students.  And, in that respect, the arguments in Pandas were the ones that really mattered.  And those arguments, as my friend Casey Luskin has implicitly admitted in his first web posting, were completely wrong.  Too bad he didn’t spin that message at the trial.

4) An “Irreducible Core?”  Here’s where things get really, really interesting.  Luskin maintains that the “irreducible core” is a “long-standing concept within ID thinking,” and argues that this concept is well-supported by current research on the system.  Well, is it? Does the blood-clotting system really contain an “irreducible core?”

Not even close.  Luskin’s own sketch of that core highlights seven (count ‘em) components in that core (click here for that image.  The core is the red box in his diagram). Those seven components are:

Tissue Factor
Factor VIII (Antihemophilic Factor)
Factor X (Stuart Factor)
Factor V (Proaccelerin)
Factor II (Prothrombin)
Factor XIII (Fibrin Stabilizing Factor)
Fibrinogen

According to Luskin, these form an “irreducible core” without which blood clotting would not be possible.

Once again, ID fails, and the culprit isn’t a liberal judge, the ACLU, or even a slick-talking smoke-and-mirrors biology prof.  It’s nature itself, in the form of a collaboration between a nasty little beast called the lamprey (Petromyzon marinus), and a pioneering scientist who has spent his career working out the evolution of the clotting cascade.  That scientist is Russell Doolittle of the University of California at San Diego Diego (which, as it happens, is the very same university where Casey got two degrees in Earth Science while simultaneously founding and managing his creationist “Intelligent Design and Evolution Awareness” [IDEA] Club).

His 2008 paper [Doolittle et al, 2008] reports on a careful search through the lamprey genome. The lamprey, as luck would have it, has a perfectly functional clotting system, and it lacks not only the three factors missing in jawed fish, but also Factors IX and V.

Now, Luskin could object that Factor IX wasn’t part of his “core,” but Factor V certainly was.  And, as Behe pointed out at length, the absence of factor IX causes potentially-fatal hemophilia in humans, which was part of his argument for the irreducible complexity of the whole system. The lamprey genome does contain a single gene, somewhat related to Factor X and Factor V, but not identical to either.  As the paper’s authors put it: “In summary, the genomic picture presented here suggests that lampreys have a simpler clotting scheme than later diverging vertebrates.  In particular, they appear to lack the equivalents of factors VIII (or V) and IX, suggesting that the gene duplication leading to these factors, synchronous or not, occurred after their divergence from other vertebrates.” [p. 195].  To make things even worse for Luskin’s “core,” a previous study from Doolittle’s lab [Jiang & Doolittle, 2003] had already shown that the bits and pieces (protein domains) of most of the clotting factor proteins are present in a primitive, invertebrate chordate.  This is exactly what one would expect from an evolutionary trajectory leading to the current system in vertebrates — the assembly of a complex pathway from pre-existing parts.

So, what are we left with?  Nothing more than a vain attempt to pretend that ID’s collapse in the Dover case was the result of misrepresentation and deception.  For Mr. Luskin and his employers at the Discovery Institute, the generation of sound and fury continues, but in scientific terms, their continuing noise signifies nothing more than the utter emptiness of their failed ideas.

(Tomorrow: The fingerprint of evolution left in whale DNA.)

References:

Pallen MJ, Matzke NJ. (2006). “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology, 4: 784-790.

Bottaro A, Inlay MA, Matzke NJ (2006) “Immunology in the spotlight at the Dover ‘Intelligent Design’ trial.”  Nature Immunology 7: 433 – 435.

Doolittle RF, Jiang Y, Nand J. (2008) “Genomic evidence for a simpler clotting scheme in jawless vertebrates.”  J. Mol. Evol. 66:185-96.

Jiang Y, Doolittle RF (2003) “The evolution of vertebrate blood coagulation as viewed from a comparison of puffer fish and sea squirt genomes.” PNAS 100: 7527-7532

Semba U, Shibuya Y, Okabe H, Yamamoto T (1998) Whale Hageman factor (factor XII): prevented production due to pseudogene conversion. Thromb. Res. 90: 31–37.

[Image courtesy of Ken Miller]

CATEGORIZED UNDER: Evolution

Comments (168)

Links to this Post

  1. The Beauty of the Interweb: Ken Miller Demolishes Casey Luskin « Cheshire | January 2, 2009
  2. News From Around The Blogosphere 01.02.09 « Skepacabra | January 3, 2009
  3. Blogging Lazy | Tangled Up in Blue Guy | January 3, 2009
  4. The True.Origin Archive: Five Major Evolutionist Misconceptions about Evolution (Part 1) « Homologous Legs | January 3, 2009
  5. Ken Miller’s Guest Post, Part Two | The Loom | Discover Magazine | January 3, 2009
  6. Florida Citizens for Science » Blog Archive » Casey Luskin And the DI Still Crying | January 3, 2009
  7. Creationism and the Real World « The Sensuous Curmudgeon | January 3, 2009
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  10. Ken Miller’s Final Guest Post: Looking Forward | The Loom | Discover Magazine | January 4, 2009
  11. Debunking Corner - Irreducible Complexity (again) › British Centre for Science Education | January 4, 2009
  12. Threads from Henry’s Web » Ken Miller v. Casey Luskin | January 4, 2009
  13. Their Own Worst Enemy « A Dark and Sinister Force for Good | January 4, 2009
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  17. Fight For Your Right to Be Ignorant | Tangled Up in Blue Guy | January 9, 2009
  18. Irreducible complexity? Ken Miller guest blogs at the Loom | FNQhome.com | January 10, 2009
  19. Sunday Links - Crab Hat Edition « The Oyster’s Garter | January 11, 2009
  20. The True.Origin Archive: Five Major Evolutionist Misconceptions about Evolution (Part 1) | Homologous Legs | January 17, 2009
  21. Darwin re-visited - Page 55 - Science Forums | January 19, 2009
  22. Darwin re-visited - Page 57 - Science Forums | January 19, 2009
  23. Intelligent Design? « valence | February 4, 2009
  24. NeuroLogica Blog » Egnor in Forbes on Evolution | February 6, 2009
  25. behe keeps the manufactroversy going « weird things | October 17, 2009
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  1. Ben

    Dr. Miller,
    Thank you for what you do. Your efforts and those of Carl Zimmer are an inspiration to those of us just beginning down the path that you and many others have so wonderfully put ablaze. I can only hope that I can contribute in any way I possibly can.

    Ben Capoccia, PhD.
    Washington University St. Louis

  2. Colin J

    Thanks for taking the time to write all of this. If only they (Luskin et al. ) would take the time to read (and understand) it, then maybe we could get somewhere instead of re-visiting the same issues over and over.

  3. Mike
  4. Ben Capoccia, PhD. wrote:
    “I can only hope that I can contribute in any way I possibly can.”

    If you want to contribute, your PhD. could be a problem when talking to average people. I’ve found many creationists to be far more ignorant of science than I first thought:
    http://normdoering.blogspot.com/2008/08/dealing-with-abysmal-ignorance.html

  5. slang

    Thanks Ken, even if it’s like shooting fish in a barrel. Poor, poor Luskin.

  6. “Judge Jones, that liberal, ACLU-friendly activist…”

    Yep, exactly the sort of judge George W. Bush is notorious for appointing.

  7. Kevin F

    Ummmmmm….this is total castration…hehehehe……nice work, can’t wait to see the next two posts….happy holidays !!!!!!!

  8. Abraxis

    What this ID people does not get is that it’s not “Evolution OR ID” – even if evolution would be disproven, it would not make ID hypothesis any more valid.

  9. As far as blood clotting is concerned, if you are proposing a darwinian origin for this mechanism, the responsibility is yours to provide the hypothetical framework, the series of steps by which this might have occurred. It is not good science to simply declare that something happened, then challenge others to prove that it didn’t. But fear not, your job has been done for you! Russell Doolittle, the worlds leading authority on the evolution of blood clotting has proposed just such a set of steps by which the mechanism of clotting might have originated. (Doolittle, R.F.(1993) “The Evolution of Vertebrate Blood Coagulation: A Case of Yin and Yang,” Thrombosis and Homeostasis, 70, 24-28)

    Yin and Yang????

    Anyway, lets see what Professor Doolittle has to say on this subject:

    “Tissue factor appears…”

    “Prothrombin appears…”

    “A Thrombin receptor is fashioned…”

    “Fibrinogen is born…”

    “Antithrombin III appears…”

    “Plasminogen is generated…”

    Antiplasmin arises…”

    “A thrombin-activatable protein is unleashed…”

    “Plasminogen activator springs forth…”

    “Stuart factor appears…”

    Wow!!! All that springing and leaping!!! With all due respect to Professor Doolittle, he attributes these leaps and springs to gene duplication and by undirected, random duplication and recombination of gene pieces. The first problem is, however, that if a gene is duplicated, it would not immediately have these new, necessary properties, it would produce a protein with the old properties! How did these new, duplicated genes acquire these new properties? If we relegate the new functions to shuffling of gene pieces or beneficial mutations, how many worthless, unusable proteins would have to be tried before the correct one was “found”? Professor Doolittle also does not answer the crucial questions of how much factor is formed, where is it formed and how fast is it formed. Any changes in the exact location, quantity and timing of the appearance of these factors would produce inappropriate clots, that would harm the organism. All of the factors have to be introduced at the same time, in the correct proportions and in the correct location for the whole system to work.

    In short, Professor Doolittle’s explanation doesn’t hold…blood :-)

  10. 'Tis Himself

    Having, unfortunately, been involved in many discussions with creationists/IDers, I’ve discovered that mere facts and logic do not sway them. Their tendency to lie about their beliefs and their opponents’ arguments doesn’t help either.

  11. gabriel

    Ken, thanks for continuing the good fight against the inanity that is the ID movement. It was a pleasure to meet you in person in Memphis this year, and I look forward to reading your upcoming posts in this series, as well as your new book (which is on my to-read list).

  12. PharmDude

    If the Discovery Institute had a corner man, he’d be obligated to throw in the towel. Good work Dr. Miller!

  13. Thank you Dr. Miller, for smashing Luskin’s feeble attempts at revisionism. But I would point out that these people won’t care; they’ll just keep trotting out the same discredited junk over and over, no matter how many times it’s debunked. There are none so blind as those who will not see. So, the cycle will continue. As long as the courts keep getting it right, that’s the important thing.

  14. Thank you for your continued effort against ID…

    I particularly liked the references to the evolution of the ID arguments:

    “clearly indicating that both were derived from a common source. That source, of course, was the author of both passages, Michael Behe.”

    I read Behe’s DBB years ago for a philosophy class and was completely underwhelmed… again, glad you put the time and effort in on these matters!

    – CA

  15. Thanks again Dr. Miller. A good friend of mine is a psychologist and he seems to think the insanity we’re seeing with ID and IC are the dying gasps of the religious. I can only hope he’s right.

  16. Sir Craig

    Charles Wagner:

    In a thread elsewhere, you stated that you would not speak to anyone with less than a PhD, deeming such lesser beings as being “too callow.” I do not have a PhD, yet I would ask you to please reply to this simple question: Why do you think there has to be a linear progression towards any kind of development, evolutionary or otherwise? I submit to you your own words:

    If we relegate the new functions to shuffling of gene pieces or beneficial mutations, how many worthless, unusable proteins would have to be tried before the correct one was “found”?

    Though I do not possess a PhD, even I know that nothing is “tried” until something useful is “found” – you are anthropomorphizing natural processes. Evolutionary theory states (I believe) that any mutation is deemed neither useful or harmful unless it benefits or damages the organism in some fashion. Most mutations are benign and do little more than sit around until some other mutation takes place. If the combination benefits or hurts, etc etc. This is something that can take literally hundreds of thousands of generations to achieve, over millions of years.

    Is it the time-frame that has you worried, because most creationists/IDers seem to have difficulty (in my experiences with debating them) with long time frames…

  17. Hey…factor V is a part of the irreducible clotting cascade?

    I have a mutation in my factor V gene…Factor V Leiden mutation.

    I’m not dead. That makes me living proof against intelligent design!

