Is Evolution Compatible with Christianity? (Video)

Is evolution compatible with Christianity? If Christians believe in evolution, what do we do with imago dei?

Comments

[Daron]

Having fun picking the slivers from your forehead, RonH? As I said, I'm not about to debate the entire premise of his book with you - the internet is already full of the exchanges (especially since I have already tested and seen how your commitment to arguments and evidence fails to live up to the hype). If you're that keen you could head over to one of the blogs dedicated to these types of arguments. If you do, I promise I'll come and watch or even join you.

A few quick points, though:
1) No, Behe does not set out to prove the system could not evolve. You need to get definitions straight (as per the OP) and you need to know Behe. If you know Behe and Irreducible Complexity you don't waste time asking questions like you did above.

2) If he runs into TTSS all he will find is another irreducibly complex system which was preceded by the BF. And he will find no step-by-step detailed explanation of how one of the systems could have evolved from another.
a) please don't waste our time with Matzke's speculations which did not satisfy this requirement, or
b) with the strawman accusation that Behe is insisting on the historical steps that did occur. The empirical part of his case demonstrates that nobody has done the science (detailed, testable models) of a plausible pathway.

3) None of this is on point.

[WisdomLover]

I note that it is suddenly up to the one who denies the existence of a thing (a naturalistic explanation for a gap) to prove its non existence.

Shouldn't it go the other way?

Unless an until evolutionists provide a 'naturalistic' explanation (whatever that is) for a given gap , shouldn't we be justified in saying that no such explanation exists?

I mean, it's not that Behe actually believes anything is it. He just doesn't believe there's a naturalistic explanation for the gap.

Or, if you like, Behe and the evolutionists are in almost total agreement about the gap. He just believes in one less naturalistic explanation than they do.

[Daron]

Lol!

I guess he has found the apologetic arguments for the naturalistic explanation unconvincing.

[RonH]

Daron,

I guess this is what you are getting at

By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution. (Darwin's Black Box p. 39)

There is the powerful challenge. Complete with wiggle words.

Later on Behe calls the routes he wants to ignore 'indirect' and 'circuitous'. He claims the likelihood of such routes 'drops preciptiously' as the complexity of the interacting system increases.

In what sense are such routes 'direct', 'indirect', or 'circuitous'? Where are the implied probabilties calculated?

RonH

[Jesse]

I wouldn't call it 'wiggle words' but one weakness I see in Behe's argument is the possible circuitous routes for building up irreducible complexity. Think of it like scaffolding.

[Daron]

Ah, the grand rescue, cooption. Glad to see you've been working your talkorigins chops, RonH.
Funny, when we talked previously I asked if you just ran off for things to support your position or if you ever tried to challenge it. As you recently said of fine-tuning, you are just hoping that the arguments will be defeated. But were you even to look at ID-critical biologists you will find that cooption is, as Behe said, highly improbable. Might it have happened some time, in some situation? Maybe. Is it a rule, law or general answer? Nope.
http://bostonreview.net/BR21.6/orr.html
Note his disdain for Behe and ID. And yet:

Second, we might think that some of the parts of an irreducibly complex system evolved step by step for some other purpose and were then recruited wholesale to a new function. But this is also unlikely. You may as well hope that half your car's transmission will suddenly help out in the airbag department. Such things might happen very, very rarely, but they surely do not offer a general solution to irreducible complexity.

Orr, of course, thinks there is a different answer: gene duplication. And yes, Behe answers that as well. The point is, once again, that the claims are not supported by science; there is no model, no calculation, nothing testable. That's what Behe argues and no amount of uber-contrarian behaviour is going to be rid of that.
http://www.arn.org/docs/behe/mb_brresp.htm

Now, have you any response at all that is relevant to what I said about the misrepresentations? Or are you going to just continue to add to the misrepresentations by making such claims as "Behe ... wants to ignore"?

[cog]

Wisdomlover,

"But there is not the slightest speck of existence that does not depend entirely on the ongoing maintenance of Almighty God. Nothing that God does can properly be called intervention. Whatever happens happens because God makes it so. There's no intervention about it."

Your statement would indicate that you have a magical worldview. In other words, there are no such things as natural laws or processes, and everything, every detail of reality, happens at the whim of God.

This view makes experimental science worthless, since any repeatable result is only repeating because of God's whim of the moment, which could change at any time.

Luckily, the alternative view that God created the universe to run, on its own, according to laws and processes that He created, is just as valid as your magical notion of the all controlling Creator.

[cog]

RonH

"Read again and see if you have not misunderstood Benner."

I read again.

What do YOU understand Benner to be saying in the SA article?

[A Soldier for Jesus]

If someone is a Bible-believing Christian, then he or she has no business attempting to mix evolution with Christianity. You begin a domino effect of compromise.

What brute, and when, became Adam? When did he sin? "It was allegory, even though it was written to appear as history." Jesus, Paul and others in the New Testament referred to Adam as an actual person, and Jesus is the last Adam. Or is Jesus a kind of New Age guru, someone who evolved consciousness beyond that of brute Adam-ape?

Also, there are other questions to be considered. "The grass withers, the flowers fade, but the word of God stands forever" (Isaiah 40.8). Do we use the ever-changing whims of man-made science philosophies to determine what God says in his Word? How much shall we accommodate so we can look intelligent to people who believe that disbelievers in evolution are automatically idiots (genetic fallacy)?

"Do not add to His words,
Lest He rebuke you, and you be found a liar." (Prov. 30.6)

[WisdomLover]

Cog-

Of course the world is magic.

What is magic but something that reliably happens but for which there is no necessity? Magic is quite reliable and discernible, otherwise what would magicians be studying the use of in their cobweb covered cells?

Wizards might even be able to 'explain' some pieces of magic in terms of others...This wand works well for charms because it's made of willow and unicorn hair, that wand works well for transfiguration because it's oak and phoenix feather, etc. This bicycle is good for sprints because it's made of aluminum, that bicycle is good for long races because it's carbon fiber, etc.

