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.

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.

“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?

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.

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.

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?

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.

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.”

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.

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.

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).

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.

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.

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.

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?

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.

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.

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.