  18. Sheridan

    Dr. Miller – I don’t understand a thing you said in your post. However, I do know the difference between science and religion. Also, I know that the ID people are trying to inject religion into science classes in the public schools. I thought that the verdict of the Dover case and the strongly worded decision by Judge John Jones would be enough to discourage the ID people from furthering their agenda. Alas, it is not to be. They are as tenacious as ever.

    I want to thank you and all the other good people who are hanging in there to defend science and progress against those who would have us all living in the Middle-Ages.

    Keep up the good fight. You have a lot of ordinary people like me who are fully supportive of you.

  19. Dave

    C’mon Charlie. Now it’s you blowing smoke. The study you point to is 16 years old. And in that time science has moved forward in attempts to prove or disprove it’s own notions. What has ID come up with? Nadda. Zilch. “Any changes in the exact location, quantity and timing of the appearance of these factors would produce inappropriate clots, that would harm the organism.” Citations please…(guffaw.

    Nice work Dr.Miller

  20. Delightfully well done, Dr. Miller! It is difficult to understand how anyone could escape the clarity of your dissection of Luskin’s “case” and sidestep all the key points in the failure of his “case” and of the claim of demonstrated “irreducible complexity” of blood-clotting mechanisms (though C^harlie W^agner’s comments up above demonstrate that by employing red herrings from a different issue one can indeed sidestep all the key points, each and every one — cognitive vigilance protecting cherished notions is an astonishing phenomena!). Here’s looking forward to the next two installments, THANKS for your time and effort on this!

  21. Michael Heath

    Could blog posts like Mr. Miller’s be the reason Mr. Luskin & the Discovery Institute doesn’t allow comments on their Internet publications?

    What I continue to find disheartening about the whole thing is how many kids are still realizing a limitation on their educational and career opportunities due partly to the efforts of people like Luskin and the rest of them at the Discovery Institute.

  22. Eric

    Great writing Dr. Miller, this biology student looks forward to parts 2 and 3.

  23. Doc Bill

    I have a PhD and I understand the subject. However, I refuse to discuss anything with Charlie Wagner until he gets an education.

    Sorry Charlie.

  24. Galapagos

    Thank you Dr. Miller. You should guest blog on The Loom more frequently, your insights are appreciated.

  25. NP

    Micheal Heath makes a good point about the DI’s “Evolution News & Views” not allowing comments. Surely they wouldn’t want their readers to actually learn something!

  26. Great post! I was reading the DI’s smoke and mirrors post and trying to figure out how to respond for my own blog. Guess I am just going to have to link right here! Dr. Miller Rocks!

  27. Gerry

    Thanks Carl and Ken.
    As a teacher, I now have more evidence to show my students how important evolution is in the study of Biology. I marvel Ken at your ability to explain things so lucidly. Any time you want to come to Australia, you would be more than welcome.

  28. That was an excellent refutation, Dr. Miller. Just another one of ID’s (irreducible) core arguments flushed down the drain.

    Does it annoy you that ID proponents are a lot slipperier than straight-out creationists? I would go insane trying to make sense of their intellectual backflips, sidesteps and smokescreens. I admire your sanity.

  29. This is why I like reading Ken Miller’s works. It allows lesser educated mortals like myself to understand complex ideas in simple terms. Cheers, Ken!

  30. lo-rez

    Thanks, Dr. Miller, for breaking it down for a layman like me. Keep up the good work.

  31. Jay Ray

    Luskin either lies or he is way out of his depth. Time and again since the very beginning, he has been shown to be the buffoon. The DI should be embarrassed and would do well to replace him or, we can hope, they might finally admit they are making it all up and pack away the not-really-all-that-big-after-all tent of theirs.

  32. MH

    truthspew wrote “Thanks again Dr. Miller. A good friend of mine is a psychologist and he seems to think the insanity we’re seeing with ID and IC are the dying gasps of the religious. I can only hope he’s right.”

    You do realise that Ken is a Catholic, don’t you? The theory of evolution is only incompatible with a *literal* interpretation of Genesis (or other creation theories).

    I shall join with you in thanking Dr Miller for this post, though. It’s always a pleasure to read his work.

  33. DB

    Thank you for fighting the good fight.

  34. Raiko

    To Kenneth Miller: You’re being quite gentle, considering that Luskin is basically lying through his teeth. I don’t think these are honest mistakes, even though you write like you’re giving him the benefit of the doubt – which I find quite noble. We’ve seen enough of the “ID”-movement to know that honesty is not part of the policy, but you’re probably aware of that. All in all, thank you for taking the time to refute these silly arguments. I am looking forward to the next part of this triology.

  35. Jeff Eyges

    Thank you, Dr. Miller. The ID’ers won’t be moved, as they cling addictively to their fundamentalist worldview, but your efforts and those of your colleagues are (hopefully) helping to educate the public as to what is and what is not legitimate science.

  36. John Kwok

    Dear Ken,

    Great job of course, and so masterfully done. After Luskin is finished in “deconstructing” blood clotting, I wonder whether he’ll set his sights next on plate tectonics. Having graduated from a leading center of research on plate tectonics, I wonder whether he’ll claim now that it is really a “fantasy” concocted by some misguided “geologists”.

    Any chance you might choose to remind Behe here at this blog that perhaps he ought to start writing the definitive textbook on Klingon biochemisty? Am sure it would be far more lucrative for him – and especially his publisher too (since it publishes the “Star Trek” books) – now that the latest “Star Trek” film will be debuting this spring. I sometimes think that he and Dembski are really in it for the money, and if that’s the chase, then what better way of promoting themselves by writing ample prose related to “Star Trek” science fiction masquerading as pseudoscience.

    A belated Merry Kitzmas and a Happy Monkey to You.

    With all best wishes,

    John Kwok

  37. John Kwok

    OOPS, some typos, so am reposting this:

    Dear Ken,

    Great job of course, and so masterfully done. After Luskin is finished in “deconstructing” blood clotting, I wonder whether he’ll set his sights next on plate tectonics. Having graduated from a leading center of research on plate tectonics, I wonder whether he’ll claim now that it is really a “fantasy” concocted by some misguided “geologists”.

    Any chance you might choose to remind Behe here at this blog that perhaps he ought to start writing the definitive textbook on Klingon biochemistry? Am sure it would be far more lucrative for him – and especially his publisher too (since it publishes the “Star Trek” books) – now that the latest “Star Trek” film will be debuting this spring. I sometimes think that he and Dembski are really in it for the money, and if that’s the case, then what better way of promoting themselves by writing ample prose related to “Star Trek” science fiction masquerading as pseudoscience.

    A belated Merry Kitzmas and a Happy Monkey to You.

    With all best wishes,

    John Kwok

  38. I think that article was the definition of “a smackdown”. Poor Casey lol.

  39. Jeff Eyges

    John, you deserve thanks, too, for arguing with the legion of morons on Amazon. You are made of far stronger stuff than I am.

  40. Lowell Luplow

    Keep up the fantastic work Ken Miller

    Happy Monkey!!

  41. Dave Vallett

    Dr. Miller> Thank you for all that you do for science… moreso because you do it in ways that Dawkins, Myers, and their colleagues simply cannot. You have managed to make the ID/Evo pseudodebate about nothing other than the science, in which ID falls hopelessly flat.

    Charlie Wagner> It’s been suggested to you in a number of places, including Pharyngula, that you actually attempt to publish your work rather than simply sniping on the web. Why haven’t you? ID falls at the first hurdle, in that it holds no predictive or explanatory power, and is not testable, and therefor it is not science. Do you think perhaps that’s why you’re limited to profressing your ignorance on your own website instead of in reputable journals?

  42. Torbjorn Larsson, OM

    Delightful! Miller provides the mirror and Luskin the smoke.

    Meanwhile, it seems clotting Charlie Wagner is still delusional:

    appears … All of the factors have to be introduced at the same time,

    Well, if it did “appear” to be 16 years ago, a common description of even significant enough results, it surely is verified today as Miller’s and Matzke’s modern references show.

    And of course the discussed evolution and specifically the lamprey example refutes the list of “all of the factors” that “have to be introduced at the same time”, but Wagner has to exemplify that he lacks “all of the factors” that it takes to understand the excellent post.

    How did these new, duplicated genes acquire these new properties?

    “Evolution, dear Wagner, evolution.” Gene duplication is a verified mechanism.

    The Wagnerian Inquisition:

    – *EVERYBODY* expects the Wagnerian Inquisition!

    Our chief weapon is repetition… repetition and dullness… dullness and repetition…

    Our two weapons are dullness and repetition… and ruthless inefficiency…

    Our three weapons are dullness and repetition and ruthless inefficiency… and an almost fanatical devotion to the Cause…

    Our four… no… Amongst our arguments… Amongst our argumentation… are such elements as dullness, repetition…

    – I’ll come in again. (Exit)

    [“stated that you would not speak to anyone with less than a PhD”.

    Hmm, so if I have a PhD (but not in biology) does that mean Wagner would actually heed my replies? Let the blood letting begin! ;-)]

  43. Torbjorn Larsson, OM

    You have managed to make the ID/Evo pseudodebate about nothing other than the science, in which ID falls hopelessly flat.

    That doesn’t pass the smell test, as the Kitzmiller vs Dover lawsuit resulted in that “The plaintiffs successfully argued that intelligent design is a form of creationism, and that the school board policy thus violated the Establishment Clause of the First Amendment to the United States Constitution.” [Wikipedia.] I.e. the context is one of a socio-political religious movement based in creationism trying to subvert science education.

    To argue the science, the law and the politics is each necessary, but so is arguing the religion and its social causes that is the origin of this parade of fools.

  44. Rev. Ryan

    Thank God for those like Dr. Miller, seeking truth under fire .
    May God bless you Dr.Miller .

  45. Chapeau. Nice way to start the Darwin year.

  46. Maezeppa

    Brilliant, and kudos. In all my years of refuting creationists I have attacked “irreducible complexity” as flawed but it never once occurred to me to expose “irreducible complexity” as an argument against evolution and not for “intelligent design”. D’oh. Thank you. That one small gem (of many) alone is worth the price of admission.

  47. david

    Very nice, Dr. Miller. Now if you could just help me understand your faith. You are quite the enigma.

  48. Dave

    David… read the posts. Understand the whole arguement. There is no requirement, or even a justificstion for needing a ‘faith’. You have certain preconceived ideas that suggest all people must have some kind of ‘faith’ in something. People who believe in reason have a faith, as you might interpret it, that two plus two equals four. But these same people would want you to be able to come to this same conclusion given the same evidence, by the same verifiable means. Two plus two is not a mystery. Science is no a mystery, nor does it want to be. Theism is a mystery and needs to be or it can’t exist. Your god, your superstition, is a mystery. One you can’t solve. And for most of the posters here a totally absurd enigma. You are the weird one.

    Dave

  49. Frank J

    Dave: I interpreted (misinterpreted?) David’s comment as questioning Dr. Miller’s Christian faith, which many “evolutionists” as well as most anti-evolutionists, see as incompatible with evolution. I don’t, BTW.

    David: Which is it?

  50. Jackson

    Really great blog entry, thanks for summarizing this part of Kutzmiller and the update. Thanks very much for the links to the corresponding diagrams in the two books -

  51. david

    I was referring to Miller’s Catholic faith. I can almost see how someone (like Miller) with an otherwise completely naturalistic world view could be a pantheist. But I simply cannot reconcile how that same person can be part of a specific sectarian belief system like catholicism. Does he really believe in the transubstantiation of the body of Christ, for example? If not, how does his congregation and his church’s religious officials feel about his participation in those ceremonies? So many questions.

  52. John Kwok

    david,

    You might get a better insight by reading Ken’s “Finding Darwin’s God”. But he isn’t the only Catholic scientist who is both deeply religious and accepts the scientific validity of evolution; the classic example of course is eminent evolutionary geneticist Francisco J. Ayala, who has written extensively about both of his keen interests in Roman Catholic Christianity and evolutionary biology.

    John

  53. Don

    We all owe you a debt of gratitude for taking the time, trouble (and the heat) to dispel the ID promoters and their thinly veiled radical Christian agendas.

  54. Zvi

    Thank you, Prof. Miller. Awesome blog post.

