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Signature in the Cell 5 – The RNA World Hypothesis (RJS)

posted by Jesus Creed Admin

Stephen C. Meyer has published a (very long, but readable) book, Signature in the Cell: DNA and the Evidence for Intelligent Design,
outlining his argument in favor of intelligent design. This book
essentially argues that life is very complex, the origin of life is a
puzzle, and the information content in DNA cannot be explained by
natural means.  Chapter 14 of his book deals with the RNA world hypothesis.(See note added at the end of post)

In a nutshell:

For life to originate we need molecules capable of self-replication with sufficient flexibility and reactivity to achieve some function that helps those same molecules self-replicate.

DNA is capable of passing information on from generation to generation – but it is not reactive and requires a complex series of reactions involving proteins for replication. Production of these proteins of require both RNA and additional proteins for transcription, and translation. The interrelated reactions are quite complex. DNA is a fairly stable (unreactive) molecule, making it good for information storage, but the chemistry of DNA is simply not rich enough for life to originate from DNA. 

Proteins have a very rich chemistry and can perform many functions. But they are not capable of replication. There are no specific interactions that allow one amino acid chain to produce an identical chain.

Therefore – life did not originate with proteins, nor did it originate with DNA.

RNA (ribonucleic acid) is a molecule similar to DNA (deoxyribonucleic acid). The added OH in RNA (circled above) makes RNA less stable than DNA and gives it a much richer, more varied chemistry. RNA is in principle capable of both self-replication and function. Chains of RNA have secondary structure (loops and folds) and tertiary structure (specific active three-dimensional shapes) and can catalyze reactions. For example ribosome is a protein-RNA complex that catalyzes peptide bond formation producing proteins. The catalytic active site of ribosome is all RNA.

RNA (or a similar “pre-RNA” nucleic acid) is a promising candidate for the initiation of the process that led eventually to life. Much work is ongoing to understand RNA chemistry – a rich and fascinating subject.

So what does Meyer have to say about the RNA world hypothesis?

Meyer outlines five problems he sees with the RNA world hypothesis:

1. RNA building blocks are hard to synthesize and easy to destroy.

This is true – we do not have a workable hypothesis yet as to how RNA bases were formed in the “primordial soup.” It is an open research question. There is a big gap in our knowledge here.

2. Ribozymes (RNA chains capable of acting as catalysts) are poor substitutes for proteins.

This is also true, but does not speak against the RNA world hypothesis. All an RNA has to do at the outset is perform a function that conveys a survival advantage for a specific RNA sequence. It does not need to perform the variety of functions proteins are responsible for in even the simplest of cells.

3. An RNA-based translation and coding system is implausible.

According to Meyer “RNA world advocates offer no plausible explanation for how primitive self-replicating RNA molecules might have evolved into modern cells that rely on  a variety of proteins to process genetic information and regulate metabolism.” (p. 305)

He is right, as far as I know, that no explanation has yet been offered.  This is not yet a solved problem, rather it is a hard problem – and one that will take a good deal of work in many labs. We simply do not know enough about the chemistry yet. There is a gap in our knowledge.

That a pathway from self-replicating RNA to a simple cell is “implausible” is a judgment statement that is impossible to defend until we know a great deal more about the chemistry of nucleic acids in general.

Finally Meyer’s discussion of the difficulties of the problem seems to start with the complexity of a simple cell and assume that much of this complexity is necessary from the beginning. This makes little sense – rather a plausible explanation will start with a very simple system and build up complexity.

4. The RNA world doesn’t explain the origin of genetic information.

And as I studied the hypothesis more carefully, I realized that it presupposed or ignored, rather than explained, the origin of sequence specificity – information – in various RNA molecules” (312)

This is the cornerstone of the argument for ID advanced by Meyer and Dembski. They propose that the information content of RNA (or DNA) cannot be “grown” from a seed.

This is also where the argument falls apart. The sequence specificity of RNA or DNA correlating specific three base codes with amino acids is more or less arbitrary. There appears to be no chemical reason why GCU codes for alanine and UCG codes for serine any more than there is a fundamental reason why  109 is the ascii code for m and 230 is the ascii code for ?. But once the code is established, specified sequences carry information. In one of the weakest arguments in the book Meyer ridicules this idea on pp. 277-279 with respect to the original proposal for DNA. He dismisses it again on p. 312-317 for RNA. 

How the code grew from sequence specificity that did arise from chemical function is an open research question (a gap in our knowledge).

5. Ribozyme engineering does not simulate undirected chemical evolution.

Many scientists, including Jack Szostak who shared the 2009 Noble Prize in Medicine and Physiology, are working on designing RNA molecules that can carry out interesting functions. Meyer claims this work demonstrates nothing useful with respect to the origin of life – but only demonstrates what an intelligence can do. According to Meyer:

Thus, even if ribozyme experiments succeed in significantly enhancing the capacities of RNA catalysts, it does not follow they will have demonstrated the plausibility of an undirected process of chemical evolution. Insofar as ribozyme-engineering experiments using a rational-design approach (as opposed to a directed-evolution approach) involve an even more overt role for intelligence, they exemplify the same problem. (321)

Meyer appears to argue that anything we discover about RNA in careful “bite-size” experiments is irrelevant because we used our intelligence to design the experiments. Clearly such experiments do not prove abiogenesis – but they do build up the background knowledge required to begin to pose plausible mechanisms and pathways.

Where does this leave us?

Meyer concludes this chapter by implying that scientists looking for solutions to all of the complex problems involved in the origin of life are paddling around in circles and making no progress.

It was demonstrably more reasonable to reject the chance hypothesis than to accept it. Theories relying on necessity awaited the discovery of an oxymoron, namely, “a law capable of producing information” – a regularity that could generate specified irregularity. Meanwhile, theories combining law and chance repeatedly begged the question as to the origin of the information they sought to explain. Theorists just spread pink stuff from one place to another, hoping in vain to make it disappear. (p. 322)

As I see it (and now we start a discussion)

1. It is demonstrably more reasonable to reject the chance hypothesis than to accept it.

2. Meyer has rightly pointed out that there are  gaps in our understanding of the origin of life. The biggest gap is actually his first problem above – the synthesis of the building blocks.