This world is so magic that once upon a time, when the fair lady and her fair lord ate the forbidden apple, not only they, but all of their kingdom were overthrown, right down to those laws you so love.

And only the Great Sorcerer who made all the magic in the first place could ever set it right. And to do it, for some reason, He had to come into the world as one of us and die and rise from the dead. And even with that, the full restoration won't happen until we all die and all the world is remade and we are raised into that new world.

Don't ask me why it had to be that way. This is deep magic!

Why would any of that make you think that empirical science is worthless?

Were God utterly capricious, you would have a point. But I have excellent evidence that God is not capricious: the very science you say is worthless on my view.

What you call His 'whims' and I call the free choices of His will are not things He changes erratically. And He has given us the means of discovering His will as He has written it in the Magic Book of Nature.

His will is so trustworthy and the words He wrote in that book so legible, that others of my race were able to use them to throw themselves all the way up to the moon, walk around and come back.

But why do the rockets fly by which my fellow men did this?

We could easily go into a long discussion of thrust and weight, fuel and oxidizers. You and I would agree on every point. As would the most hardened atheist. God wrote His will into His Book of Nature for all to see. Even those who hate Him. But that will just beg more questions. And when we are finished answering those questions, we will still have more.

In the end, you will have to say that it is because that's just the way things are.

But I will do you one better by saying that the Great Wizard even now makes all the world, from the smallest quark to the largest star, obey His will. So why do the rockets fly?

Because they are bewitched.

[WisdomLover]

Cog-

This view makes experimental science worthless, since any repeatable result is only repeating because of God's whim of the moment, which could change at any time.

And the existence of laws that operate without God's intervention would prevent that how?

If the whim takes Him, which according to your fear, could happen at any moment, He'll just change the law.

If you say that He's not taken by such whims, then what happens to your initial criticism?

Luckily, the alternative view that God created the universe to run, on its own, according to laws and processes that He created, is just as valid as your magical notion of the all controlling Creator.

No. It's not just as valid. Things that exist without the sustainer of existence are round squares. It does not matter whether they originally came into being because God created them. The claim that they exist now without Him is a contradiction. This general rumination applies both to physical objects and the laws they obey.

The law of gravity is a law today because God wills it to be so, and only because God wills it to be so. And the law is given its power to draw all things to their center, not because they have an attractive 'power', or because the law 'constrains' them, or even because space is curved (the curvature of space 'explains' gravity only on the assumption that things follow geodesics--the curved space equivalents of straight lines.) Things are drawn to the center, in the end, because that is the way God has decided it will be, and for no other reason.

[Loki]

WL

"Things that exist without the sustainer of existence are round squares."

Why? You havent explained why Cog is wrong. You've just said he is. How do we decide between these 2 alternate views?

[Brad B]

God's whim...like raising Lazurus from the dead? Yes He has suspended natural processes at times, even just for His own glory, why do you associate that to be something bad? Dont you trust Him?

[Brad B]

Oh,btw Cog, where do you justify the statement that:

"God's whim could change at any time?"

It's not biblical, so where does this thought originate from?

[Loki]

Brad B

"Yes He has suspended natural processes at times, even just for His own glory"

How do you know natural processes were supsended?

[RonH]

Cog,

Looking at life on Earth, says chemist Steven Benner of the Foundation for Applied Molecular Evolution in Gainesville, Fla., “we have no way to decide whether the similarities [such as the use of DNA and proteins] reflect common ancestry or the needs of life universally.” But if we retreat into saying that we have to stick with what we know, he says, “we have no fun.”

I read this as follows:

Either...

1) All life has DNA and proteins or...
2) Other systems that use different chemistry exist.

If #1 is true, then that is why life on Earth has DNA and proteins.

If #2 is true, then life on Earth has DNA and proteins because it shares common ancestry.

Here is more from Benner

While "life" may universally be a self-sustaining chemical system capable of Darwinian evolution, alien life may be quite different in its chemistry from the terran life that we know here on Earth. In this case, it will be difficult to recognize, especially if it has not advanced beyond the single cell life forms that have dominated much of the terran biosphere. This review summarizes what we might infer from general physical and chemical law about how such "weird" life might be structured, what solvents other than water it might inhabit, what genetic molecules it might contain, and what metabolism it might exploit.

What do you say?

RonH

[RonH]

Daron,

Evolution is driven by reproductive fitness, not preservation of function.

Behe classes evolutionary paths as 'direct' or 'indirect/circuitous' based upon some idea he has (and/or thinks others will buy) regarding evolution 'wanting to' preserve function or 'trying to' go the 'direct' route.

But evolution is 'interested in' function only secondarily: only in service to reproductive fitness.

If function is changed along some evolutionary path evolution is 100% blind to that change.

Evolution neither seeks nor avoids change in function.

Reproductive fitness forces the path of evolution. A change in function is no obstacle whatsoever.

Evolution will not 'consider' a path containing a change in function 'indirect' or 'circuitous'.

Evolution will not 'consider' a path in which function is not changed 'direct'.

The repetition here above intentional.

BTW, the cooption metaphor should not have purpose is read into it. It's just a way of saying: a change in function can/did occur on an evolutionary path.

I don't understand the splinters thing. Please tell me what it means.

RonH

[Daron]

"Evolution is ...
Evolution neither ...
Evolution will ... "

What am I reading, your prayer? Or incoherent poetry?

"Evolution is driven by reproductive fitness, not preservation of function."
Right, that's what I said. And if a function does not aid in reproductive fitness it is not selectable. If it is not selectable then it is built by chance. Regardless of whether it happened all at once, or blindly attached with no necessary relationship to some other selectable feature, when the complexity discussed arises by chance even those like Dawkins say it would be miraculous. Dawkins gives himself a few lucky breaks to get started, but even he insists you need a ratchet to get this kind of complexity regularly.

The splinters are from running headlong into trees which keep you out of the forest. Being a perpetual contrarian whose only purpose seems to be to gainsay whatever you possibly can you belie your self-aggrandizing claims to be an evidence-based truth seeker.

What you are is a rebel against your Creator.