  55. who cares

    Regardless of what you believe, evolution or ID what is wrong with teaching the possibility of both. They are both THEORIES. Theories are not fact. I personally think both should be taught so that a student can make up their own mind.

  56. John A. Davison

    Design is apparent in every aspect of the universe. I cannot imagine a scientist of any stature that would be so weak minded as to deny or even challenge the idea that every aspect of the world, animate and inanimate WAS designed. Intelligent Design is a starting point for any serious discussion of the real world. There is absolutely nothing in the atheist Darwinian fairy tale that ever had anything whatever to do with creative, ascending evolution.

    Natural selection, the sine qua non of neo-Darwinism, is very real. Its function now as in the past is the same. It is to prevent evolution, to maintain the status quo for as long as possible, only finally for the selected organisms to succumb to extinction which is the history of the fossil record. Natural selection, allelic mutation, Mendelian genetics and sexual reproduction are all anti-evolutionary. All ascending evolution was emergent, predetermined and planned, arising on schedule from those relatively few organisms that were able to leave progeny markedly different from themselves. It is likely that such creatures no longer exist.

    The present biota is probably the terminal one for life on this planet. There hasn’t been a new Genus in two million years or a new verified true species in historical times. All we now see is rampant extinction with no new species replacing those that have become extinct.

    Just as ontogeny terminates with the death of the individual, so phylogeny is apparently also now finished and will terminate with the extinction of its products, including one of its last – ourselves, probably not more than 100,000 years old.

    For more heresy, with full documentation, I recommend my weblog where everyone is welcome but very few venture.

    jadavison.wordpress.com

  57. SkasasParadigm

    I would say if Dawkins is Darwin’s bull dog Ken miller is Darwin’s court jester. The point isn’t getting I.D. in schools it’s teaching people why Darwinian evolution is B.S. which is out of the bag.

  58. Anonymous Benefactor

    Its a good thing I never read any of those long 1000 page Ken Millers textbooks, John A. Davison provides all the necessary information I need at this point. It seems quality is much more substantial to me then quantity.

    Well now with Darwinism almost completely dead, what will you do with all those outdated useless textbooks you have written Ken Miller? Let me rephrase that question, what will all those poor students of Biology do with all those outdated and useless textbooks you have written? I have but one suggestion, when the “Darwinism is dead” museum opens, you can put them there.

    [Carl: Um…the email for this comment starts “jadavison” Coincidence? I think not. Please, no sock puppets, folks.]

  59. Anonymous Benefactor

    Hear is Ken Miller blithering away:

    “ID is false, Darwinism is true, I’m a theist and God likes to play with dice”

    Makes any sense? No, of course it doesn’t.

    [Carl: Yep, that’s Davison, too. I guess I have to remind everyone, sock-puppetry is a bannable offense.]

  60. tresmal

    SkasasParadigm Says:
    “The point isn’t getting I.D. in schools it’s teaching people why Darwinian evolution is B.S. which is out of the bag.”
    Funny that precious few scientists have heard the news. Or did you specify “Darwinian” evolution to point out that that has been completely subsumed by the Modern Synthesis?

  61. John A. Davison

    Carl:

    Anonymous benefactor is not a sockpuppet. His email is not my email. He is not I and I have no idea who he is. He helps me some with the administration of my weblog. Apparently, from his comments here, he happens to agree with me about the Darwinian fairy tale. I recommend you accept this analysis as it is entirely accurate.

    “Darwinians of the world unite. You have nothing to lose but your natural selection.”
    after Karl Marx

  62. truth machine

    if you are proposing a darwinian origin for this mechanism, the responsibility is yours to provide the hypothetical framework

    As always, Charlie lies. It is Behe’s claim that there is no evolutionary pathway; the burden is on him to demonstrate that claim; evolutionary biologists have no responsibility to provide anything in regard to Behe’s examples — and yet, they have, contrary to Charlie’s other lies.

  63. truth machine

    Regardless of what you believe, evolution or ID what is wrong with teaching the possibility of both. They are both THEORIES. Theories are not fact. I personally think both should be taught so that a student can make up their own mind.

    Sorry, but doing that will just produce people as grossly ignorant as you are. Schools are places where accumulated human knowledge is passed on to students, not a place for students to decide on their own what is or is not true. And part of accumulated human knowledge are the vast number of facts indicating that evolution occurs, and the explanatory framework for those facts that is known as the theory of evolution — “theory” not meaning guess or hypothesis, contrary to your gross ignorance.

  64. truth machine

    I simply cannot reconcile how that same person can be part of a specific sectarian belief system like catholicism.

    Then you have a grossly erroneous concept of human cognition. Alonzo Church was both a great logician and a surly racist and sexist, despite racism and sexism not being products of logic.

  65. John A. Davison

    There is at present no “evolutionary theory,” sensu strictu. Theories are verified hypotheses and neither Lamarckism nor Darwinism satisfy that criterion. The only substantial issue has always been the “mechanism” by which evolution took (past tense) place. There are two current hypotheses that each incorporate the findings of the experimental laboratory, my Prescribed Evolutionary Hypothesis (PEH) and the Universal Genome Hypothesis (UGH).

    There is nothing in the fossil record to support the gradual Darwinian model, absolutely nothing. Intermediate forms support evolution but not their gradual transformation each from a known predecessor.

    “The first bird hatched from a reptilian egg.” and “We might as well stop looking for the missimg links as they never existed.”
    Otto Schindewolf

    I welcome Carl Zimmer or anyone else to further discuss the great mystery of organic evolution either on my “Evolution is finished!” thread, here or anywhere else where that can be arranged to take place without rancor, threat or personal insult. That is a tall order these days!

    “A past evolution is undeniable, a present evolution undemonstrable.”

    jadavison.wordpress.com

  66. John A. Davison

    I agree with Behe that there were no precursors to flagella either of the prokaryoyic or the eukaryotic variety. I further believe that mitochondria, centrioles, centromeres, microtubules, cellular membranes, nuclear membranes, ribosomes and all the other cellular organelles first appeared in their present configurations and had no simpler antecedent structures from which they gradually “evolved.” It is a serious error to assume otherwise when there is absolutely no reason to do so.

    jadavison.wordpress.com

  67. John A. Davison

    Don’t take my word for it –

    “It is undesirable to believe a proposition when there is no ground whatsoever for believing it to be true.”
    Bertrand Russell

  68. John A. Davison

    How about a translation for this most recent message?

    It is hard to believe isn’t it?

    jadavison.wordpress.com

  69. RickK

    I’m a newcomer to arguments like this. But if biological evolution is not true, why do we use it to successfully predict intermediate forms that we later find? If the fossil record holds no evidence of biological evolution, why did we find tiktaalik? Why do we now find in China those feathered dinosaurs predicted by Robert Bakker?

    I think if something has an explainable mechanism, is demonstrable, is testable, and makes successful predictions, then it’s pretty hard to refute that it is a working scientific theory.

    “The first bird hatched from a reptilian egg.” This is the kind of statement that 100 years ago was provocative, but now is the sort of response one would expect on Yahoo!Answers today.

    As for the row over blood clotting, it’s the same argument made about the human eye 150 years ago. But we don’t hear the eye being front and center in the irreducible complexity arguments because we understand so many intermediate forms that paint a quite sensible picture of how the eye could have evolved. Focusing now on blood clotting, or on bacterial flagella seems to me like someone finding a loose brick in the Empire State Building, pointing at it, and saying “see, there’s no WAY this building can stand.” It sounds way too much like using polonium halos to prove the Earth is 6000 years old.

  70. John A. Davison

    RickK, whoever that is.

    You are apparently just another anyonymous blowhard, afraid to reveal his name and credentials which he probably doesn’t have anyway.

    “The first bird hatched from a reptilian egg” came from the pen of Otto Schindewolf, the greatest paleontologist since Cuvier.

    “A past evolution is undeniable, a present evolution undemonstrable.”

  71. Antaeus Feldspar

    John A. Davison, if you are interested in participating in civilized debate, you will first have to learn to conduct yourself according to the rules of civilized debate. Your current behavior suggests that you do not know these rules, or, more precisely, do not understand that they are something for YOU to follow as well, rather than simply being rules for everyone else. You say that ‘very few” venture onto your weblog. I think the reason for that is fairly obvious: people who want to sound big and important, who think they have big and important things to say, but who have nothing to support their assertions except their own pomposity, are neither in short supply nor significant demand. People listen to Ken Miller because he can make a statement and then support it with reasoned argument and appropriately cited fact. Not everyone possesses that skill — and you are a living demonstration of that.

  72. Okay, the thread hijacking has gone on long enough.

  73. Earle Jones

    Casey Luskin is an attorney and a geologist. Why would one expect anything of consequence from him on the subject of biology? Thanks to Ken Miller and to Carl Zimmer for this enlightening piece.

  74. http://blogs.discovermagazine.com/loom/2009/01/02/smoke-and-mirrors-whales-and-lampreys-a-guest-post-by-ken-miller/

    “In Chapter 4 of Darwin’s Black Box I first described the clotting cascade and then, in a section called “Similarities and Differences”, analyzed it in terms of irreducible complexity. Near the beginning of that part I had written, “Leaving aside the system before the fork in the pathway, where details are less well known, the blood clotting system fits the definition of irreducible complexity… The components of the system (beyond the fork in the pathway) are fibrinogen, prothrombin, Stuart factor, and proaccelerin.” Casey Luskin concludes that from that point on I was focusing my argument on the system beyond the fork in the pathway, containing those components I named. That is a reasonable conclusion because, well, because that’s what I said I was doing, and Mr. Luskin can comprehend the English language.

    Apparently Prof. Miller can’t. He breathlessly reports that one page after I had qualified my argument I wrote “Since each step necessarily requires several parts, not only is the entire blood-clotting system irreducibly complex, but so is each step in the pathway” and Miller asserts that meant I had inexplicably switched back to considering the whole cascade, including the initial steps. It seems not to have occurred to Miller that that sentence should be read in the context of the previous page…”

    [Carl: Geoff is quoting from Michael Behe’s latest Amazon blog post. Behe does not allow comments there. Comments are welcome here.]

  75. Joe G

    According to Dr. Behe, the author of “Darwin’s Black Box”- the book that Dr Miller said he read, his discussion was about just part of the blood-clotting cascade.

    So who are we to believe- the author or the reader?

    Now I understand why the anti-IDists want to believe the reader but that just doesn’t make any sense at all.

  76. According to Luskin, these form an “irreducible core” without which blood clotting would not be possible.

    In HUMANS!

    The lamprey, as luck would have it, has a perfectly functional clotting system, and it lacks not only the three factors missing in jawed fish, but also Factors IX and V.

    Last I checked lampreys were/ are not HUMANS!

    So the bottom-line is you people A) cannot read and B) cannot stay on-topic.

    When someone discusses a system in one organism and you turn around to say something about another organism that is plain ole dishonesty.

    But dishonesty is all you have.

    Ya see “evolution” is NOT being debated. The debate is all about directed processes vs undirected processes.

    And until you get that through your thick heads all you will ever produce are stawman arguments against ID.

  77. Antaeus Feldspar

    Joe G says:

    “When someone discusses a system in one organism and you turn around to say something about another organism that is plain ole dishonesty.”

    For you to say so indicates that you don’t actually understand what the discussion is about. Despite your mystifying assertion that “‘evolution’ is NOT being debated”, that’s exactly what we’re debating — and evolution is the process by which, according to the mainstream scientific view, one organism becomes another organism.

    Behe’s argument that the blood-clotting cascade must have resulted from design by some intelligence absolutely depends upon his ruling out all other possibilities, such as evolution from simpler versions. His attempt to rule out evolution from simpler versions absolutely depends upon the assumption that any simpler version would provide no survival value whatsoever. As soon that assumption is disproved, Behe’s argument evaporates.

    Does it matter that we find our proof that a simpler version of the system can exist and provide survival value in the lamprey, rather than in some animal closer to humans in the evolutionary tree? Not in the least. All that’s needed is to prove the possibility. As soon as you prove the possibility, you disprove the claim of impossibility.