3. He suggests that lack of current understanding means that no mechanism or pathway will be forthcoming.

4. He misunderstands scientific method and thinking.

5. He attaches far too much importance to the “information problem” and will not think outside of the box about mechanisms for the growth of complexity.

So some questions:

Does Meyer convince you? If so why?

and

Do you think that Meyer’s arguments against an “RNA world” type hypothesis are essentially gap arguments? If not, why not? If so, why should we think that these gaps are permanent?

If you wish to contact me, you may do so at rjs4mail[at]att.net

Note added: Coincidentally Stephen Meyer has written a response to Darrel Falk’s review of his book. It is published today on Science and the Sacred. In his r
esponse Meyer deals with this chapter and he reiterates one of the arguments that I find problematic – that designed experiments only prove the power of design, not the plausibility of natural process.  Read his response and comment – either there or here.



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pds

posted January 28, 2010 at 7:33 am


http://thedesignspectrum.wordpress.com/
RJS,
You are not addressing Meyer’s argument in its strongest form, and you don’t really address his strongest point- there is no feedback mechanism to produce information until there is function. There is no function until you reach a certain level of complexity. I recommend that people read Meyer for themselves. This summary does not do him justice.
This is not about what we don’t know. It is about what we know about the assembly of highly specified information. It is about what we know about the probability of self-assembly by pure chance and serious plausibility analysis. It is about reasoned tentative inferences based on that.
I don’t think you understand the scientific method of the “inference to the best explanation.” What is your best explanation and why do you draw that inference? How do you think Meyer gets the scientific method here wrong?
You seem to saying, “Hey, anything is possible.” or “Hey, you never know!” That is not a serious inference to the best explanation.
He is not saying it is “impossible,” or that’s not necessary to his argument. He is saying design is the best inference.
I would add that the design inference in the origin of life is consistent with the evidence of design in the fine-tuning of the universe. Why shouldn’t we make that tentative inference?



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RJS

posted January 28, 2010 at 7:42 am


pds,
You say “There is no function until you reach a certain level of complexity.” This is the problem in all this “information” argument for ID. There can be a function that gives the necessary feedback with very little complexity.
But you never really explain why you think Meyer’s proposal is not a “gap” argument. It seems rather clear to me that it is all an argument from ignorance and makes the same mistakes as Paley’s watchmaker argument.



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Hrafn

posted January 28, 2010 at 8:17 am


No PDS, it is *you* who fails to understand “inference to the best explanation”. ID is not the “best explanation”, it is arguably one of the worst possible explanations — as it confers no understanding whatsoever of the processes involved. It in fact bears considerable resemblance to this example from Peter Lipton:
“For example, if one says that smoking opium tends to put people to sleep because opium has a ‘dormative power’, one is giving an explanation that is very likely to be correct but not at all lovely: it provides very little understanding.”
http://www.hps.cam.ac.uk/people/lipton/inference.pdf



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Hrafn

posted January 28, 2010 at 8:34 am


Further from the same article:
“Better explanations explain more types of phenomena, explain them with greater precision, provide more information about underlying mechanisms, unify apparently disparate phenomena, or simplify our overall picture of the world.”
This failure to give ANY “precision” or “information about underlying mechanisms” is precisely what I’ve been complaining about the bald assertion of ID as an ‘explanation’.



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RJS

posted January 28, 2010 at 9:08 am


pds,
I also recommend that those who are truly interested read Meyer’s book, and then enter into conversation to look at the strengths and weaknesses of his argument. I have tried to give a summary here to start a conversation – but it is short.
It seems likely that the DNA and RNA code in the cell is “accident remembered.” An example was used of a combination lock – before the lock is “set” any combination will work. After it is set only one will work. The DNA code we see now is “after the lock is set” so the sequence is specified.
Meyer claims this analogy is poor, and he claims that because intelligence is involved in the design of the lock it proves nothing about origins. This gets to your point about complexity, and my comment about the flaw in ID reasoning. Complexity and the specificity of the DNA/RNA code grow together – the original system need not have any significant complexity. The RNA (or “pre-RNA nucleic acid”) need only have a sequence that performs a function. The function must in a small way increase the likelihood that that sequence will replicate.



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Dan

posted January 28, 2010 at 9:38 am


Seems to me there is a double standard here.
There is an admission that science has no mechanism to explain certain aspects of the origin of life. One suggestion, the evolutionary one, is that mechanisms may yet be discovered, based in the faith that plausible natural law explanations for many features of the evolutionary model have been found. The other suggestion from the ID side is that purely naturalistic mechanisms will not be discovered based on the sheer magnitude of the number of chance occurrences that must all come to pass in harmony with each other and based on the inference that complex information that we currently observe always comes from a designer.
The double standard is that RJS and others are willing to reject Meyer’s argument, not based on evidence, but based on a faith commitment that naturalistic mechanisms that do not as yet exist will be found, while at the same time accusing Meyer of advancing a theory based on “gaps”. How ironic.
It seems to me the reason for rejecting ID at this point, is based on a particular definition of science that is completely beholden to naturalism, which means nothing ID can ever propose will suffice. Meanwhile, the reason for accepting naturalistic mechanisms that do not yet exist is merely a belief that natural mechanisms will be found because they must be found to maintain the narrow definition of science as a purely naturalistic enterprise.
It seems when we reach that stage, there is no point in carrying on the discussion. Naturalists will not, have not and can not ever entertain the notion that something might have a cause that is beyond nature. It is functional atheism. Nor can they entertain the notion that if a being exists that is outside of nature and acts within nature, we might see the effects of such action but not be able to explain the cause. This to them appealing to any cause beyond nature is anti-science even if it might be true, simply because science is enslaved to naturalism.



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Daniel T.

posted January 28, 2010 at 9:46 am


It’s the same old argument from ignorance that the ID proponents always use. “We don’t know how something happened, therefore it can’t possibly have happened naturally.” We’ve been down this road many times now.
The Discovery Institute has contributed absolutely nothing to the debate on how life came into being or on how evolution works. They have taken on as their mission, tearing down understanding, not building it up, and that is a recipe for disaster.



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pds

posted January 28, 2010 at 10:06 am


RJS #2,
You said,

But you never really explain why you think Meyer’s proposal is not a “gap” argument. It seems rather clear to me that it is all an argument from ignorance and makes the same mistakes as Paley’s watchmaker argument.