[Daron]

He answered, "You shall love the Lord your God with all your heart, with all your soul, with all your strength, and with all your mind [Deuteronomy 6:5]; and your neighbour as yourself [Leviticus 19:18]."

[Jesus] said to him, "You have answered correctly. Do this, and you will live."

But he, desiring to justify himself, asked Jesus, "Who is my neighbour?"

And he asked, what is life? what is "not selectable"?, what splinters?

[WisdomLover]

Soldier-

I think you put your finger on the key problem with theistic evolution in your second paragraph.

It is quite true that the Bible does sometimes engage in metaphor, and we might as well acknowledge that. Good Heavens, that's how Jesus taught! So we can't rule out of hand the claim that Genesis 1-3 might be one of those metaphors. I'm pretty sure that we can't put ourselves down for saying that they are strict chronologies. We actually get ourselves into logical difficulties if we do, since the Genesis 1 and Genesis 2 chronologies conflict. The conflict is so obvious that I think we have to assume that Moses himself did not intend it as a strict chronology.

BUT

Jesus and the NT writers spoke about Adam in such a way that we just have to rule out the idea that Genesis 1-3 are nothing but metaphor.

There had to be this one father, and this one mother, of the human race. Created separately from the animals and given dominion over them in a perfect creation not subjected to frustration and enslaved to corruption. Evolution with its competition and brutal regime of death and survival had not part of that.

And they fell into sin. And in their fall we all fell and the world itself was cursed.

Without that what are we to make of the claim that there is one Christ, God-Incarnate who came to undo the curse that that one Adam brought upon us?

If you give up the special creation of Adam and Eve and their fall from grace, you give up the Gospel and the Work of Christ. That is to say, you give up Christianity.

If you are going to fit evolution anywhere into this picture, it has got to go in after the fall. So it cannot explain the origins of Man.

[WisdomLover]

Loki-

Let me break it down.

The "sustainer of existence" means "that which sustains the existence of all existents".

"X exists without Y" means "X is an existent, but Y does not sustain the existence of X".

Thus "X exists without the sustainer of existence" means "X is an existent, but that which sustains the existence of all existents does not sustain the existence of X"

To put it a little differently "That which sustains the existence of all existents does not sustain the existence of at least one existent (namely X)"

Or, "That which sustains the existence of all existents does not sustain the existence of all existents."

I'm pretty sure that that's a garden variety contradiction.

So what is Cog going to say? That God is not the sustainer of existence? That the things he was talking about were not existents? Or what?

[Loki]

From The Origin Of Species To The Origin Of Bacterial Flagella by Mark J. Pallen & Nicholas J. Matzke, Nature Reviews Microbiology, 4(10): 784-790 (October 2006).

For those unfamiliar with the background, Nick Matzke was the author of an interesting article, namely this one (http://www.talkreason.org/articles/flag.pdf), which hypothesised that the various proteins that are found in the bacterial flagellum would be found to be homologous with other proteins belonging to other metabolic systems, and that as a consequence, the bacterial flagellum would eventually be found to be the result of co-opting existing, earlier systems and re-using them for another purpose - a classic evolutionary process. Needless to say, a lot of noise was emitted by the ID brigade to the effect that Matzke's ideas were "speculation", and the rest of it, but, the point here is that Matzke made testable predictions in his article, and in doing so provided evolutionary biologists with real substance that they could pursue in the laboratory. The following quote from the abstract of Matzke's original paper is apposite:

Matkze, 2001 wrote:A new model is proposed based on two major arguments. First, analysis of dispersal at low Reynolds numbers indicates that even very crude motility can be beneficial for large bacteria. Second, homologies between flagellar and nonflagellar proteins suggest ancestral systems with functions other than motility. The model consists of six major stages: export apparatus, secretion system, adhesion system, pilus, undirected motility, and taxis-enabled motility. The selectability of each stage is documented using analogies with present-day systems. Conclusions include: (1) There is a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F1F0-ATP synthetase. (2) Much of the flagellum’s complexity evolved after crude motility was in place, via internal gene duplications and subfunctionalization. (3) Only one major system-level change of function, and four minor shifts of function, need be invoked to explain the origin of the flagellum; this involves five subsystem-level cooption events. (4) The transition between each stage is bridgeable by the evolution of a single new binding site, coupling two pre-existing subsystems, followed by coevolutionary optimization of components. Therefore, like the eye contemplated by Darwin, careful analysis shows that there are no major obstacles to gradual evolution of the flagellum.

Now, note that specific predictions were made with respect to the homologies involved, namely that homologies would be found between flagellar proteins and those of the Type 3 Secretory System, plus an enzyme called F1F0-ATP synthetase. I'll leave the latter enzyme aside for a moment, but return to it because this one turns out to play an important role. Stay tuned for the fun revelations!

Now, first of all, the paper from Nature Reviews Microbiology I cited above by Matzke & Pallen itself dispenses wholesale with the idea of the bacterial flagellum being "irreducibly complex", because, lo and behold, there are bacteria with flagella that are missing numerous components. From that paper, I copy the following details with respect to the presence or absence of specific flagellar proteins in various bacteria possessing flagella:

FlgA (P ring) - Absent from Gram-Positive bacteria
FlgBCFG (Rod) - universal
FlgD (Hook) - universal
FlgE (Hook) - universal
FlgH (L Ring) - Absent from Gram-Positive bacteria
FlgI (P Ring) - Absent from Gram-Positive bacteria
FlgJ (Rod) - FlgJ Rod N-terminal domain absent from some systems
FlgK (Hook-Filament Junction) - universal
FlgL (Hook-Filament Junction) - universal
FlgM (Cytoplasm & Exterior) - Absent from Caulobacter
FlgN (Cytoplasm) - Undetectable in some systems
FlhA (T3SS apparatus) - universal
FlhB (T3SS apparatus) - universal
FlhDC (Cytoplasm) - Absent from many systems
FlhE (Unknown) - Mutant retains full motility
FliA (Cytoplasm) - Absent from Caulobacter
FliB (Cytoplasm) - Absent from Escherichia coli
FliC (Filament) - universal
FliD (Filament) - Absent from Caulobacter
FliE (Rod/Basal Body) - universal
FliF (T3SS apparatus) - universal
FliG (Peripheral) - universal
FliH (T3SS apparatus) - Mutant retains some motility
FliI (T3SS apparatus) - universal
FliJ (Cytoplasm) - Undetectable in some systems
FliK (Hook/Basal Body) - universal
FliL (Basal body) - Mutant retains full motility
FliM (T3SS apparatus) - universal
FliN (T3SS apparatus) - universal
FliO (T3SS apparatus) - Undetectable in some systems
FliP (T3SS apparatus) - universal
FliQ (T3SS apparatus) - universal
FliR (T3SS apparatus) - universal
FliS (Cytoplasm) - Absent from Caulobacter
FliT (Cytoplasm) - Absent from many systems
FliZ (Cytoplasm) - Absent from many systems
MotA (Inner membrane) - universal
MotB (Inner membrane) - universal

So, the mere fact that there are in existence bacteria with missing proteins from the above list whose flagella still function rather makes a mockery of the "irreducible complexity" assertion to begin with. But, this is only part of the story. The same paper continues with the following:

Pallen & Matzke, 2006 wrote:Many paths to motility

Although the evolution by random mutation and natural selection of something as complex as a contemporary bacterial flagellum might, in retrospect, seem highly improbable, it is important to appreciate that probabilities should be assessed by looking forward not back2. For example, from studies on protein design it is clear that creating proteins from scratch that, like flagellin, self-assemble into filaments is not very difficult39,40. Furthermore, it is clear that there are many other filamentous surface structures in bacteria that show no apparent evolutionary relationship to bacterial flagella41,42. In other words, there are plenty of potential starting points for the evolution of a molecular propeller. Evolution of something like the flagellar filament is therefore far less surprising than it might at first seem. In fact, microorganisms have adopted other routes to motility besides the bacterial flagellum43. Most strikingly, although archaeal flagella superficially resemble bacterial flagella, in that they too are rotary structures driven by a proton gradient, they are fundamentally distinct from their bacterial counterparts in terms of protein composition and assembly.

Intermediate forms

What about intermediate forms between bacterial flagella and other biological entities? Darwin encountered a similar argument about gaps in the fossil record, and in response he pointed out how improbable fossilization was, so that little of any extinct biosphere could ever be expected to appear in the fossil record14. Although fossils are of no use in reconstructing flagellar evolution, similar arguments might be made at the molecular level. Despite a decade of bacterial genome sequencing, we have scarcely begun to sample the molecular diversity of the biosphere. Yet even with the scant coverage of genome sequence data to date, several curiosities have already been revealed. For example, there is growing evidence that flagellin and the flagellar filament are homologous to the NF T3SS protein EspA and the EspA filament, respectively35,44–48. The EspA filament therefore provides a model for how the ancestral flagellar filament might have functioned for purposes other than locomotion (adhesion or targeted protein secretion). Furthermore, the EspA protein from E. coli initially seemed to be one of a kind. However, thanks to genome sequencing, related proteins have been identified in several bacteria occupying diverse niches, including: S. typhimurium, Edwardsiella ictaluri, Shewanella baltica, Chromobacterium violaceum, Yersinia frederiksenii, Yersinia bercovieri and Sodalis glossinidius. In addition, proteins that resemble flagellar components but that are encoded in the genomes of bacteria that do not engage in flagellar motility have also been identified. The first example of these potential ‘missing links’ came from the chlamydias49. More recently, flagellar-related genes have been detected in the genome of the soil bacterium Myxococcus xanthus, which uses gliding rather than flagellar motility35. It seems likely that other examples of potential evolutionary intermediaries will be found as we sequence an increasing proportion of the biosphere.

The paper continues with:

Pallen & Matzke, 2006 wrote:Towards a plausible evolutionary model

From the above discussions of sequence homologies and modularity, it is clear that designing an evolutionary model to account for the origin of the ancestral flagellum requires no great conceptual leap. Instead, one can envisage the ur-flagellum arising from mergers between several modular subsystems: a secretion system built from proteins accreted around an ancient ATPase, a filament built from variants of two initial proteins, a motor built from an ion channel and a chemotaxis apparatus built from pre-existing regulatory domains (FIG. 1). As we have seen, each of these function in a modular fashion and share ancestry with simpler systems — thereby answering the question ‘what use is half a flagellum?’ Furthermore, it is not hard to envisage how an ancestral crude and inefficient flagellum, if it conferred any motility at all, could function as the starting material for natural selection to fashion today’s slicker flagellar apparatus.

However, one could still question how, from such bricolage, natural selection could lock on to an evolutionary trajectory leading to an organelle of motility in the first place, when none of the components alone confer the organism with a selective advantage relevant to motility. The key missing concept here is that of exaptation, in which the function currently performed by a biological system is different from the function performed while the adaptation evolved under earlier pressures of natural selection50. For example, a bird’s feathers might have originally arisen in the context of selection for, say, heat control, and only later have been used to assist with flight51,52. Under this argument, a number of slight but decisive functional shifts occurred in the evolution of the flagellum, the most recent of which was probably a shift from an organelle of adhesion or targeted secretion, such as the EspA filament, to a curved structure capable of generating a propulsive force.

Now, as a slight tangential diversion, which along the way provides yet more evidence for evolutionary hypotheses, one avenue of attack being considered with respect to the development of the bacterial flagellum is the reconstruction of earlier, more ancient versions of the proteins responsible for the construction of this structure. Precedents already exist with respect to the reconstruction of ancient genes, and the following four papers are examples thereof:

Crystal Structure Of An Ancient Protein: Evolution By Conformational Epistasis by Eric A. Ortlund, Jamie T. Bridgham, Matthew R. Redinbo and Joseph W. Thornton, Science, 317: 1544-1548 (14 September 2007)

Resurrecting Ancient Genes: Experimental Analysis Of Extinct Molecules by Joseph W. Thornton, Nature Reviews: Genetics, 5: 366-375 (5 May 2004)

Resurrection Of DNA Function In Vivo From An Extinct Genome by Andrew J. Pask, Richard R. Behringer and Marilyn B. Renfree, PLoS One, 3(5): e2240 (online version, May 2008)

The Past As The Key To The Present: Resurrection Of Ancient Proteins From Eosinophils by Steven A. Benner, Proc. Natl. Acad. Sci. USA., 99(8): 4760-4761 (16 April 2002)

From the paper by Pask et al above, we have:

Pask et al, 2008 wrote:

There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.