  78. Jack

    “For Mr. Luskin and his employers at the Discovery Institute, the generation of sound and fury continues, but in scientific terms, their continuing noise signifies nothing more than the utter emptiness of their failed ideas.”

    Poetry. Thank you Dr. Miller.

  79. leebowman

    “Does it matter that we find our proof that a simpler version of the system can exist and provide survival value in the lamprey, rather than in some animal closer to humans in the evolutionary tree? Not in the least.”

    Two points. The fact that a simpler version exists neither confirms evolution by natural processes, nor disproves IC. It is evident that natural processes do offer adaptive changes. As I have stated elsewhere, that function of evolution is likely a ‘designed in’ process, i.e. a form of self-correction of species to aid in survival. Past designer(s) would have better things to do than to intervene continually, or even only as needed. But that process has (adaptive evolution) obvious limits, and radical speciation is beyond its ability.

    A prediction:

    The ‘software’ of zygote progression forms biologic constructs. Never was there a goddidit ‘poof’ event, at least not in evidence. And the complexity of what’s out there today, along with the plethora of extinctions, progressed via evolutionary processes, and of course embryogenesis, from monocellulars. The ID distinction, and where it diverges with evolutionary theory, is the method of novelty and complexity additions that are beyond the ability of undirected processes. Further, the genetic ‘software’ itself appears designed, and with data input at points in time added by intervention. It is a combination of both.

    A crude but viable analogy is the microprocessor. Designed by men, but without automated processes to incorporate revisions, and produce the templates for fabrication, could never have been accomplished manually. Today’s processors are approaching 2 billion transistors, with virtually miles of conductive pathways, yet on a (typically) one millimeter square chip of silicon. The motherboards that they sit on are even more complex (regarding pathways), since they now are comprised of as many as seven layers molded together, with thousands of pathways laid out in three axes (x,y,z).

    No human mind could fashion one without software. By extension, it is likely that no cosmic entity(ies) could have fashioned biologic life without engineering as well, and the construct of evo- & embryo- processes. The vast times involved, and the genome itself contains the evidence.

    So as to not be ‘off topic’, this prediction, if valid, rules out a totally naturalistic cascade of events. The fact that intermediates are found, does in some cases indicate transitional states. In the case of the flagella, I agree with Davison that another device (TTS) with a subset of proteins in no way validates either of those constructs forming on their own, and by selective pressure. One is a syringe, the other a propelling device. The use of some common proteins is a big ‘so what’. Both, and in particular the flagella, show earmarks of design.

    Finally the blood-clotting cascade. As stated by you know who, it has core components that are irreducible in all of its various iterations. The core components, found in lineages totally separate from each other, are the evidence of a common design team, NOT of multiple selectable mutational sequences, independent of each other. And to go a bit further, the same logic applies to virtually everything found in nature, but that point is opinion based.

    To conclude, theodicy is essentially all that is left to refute ID, and it fails on this basis. Where is it written, or demonstratable, that life on ‘theme park earth’ was intended to be Utopian? It is obviously not, and neither the Super Bowl, nor the Roman chariot races (with death as second prize) offer a more difficult or challenging quest. If anything, it exposes the competitive nature of the designer(s).

  80. leebowman

    Correction:

    Regarding the microprocessor ‘chip’, “one millimeter” is a bit of a stretch (maybe someday, when constructed on a molecular level). I meant ~ one centimeter.

  81. Antaeus Feldspar

    “The fact that a simpler version exists neither confirms evolution by natural processes, nor disproves IC.”

    By the definition of IC, it does. Why would you try to participate in this discussion if you have no idea of what the terms involved mean?

  82. david

    John Kwok, thanks for the reminder. I will endeavor to check out Miller’s, “Finding Darwin’s God.”

    — So many books. So little time.

  83. ScienceVsDarwin

    Unfortunately Miller’s lengthy article is based on poor his comprehension skills, as Behe details on his blog.

    “It seems not to have occurred to Miller that that sentence should be read in the context of the previous page, so he focuses on the components before the fork, the better to construct a strawman to knock down. In fact, in that section containing the second quote (“Since each step…”) I was arguing about the difficulty of inserting a new step into the middle of a generic, pre-existing cascade … He ignores (or doesn’t comprehend) context, ignores (or doesn’t comprehend) the distinctions an author makes, and construes the argument in the worst way possible.”

    Apparently many readers were impressed by this wholly misdirected attack. I shudder for the future of science when emotion so easily trumps logic and rationality.

    And I shudder for the clueless who are totally unaware of Darwinism’s triumph – in Hitler’s Holocaust, as documented in Weikart’s “From Darwin to Hitler” – “”The philosophy that fueled German militarism and Hitlerism is taught as fact in every American public school, with no disagreement allowed. Every parent ought to know this story, which Weikart persuasively explains.” (Phillip Johnson)

  84. ScienceVsDarwin

    BTW, anyone interested in the cogitations of a more … shall we say … *reliable* intellect … should read ex-atheist Antony Flew’s “There Is a God”. Warning: For the open-minded thinker only.

  85. ScienceVsDarwin

    More on Weikart’s long-overdue book on Darwinism and Hitler:

    “Richard Weikart’s outstanding book shows in sober and convincing detail how Darwinist thinkers in Germany had developed an amoral attitude to human society by the time of the First World War, in which the supposed good of the race was applied as the sole criterion of public policy and ‘racial hygiene’. Without over-simplifying the lines that connected this body of thought to Hitler, he demonstrates with chilling clarity how policies such as infanticide, assisted suicide, marriage prohibitions and much else were being proposed for those considered racially or eugenically inferior by a variety of Darwinist writers and scientists, providing Hitler and the Nazis with a scientific justification for the policies they pursued once they came to power.” — Richard Evans, Professor of Modern History, University of Cambridge, and author of The Coming of the Third Reich

    “This is one of the finest examples of intellectual history I have seen in a long while. It is insightful, thoughtful, informative, and highly readable. Rather than simply connecting the dots, so to speak, the author provides a sophisticated and nuanced examination of numerous German thinkers of the late nineteenth and early twentieth centuries who were influenced to one degree or another by Darwinist naturalism and their ideas, subtly drawing both distinctions and similarities and in the process telling a rich and colorful story.” — Ian Dowbiggin, Professor of History, University of Prince Edward Island and author of A Merciful End: The Euthanasia Movement in Modern America

    “This is an impressive piece of intellectual and cultural history–a well-researched, clearly presented argument with good, balanced, fair judgments. Weikart has a thorough knowledge of the relevant historiography in both German and English.” — Alfred Kelly, Edgar B. Graves Professor of History, Hamilton College, and author of The Descent of Darwin: The Popularization of Darwinism in Germany, 1860-1914

  86. ScienceVsDarwin

    Would he care to live in a society shaped by Darwinian principles? The question was asked of Richard Dawkins.

    Not at all, he at once responded.

    And why not?

    Because the result would be fascism.

    In this, Richard Dawkins was entirely correct; and it is entirely to his credit that he said so. (David Berlinski, “Connecting Hitler and Darwin”, Human Events)

  87. ScienceVsDarwin

    From the same article (Berlinski):

    Visiting the site at which those judged defective were killed — a hospital, of course — the narrator, Ben Stein, asks the curator what most influenced the doctors doing the killing.

    “Darwinism,” she replies wanly.

    [Carl: This series of comments from ScienceVsDarwin is a classic example of how not to leave comments on my blog. Ben Stein, to my knowledge, doesn’t have much bearing on blood-clotting. Back to the topic at hand, please.]

  88. ScienceVsDarwin

    Well, apparently Ben Stein knows about as much as Miller does about the evolution of blood clotting :)

    At least Stein is demonstrably more capable of following an argument in context. But, in fairness, it would have been difficult for anyone to respond to Behe’s *actual* argument, i.e. doing the hard work of considering and explaining away the clotting cascade “after the fork.”

    As wise man say, “Random mutation/natural selection works great in folks’ imaginations, but it’s a bust in the real world.”

  89. Antaeus Feldspar

    The blood-clotting cascade was claimed as an example of something that was “irreducibly complex”. The existence of a simpler version which nonetheless provides survival value falsifies that claim. Luskin’s attempts to retroactively claim that Behe’s argument about the blood-clotting cascade was something DIFFERENT than what Behe himself said in court that it was are doomed to failure — they are only attempts to obscure.

  90. ScienceVsDarwin

    “The existence of a simpler version which nonetheless provides survival value falsifies that claim.”

    First of all, Doolittle’s arguments are tentative stabs at the problem, still awaiting experimental support.

    Second, I see some education regarding the nature of the ID challenge is in order. (This was spelled out in Behe’s book, but I guess it’s on the forbidden list.) Here goes:

    The existence of a simpler cascade does not impinge upon the problem that Miller tries so hard to avoid addressing. If the lamprey is indeed relevant, falsification requires showing how the simpler system leads to the mind-bogglingly complex system by an unbroken (i.e. non-fatal) series of changes via random mutation or natural selection.

    We would do well to make a distinction between science fact and science “stories”. Doolittle’s claim is, for now, a story, charming though it may be, not to belittle Doolittle.

    If/when it becomes supported by actual data or experiment, then the really hard work begins, of demonstrating how it could change into the more complex cascade. (When we say “demonstrate”, it must be remembered, we must not mean vague glosses involving “springing forth” and the tao.) This is how science should progress, and Darwinism should not get a waiver just because it is the preferred faith.

  91. ScienceVsDarwin

    P.S. we should bear in mind that umpteen choruses of “bravo” and “good job” to Miller – some from people who admit they don’t even understand the content of his article – does not make it science. To those who are unaware of the many foibles of the “science mob”, let us recall h. pylorii and plate tectonics, whose existence was shouted down by the mob majority, and whose proponents were mercilessly ridiculed.

    I am completely open to Miller and Doolittle’s speculations being (eventually) proven right. However, these are not matters to take on faith. If we choose to believe such stories without scientific backing, we do not deserve to count ourselves among the supporters of science, but merely sycophants.

  92. Antaeus Feldspar

    “The existence of a simpler cascade does not impinge upon the problem that Miller tries so hard to avoid addressing. If the lamprey is indeed relevant, falsification requires showing how the simpler system leads to the mind-bogglingly complex system by an unbroken (i.e. non-fatal) series of changes via random mutation or natural selection.”

    Not so. Behe claimed the system to be irreducibly complex. When a simpler system is shown to be functional, that destroys the claim of irreducible complexity right there. You seem to be completely ignorant of where the burden of proof lies — it is with Behe, who is making the extraordinary claim.

    You must remember that Behe’s argument is an argument by elimination. Let us assume, for argument’s sake, that the only options for explaining the blood-clotting cascade are either intelligent design or evolution — Behe’s argument dissolves into nothingness without this assumption, so let us grant it for argument’s sake.

    Behe’s second premise is that he has disproven the possibility of evolution being responsible for the blood-clotting cascade. Now IF his two premises (it’s either intelligent design or evolution; and, it ain’t evolution) were sound, then the conclusion that it’s intelligent design would be sound as well. BUT HE MUST PROVE HIS PREMISE.

    How did Behe attempt to prove his second premise? Again, through an argument by elimination, which runs something like the following:
    * If a species without a blood-clotting cascade had evolved into a species with the complete blood-clotting cascade known today, it could have only done so by:
    * All the needed genetic changes happening ALL AT ONCE to ONE individual member of the species, OR,
    * A simpler version of the blood-clotting cascade arising first through genetic variation, natural selection favoring that simpler version because it provides survival value, and then genetic variation producing the version of the blood-clotting cascade known today.
    * But the chances of all the needed genetic changes happening ALL AT ONCE are too fantastically improbable to merit serious consideration.
    * Meanwhile, the possibility of the complete blood-clotting cascade evolving from a simpler version that itself became represented in the population because it provided survival value can be eliminated because NO SUCH SIMPLER VERSION IS POSSIBLE. (Emphasis added.)
    * Therefore, all the possibilities for the blood-clotting cascade arising through evolution have been eliminated; therefore, the blood-clotting cascase DIDN’T arise through evolution.