I already did in other comments. Also here:
http://thedesignspectrum.wordpress.com/2009/11/18/the-form-of-design-arguments-from-nature/
Prong 1 of the design argument is a positive argument based on positive evidence from analogy. We all know this evidence by observing the world around us. We often forget that this is scientific data. As Nobel laureate Francis Crick put it, “Biologists must constantly keep in mind that what they see was not designed, but rather evolved.” Why do they need to remind themselves of this? Because the positive evidence for design is overwhelming. If naturalistic explanations fail, there is no reason to keep reminding ourselves that it was not designed.



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pds

posted January 28, 2010 at 10:28 am


The Design Spectrum
RJS,
You said,

It seems rather clear to me that it is all an argument from ignorance and makes the same mistakes as Paley’s watchmaker argument.

You seem to be saying that all design arguments are “gap” arguments and “arguments from ignorance.” If so, then you are concluding that the design arguments made by Dallas Willard, Peter Kreeft, Thomas Aquinas, Tim Keller and Francis Collins are all bad arguments.
If not, then you need to explain why Meyer’s argument is bad, while the others you might distinguish are good.
Here is a quote from Tim Keller that summarizes his design argument in The Reason for God:
http://thedesignspectrum.wordpress.com/2010/01/28/tim-kellers-design-argument/
Do you think Keller’s argument is an “argument from ignorance” and therefore invalid?



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pds

posted January 28, 2010 at 10:37 am


The Design Spectrum
Dan #6,
Excellent comment! Very well put.
Daniel T. #7,
Not so much.



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dopderbeck

posted January 28, 2010 at 10:40 am


As described, it seems clearly to be a gap argument to me. The “gap” is that there can be no “cause” for the emergence of “information.” “Information” is seen ontologically as a basic constituent of the universe, along with energy and matter. It is a way of trying to describe mathematically the “divine energies” of Eastern Christian / Patristic thought.
pds (#8) — again, your approach is highly problematic. You assume that the categories of “designed” and “known natural processes” are contradictory. If in your second prong “known natural processes” could account for the apparently designed feature, by your logic, we must infer that the feature was NOT designed. But that directly contradicts Christian theological presuppositions, which assume that ALL of nature is “designed,” including any “known ‘natural’ processes.” So, from a Christian perspective, it seems clear to me that the way you frame the argument fails (and I also don’t think it’s consistent with classical theistic arguments for design).
I think a a more accurate and sophisticated way to frame the argument would be this:
1. “Information” is a basic property of the universe.
2. Specified information cannot be caused by chance.
3. Therefore, the cause of specified information must be a will.
4. There must be ultimately in the chain of causes a will that is uncaused.
This, I think, would be something like Aquinas’ five ways. A key argument for ID, then, would be prong 2: can “information” emerge from stochastic processes or must the presence of “information” always involve a teleological cause?



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bob johnson

posted January 28, 2010 at 10:44 am


The whole idea of ID comes down to the fact scientists don?t know exactly how self replicating molecules can start functioning. Because of the lack of this knowledge there must be a designer and because of this designer there is no reason to continue to look. I am afraid when scientists do understand how life began the ID people will say ?Oh yes look how the designer did it.?
There is no double standard. I don?t have to have faith to believe scientists will find a natural explanation on how life started. I can just look at the track record of explanations by a natural process and by the process directed by an invisible designer. Designer explanations from lighting to why Haiti was destroyed have all failed. So until the designer?s record improves I will keep my money on a natural explanation



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dopderbeck

posted January 28, 2010 at 10:48 am


pds (#9) — the quote you give from Keller is not a very well formulated argument. I take it to be more a version of Pascal’s Wager than a true design argument. So, in a sense, I would say, yes, this particular argument of Keller’s is a “gap” type of argument and ultimately is a default to Pascal’s Wager.
A better way for Keller to have framed this, I think, and more line line with Reformed thinking (IMHO), would be to say:
Christian theology asserts that all the universe is “creation,” designed by God. Christian theology and the Bible also teach us that our finite human minds, particularly as they are darkened by sin, cannot fully comprehend or understand this — indeed, that we suppress the knowledge that “nature” is God’s creation. We cannot look to “nature,” therefore, to “prove” God.
Once we have come to understand something of who God is, however, our eyes can be opened to the amazing ways in which the claim that God is creator is fully compatible with our observations of nature. The remarkable “coincidences” of life, which are “stochastic” or “random” from a statistical perspective, can be understood as the gracious operation of God’s providential care for all of creation and for us. We can declare with the Psalmist that
all of creation shouts God’s glory — His beauty, wisdom, and care. This change in perception all begins with the spark of faith.



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pds

posted January 28, 2010 at 11:14 am


David O. #11,
Based on your comment, I updated that post to make explicit what I think was fairly clearly implied – that the “known natural processes” are without recourse to design input. So now it reads: “Known natural processes could produce the feature (without design)”
With that clarification, I think your comment does not hold.
We also need to distinguish what we know by science and what we know by faith — what design is seen in nature and what design is only known by faith.



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ron

posted January 28, 2010 at 11:16 am


It seems to me that having faith that mechanisms will eventually be found that provide an explanation for the origin of life is at least as reasonable as having faith that they won?t (which is one way to put the ID ?theory?). In fact, there is precedent from other areas of science for this former kind of faith. In cosmology production of the elements in stars was explained, in principle through nuclear fusion where, beginning with hydrogen, progressively heavier and heavier elements are formed through the combination of lighter ones. However when the process was modeled using known properties of nuclei, an apparent show stopper was found at a key isotope for the element beryllium, which isotope does not exist naturally. One could have concluded at the time that cosmological evolution was impossible, asserting in ID fashion that a miraculous intervention would be required. In fact a resonant state was discovered in carbon, the next key element in the fusion chain, and this state allows the process of nuclear synthesis in stars to proceed to heavier elements in the periodic table.
Looking at this story metaphysically, one can take the point of view of Dawkins & Co. that the evolution of nature is a completely naturalistic process and there is therefore no need for a creator. Or one marvel at the seeming arbitrary fact of the existence of this resonant state ? one example of the numerous properties of matter that many point to as evidence of ?fine tuning? of the universe ? and suspect or believe (as many scientists of faith and non-faith did) that it points to, or alludes to, an incredibly subtle intelligence behind the existence of all there is. Indeed, what is more impressive ? an intelligence that created the universe that sorta-kinda evolves, but in which this intelligence nevertheless finds it necessary on occasion to miraculously intervene in order to kick the evolutionary can down the road? Or an intelligence that designed in from the beginning all the evolutionary pathways that are needed for the evolution of not only the universe but the life forms within it? In my view ID constrains us to the former type of deity; whereas a theology that is sympathetic and not hostile to science allows us to conceive of the (infinitely greater?) latter type of God.
I just concluded a scientific career in an R&D organization, and I never saw a single project that was designed correctly from the get-go. For a human to get it right the first time would be impressive; to imagine a creator who could do it for everything that exists is impressive indeed. ID philosophy, perhaps unintentionally, sells God short, rendering him (or her) less intelligent, less immanent, than what we might expect from a ?naturalistic? view of nature. Perhaps it even anthropomorphizes the deity, implicitly saying that because we can?t (yet) understand how something can occur naturally, it must also be impossible for God to figure out a way for it to happen naturally as well.