So scientists are already resurrecting ancient proteins and testing their functionality in model organisms. Indeed, one of the results in the scientific literature comes courtesy of this paper:

Resurrecting The Ancestral Steroid Receptor: Ancient Origin Of Oestrogen Signalling by J.W. Thornton, E. Need and D. Crews, Science, 301: 1714-1717 (2003)

in which the scientists determined that the modern receptors for steroid hormones in modern organisms are traceable to an ancestral receptor dating back 600 million years, and reconstructed the ancestral steroid receptor in the laboratory to determine that it worked.

So, given that precedents already exist for the successful reconstruction of ancient proteins and the genes coding for them, this avenue of attack is likely to prove highly instructive with respect to the bacterial flagellum. Indeed, Pallen & Matzke make this very observation in their paper:

Pallen & Matzke, 2006 wrote:But obviously, one cannot model millions of years of evolution in a few weeks or months. So how might such studies be conducted? One option might be to look back in time. It is feasible to use phylogenetic analyses to reconstruct plausible ancestral sequences of modern-day proteins, and then synthesize and investigate these ancestral proteins. Proof of principle for this approach has already been demonstrated on several NF proteins69–75. Similar studies could recreate plausible ancestors for various flagellar components (for example, the common ancestor of flagellins and HAP3 proteins). These proteins could then be reproduced in the laboratory in order to examine their properties (for example, how well they self-assemble into filaments and what those filaments look like). An alternative, more radical, option would be to model flagellar evolution prospectively, for example, by creating random or minimally constrained libraries and then iteratively selecting proteins that assemble into ever more sophisticated artificial analogues of the flagellar filament. Another experimental option might be to investigate the environmental conditions that favour or disfavour bacterial motility. The fundamental physics involved (diffusion due to Brownian motion) is mathematically tractable, and has already been used to predict, for example, that powered motility is useless in very small bacteria76,77.

However, let us move on to the more recent developments.

Now, back in 2006, Pallen & Matzke listed some known homologies, and once again, I reproduce their results from the table in the paper:

FlgA (P ring) - CpaB
FlgBCFG (Rod) - FlgBCEFGK
FlgD (Hook) - none specified
FlgE (Hook) - FlgBCEFGK
FlgH (L Ring) - none yet known
FlgI (P Ring) - none yet known
FlgJ (Rod) - none yet known
FlgK (Hook-Filament Junction) - FlgBCEFGK
FlgL (Hook-Filament Junction) - FliC
FlgM (Cytoplasm & Exterior) - none yet known
FlgN (Cytoplasm) - none yet known
FlhA (T3SS apparatus) - LcrD/YscV
FlhB (T3SS apparatus) - YscU
FlhDC (Cytoplasm) - Other activators
FlhE (Unknown) - none specified
FliA (Cytoplasm) - RpoD, RpoH, RpoS
FliB (Cytoplasm) - none specified
FliC (Filament) - FlgL, EspA
FliD (Filament) - none yet known
FliE (Rod/Basal Body) - none yet known
FliF (T3SS apparatus) - YscJ
FliG (Peripheral) - MgtE
FliH (T3SS apparatus) - YscL, AtpFH
FliI (T3SS apparatus) - YscN, AtpD, Rho
FliJ (Cytoplasm) - YscO
FliK (Hook/Basal Body) - YscI
FliL (Basal body) - none yet known
FliM (T3SS apparatus) - FliN, YscQ
FliN (T3SS apparatus) - FliM, YscQ
FliO (T3SS apparatus) - none
FliP (T3SS apparatus) - YscR
FliQ (T3SS apparatus) - YscS
FliR (T3SS apparatus) - YscT
FliS (Cytoplasm) - none yet known
FliT (Cytoplasm) - none yet known
FliZ (Cytoplasm) - none yet known
MotA (Inner membrane) - ExbB, TolQ
MotB (Inner membrane) - ExbD, TolR, OmpA

Now, as Pallen states in his blog entry as linked above, out of this list of proteins, only two were listed as being both essential to all bacterial flagella AND possessing no known homologues in 2006. Those proteins were FliE and FlgD. From the 2006 update of Matzke's original 2003 paper, we read:

Matzke, 2003 wrote:Many of the homologous and/or inessential proteins found in Table 1 of Pallen and Matzke 2006 were cited in the 2003 paper, but the 2006 table is an authoritative update and supercedes what is said here. The important overall point, as discussed in my blog post, is that of the 42 proteins in Table 1 of Pallen and Matzke, only two proteins, FliE and FlgD, are both essential and have no identified homologous proteins. This is substantially more impressive than the situation in 2003, and means that the evidence for the evolutionary origin of the flagellum by standard gene duplication and cooption processes is even stronger than in 2003. Important specific updates include: a homolog of FlgA has been confirmed (along the lines that I suggested in 2003); FliG has no homolog in NF-T3SS or the Exb/Tol systems, rather it may be homologous to the magnesium transporter MgtE; and the flagellar filament protein FliC (and its sister FlgL) is probably homologous to EspA and other pilus proteins found in NF-T3SS. I still suspect that all of the axial proteins (including FliE and FlgD) are homologous to each other and therefore to pilus proteins in NF-T3SS, but only the confirmed homologies are reported in Pallen and Matzke 2006.

At least, this was the situation back in 2006. However, science moves on!