    Now, I hope you’ve been following carefully, ScienceVsDarwin (actually, I know you HAVEN’T; what I really hope is that someone who might otherwise be deceived by your arrogant assertions will be following carefully.) Anyone who’s been following carefully has realized that Behe’s argument is ABSOLUTELY dependent upon the premise that no version of the blood-clotting cascade simpler than the complete cascade provides any survival value. As soon as that premise was shown to be false, Behe’s argument was dead and could not be resurrected.

    “– falsification requires showing how the simpler system leads to –” No. No. Sorry, reality intrudes on your fantasy world here, falsification HAS ALREADY OCCURRED. The EXISTENCE of the simpler system falsifies Behe’s arguments. You may WISH that the burden of proof went in the other direction, just as Luskin obviously WISHES that Behe had only claimed that the “core” of the blood-clotting cascade was IC instead of claiming that the whole thing was — but you both are just going to have to come to grips with reality.

    Your failure to recognize where the burden of proof lies makes all the rest of your rhetoric empty, and your claim to be the representative of “science” here just risible.

  93. Tx skeptic

    The preceding discussion affirms that Miller has indeed refuted Behe’s argument for irreducible complexity based on the blood clotting cascade. However, this does not help the argument for common ancestry. Since nature has hidden the circumstances of the origin of life itself, it is pure speculation to assume that all life sprung from a common ancestor.

    What natural law prohibits the appearance of multiple unrelated lineages of life? Natural selection has been demonstrated with respect to members of the branches of the “tree of life,” but what’s missing is any observable evidence about the “trunk” of this “tree.” It appears that there is insufficient information to assert that all life shares a common ancestor.

  94. Antaeus Feldspar

    “Since nature has hidden the circumstances of the origin of life itself, it is pure speculation to assume that all life sprung from a common ancestor.”

    What do you mean “nature has hidden the circumstances of the origin of life itself”, Tx skeptic? If you mean that we have no information from the fossil record or from molecular biology to support the theory of common ancestry, then you’re quite simply wrong, and need to remedy the gaps in your own knowledge before you can expect to be taken seriously.

    Thankfully, I’m sure that other readers will be happy to suggest some remedial reading you might do to cure your mistaken belief that we are “missing … any observable evidence” about the common ancestry of life forms; my own suggestion is Donald Prothero’s excellent “Evolution: What the Fossils Say and Why It Matters.”

  95. Tx skeptic

    Antaeus, How do you know that life only began one time? How do you know that all metazoa share a common ancestor with protozoa, or even that all protozoa share a common ancestor? Where is the fossil evidence that eucharyotes share a common ancestor with prokaryotes?

  96. Antaeus Feldspar

    Tx skeptic —

    If that’s what you meant, you could have expressed yourself much more clearly. Saying, as you did, that we are missing “any observable evidence about the ‘trunk’ of this ‘tree'” is, again, simply false. We have plenty of observable evidence about the trunk. If you had instead asked “What observable evidence is there to indicate that there is only one trunk, and not more than one?” it would have been a far more meaningful query.

    If that was actually your intention — to query whether every single life form that has ever existed on Earth can be linked to each other by common ancestry — then you chose an extremely unfortunate way of doing so. By presenting it as if it was relevant to “Miller has indeed refuted Behe’s argument for irreducible complexity based on the blood clotting cascade,” indeed inviting people to draw the conclusion that you were somehow presenting arguments which in turn refuted Miller by starting your very next sentence after that admission with “However,” you made it seem as if you were claiming there was no evidence for common ancestry of the kind Behe thought he could rule out if the blood-clotting cascade was “irreducibly complex”. Not the wisest choice, if what you really meant to suggest was that perhaps the circumstances that brought forth the simplest forms of life from non-life could have done so more than once.

  97. Tx skeptic

    My apologies for not being clear. The point is that refuting a single argument for ID does not vindicate all of Darwinian dogma. A universal claim of Darwinian evolution is that all life came from a single common ancestor. So I ask: what is the scientific evidence for the “single tap root” and the “single trunk” of the “tree of life?”

    Re: Prothero, would you be referring to his presentation of the panspermia theory on p. 148? Or how about “the genetic take-over event where high-tech nucleic acids” replaced clay templates formed by a series of mysterious replication cycles? (p. 153). [Neither of which is able to generate life.]

    Or, perhaps the fact that fossils represent a fraction of one percent of the total number of species that have lived in the last 600 million years? (p. 52) [Inductive reasoning based on a fraction of 1% of anything is questionable.]

    Or, “The oldest truth of paleontology proclaimed that the vast majority of species appear fully formed in the fossil record and do not change substantially during the long period of their later existence.” (p. 81, quoting Gould)

  98. Antaeus Feldspar

    Ah, so you are intentionally trying to change the subject. Somehow I suspected that was the case, really.

  99. Mel

    Wow. Dishonest quote-mining used to make sweeping generalizations about evolutionary biology by and ID creationist clearly not versed in evolutionary theory, its claims, or the evidence supporting those claims. Fancy that. I expect that Tx skeptic will soon be demanding to be shown evidence of this and that rather than doing the hard work of an honest individual that would involve actually going to an academic library and going over the primary literature that is the stuff of real science.

  100. Tx skeptic

    Well, excuse me for responding to some of the broader comments on this post…

    But, A. F., you were the one who suggested Prothero. Is it not fair to comment on what he says about the question I asked?

  101. Antaeus Feldspar

    Exactly, Mel. It really says something that, with the whole Prothero book in front of him, “Tx skeptic” can’t even find sufficient quotes from Prothero to respond to — he has to find a quote from Gould in Prothero, and respond to that! Well, since “Tx skeptic” quotes Gould from page 81 of Prothero, I’ll quote Prothero himself from page 82:

    “Through all this intense debate within evolutionary biology, the creationists are constantly on the lookout for some tidbit they could quote out of context to say just the opposite of the author’s meaning. Sure enough, many of the quotations about punctuated equilibrium are misconstrued to indicate that Gould and Eldredge claim there are no transitional forms or that the fossil record doesn’t show evidence of evolution! Typically, these “quote-miners” pull a single short section out of a longer quotation that gives exactly the opposite impression of what the author really said. Such a practice suggests that the creationists either can’t read and don’t understand the entire quote or are intentionally trying to deceive their own readers by claiming that Gould and others have said just the opposite of what they actually meant (which means they are dishonest and deceitful)!”

    If “Tx skeptic” had deliberately set out to prove Prothero right about creationist quote miners, I doubt he could’ve done much better than he has already.

    By the way, anyone know where “Tx skeptic” got his bizarre idea that “A universal claim of Darwinian evolution is that all life came from a single common ancestor”? It is of course in keeping with the principle of parsimony not to postulate multiple occurrences of abiogenesis where one will do, but I have never heard of this supposed “universal claim”.

  102. Tx skeptic

    Touche! It is fair to quote someone in order to demonstrate the irony of their position which is inconsistent with the facts. The facts that Gould mentions are fair game for both sides of the argument.

    It is odd that you do not recognize the logical conclusion that every textbook on evolution presents with its diagram of the “tree of life” – the diversity of life is always represented with one trunk, not multiple independent “bushes” (borrowing from Gould again). Perhaps the latter is just be too suggestive of an alternative narrative that most evolutionists would view as heretical.

  103. Antaeus Feldspar

    It’s not “heretical” so much as “pointless and unnecessary”. The whole point of devising hypotheses is to explain the evidence, and you’ve yet to provide any evidence for which “multiple independent trees of common descent” is any better of an explanation than “a single tree of common descent.” In any case, a) it’s off-topic, because the subject is evolution, and how life came from non-life is a different subject entirely, and b) even if the subject was worth pursuing, there’s no sense in pursuing it with a dishonest quote-miner.

  104. Mel

    There are valid questions concerning if there were multiple trunks in the very earliest era of life, with later coalescence into a single one. There is nothing right now to prove or disprove such a hypothesis. Given that horizontal gene transfer was likely to have been far, far more prevalent in those early times, it is doubtful that we could pick up any signal of such multiplicity of early life lineages. What is undeniable at this point is that all life (save perhaps for some times of viruses) is related, and shows the indelible trace of common ancestry, whether vertical or horizontal (it depends on the taxon and the degree to which horizontal gene transfer dominates genetic transmission). You speak of the fossil record, and what you don’t seem to realize is that the record of common descent that is evident in genome sequences is actually far better. I would suggest you take some time to go over the research that supports these findings and assertions. I would suggest the first place to start would be Sean Carrol’s wonderful “The Making of the Fittest”. It is well written and accessible, and would give you a feel for the data and how to interpret it. Then, I would recommend you go through its works cited list, find the original research papers he cites, and read them. As it stands, it seems that you are making broad assertions about science without having made the effort to learn or understand the science itself. This does not speak well for you, and you should take this opportunity to show that you are of good faith.

  105. Tx skeptic

    I’m simply saying that common ancestry is not based on evidence per se, but rather on inference from correlating data. But this is a circular argument: you assume common ancestry because you can correlate traits (morphological or by DNA). Sure, all life shares common things such as carbon, water, etc., and information is carried in common structures built from common materials. But you would not apply such reasoning to inanimate objects (e.g., all sugar crystals don’t come from a common source). Correlation should not be confused with causation. And doesn’t the notion of evolutionary convergence make common ancestry unnecessary?

  106. Tx skeptic

    “Given that horizontal gene transfer was likely to have been far, far more prevalent in those early times, it is doubtful that we could pick up any signal of such multiplicity of early life lineages.”

    On what basis do you assert that horizontal gene transfer was “far, far more prevalent in those early times?” Any characterization of “early times” is beyond observation.

  107. Mel

    First, you will notice the term “likely”. I did not assert, either. I am going based on models put forth by Carl Woese and others. One thing that comes out of such models is that barriers to gene flow that maintain species would have taken a while to evolve. If so, then horizontal gene flow, which is still rather prevalent today in a relative sense, would have been greater during the era of early life. Again, I would recommend that you do some reading in the primary literature. I notice that you chose to dodge my recommendation that you do so in order to engage in a rhetorical attack.

    Any characterization of “early times” may be beyond direct observation (save for to the extent that we can replicate early life and early Earth conditions in the lab – and if current efforts to do this do not satisfy you, then I would recommend that you wait a while, as science is still young, and we have tens of thousands of years worth of work still to do), but it is not beyond inference based on data we have from life and the processes of life. Again, I would recommend you do some reading of the primary literature if you don’t understand this. You might also want to enter a basic nature and practice of science class at a local university if you don’t grasp that inference is a crucial and key part of science.

    As to your earlier point about common ancestry, you again display a woeful lack of understanding of the underlying evidence. It is not simply a matter of correlation, nor could all evidence from DNA sequences be useful equally to a hypothesis of convergence and a hypothesis of common ancestry. For instance, whales carry olfactory genes that are homologous with those that we carry, but all of theirs are dysfunctional due to mutations (whales can’t smell – they use their nasal passages for other things, after all). That would make no sense under a hypothesis of convergent evolution, as the dysfunctional genes don’t do anything. However, if whales descended from a common ancestor it shared with humans, then you would expect both to have similar sets of olfactory genes, but that the whale lineage would end up losing function in those genes following loss of importance and function in their olfactory sense. If you study comparative genomics, you find that genomes are rife with data like this, where there are dead genes lying around that don’t do anything, but are there simply because they were once useful in an ancestral genomic context. Again, an accessible introduction to this written for the lay person is Sean Carrol’s “The Making of the Fittest”, and after that, I suggest, again, that you go to an academic library and delve into the primary literature itself. Otherwise, I will be forced to assume that you are the typical ID creationist troll who is just playing the usual dishonest word games.

  108. Antaeus Feldspar

    Unfortunately, Mel, “Tx skeptic” is proving he is not just ignorant of “the science”, but of science, period. Examples:

    * his February 9, 2009 9:42 pm post, in which he discusses the off-topic subject of two hypotheses that have been proposed for how the first life was generated from non-life, and follows it with the comment “Neither of which is able to generate life.” Well, wow! I bet you all those scientists who have done actual work attempting to falsify hypotheses feel really silly! According to “Tx skeptic”, all you have to do is just assert that something isn’t possible and that’s all that’s needed! (The hypocrisy of such a manuever coming in the same post where he whines about “Darwinian dogma” is absolutely marvelous.)