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dopderbeck

posted January 28, 2010 at 11:43 am


pds (#14): no, my objection still holds, because THERE ARE NO ‘NATURAL PROCESSES WITHOUT DESIGN! The distinction between “nature” and “design” is heretical from a Christian perspective. All of “nature” is “creation,” and all of “creation” is God’s design.
And I disagree with the “distinction” between what we “know by science” and what we “know by faith.” This buys into Englightenment / Cartesian / Kantian epistemology. All human knowledge claims are rooted in some fiducial commitments. In this sense, there is no neat distinction between “science” and “faith.”
A better distinction is this: we need to distinguish between those aspects of reality that are best investigated through tools and methodologies we call “natural science” and those aspects that are best investigated through tools and methodologies we call “theological science.”



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pds

posted January 28, 2010 at 12:13 pm


David O. #16,
Hey, you callin’ me a heretic?!? :)
But seriously, if you define “design” as “all natural processes” or “everything that happens,” then it will be hard to have a conversation. That is not what I mean when I say “design,” and it is not the meaning of most people.



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pds

posted January 28, 2010 at 12:23 pm


The Design Spectrum
Ron #15
You said,
“Or an intelligence that designed in from the beginning all the evolutionary pathways that are needed for the evolution of not only the universe but the life forms within it?”
That is an intelligent design scenario. It is called “front-loading.”
The question ID asks is not when the design took place, but whether the design is detectable, and whether non-design processes could produce what appears to be designed.



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dopderbeck

posted January 28, 2010 at 12:38 pm


pds (#17) — but that’s exactly the problem! The conversation should be about the theological claim that all creation is designed. If our apologetic has to involve making up categories that are theologically suspect (not-designed nature), then something is amiss, IMHO.
I’ve tried to convince the biologos folks to have a heretic’s book burning of ID books, but they won’t bite… ;-)



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RJS

posted January 28, 2010 at 12:42 pm


pds,
All Christians are somewhere on the design spectrum because we all believe that God created the world and interacts with the world he creates.
Now the question here is whether the laws of chemistry and physics designed into the universe are sufficient – or whether God had to step in and add something more in the initiation of life. I think that the argument that he had to step in is an argument from ignorance.
The other piece of the design discussion is evolution once we have life (single cells). Did God have to step in again to create diversity – or did this happen by “natural” mechanism understood from scientific investigation?
I also think that David hits a key point – we do not need to make room for God, he is in all and all is created by him. To try to separate designed processes from natural processes starts the discussion off on the wrong foot. John 1: 1-3 In the beginning was the Word, and the Word was with God, and the Word was God. He was in the beginning with God. All things came into being through Him, and apart from Him nothing came into being that has come into being.



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Dan

posted January 28, 2010 at 1:01 pm


RJS wrote: I think that the argument that he had to step in is an argument from ignorance. That is precisely what frustrates me. Why is the argument that God MAY have worked outside of natural law out of bounds? Especially for a Christian?
Here is where the double standard exists in objections to ID. Consider the following chain of reasoning as a regular criticism of both ID and various forms of creationism.
1. Evolution has no current explanation for a particular biological feature.
2. ID suggests this gap is evidence against evolution, and as such favors but does not prove design.
3. ID is accused of “God of the Gaps” reasoning, that “negative” evidence is not evidence for design.
Naturalists, in the process ignore many of the the additional arguments ID makes that are not based in “gaps”, but that is a separate issue. Now consider the converse:
1a. ID, it is asserted, does not suggest a naturalistic mechanism to demonstrate how a designer acted in nature to produce a specific biological feature.
2a. Naturalists, Evolutionists, and Theistic Evolutionists argue this is a completely disqualifying gap in the ID model and as such favors theories based in natural processes.
3a. Naturalists do not think this to be “Darwin of the Gaps” reasoning, but pat themselves on the back for exposing the “anti-science” foolishness of those who posit causes that are not based in natural mechansims. Because ID does not advance a naturalistic process as an explanation to a particular thing (while acknowledging natural causes of most things), it completely violates the rules of the game and does not deserve even cursory respect. It is ridiculed as fundamentally “not science”.
It is a classic case of winning the game by controlling the rules. ID is asked to produce a testable natural mechanism for how things may have occurred. But one of the key points ID is trying to make is that it must be considered at least a possibility that no natural mechanism can account for at least some features of biological life. While accepting natural selection as an explanation for change within limits, for example, ID suggests that some of the changes are beyond the scope of natural selection alone, that the reason the “gaps” exist is precisely because nature is not enough. To insist ID provide a natural mechanism is asking ID to abdicate its very position. It is a case of naturalism assuming the thing it is trying to prove (all things have purely natural causes) and insisting ID accept the same assumption.
But If an intelligence exists outside of nature, what natural mechanism is necessary for that being to act? And here is the critical disconnect: The possibility that such activity may be outside of the reach of natural science does not mean it may not be the truth. It only means that the “evidence” for such causes may require something in addition to natural science. It simply does not do to say “but science only deals with nature” when the question being asked is whether “nature” is all there is. To object to ID on the basis that science only deals with natural phenomena is both unfair and unreasonable unless one bars the supernatural from the discussion before the discussion begins.
This is the blind spot naturalistic scientists refuse to see, but the average person who is not totally committed to naturalsim sees as plain as the nose on Darwin’s bust. This is at least one reason why after 150 years of Darwinism having near complete control of the universities, public schools and public media, the majority of Americans still are unconvinced of Darwinism. When one is considering the origin of life and the question at hand is whether nature alone did it or whether God played an active role in it, one cannot begin the conversation by insisting that the only truly “scientific” explanations that will be tolerated are the ones that appeal to natural processes. Presumably, if something beyond nature exists, he/she/it is not bound by our definitions of science. We may see the effects of supra-natural activity in the natural realm, but may never know the mechanisms.
The science acedemy must either allow for the possibility that an explanation that is not a natural mechanism might be the true explanation, even if that is beyond the reach of science, or it must drop the pretense that science is neutral toward religious ideas about origins. If we are open to the barest possibility that God might exist, then we must allow for the possibility that some things in nature might not be explained by appeal to natural processes alone. (For any Christian who believes in a creator and an incarnate savior, the natural and supernatural coexisting seems to me fundamental. Yes, Dopderbeck, God may work within natural law – but he is not required to.) And if we allow for that, then the inference that complex, information rich and functional processes in cells are positive evidence for design is valid, just as a computer program is evidence of a programmer, and such reasoning is not merely an argument from gaps, it is an inference from what we observe to what we can never observe, but which may be exceedingly reasonable.