First, take a look at this site, which is the site devoted to ATP synthase. Now, one of the homologies that Matzke originally hypothesised was that at least one of the flagellar proteins would prove to be homologous to proteins in the ATP synthase group, in particular the awkwardly named F1F0-ATP synthetase. Now it turns out that ATP synthases are themselves complex entities, and indeed F1-ATPase rotates on an axis as it performs its synthesis! However, as this paper:

Axle-Less F1-ATPase Rotates In The Correct Direction by Shou Furuike, Mohammad Delawar Hossain, Yasushi Maki, Kengo Adachi, Toshiharu Suzuki, Ayako Kohori, Hiroyasu Itoh, Masasuke Yoshida and Kazuhiko Kinosita, Jr., Science, 319: 955-958 (No. 5865, 15 February 2008)

reveals very succinctly, dismantling this structure so that it no longer has an axle to rotate about does not stop it from functioning! Here's the abstract:

Furuike et al, 2008 wrote:F1–adenosine triphosphatase (ATPase) is an ATP-driven rotary molecular motor in which the central γ subunit rotates inside a cylinder made of three α and three β subunits alternately arranged. The rotor shaft, an antiparallel α-helical coiled coil of the amino and carboxyl termini of the γ subunit, deeply penetrates the central cavity of the stator cylinder. We truncated the shaft step by step until the remaining rotor head would be outside the cavity and simply sat on the concave entrance of the stator orifice. All truncation mutants rotated in the correct direction, implying torque generation, although the average rotary speeds were low and short mutants exhibited moments of irregular motion. Neither a fixed pivot nor a rigid axle was needed for rotation of F1-ATPase.

Another blow to "irreducible complexity" (Hermann Müller would doubtless have smiled wryly over this!), but this isn't all. Returning to Pallen's blog, we find this:

Pallen, 2008 blog post wrote:Since the early 1990s, it has been known, from sequence comparisons, that the flagellar ATPase (FliI) is homologous to the alpha and beta subunits of the F-type ATPase, a transmembrane protein complex (see figure) found in bacteria, mitochondria and chloroplasts (see http://www.atpsynthase.info).

In 2003, Nick Matzke (then at the NCSE and so a couple of years later science adviser to the plaintiffs in the Dover trial) wrote an essay summarising plausible evolutionary scenarios for the origin of the bacterial flagellum. He noted a couple of previous suggestions that the proto-flagellum might have originated from the F-type ATPase. Crucially, he predicted that additional homologies would be found between components of the F-type ATPase and the flagellar protein export apparatus, for example between the b subunit of the ATPase and FliH and between the delta subunit and FliJ.

In 2006, I confirmed one of Nick's hunches through homology searches, showing that part of FliH was homologous to the b subunit. However, things turned out slightly different from Nick's predictions in that FliH is actual of a fusion of domains homologous to the b subunit and the delta subunit.

Last year Namba's group published the structure of FliI and confirmed the striking homology with the F-type ATPase enzymatic subunits. At that stage in the game, it had become clear that the ATPase was a universal component not just of flagellar export systems but also of non-flagellar type III secretion systems. Also, if it was also clear that if one knocked out the gene for FliI, one abolished flagellar biosynthesis. Thus, just about everyone in the field accepted that FliI was an essential component of the flagellar apparatus and that it energised secretion of proteins through the protein export system. In other words, if there were anything to the idea, put forward by Behe and others in the ID movement, that the flagellum showed "irreducible complexity", even experts might have accepted that FliI was one of the "irreducible" components!!

BUT earlier this year, Minamino and Namba (and independently a team headed by Kelly Hughes in the US) overturned all our assumptions by showing that it was perfectly possible to make flagella without FliI--what you needed to do was knock out FliH at the same time. Somehow or other FliH, which usually interacts with FliI, gums up the export apparatus in the absence of FliI. So, bang goes another pillar of support for the ID argument! In fact, it appears that flagellar protein export is powered not primarily by the ATPase but by the proton-motive force.

So, the FliI protein appeared on the face of it to be essential, because knocking out the gene for FliI synthesis destroyed flagellar biosynthesis. But, and here's the part that really throws the spanner into "irreducible complexity" as espoused by Behe, if you knock out the gene coding for FliI, but in addition knock out the gene for FliH, flagellar biosynthesis returns! This rather buggers up "irreducible complexity" in a spectacular manner.

Yet even this is not the whole story. Believe it or not, there is more! Returning to Pallen's blog, we read:

Pallen, 2008 blog post wrote:Namba and colleagues have now solved the structure of FliJ, another protein that interacts with FliI and FliH. And what they found was clear evidence of homology with yet another protein from the F-type ATPase--the gamma subunit!

So, now we have deep and broad homologies between the flagellum and the F-type ATPase, just as Nick predicted. This provides another nail in the coffin of the idea that flagellum was intelligently designed. If the flagellum were the product of intelligent design, particularly by an omniscient deity, the designer could have custom-built it from scratch, so it need not resemble anything else in nature. By contrast, the processes of evolution tends to cobble together and tweak already existing components (something Francois Jacob called bricolage)--and slowly but steadily it is become clear that the flagellum has been built this way.

Incidentally, the paper covering the homology between FliI and the alpha and beta subunits of the F-type ATPase is this paper:

Salmonella typhimurium Mutants Defective In Flagellar Filament Regrowth And Sequence Similarity Of FliI to F0F1, Vacuolar, And Archaebacterial ATPase Subunits by Alfried P. Vogler, Michio Homma, Vera M. Irikura and Robert M. McNab, Journal of Bacteriology, 173(11): 3564-3572 (June 1991) [Full paper downloadable from here]

so this homology had actually been known even before Behe made his assertions about "irreducible complexity", something he would have known if he had bothered to perform a basic literature search. After all, he has institutional access, whereas I don't currently, yet I was able to find this paper once pointed in the right direction. This paper also covers the knocking out of the gene for FliI and the effect on flagellar biosynthesis.