    * his February 11, 2009 7:46 pm post, which — oh Lord, let’s just count, shall we?
    1) Attempting to find “circular logic” in stating the same fact two ways
    2) Attempting to invent an impenetrable and baffling difference between “data” and “evidence”
    3) Attempting to analogize from sugar molecules which have a few dozen atoms to DNA which may have that many chromosomes
    4) Throwing in “Correlation should not be confused with causation” with no relevance to the current conversation
    5) Finally, invoking a principle of evolutionary theory to try and argue against the logical implications of evolution!

    * his February 11, 2009 7:53 pm post, in which he shows ignorance of what “observation” means.

  109. Tx skeptic

    Your ad hominem attacks accusing me playing “dishonest word games” and hypocrisy are neither warranted nor appreciated. My premise, stated in my first post, is that not knowing the origins of life makes models of its early development highly speculative. As an engineer, I may be awkward in expressing my thoughts on this subject, but I am not being dishonest nor hypocritical.

    You don’t know what you don’t know. Instead of acknowledging this, you tell me that you can extrapolate backwards through fossils (Prothero) and DNA (Carroll) to the origins of life. As I mentioned in my response on Prothero, a 1% fossil record does not impress me as sufficient for inductive conclusions about origins. Nor has any one adequately dealt with Gould’s statement about the nature of the fossil record. Amino acids and a few proteins in the lab are insignificant with respect to the question of the origins of life.

    Re: DNA, as an engineer, I can assure you that the presence of “copied” and “similar” components in electronic products are evidence of a common designer and/or common components, not “common ancestry.” Design reuse is highly valued, and innovation often leads to extremely similar designs even from independent designers. I acknowledge my bias toward a designer viewpoint, but so far I haven’t found anything to persuade me to change my mind. Your literature appears to present a non-falsifiable system. When natural selection doesn’t explain something, then evolutionary convergence or horizontal gene transfer is called to the rescue. Previous classifications of clades reflecting close ancestral relationships are now considered polyphyletic clades, presented with appeals to evolutionary convergence. Evolution is evolving well beyond the rule of natural selection because it no longer appears adequate to explain the data.

  110. Mel

    I guess that answers my question about the dishonesty. Seriously, go to the library and do some reading. I’m not going to bother dealing with you any more. It is simply research time wasted (I am an evolutionary biology graduate student, I get really sick of people like you who clearly have never delved into the work that I and others in the field do, and yet feel fully justified in making sweeping judgments about the field despite your ignorance. I do wonder, have people like you any honor or scruples?).

  111. Mel

    And one last thing: You wrote:

    “Evolution is evolving well beyond the rule of natural selection because it no longer appears adequate to explain the data.”

    This statement alone shows incredible ignorance of evolutionary biology, and forces involved in evolution other than natural selection have been recognized and studied for going on a century now. Ever hear of genetic drift, for instance? Natural selection is likely the dominant force in evolution, and certainly the only one that can lead to adaptation and fitness of organisms to their environment, but it is not the only force, and this is neither a new concept, nor a hidden one. Heck, without even going to the primary literature, you can pick up Ridley’s textbook “Evolution” that is used at the undergraduate level and learn that.
    If you are showing ignorance that would embarrass an undergraduate biology major, you might want to reconsider your arrogance about evolutionary biology. I certainly wouldn’t display such about any area of engineering.

  112. Antaeus Feldspar

    “Your ad hominem attacks accusing me playing “dishonest word games” and hypocrisy are neither warranted nor appreciated.”

    Ah, so to the already sizable lists of things you try to talk about despite not really understanding them, we can add the concept of the ad hominem fallacy. For your information, ad hominem is not merely saying something about you and your ideas that you don’t appreciate; it’s saying that something is bad about you and falsely suggesting that this automatically carries over to your ideas. Pointing out that your argumentation abounds in dishonest quote-mining, in logical fallacies that a bright middle-schooler could see through, in evidence that you do not actually take the time or give the effort to understand the ideas you think you are talking about, but simply toss them out glibly wherever they sound good (“Evolutionary convergence” makes common ancestry unnecessary! Abracadabra hey presto! Now “evolutionary convergence” is an excuse made for evolution!) We are saying that your ideas are wrong, and you’re dishonest intellectually and otherwise. Not that your ideas are wrong because of your being dishonest intellectually and otherwise.

  113. Tx skeptic

    Mel: my statement about natural selection is in response to the continuing claims of Darwinists re: the vertical axis (not the horizontal, for which genetic drift is relevant). As for the gaps in my knowledge, I’m happy to continue reading… When I’ve had the opportunity to read Carrol’s book I’ll get back to you.

    Antaeus: what inspired you to choose “giant rock” (perhaps you had something else in mind) as your moniker? You certainly have a talent for insult. Please explain how I have been intellectually dishonest? I never suggested that my interpretation of Prothero’s book agreed with his conclusions. That said, how are my observations about his quotes dishonest? Are his statements not fair game for analysis either for or against his conclusions? It seems like “quote mining” is standard practice against ID.

    Back to dogma: “What elevated common descent to doctrinal status almost certainly was the much later discovery of the universality of biochemistry, which was seemingly impossible to explain otherwise. … In questioning the doctrine of common descent, one necessarily questions the universal phylogenetic tree. That compelling tree image resides deep in our representation of biology.” [Microbiology and Molecular Biology Reviews, June 2004, p. 173-186, Vol. 68, No. 2. article A New Biology for a New Century by Carl Woese]

    Of course, Woese suggests a new interpretation based on his theory of horizontal gene transfer (HGT), but my earlier statement about dogma seems to be supported in the literature. The HGT theory sounds speculative to me. What evidence is there that bacteria and archaea (and even eucharya) swapped genes between the two (three) domains?

  114. Mel

    “my statement about natural selection is in response to the continuing claims of Darwinists re: the vertical axis (not the horizontal, for which genetic drift is relevant).”

    A statement that shows you don’t understand what genetic drift is.

    “What evidence is there that bacteria and archaea (and even eucharya) swapped genes between the two (three) domains?”

    A question that shows you have not examined the wealth of papers on this subject that have been published over the last three decades.

    Again, arrogance founded on ignorance of the published record of data. Your statements continue to betray a lack of honor, comprehension, or intellectual honesty. At least take a class or two and do some reading before deciding to denigrate an entire field of research with tens of thousands of practitioners and hundreds of thousands of papers covering the findings and backing up the assertions of the field.

  115. Antaeus Feldspar

    “Please explain how I have been intellectually dishonest?”

    If you had actually read the answers you had purportedly been looking for, you’d know the answer to that question. It’s been spelled out in detail. Because there might be readers who don’t know exactly how you twisted the quote you ripped blatantly out of its context in the Prothero book, I’ll spell it out for them and not for you.

    Picture a large graph. And by large, I mean large. Like, picture it as large as you could make it — and then picture it even larger than that. Now place a spot at the origin; we will call this spot “point A”. Move a fairly long distance along the X axis, and then move a somewhat smaller distance perpendicular to the X axis, and mark a new spot; we will call this “point B”.

    What do our X and Y axes represent? The X axis represents time — a geological amount of time. The Y axis represents development of a particular line of genetic descent. (Obviously ‘development’ is so complex that it cannot really be reduced to a one-dimensional spectrum, but for purposes of this demonstration such a simplification will harm nothing. Just remember that while distance between two points on the Y axis means a great difference between the phenotypes represented by those points, it does not automatically mean the superiority of one over the other.) What do spot A and spot B represent? Spot B represents a species as it exists at one point in geological time; spot A represents the ancestors of that species as they existed at some far previous point in geological time.

    Now why is it relevant to say, as we did, that the graph is really, really large? To give everyone an intuitive understanding of why it’s no simple matter to say “what is the overall shape of that line?” and why there could be legitimate disputes on that answer and would be even with access to 100% of the evidence. It’s easy to say “Oh, that’s a straight line” or “oh, that’s a slightly curved line” or “oh, that’s a jagged line” if you’re looking at it drawn on a piece of paper on your desk. If it’s drawn on the Salar de Tunupa, it’s going to be a lot harder to make an assessment on what that overall line shape is.

    Now at one point the prevailing opinion about the overall shape of the line between spot A and spot B was that it should be pretty much a straight line. This is known as “gradualism” or “phyletic gradualism”. Remember, we’re talking about the overall shape of a very, very, very large line — so even if you happen to find a spot along the line where the slope is obviously far, far different from what the slope of a straight line between point A and point B would be, it’s not exactly something that you could jump up and say “Whoa! This totally disproves the ‘straight line’ hypothesis!” because after all the hypothesis is about the overall shape of the line.

    But eventually Gould and Eldredge proposed an alternate hypothesis about the overall shape of the line: that instead of a single straight line that never changed slope, it was actually composed of some line segments that ran nearly parallel to the X axis, joined to each other at their ends by line segments with much steeper slopes. This hypothesis was called “punctuated equilibrium”, and it has now displaced phyletic gradualism as the prevailing opinion (though some suggest that constant-rate gradualism was never as strongly believed as Gould and Eldredge suggested, that they painted their idea as more distinct from the prevailing opinion than it actually was. Darwin himself in The Origin of Species commented that “the periods, during which species have undergone modification, though long as measured by years, have probably been short in comparison with the periods during which they retain the same form” which hardly fits constant-rate gradualism.)

    Here is why Tx skeptic is intellectually dishonest: he freely admits that he took the Gould quote not even from Gould, but from Prothero describing how the ideas of Gould and Eldredge became the accepted view. So he knows very well the context. He knows that Gould and Eldredge are arguing against a straight line between points A and B, and for a jagged line, composed of long level segments and short steep segments. But Tx skeptic pulls from Gould only those quotes which talk about the existence of long level segments and tries to argue that this supports the non-existence of anything else!

    Okay, let’s even pretend for the sake of argument that Tx skeptic didn’t read Gould in the context of Prothero, who as we already saw hit Tx skeptic dead-center by noting that “creationists … on the lookout for some tidbit they could quote out of context to say just the opposite of the author’s meaning … [misconstrue] many of the quotations about punctuated equilibrium … to indicate that Gould and Eldredge claim there are no transitional forms or that the fossil record doesn’t show evidence of evolution”. Let’s pretend for a second that Tx skeptic didn’t read Prothero saying “this is what dishonest quote-miners do” and then proceed to do exactly that. Even if we pretend — isn’t it obvious? Isn’t it obvious that “there’s more nitrogen in the atmosphere than mainstream science thinks there is” doesn’t support a claim that “there’s no oxygen in the atmosphere, the way mainstream science thinks there is”? Isn’t it obvious that it’s dishonest to treat Gould as an authority on the evidence, but only on the evidence you want there to be?

    The answer is: yes. Yes. It’s very obvious that it’s dishonest. And Tx skeptic made the choice to be dishonest.

  116. Tx skeptic

    After all that you have said, evidence that all life sprung from a common ancestor remains elusive.

    Gould & Prothero do not shed light on the origins of life. As I said earlier, Prothero’s examples of ridiculous hypotheses from the scientific community about those origins are not persuasive.

    Furthermore, Woese’s horizontal gene transfer work calls into question whether the notion of a last universal common ancestor is even verifiable. The literature that I have read (including Woese) assumes that there is a common ancestor, and does not address how this assumption can be tested. That boils down to circular reasoning.

    You appeal to “tens of thousands of practitioners and hundreds of thousands of papers covering the findings and backing up the assertions of the field.” But those practitioners and papers cover the whole gamut of evolution, so the vast majority of that work is irrelevant to the issue I raised.

    You are the experts, so instead of attacking me, can you not tell me how this doctrine of common ancestry has been verified? Or how this doctrine is falsifiable?

  117. Antaeus Feldspar

    After all that you have said, questions about abiogenesis remain off-topic, as abiogenesis is not a part of the theory of evolution. And dignifying the discourse of a dishonest quote miner remains a waste of time and energy.

  118. Mel

    Antaeus Feldspar, I think you are right. His incoherence doesn’t help his case to be taken seriously, either (really, in what sick mind does it even make sense to mine a quote concerning punctuated equilibrium, which is an explanatory model created to explain macroevolutionary patterns, in order to use it to attack abiogenesis and the unity of life?).