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pds

posted January 28, 2010 at 1:07 pm


RJS #20,
You have not answered the questions I raised in #1 and #9. Without that, your critique of Meyer rings hollow.
If you reject the design arguments of leading thinkers like the ones I name in #9, you are putting yourself at the extreme end of the design spectrum.



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RJS

posted January 28, 2010 at 1:32 pm


pds,
With respect to the people you list … Dallas Willard, Peter Kreeft, Thomas Aquinas, Tim Keller and Francis Collins.
I don’t think that I am saying anything that Collins would not say. David (#13) did a good job of addressing the comments by Keller. I enjoy reading Willard, he has great insight, but you would need to give a specific example I could interact with. I’ve never read Kreeft. I would love to sit down and talk with any or all of these people (well – except Aquinas, that will have to wait). But none of them are “authorities” on all subjects.
In #1 – what do you mean by design in the origin of life? How would this design be manifest?



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Unapologetic catholic

posted January 28, 2010 at 1:32 pm


The existence of single strand and double strand RNA viruses seems to refute Meyer’s arguemtn by their very existence.
“If you reject the design arguments of leading thinkers like the ones I name in #9, you are putting yourself at the extreme end of the design spectrum.”
No, you’re misreading Aquinas, who in any event pre-dates scientific advances in this field.



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RJS

posted January 28, 2010 at 1:35 pm


Dan (#21)
You say: But one of the key points ID is trying to make is that it must be considered at least a possibility that no natural mechanism can account for at least some features of biological life.
Given this hypothesis, how would one go about testing it?



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pds

posted January 28, 2010 at 1:44 pm


The Design Spectrum
RJS #23,
In #9, I asked, “Do you think Keller’s argument is an “argument from ignorance” and therefore invalid?”
David O. did not address that.
Same question about Collins’ argument based on fine-tuning in The Language of God.
If these are not arguments from ignorance, why is Meyer’s?
I would say that none of them are arguments from ignorance, because they all involve reasonable inferences after carefully considering the plausibility of alternative explanations.



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RJS

posted January 28, 2010 at 2:01 pm


pds,
Keller says this (In his chapter on “The Clues of God”) I copied from your post, but actually happen to have the book at my desk:

It is technically possible that we just happened to be in the one universe in which organic life occurred. Though you could not prove that the fine-tuning of the universe was due to some sort of design, it would be unreasonable to draw the conclusion that it wasn?t. Although organic life could have just happened without a Creator, does it make sense to live as if that infinitely remote chance is true? Timothy Keller, The Reason for God, pp. 131-132.

I have no quarrel with Keller here, and I don’t think that it is an argument from ignorance – but I don’t see how it makes your point. What Keller seems to be saying is that even with natural explanations for everything, why rule out a creator. Why live as if there is no creator? The majesty of creation is a clue for the creator.
Meyer is saying something at its core very very different. He is saying that there is no “natural” mechanism God could have used in his creation to produce the information content of a simple cell. It could not have grown from precursors. How does one go about testing this hypothesis? I assume that one does this by continuing the search for natural mechanisms (God’s mechanisms) not by assuming God God could not have used natural mechanism.



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RickK

posted January 28, 2010 at 2:11 pm


Meyer has convinced me of nothing, because all he is arguing is that there is a gap in our knowledge, and I knew that already. Anyone who knows history can see in the Intelligent Design argument nothing more than the latest “God of the Gaps” argument.
Early humans saw things in nature which he could not explain, and therefore imbued all things with divine or supernatural essence to explain the gaps in his knowledge. They were wrong.
In the Middle Ages, people didn’t understand schizophrenia or epilepsy, and filled in the gap in their knowledge by attributing them to demonic or divine possession. They were wrong.
Sir Isaac Newton worked out the mechanics of gravity, and concluded that some being (Aristotle’s “Prime Mover”) must have put the planets and stars in motion. Newton didn’t understand stellar and planetary formation, and so appealed to divine causes to fill in the gaps in his knowledge. He was wrong.
Throughout history, people of different lands and faiths have lacked an understanding of how the Earth and its life could have come into being. Before the days of Charles Lyell and Charles Darwin, many assumed the world appeared in some great supernatural creation by the divinity of their choice. They were wrong.
Now we’re down to saying “we don’t understand how the spinning whip on the bum of germ came into being, so it must have been an ‘intelligent creator’ of nature”, or “we don’t understand how these molecules stuck themselves together 3.5 billion years ago, so it must have been an ‘intelligent designer'”.
All of the people I’ve listed above had really good arguments for what they believed. But the only consistent fact that we’ve learned through the centuries, the one fact proved time and time and time again, is that natural phenomena have natural causes.
And so here we sit, wasting energy on yet another cleverly presented ‘god of the gaps’ argument when we could be asking the RIGHT question – how did life first evolve?
What is disturbing about Meyer, however, is that he has absolutely no interest in answering that question. His entire motivation, clearly stated in his own writings, is to twist and confuse public discourse on evolution so as to keep open a gap big enough for the interventionist god of the Christian Bible. He stated as much in the “Wedge Document”, and he tips his hand in “Signature” when he rejects the ability of any laboratory experiment to tell us anything about the creation of life. By saying this, Meyer says essentially: “nothing science discovers should convince you, dear reader, that life could have evolved naturally.”
And fundamentally, he has directed this science-sounding book not at scientists or mathematicians, but at the general public who are not equipped to address his more technical arguments. So his approach is clearly to advocate for his faith, and NOT to engage in open inquiry.
Meyer is an enemy of rationality, an enemy of education, and an enemy of anyone who doesn’t want their children taught the Christian Bible in public school science classes.