More pertinently, the following paper:

Evolutionary Links Between FliH/YscL-Like Proteins From Bacterial Type III Secretion Systems And Second-Stalk Components Of The F0F1 And Vacuolar ATPases by Mark J. Pallen, Christopher M. Bailey and Scott A. Beatson, Protein Science, 15: 935-941 (2006) [Full paper downloadable from here]

is the one containing the confirmation by Pallen of one of Matzke's predictions as cited above. Another homology was confirmed courtesy of this paper:

Structural Similarity Between The Flagellar Type III ATPase FliI And F1-ATPase Subunits by Katsumi Imada, Tohru Minamino, Aiko Tahara and Keiichi Namba, Proceedings of the National Academy of Sciences of the USA, 104(2): 485-490 [Full paper downloadable from here]

This paper:

Distinct Roles Of The FliI ATPase And Proton Motive Force In Bacterial Flagellar Protein Export by Tohru Minamino and Keiichi Namba, Nature, 451: 485-489 (24th January 2008) [Full paper downloadable from here]

is the paper that covers the knocking out of FliH and FliI resulting in restoration of flagellar biosynthesis.

So, now the only two proteins remaining to find homologies for are FliE and FlgD, and you can bet that this is being worked upon as I type this.

Behe's "irreducible complexity" nonsense was known to be a canard by actual biologists the moment he aired it in public.

Of course, Behe's failure to perform the requisite literature search, and realise that this problem had, in essence, been solved back in 1918, merely set a precedent that he was to revisit during the Dover Trial, where he asserted that evolutionary biology not only had no answer to the "problems" purportedly posed by the vertebrate blood clotting cascade, but that evolutionary biology never would find any answers. His rashness in uttering this was sharply exposed, when the cross examining counsel presented Behe with no less than fifty-eight peer reviewed scientific papers, and nine university textbooks, containing the very material Behe had claimed would never exist.

Likewise, his arguments with respect to the bacterial flagellum revealed that he had not bothered performing even the most perfunctory of literature searches. Not least because scientists were publishing papers containing research unravelling the secrets of the bacterial flagellum several years before it was erected as a purported "poster child" for "intelligent design". However, it appears that the situation is now even worse for the IDers with regard to the bacterial flagellum.

(With thanks to Calilasseia - his work repeated above)

Anything to say about that Daron?

[Daron]

Yeah, nice spam.
Go read the responses to Matzke.

[Daron]

This is known as a literature bluff and is the same stunt to which you allude with your "58 papers" in Dover canard.
None of those papers addressed Behe's project.

If you think the BF is not IC you're ignoring facts that even Behe's opponents acknowledge.
If you think I'm going to waste my time trying to prove Behe's case you're ignoring all my comments here.
If you take your dog and pony show to Telic Thoughts or Uncommon Descent I'll go watch you try to defend just as I said I would for RonH. If you search those sites you'll find this has already been dealt with in depth.

[Loki]

Nice try at sticking your fingers in your ears and screaming "Im right Im right Im right" rather than looking at the evidence from reality.

The Bacterial Flagellum is not irreducibly complex.

And its not literature bluff. Its called making an argument. The fact you dont like it and cant be bothered to read it is neither here nor there.

[WisdomLover]

Loki-

Was there a reason you felt the need to do the whole Ctrl-C/Ctrl-V dance?

Couldn't you have just linked to Calilasseia's article instead of giving us a word for word copy?

Unless of course, the goal was to so amaze and impress Daron with the depth of your (or really, Calilasseia's) knowledge of sciencey stuff that he would be struck dumb.

Just as a hint copy-and-paste isn't really all that impressive.

[Daron]

Like I said, Loki ...

[WisdomLover]

Thanks Daron, for not being struck dumb and seeing through the ploy.

[Daron]

BTW Loki,
I doubt you understand what you spammed. But let's see if you understand me.
If I'm claiming "I'm right, I'm right, I'm right" what is it I am claiming to be right about?

[Loki]

Is there a reason why you choose to ignore the substantive issues?

And attack me for posting and citing correctly?! Too funny.

Tell me what is wrong with what I have done?

[SteveK]

Daron,
In response to this:

And its not literature bluff. Its called making an argument.

Maybe you can link to every ID book on Amazon and a few ID blogs as a way to give a better argument - the more voluminous, the better the argument. Will she plug her ears or will she actually look at the evidence?

[Daron]

I already did, Loki.
And I am not arguing the "substantive" issues, by which I presume you mean whether or Behe is right or wrong. If you think you'd get a few kicks out of it I've told you where you can go to find people also interested in doing it. I've played that game for far too long and am not interested in it any longer. The arguments are all out there, one click away, and the interested person can go find them hashed out by people who know what they are talking about.

If you actually know what you are talking about and think you have something relevant to add to the debate give me a link to where you are discussing it. I'll gladly check it out.

Since you can't quite understand me I will lay it out again. People early in this thread made statements implying that ID proponents are heretical, that they are envisioning a false god and calling Him God. I challenged that and their characterizations of the ID arguments. I am not arguing the merits of the case.

Dr. Beckwith issued one response but has left, apparently with better things to do. I don't blame him. Do you have anything of interest to add to their position?

Of course RonH posted a series of questions designed to show he knows a little bit about this subject and to fling some stones here and there. I responded to him on the basics and told him I am not going to waste my time trying the Behe case yet again.

Now you've done the same with your spam-attack.
If anyone cared about the Matzke (which I've read and had suggested early on that RonH not go find and post because it is a waste of time and not the issue) they could go read it. If they wanted to know if it actually addressed Behe they could find that out, too.

If you are convinced by Matzke, Panda's Thumb, talkorigins, etc., good for you. You aren't alone, so that should give you comfort.

[Loki]

Daron

You are arguing that because science hasnt propose a detailed testable model of a proposed pathway to acheive an "IC" system science has failed.

And instead you can conclude that ID is the winner. Without actually demonstrating that the sytem is designed. You are just concluding that because you claim it hasnt arisen by chance and it isnt natural.

So really you dont know that it *was* designed. You are simply claiming that it ISNT chance/natural.

[SteveK]

Question for the experts here. What is doing the selecting when it comes to natural selection? Nature? That seems redundant but at the same time not really selecting in the sense that the terms actually means. Nothing is driving any process as a means of secure a fitness benefit. It's just happening.