    I wonder if he brings this same level of dishonesty, incoherence, and arrogant ignorance to understanding everything (yeez, what if he really is an engineer? What a threat the projects he works on must be to the life and limb of all involved?)? Let’s imagine, for instace, Tx skeptic discussing “A Tale of Two Cities”:
    There is no evidence of any tragedy or bad events in “A Tale of Two Cities”. Indeed, all evidence points to it being a bright and happy story. After all, the author himself opens by stating very clearly “It was the best of times…” That is really open and shut and cannot be denied. I don’t think there is any way to prove me wrong.
    What? You say that the entire rest of the book proves me wrong? Why, I have not heard of the rest of the book. I doesn’t contradict anything I have said anyway.
    <>
    I still see no evidence that “A Tale of Two Cities” is about anything other than the pure happiness of the best of times, just as the authors says right there in the beginning. In fact, I have read all of “Moby Dick”, and it says nothing about there being any tragedy in “A Tale of Two Cities”. Clearly you Dickensist don’t know what you are talking about.

  119. Tx skeptic

    Very clever, Mel, but you have hypothesized a story around a book for which the first chapter (not merely part of the first sentence) is missing. You have supplied your own ideas about the first chapter and proceeded from there. As you continue to substitute insults for substance, it only reflects poorly on you.

    Abiogenesis is irrelevant only for those who beg the question about the power of evolution to unify the whole story of life. You don’t want to talk about it because you have no substantive argument either for or against it.

  120. Antaeus Feldspar

    What? Did the dishonest quote-miner say something? I think it might have been another attempt to try and drag the discussion off-topic onto abiogenesis, which has nothing to do with evolution. The theory of gravity is about forces that act upon matter; the question of where the matter came from is a completely different subject. In the same manner, the theory of evolution is about what happens to life from generation to generation, and the question of how the first generation came into being is a completely different subject.

  121. Post Scriptum

    Tx skeptic

    It would be interesting to hear what your theory for the origin of life is. Since you brought up the subject, it’s surely not too much to ask for you to provide one.

    I must however say that I don’t expect much of it since you are criticizing a theory (evolution) which does not propose to describe the origin of life for not describing the origin of life. This is like criticizing evolutionary theory for not providing information about the origin of the universe (or the existence of milk shakes for that matter). Even if it was for just that reason (and it is not) I would have to agree with the conclusion that you are being intellectually dishonest.

    I would like to add a more general remark: The hole that Behe et al. have tried to squeeze their god into appears to be getting somewhat tight and it is inevitable that people start looking for yet another convenient hole to pop a deity into. Obviously the origin of life is one such hole (for the moment). Personally if I believed in a deity I certainly wouldn’t want it to be one who, under fire from progressing scientific understanding, spends his time moving from one manhole (or godhole?) to the next.

  122. Mel

    Thankfully biologists and origin of life researchers do not require the belief, acceptance, or permission of internet cranks to do their work. The work goes on, and will go on for a very long time to come. Many will continue to ignore the findings that come out, refuse to hear the answers that are obtained, or even bother to read the papers. Indeed, as findings are amassed, many will continue to deny that there are any findings (just as a certain someone will continue to say that there is no evidence to support HGT between domains no matter how many papers are out there for the finding upon some rather simple searches), but they will be out non-the-less.

  123. Tx skeptic

    Evolution is about from/to development, and thus cannot be isolated from knowledge of starting points. Therefore, origins are relevant to the discussion of evolution. However, since you appear to lack scientific evidence for a universal common ancestor you can only speculate about the role of evolution in early life on earth. From what I’ve always been told, such speculation should not be called science.

    Where this overlaps with the debate between Behe and Miller is that Behe questions the starting point and the evolutionary path to the current human blood clotting system. In response to comments on this blog, Behe would say that the lamprey’s system does not refute his argument of “irreducible complexity” of the human system because it has not been established that the lamprey is an evolutionary ancestor of humans. Behe’s question is: what is the starting point for the alleged evolution of the human blood clotting system and does the mechanism of natural selection explain the transition? I’m not defending Behe’s conclusions, but merely commenting on his logic.

    I don’t subscribe to a god of manholes, but you have switched contexts from science to philosophy/theology. In the latter context, it is valid to recognize both primary and secondary causes. Theists like Miller can affirm that God established the natural laws that govern the universe; hence, evolution may be viewed as the secondary cause of that for which God is the primary cause.

    Why not admit that discussions of origins and the early role of evolution are philosophical and not scientific?

  124. Mel

    “Why not admit that discussions of origins and the early role of evolution are philosophical and not scientific?”

    Because, whether you choose to realize it or not, such investigations are the domain of science. That you don’t understand that is not surprising, as you have shown repeatedly that you don’t understand the nature and practice of science (nor apparently that the origin of life and the existence of a common ancestor are very much separate issues ). Again, thankfully, scientific inquiry is not contingent upon the acceptance or blessing of intellectually dishonest internet cranks. Of course, those cranks will never recognize this, and will continue with their delusions of relevance.

  125. Antaeus Feldspar

    “Evolution is about from/to development, and thus cannot be isolated from knowledge of starting points.”

    Sure, right. Just as you can’t possibly discuss how gravity pulls an apple to the ground without talking about how the apple tree got there. Oh, wait, you can.

    “Where this overlaps with the debate between Behe and Miller is that Behe questions the starting point and the evolutionary path to the current human blood clotting system.”

    In other words, it doesn’t overlap at all. Perhaps it might if Behe had managed to prove that the ancestry of humans led back to some abiogenetic event that was not the same abiogenetic event that led to other species, but in point of fact, he did not prove that or anything like it.

    “In response to comments on this blog, Behe would say that the lamprey’s system does not refute his argument of “irreducible complexity” of the human system because it has not been established that the lamprey is an evolutionary ancestor of humans.”

    And if Behe made that fallacious response it would be nothing but garbage. Reality time: the burden of proof is on the party making the extraordinary claim. Behe is that party; he claims that he has proven that the human blood-clotting system is the product of intelligent design by disproving ANY POSSIBILITY that it came about by evolution. He claims that he has disproven any possibility that the HBCS came about by evolution because there is NO simpler system that is adaptive from which the HBCS could have evolved. But we already know that that assertion, the linchpin of his claim, is FALSE.

    Idiots and scoundrels may try to reverse the burden of proof and claim that, in order to refute Behe, mainstream science must not only show that there IS a simpler system that is adaptive but also show that it was THAT simpler system and no other from which the HBCS evolved. To which the correct response is: Bull-puckey. Behe’s argument was always shaky, based as it was on an assumption that “we know of no such system” means “no such system exists”. But the minute it was shown that such a system DID exist, Behe’s argument, which was ENTIRELY DEPENDENT upon the premise that NO SUCH SYSTEM EXISTED — are you comprehending this? — dissolved in failure.

  126. Post Scriptum

    You seem pretty confused. For one you keep conflating evolutionary theory and the problem of the origin of life despite the fact that the difference has been pointed out to you several times now.
    You ask: “Why not admit that discussions of origins and the early role of evolution are philosophical and not scientific?”
    Let me try to answer that: Might it be because they are not? Since organic matter is constructed from the same basic materials as inorganic matter it is not a philosophical problem how it came into existence. There is no problem of dualism here. The question of the origin of life is simply the question how matter came to be assembled in a specific configuration. That question is a completely legitimate scientific question and is indeed being studied as such.
    The fact that there is currently no well tested and supported theory and that you personally can’t see such a theory (or evidence supporting it) being found is completely irrelevant to the matter of it being a scientific question. By the way, I hope you noticed that you have invoked one of the typical fallacious ID arguments here? In case you hadn’t realised, I am referring to the argument from personal incredulity.

    You add that I switch contexts from science to philosophy/theology. You still don’t seem to realize that ID IS theology and that only for that reason my remark is neccesarily in that context. I haven’t switched contexts, I have just not been as confused as some people about the fact that the “god of holes” approach to scientific knowledge (of which ID is only one incarnation) IS and always has been THEOLOGY.

  127. Tx skeptic

    “…the origin of life and the existence of a common ancestor are very much separate issues”

    Your unstated assumption that life only started once is unverifiable; hence there is no basis for your conclusion.

    “The question of the origin of life is simply the question how matter came to be assembled in a specific configuration.”

    There are non-living organisms everywhere that are fully assembled for life. Try again.

    Back to the two lines of evidence that you appeal to for explaining early life on earth: fossils and DNA. Scientists claim that life on earth can be traced back 3.5 B years. Yet neither fossils nor DNA are available for the first 3 B years. Recalling your illustration from A Tale of Two Cities, you make a lot of claims based on having “text” from only the last 14% of the book, of which only a fraction of 1% of the “words” is available (by Prothero’s account, which greatly exceeds the DNA evidence available).

  128. Mel

    Your unstated assumption that life only started once is unverifiable;

    The common ancestor came long after the origin of life. How many independent origins of life there initially were is irrelevant, as life bears the stamp of common lineage. It is possible that life arose multiple times, and either all descendants of all but one of these multiple ur-lineages died out, leaving the one that remains, or all came to be meshed prior to the common ancestor. Regardless, you don’t need to know the exact details of the origin of life to be able to study and discern how life evolved and diversified after the last common vertical ancestor. It really isn’t all that hard to understand. Of course, I can’t expect someone who doesn’t understand what genetic drift is and who insists that there is no evidence for horizontal gene transfer between domains despite the existence of such evidence if he bothered to do a PubMed search to understand such things. Really, Tex, you just continue to shame yourself as dishonest and incoherent.

    And, yes, there are fossils available from almost 3 billion years ago:
    Lepot, Kevin; Karim Benzerara, Gordon E. Brown, Pascal Philippot (2008). “Microbially influenced formation of 2,724-million-year-old stromatolites”. Nature Geoscience 1: 118–21. doi:10.1038/ngeo107. ISSN 1752-0894.

    There are microfossils from even earlier. Again, do you ever do any research before you make your claims?

    I think you missed the point of the “A Tale of Two Cities” example, and in the process are demonstrating its aptness in describing your dishonesty and inability to comprehend what you read.

  129. Tx skeptic

    “How many independent origins of life there initially were is irrelevant, as life bears the stamp of common lineage.”

    Common lineage assumes a lot for the connection between e.g., prokaryotes and humans, particularly since there is no verifiable family tree or step-wise verification of the development of any primitive genome to that of humans. A Ford and a bicycle have much more in common than a bacteria and a human, yet no common lineage. What is common to all life are the building blocks and mechanisms and the “spark of life.” You have no reason, other than a presumption, for dismissing the possibility of a common designer.

    Re: HGT, the earliest DNA available is from the Cambrian era. Hence, any papers on HGT occurring prior to that are sheer speculation. But common lineage presumes a link prior to that – so your argument begs the question.

    Please excuse my mistake regarding pre-Cambrian fossils. However, consider the following:

    1. The supposed stromatolites found in 3.5 Ba sediments have been challenged by Donald Lowe, whose well-known research attributes the patterns to abiotic sources.

    2. The dates of artifacts attributed to biotic origins found in sedimentary rock should not be confused with the age of the surrounding rock, any more than the dates of shells washed ashore should be associated with the age of the sand surrounding it. The dating techniques used rely on igneous rocks, which are dated to their molten phases, during which any soft-bodied life would have vaporized. As an article on Geochemisty in Science (23 January 2009) noted, “However, these [dating] measurements were performed on a bulk rock sample, and there is no context information about the environment of formation of the rocks or the kinds of life forms they could contain.” This article also says that your 2.7 Ma stromatolites are “now reidentified as recent contamination.” The only thing that can be concluded is that artifacts found in rock were deposited no earlier than the date the rock underwent its last molten phase.

    3. The discovery of early stromatolite fossils is evidence only of common ancestry for present-day stromatolites, not other life.

    4. Porthero has conceded that the paucity of fossils prior to the Cambrian era does not contribute to the argument for a universal common ancestor.

    Re: Lowe’s work, see:
    http://www.space.com/scienceastronomy/astrobio_paleontology_030407.html
    (Earth’s Oldest Fossils Reverse Course, April 7, 2003).