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Ray Ingles

posted January 28, 2010 at 2:12 pm


BTW, regarding the synthesis of nucleobases – recent research has found some very interesting candidates for processes that can naturally generate them:
http://discovermagazine.com/2008/feb/did-life-evolve-in-ice
“Miller had filled the vial in 1972 with a mixture of ammonia and cyanide, chemicals that scientists believe existed on early Earth and may have contributed to the rise of life. He had then cooled the mix to the temperature of Jupiter?s icy moon Europa?too cold, most scientists had assumed, for much of anything to happen. Miller disagreed. Examining the vial in his laboratory at the University of California at San Diego, he was about to see who was right.
As Miller and his former student Jeffrey Bada brushed the frost from the vial that morning, they could see that something had happened. The mixture of ammonia and cyanide, normally colorless, had deepened to amber, highlighting a web of cracks in the ice. Miller nodded calmly, but Bada exclaimed in shock. It was a color that both men knew well?the color of complex polymers made up of organic molecules. Tests later confirmed Miller’s and Bada?s hunch. Over a quarter-century, the frozen ammonia-cyanide blend had coalesced into the molecules of life: nucleobases, the building blocks of RNA and DNA, and amino acids, the building blocks of proteins.”
“Biebricher sealed small amounts of RNA nucleobases?adenine, cytosine, guanine?with artificial seawater into thumb-size plastic tubes and froze them. After a year, he thawed the tubes and analyzed them for chains of RNA.
For decades researchers had tried to coax RNA chains to form under all sorts of conditions without using enzymes; the longest chain formed, which Orgel accomplished in 1982, consisted of about 40 nucleobases. So when Biebricher analyzed his own samples, he was amazed to see RNA molecules up to 400 bases long. In newer, unpublished experiments he says he has observed RNA molecules 700 bases long.”



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Ray Ingles

posted January 28, 2010 at 2:24 pm


Meyer appears to argue that anything we discover about RNA in careful “bite-size” experiments is irrelevant because we used our intelligence to design the experiments.

That kind of argument always bugged me. We can build conditions that simulate tornadoes. Sometimes you see them at science museums. Does that mean that all tornadoes need intelligent intervention to arise?



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pds

posted January 28, 2010 at 2:26 pm


The Design Spectrum
RJS #27,
Your summaries of Keller and Meyer are full of spin. I think both of them are making an “inference to the best explanation.”
Keller’s inference is based on his conclusion that a non-design explanation is “infinitely remote.” His conclusion is based on the lack of current plausible non-design explanations, and the weakness of the ones put forth like the multi-verse hypothesis. Exactly the reasoning Meyer uses.
Meyer does not talk about God in his main argument. His main argument is similar to Keller’s. Meyer does not talk about “natural” so much as whether the processes are designed or not.
Meyer’s argument is much fuller and has more positive evidence. But of course, he had 600 pages to work with.



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Your Name

posted January 28, 2010 at 2:26 pm


RJS
“You say: But one of the key points ID is trying to make is that it must be considered at least a possibility that no natural mechanism can account for at least some features of biological life.
Given this hypothesis, how would one go about testing it?”
I think this is one strand of ID, but not all of it. I think this is where complexity of information comes into play, and probabilities lead to reasonable inferences while improbabilities lead to unreasonable inferences. ID says that if something is highly improbable, then it is not likely a good explanation. Naturalism says that if something is highly improbable but there is no other “natural” explanation, then the natural explanation must be tentatively accepted, no matter how unlikely.
I am skeptical of someone solving rubrics cube blindfolded because it is improbable, though not theoretically impossible. I am skeptical of many aspects of evolution for the same reason. You seem to reject Meyer’s argument in part because “improbable” does not mean “impossible”. But I think Meyer would say there is a difference between improbable and mathematically prohibitive, and that is part of the design/information theory case some make. Random, undirected shuffling of chemicals leading to complexity strains credulity, so why insist it must have an undirected natural mechanism as its source, unless one is predisposed to rejecting that which is beyond nature. And it is not that one event is improbable, it is that whole series of interdependent events must all work together, exponentially increasing the difficulty.
But I think ID and TE will remain at an impasse, because TE seems unwilling to forsake methodological naturalism.



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Unapologetic catholic

posted January 28, 2010 at 2:31 pm


Does Singature inthe cell differ appreciably in any way from Meyer’s earlier 1998 article onthe same subject?
http://www.discovery.org/a/2074
It appears to me that Signature in the Cell is an exopanded re-hash of the1998 article
And does he address the scientific advacnes in abiogenesis since 1998?



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AHH

posted January 28, 2010 at 2:37 pm


Regarding the discussion about “design” between pds and dopderbeck, where dopderbeck rightly points out that good Christian theology sees God’s design in all of creation and suggests that we not do apologetics on a playing field that implicitly denies God’s transcendence over all nature:
1) Some have suggested that a more accurate name for the ID movement would be Intelligent Assembly. If one thinks of the analogy to human design, it is really the assembly of the designed object (mousetrap, for example) that is alleged to be outside the capabilities of nature. Unfortunately this suggestion has not caught on.
2) I don’t remember the details, but in some context of the American Scientific Affiliation, Loren Haarsma of Calvin College challenged some ID advocate (Nelson?) to answer the question “Is the Sun designed?” No answer was provided to this question which (with Gen. 1:14-18) illustrates David’s point.
[Aside: Loren's book with his wife and fellow Prof Deborah Origins: A Reformed Look at Creation, Design, and Evolution is an excellent introduction to these issues.]