Am I correct in saying that natural selection means 'what occurred' not 'what benefits'?

[Loki]

Daron

Do you think science can provide evidence for god?

[Loki]

And truly, apologies if you thought that post was spam. I honestly thought you'd find it interesting and I missed your previous post about Matzke.

Sorry. If someone can delete it please do.

[RonH]

What are these facts that Behe's opponents acknowledge?

Let's say if you take a 'part' from a BF it won't work - at least not as a BF.

In other words, let's say the BF is IC.

Is that one of these facts?

Let's acknowledge it!

The BF is IC! The BF is IC!

So what?

The IC-ity of the BF is not "a powerful challenge to Darwinian evolution".

It's no challange at all, because taking a 'part' from the BF is reversing the last step of one possible path the evolution of the BF.

The IC argument just ignores almost ALL the possible paths of the evolution of an IC system.

Oh, Behe says those paths have a precipitously dropping likelihood. But he gives no reason to believe those thousands of paths are any less likely than the few very paths the IC argument pertains to.

RonH

[SteveK]

Do you think science can provide evidence for god?

Depends on what you would count as evidence. Suppose the resurrection was filmed in HD in the midst of a room full of people in lab coats - you included? Evidence for God or evidence for the mystery of nature?

[Daron]

Loki,

You are arguing that because science hasnt propose a detailed testable model of a proposed pathway to acheive an "IC" system science has failed.

Np, I'm not. But nice try.

You are just concluding that because you claim it hasnt arisen by chance and it isnt natural.

Still wrong. Your understanding is weak.

So really you dont know that it *was* designed. You are simply claiming that it ISNT chance/natural.

I'm pretty sure I didn't say that, either.

I happen to know that everything was designed. And I know that since the creation of the world God's invisible qualities--his eternal power and divine nature--have been clearly seen, being understood from what has been made, so that men are without excuse.

Do you think science can provide evidence for god?

Did you mean 'God'? He is a Person and we use God as His name. Of course it can.

[Loki]

Daron

"I happen to know that everything was designed." How?

How can science provide evidence for God? Science deals with observational reality and doesnt have the tool kit to be able to study the supernatural.

[Daron]

Let's acknowledge it!

The BF is IC! The BF is IC!

So what?

So don't say it isn't.

The IC-ity of the BF is not "a powerful challenge to Darwinian evolution".

Good for you. Have an opinion, just don't claim things that aren't true.

The IC argument just ignores almost ALL the possible paths of the evolution of an IC system.

It doesn't ignore anything and you are speaking untruths.

Oh, Behe says those paths have a precipitously dropping likelihood. But he gives no reason to believe those thousands of paths are any less likely than the few very paths the IC argument pertains to.

He does give a reason. You are speaking untruths again. He cites and agrees with even evolutionary biologists who see the unlikelihood of cooption and he points to the absence of literature meeting his challenge. You can literature bluff like Matzke did in Dover, but when you look into the bluff you find that Behe's challenge is not met in that literature.

All you are left with is to say that Behe's challenge (and don't call it moving goal-posts, as they have never moved) is irrelevant, unfair, unrealistic, or some such thing.
Fine. Have an opinion.

[Daron]

"I happen to know that everything was designed." How?

Divine revelation.

How can science provide evidence for God? Science deals with observational reality and doesnt have the tool kit to be able to study the supernatural.

You'd have to be familiar with the term "evidence" to understand. Ask RonH, he's got a grasp on it.

[Loki]

Daron

It was a perfectly civil question. Science is absolutely incapable of providing evidence for God.

So your definition of science is not the one scientists actually use and you are wrong.

"Divine revelation" What is this?

[Daron]

Loki,
I missed your follow-up about the homology review. Thanks, that was nice.

Science is absolutely incapable of providing evidence for God.

I say it provides evidence and you say it doesn't. Well, an element of conflict in any discussion's a very good thing. It means everybody is taking part and nobody is left out.

evidence= a reason to believe in a proposition.

What's this special definition you and the scientists use by which you've declared me wrong?

Divine revelation = God's revealed Word in the Holy Bible and His revealed will in Nature.

For by him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things were created by him and for him.

[Daron]

SteveK,
I missed your comment as well - about linking to ID books. Indeed, the battle of dueling opinions about dueling authorities expressing their opinions.
:)

[Loki]

Daron

Try this link (apologies if you consider this spam but Ill post the link as well)

"Misunderstandings of the limits of science [.......]

Because science deals only with natural phenomena and explanations, it cannot support or contradict the existence of supernatural entities — like God."

http://undsci.berkeley.edu/teaching/misconceptions.php#c1

So as long as we are clear that as soon as you start talking about God you arent doing science then we may be in agreement.

[SteveK]

Science is absolutely incapable of providing evidence for God.

Science is capable of providing the raw data/evidence that rational minds can use to reach jusified conclusions. As an example, you'd agree that science has given us evidence for the uniformity of nature, right?

[Daron]

I think you are talking about conclusions within the realm of science, qua science. What you asked about were reasons to believe in God that came as data points from empirical observation.

Allan Rex Sandage (famous astronomer, dubbed the “Grand Old Man of Cosmology” by the New York Times, and a former atheist): “It was my science that drove me to the conclusion that the world is much more complicated than can be explained by science. It was only through the supernatural that I could understand the mystery of existence.”

http://www.bethinking.org/resource.php?ID=133

Allan Rex Sandage, probably the greatest observational cosmologist in the world, shocked everybody several years ago at a seminar in Dallas when he announced that he had become a believer in God because of the scientific evidence that he had encountered.

http://www.beliefnet.com/story/154/story_15485_1.html

[SteveK]

Evidence for God can take the form of evidence consistent with the God hypothesis. That's science, isn't it?

[Daron]

Dawkins certainly thinks the existence of God is a scientific question.
Then again, to ask, or categorically demand, that "science" is this or that one thing, ignores the demarcation problem in the philosophy of science.