    So modify my analogy based on A Tale of Two Cities to include a few random “words” in the early chapters of the book. Your story is based on conjecture and speculation, not scientific evidence. Common lineage, is as Woese called it, a doctrine.

  130. Mel

    Okey-doke, Tex, I get it. You don’t understand evolution. You don’t understand the evidence behind evolutionary biology. You haven’t done much research beyond looking for even the most tenuous basis to reject your understanding of evolution (hence the magnificent examples of quote mining and egregious intellectual dishonesty). You don’t understand the nature and practice of science. You really, really, really don’t want to accept evolution, and it is clear nothing will ever change that. Fine. Have fun with that.

  131. Antaeus Feldspar

    “You have no reason, other than a presumption, for dismissing the possibility of a common designer.”

    Tex once again demonstrates that he doesn’t bother reading. Didn’t we just cover the issue of the burden of proof? If someone wants to postulate the involvement of a “designer” in the creation and development of life, the burden of proof is upon that person to justify the involvement of such an entity, not on anyone else to justify its exclusion.

    Behe claimed he had met the burden of proof by showing that evolution could not be responsible for the development of the human blood-clotting system. However, as we saw, one of the premises which absolutely has to be true for Behe’s claim to hold together is in fact false, so Behe failed to meet the burden of proof. You tried to resurrect Behe’s claim by … well, basically by being a poor/dishonest logician and trying to move the goalposts to hide the fact that Behe’s claim is already collapsed beyond repair.

    Now what do you try to offer to meet the burden of proof, to justify why some “common designer” had to be involved? Let’s see… … … what, you mean this is it? “A Ford and a bicycle have much more in common than a bacteria and a human, yet no common lineage.” That pathetic analogy is all you have to offer? I mean — you expected that to be taken seriously?

    All right, let’s expose your idiocy for what it is:

    * Ford and bicycles do not create modified copies of themselves. Bacteria and humans do.
    * The predecessors of modern bicycles, push bikes, first appeared around 1818-1819. The first Fords came out in 1902-1903. That means that less than 100 years elapsed between the first bicycles and the first Fords. By contrast, bacteria first appeared about 3,500,000,000 years ago, and modern humans first appeared about 200,000 years ago.
    * So with the stupid parts spelled out, your analogy is “If the only way to explain the common appearance of two machines which made their first appearances about a century apart is that they had the same designer, obviously that’s the only way to explain any commonalities between two organisms which made their first appearances over 3.499 million centuries apart! Clearly, we can dismiss any possibility that imperfect replication over a little matter of 3.499 million centuries could account for any differences between the two organisms, not because we have any reason to think that imperfect replication ever stopped during that 3.499 million centuries but just because we can be pretty sure that imperfect replication didn’t affect the mechanical devices. Which don’t replicate.”

  132. Tx skeptic

    “Okey-doke, Tex, I get it.”

    No, Mel, you don’t get it. I am simply questioning the evidence for the universal common ancestor, not the evidence for evolutionary diversity. BTW – I feel sorry for people who thrive on insulting others. I don’t claim to understand everything, but dishonest, I’m not.

    Feldspar: Burden of proof? Where did DNA come from in the first place? Sure life makes copies of itself; but its ability to make these copies came from an external source. You assume that original source disappeared. On what basis?

    “If the only way to explain the common appearance of two machines which made their first appearances about a century apart is that they had the same designer…”

    I never claimed that a bicycle and a Ford had the same designer, merely that they came into existence independently from external sources. It is you who are being intellectually dishonest.

  133. Antaeus Feldspar

    Tx credulous —

    Once again, you are pursuing the wholly off-topic issue of abiogenesis. We’ve only explained, what, five times why abiogenesis and evolution are two separate subjects? Your insistence on trying to drag the conversation off-topic yet again sure looks like dishonesty to me. Even if the topic were abiogenesis, your claim that life’s ability to replicate ‘came from an external source’ is unsupported, making your claims about what others assume about that supposed external source misguided.

    As for your bicycle and Ford argument, I thought I was giving YOUR argument the benefit of the doubt by considering that since bicycles and Fords are both designed by humans, that could count as a ‘common designer’. If that wasn’t to your liking, then I officially have no idea what the hell the point you were trying to make with that blather about Ford and bicycles. WAS there a point, or have you resorted to just pure obfuscation now that your quote-mining has been exposed?

  134. Tx skeptic

    Feldspar: you appear not to have understood my explanation that abiogenesis is indeed relevant to the question of common ancestry. If there were more than one lineage of life, it is reasonable that the descendants of those lineages would not share a common ancestor. Re: the Ford & bicycle, I explained that the point was both were the products of external sources. Apparently you have trouble relating that concept to design?

    Below is a link to an article summarizing the findings to date from genomics. What I find interesting is that it argues for new paradigms to explain evolution because the results of the research don’t fit the traditional models. The continual revision of evolutionary explanations persuade me that science hasn’t really figured out what it dogmatically teaches after all.

    http://nar.oxfordjournals.org/cgi/content/full/gkp089v1
    Darwinian evolution in the light of genomics, by Eugene V. Koonin
    Nucleic Acids Research, Feb 12, 2009

    Selected quotes:
    The existence of a ‘species tree’ for the entire history of cellular life, is falsified by the results of comparative genomics. [What, no universal common ancestor?]

    Major gaps in the reconstructed gene set of LUCA … the lack of conservation of central cellular systems among the domains of life indicates that the early stages of cell evolution involved radical changes which are hardly compatible with uniformitarianism. [a corollary of common ancestry is uniformitarianism.]

    The modern-type DNA replications systems and membranes evolved at least twice independently in two domains of life (assuming a symbiogenetic origin for eukaryotes). [Since the basic DNA replications systems of bacteria and eukaryotes evolved independently, one might reasonably question common ancestry.]

    There are major differences in the genome layouts between different lines of life evolution. [Another reason to question common ancestry.]

    There is every reason to believe that, even prior to the radiation of all major lineages known today, the distribution of genome sizes and the mean complexity in prokaryotes was (nearly) the same as it is now. [Yep, those 3.5 Ba cyanobacteria that left stromatolites look the pretty much the same in today as they did back then. It appears that bacteria didn’t grow up to be fish or birds or animals after all.]

    Whether the TOL can be salvaged as central trend in the evolution of multiple conserved genes or this concept should be squarely abandoned for the Forest of Life image remains an open question. [The “tree of life” concept just doesn’t look like it will survive the scrutiny of genomics.]

    The theoretical and empirical studies on the evolution of genomic complexity suggest that there is no trend for complexification in the history of life and that, when complexity does substantially increase, this occurs not as an adaptation but as a consequence of weak purifying selection, in itself, paradoxical as this might sound, a telltale sign of evolutionary failure. It appears that these findings are sufficient to put to rest the notion of evolutionary ‘progress’, a suggestion that was made previously on more general grounds. [So Darwin seems to have been mistaken after all.]

    Did alternative splicing evolve as a functional adaptation? In all likelihood, no. [Another hole in Darwin’s theory.]

    Genomic complexity is not, originally, adaptive but is brought about by neutral evolutionary processes when purifying selection is ineffective. [Where’s Darwin when you need him?]

    The insistence on adaptation being the primary mode of evolution … became deeply suspicious if not outright obsolete, making room for a new worldview that gives much more prominence to non-adaptive processes. [Looks like the theory of evolution is due for major renovations.]

    All of the above demonstrate why I’m skeptical of the explanations of the history of life coming from the proponents of evolution. The burden of proof is yours.

  135. Antaeus Feldspar

    “you appear not to have understood my explanation that abiogenesis is indeed relevant to the question of common ancestry.”

    Only if you define “the question of common ancestry” as something that is itself irrelevant to the current discussion. As far as I can tell, it’s not only irrelevant to the current discussion but boring and pointless in its own right, ranking below “how many angels can dance on the head of a pin” in the category of “questions that ever have a chance of being worth the time it takes to discuss them.”

    “Selected quotes:” Oh yes. I’m sure they’re quite carefully “selected”, probably in the same manner that you “selected” quotes from Gould out of Prothero. If you think anyone would waste time with your dishonest quote-mining, you’re out of your head — especially as even a casual skimming of the quotes shows that Koonin’s thesis is “in ‘descent with modification’, the ratio of ‘modifying’ events to ‘selecting’ events is higher than previously thought” and not even close to your “descent with modification is defeated, long live a nebulous common designer!”

    “All of the above demonstrate why I’m skeptical of the explanations of the history of life coming from the proponents of evolution. The burden of proof is yours.” Once again you show that you (deliberately, probably) misunderstand the burden of proof.

    The dominant scientific theories are that a) life started for the first time through some chain of circumstances, the chances of which occurring any one time might be highly improbable, but which was in fact likely to happen overall, given the size of the planet and the huge lengths of time involved; and b) from that abiogenetic event (or events, plural — contrary to your misguided fixation, it doesn’t make a great deal of difference) life thereafter developed according to the known and pretty well understood mechanisms of evolution.

    Your favored theory is that an unknown “designer” who has never been shown to exist in any scientific sense, acting by absolutely unknown mechanisms, made numerous interventions in the development of life on this planet — including creating it for the first time — and went on to deliberately intervene as many times as are conceptually needed for you to be able to deny that evolution played the major role. If you think the burden of proof is on everyone else to disprove the existence of your unknown “designer” and its unknown powers, you’re thoroughly deluded.

  136. Antaeus Feldspar

    Oh, and just to highlight Tex’s problems with logic

    “Re: the Ford & bicycle, I explained that the point was both were the products of external sources. Apparently you have trouble relating that concept to design?”

    I have trouble seeing how you think it supports your point. If you do not count Fords and bicycles as having the common designer of “humanity” then your argument seems to go as follows:

    “Fords and bicycles have a lot of similarity of design, but if we inferred from similarity of design that they must have a common designer, we would be mistaken. Therefore, when we look at bacteria and humans, which have even less similarity of design, we should conclude that they do have a common designer.” Less similarity of design argues for a common designer, Tex? Really? This is what passes for logic on your planet?

  137. August Berkshire, of Minnesota Atheist fame, has written a review of Ken Miller’s talk in the Twin cities. The post is “Losing Miller’s God.” It is getting a certain amount of attention.

  138. David

    Mr. Miller starts out talking about the Kitzmiller case, which was in 2005, and then cites as evidence that the case was fairly decided, a 2008 paper by Doolittle et al. mentioning that the lamprey clotting cascade lacks five of the factors found in the human cascade.

    But it is unclear whether the absence of the factors in the lamprey cascade was known in 2005, and if so, whether this was entered into evidence at the trial.

    Intelligent Design may be completely wrong (I suspect it is), but the fairness or unfairness of the Kitzmillar trial is a completely separate issue, and if the missing lamprey factors were not entered into evidence at the trial, they cannot be relevant as to whether the trial itself was fairly decided.

  139. Jennifer

    David,

    Professor Miller isn’t using more recent data unfairly. Luskin made two separate claims regarding Professor Miller’s positions: (1) Luskin claimed that Professor Miller misrepresented Professor Behe’s arguments at trial by stating that Professor Behe argued that the entire blood clotting cascade was irreducibly complex and (2) Luskin claimed that the “core” components of the blood clotting cascade are irreducibly complex.

    Professor Miller countered the first claim by demonstrating that Behe argued in both Pandas and DBB that the entire blood clotting cascade was irreducibly complex. He then highlighted that these arguments were negated at trial by showing that some species lack certain components of the blood clotting cascade.

    Professor Miller then addressed Luskin’s claim that the “core components” of the blood clotting cascade are irreducibly complex. Professor Miller refuted these claims by pointing to Dr. Doolittle’s more recent research.

    You see, Professor Miller isn’t refuting Behe’s statements at trial using data that couldn’t have been “entered into evidence.” He’s refuting the new argument that ID manufactured after Behe’s original statements bit the dust in the Dover trial.

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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.

About Carl Zimmer

Carl Zimmer writes about science regularly for The New York Times and magazines such as DISCOVER, which also hosts his blog, The LoomHe is the author of 12 books, the most recent of which is Science Ink: Tattoos of the Science Obsessed.

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