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dopderbeck

posted January 28, 2010 at 2:51 pm


RikK (#28) said: Meyer is an enemy of rationality, an enemy of education, and an enemy of anyone who doesn’t want their children taught the Christian Bible in public school science classes.
I respond: This illustrates the other side of the problem with debating ID. I mean, really — next thing you know you’ll be accusing Meyer of being a secret burqa-wearing terrorist. The real “enemy of rationality” is naked ad hominem.
PDS (#31 et al.) — who really cares what Keller, Moreland, Willard, or even F. Collins have said? Even very smart and very sincerely Christian people are capable of making dumb arguments — or smart arguments that happen upon careful inspection to be wrong. And as I’ve noted before, Moreland and Willard are situated in a particularly rationalist Evangelical neo-Thomistic school of thought that is by no means the only “Christian” way of approaching questions of faith and reason. There is likewise a “spectrum” of Christian theological reflection on faith, reason, and natural theology. I happen to think Barth, T. Torrance, and Alister McGrath are closer to the mark than Thomas Reid, Moreland, and Willard.



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pds

posted January 28, 2010 at 3:10 pm


AHH #34,
I agree that we should see God’s design in all of creation (theologically). But as I said, the issue is how we see it. In some cases the evidence of God’s design is more obvious in certain features of nature.
“Is the sun designed?” Yes, in some sense. God created it and designed it. But is the evidence of its design as obvious as in the origin of life or the fine-tuning of the universe? I don’t think so.
Why do Keller and Collins not refer to the sun in their arguments?



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pds

posted January 28, 2010 at 3:22 pm


The Design Spectrum
Dop #35,
“Who really cares what Keller, Moreland, Willard, or even F. Collins have said?”
In part because Collins strongly attacks ID proponents in his book. Collins is inconsistent in his reasoning and sets a bad example for the church. He is adding fuel to the fire of the existing cultural hostility to ID proponents.
RJS says Meyer’s is an “argument from ignorance” which is a means of dismissing it and marginalizing any scholar who agrees or is sympathetic to Meyer’s arguments.
I think we can increase acceptance of good science in the church. But we will not do it by demonizing Christian scientists who are making very good arguments based on sound reasoning.



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RJS

posted January 28, 2010 at 3:54 pm


pds,
My post puts out some of what I think about Meyer’s argument and then asks:
Do you think that Meyer’s arguments against an “RNA world” type hypothesis are essentially gap arguments? If not, why not? If so, why should we think that these gaps are permanent?
Can you answer these questions?
A gap can be evidence for design – but then we have to argue why the gap is permanent rather than “from ignorance.” Meyer and Dembski realize this and try to develop an argument for the permanence of the gap with their discussion of information. The real question at the root here is whether they are right about the inability of natural process to create information.



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RJS

posted January 28, 2010 at 4:06 pm


Your Name (#32)
Probabilities for processes such as the ones we are talking about can only be calculated, or even estimated once we know enough about the “landscape” of the problem. Meyer points out that random chance on a level playing field won’t do it. I agree – this is prohibitively improbable.
Now we have to start looking at the nature of the landscape. Is there a pathway that is not improbable? I brought up the protein folding problem in the last post. Given that it is astronomically improbable for a protein to fold by random chance scientists started to look for other mechanisms and features of the landscape that would result in folding.
On the origin of life problem … when a puzzle confronts the only approach is to search for solutions. Will we find solutions? If the ID people are right – no, we will search for centuries and not find a pathway sufficiently probable to gain wide acceptance. But why should we assume that they are right?



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Unapologetic catholic

posted January 28, 2010 at 4:24 pm


For PDS and Dopderbeck,
Here is a very detailed thoughtful and scholarly anlaysis of why Thoams Aquinas would reject modern day Intellgient Design.
http://guweb2.gonzaga.edu/faculty/calhoun/socratic/Tkacz_AquinasvsID.html



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pds

posted January 28, 2010 at 4:28 pm


Dan #21,
Another excellent comment.
The reasoning I see in RJS suggests that her “methodological naturalism” looks and feels a lot like “philosophical naturalism,” at least in the realm of biology. And then she or her allies suggest that anyone who does not share it is “anti-science.” This is a tragedy for the church.
RJS #38,
I think Meyer has answered your questions as well as can be done. He has made a good case for his “best explanation.”



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RJS

posted January 28, 2010 at 5:07 pm


Dan #21,

The inference that complex, information rich and functional processes in cells are positive evidence for design is valid, just as a computer program is evidence of a programmer, and such reasoning is not merely an argument from gaps, it is an inference from what we observe to what we can never observe, but which may be exceedingly reasonable.

If 10 or 50 or 100 years from now someone proposed a “natural” mechanism and demonstrated a probable pathway for the development of complex information rich functional processes would it undermine your faith (assuming you lived that long)? Would such a demonstration undercut the Christian faith?
I don’t care how God created the universe or life. I think that we can search for evidence of natural mechanism without fear and go where the evidence leads. The presence or absence of such evidence does not negate the power and majesty of God, nor should it diminish the wonder and awe we experience looking at creation.



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R Hampton

posted January 28, 2010 at 5:17 pm


pds,
What does Meyer say specifically about the “lipid world” model of abiogenesis or other pre-RNA/DNA models?



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R Hampton

posted January 28, 2010 at 5:47 pm


The reasoning I see in RJS suggests that her “methodological naturalism” looks and feels a lot like “philosophical naturalism,” at least in the realm of biology.
And that’s precisely why Intelligent Design was invented. This is what Francis Collins had to say about the flawed purpose of ID at the 2009 Vatican Conference on Evolution:
Certainly, in many of the fundamentalist very conservative Christian seminaries the notion of intelligent design or even Young Earth Creationism is the accepted norm for how theology is presented to future pastors, very much saying that, if science disagrees with the literal interpretation of Genesis I and II, then science must be wrong and it is the duty of the Christian to resist what is seen as a materialist perspective derived from these insights … I think this is a disaster for the Protestant Church in the US, because ultimately it will fail.
One hope would be that sometime in the not too distant future that realisation will begin to sink in and that, by a true and effective dialogue about the facts as opposed to the strong crusading feelings of some, it might be possible to develop a much more effective theology, a theology that celebrates what science is teaching us about the universe as manifestations of God?s awesome creation as opposed to a theology that seems to be afraid of science and defensive about what science is teaching us, as if, somehow, our puny minds, in understanding the universe, could threaten God Almighty.



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Dan

posted January 28, 2010 at 5:47 pm


RJS 42
Let me get back to the philosophical assumption problem this way.
Would you, as a Christian, look for a natural explanation for the resurrection or the virgin birth? Presumably, those are events which science can examine and look at the effects (Jesus would have had no pulse on Friday but a pulse on Sunday), but cannot get at the “mechanism”. That is by definition, a miracle. Christianity for 2000 years has held a miracle as the central event of its faith.
Does that alter your view of science? Is belief in the resurrection unscientific if we cannot explain it with a naturalistic mechanism?
If you would not demand that the resurrection or virgin birth be explainable by a natural mechanism, then what is the necessity that events in the origin of life be explained by a natural mechanism?
The problem for me isn’t that science might someday show a possible mechanism for the origin of life, the problem is that the possibility of a cause that is not in the naturalistic system is always, without exception, vociferously dismissed and ridiculed, even here. There is no room for anything but naturalism in the secular scientific world and increasingly Christian higher ed is moving in the same direction. Why the totalizing metanarrative of naturalism crushing all dissent? Just because certain things might be explained by natural cause and effect does not meant all things MUST be.



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pds

posted January 28, 2010 at 6:17 pm


The Design Spectrum
#44,
Wow. Saint Francis is sounding a whole lot like ranting Rick in #28 (“Meyer is an enemy of rationality, an enemy of education”).
That’s scary. He has got to know how much he is misrepresenting ID.



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BradK

posted January 28, 2010 at 6:26 pm


Saint Francis? Isn’t name calling inappropriate for this discussion?
Wasn’t it you who recently made a comment about setting a bad example for the church?



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Unapologetic catholic

posted January 28, 2010 at 6:42 pm


Good questions Dan,
I’ll take a stab.
“Would you, as a Christian, look for a natural explanation for the resurrection or the virgin birth? Presumably, those are events which science can examine and look at the effects (Jesus would have had no pulse on Friday but a pulse on Sunday), but cannot get at the “mechanism”.”
There is no theoretical reason why natural explanations for the resurrection or virgin birth could not be explored. There are practical limitations–passage of time–that make the search for such explanations extremely unlikely to be productive. But, when evidence capable of being evaluated by science is proffered–shroud of Turin, for example, isn’t science applied?
?Does that alter your view of science??
Not at all.
?Is belief in the resurrection unscientific if we cannot explain it with a naturalistic mechanism??
An unqualified “Yes.”
?If you would not demand that the resurrection or virgin birth be explainable by a natural mechanism, then what is the necessity that events in the origin of life be explained by a natural mechanism??
Nobody is asserting such necessity. There is a difference between ?necessity? and ?capability to explain.? The origin of life is capable of explanation by natural mechanisms. It?s not that God couldn?t have used a miracle to create life on Earth, but we have no evidence that He did so and there?s no reason to think He chose that method.
I use the weather analogy. Hurricanes arise by purely natural processes, fairly well (but not perfectly) understood. It is entirely possible that God steered Hurricane Katrina right into New Orleans. But natural processes adequately explain that result. God is certainly capable of steering Hurricane Katrina into New Orleans undetected by simply counter-acting the natural coriolis forces, but there?s no necessity to invoke that explanation at all for what happened.
The origin of life is exactly the same. There is no requirement for a miracle to have occurred. That is a different statement than one asserting God created life using purely ?natural? means or by miracles that could not be detected by mere mortals.
?There is no room for anything but naturalism in the secular scientific world and increasingly Christian higher ed is moving in the same direction. Why the totalizing metanarrative of naturalism crushing all dissent??
Here you subtly switched terms and mistakenly inject post-modernist thought into the discussion. Science limits itself to natural events. It is after all the study of the natural world. As a self-limiting means of subject matter control, science excludes the study of supernatural events. It doesn?t say these can?t or don?t happen?it says science cannot make any meaningful studies of such events. They aren?t science, they lie in some other field of study.
Unfortunately for the proponents of miracles, this self-limiting feature of science also has resulted pragmatically in huge successes for scientific achievement not matched by any other field of study. Now, everybody wants to be considered ?science? because it has the cachet of truthfulness. However, unless the methodological naturalism is rigorously applied, the result isn?t science?but may or may be true!
There is no ?dissent? in science. That concept is post modernist B.S., frankly. There are things that are correct is science whether or not you dissent. Your dissent and hurt feelings are irrelevant. If you dissent from the scientific consensus that the acceleration due to gravity is 9.8 meters per second squared, you are free to show your work. Until then your ?dissent? simply a mix of hurt feelings and ignorance?unless you jump out of an airplane?then your dissent will be both swift and fatal.
You can ?dissent? from that idea that each organism inherits dna from its parents and there are also random mutations in every generation, but that fact occurs despite your dissent. Your dissent would be harmless unless you refuse to vaccinate your children from mutating flu viruses. You can dissent from the fact that dna testing can determine paternity and ancestry?but you would be wrong and harmful if you refused to consider genetic testing for certain diseases.
So has Meyers made his case? No. This is a man who testified under penalty of perjury that ?force fields, atoms and quarks are all unobservable.? I conclude two things from his testimony: (1), he?s never been introduced to a compass, and (2) he is ignorant on science.



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R Hampton

posted January 28, 2010 at 6:50 pm


pds,
I’ll help you out (with the “lipid world”) comment. Dr. Meyer has retracted in his assessment of the intractable problems with an evolutionary origin of life:
The central problem facing origin-of-life researchers is neither the synthesis of pre-biotic building blocks (which Sutherland?s work addresses) or even the synthesis of a self-replicating RNA molecule (the plausibility of which Joyce and Tracey?s work seeks to establish, albeit unsuccessfully). Instead, the fundamental problem is getting the chemical building blocks to arrange themselves into the large information-bearing molecules (whether DNA or RNA).
Essentially, Dr. Meyer has admitted that if Science should prove (to his satisfaction) that nature can (and does) synthesize pre-biotic building blocks and/or synthesize a self-replicating RNA molecule, there would still be room for an Intelligent Designer (God) . Ultimately what nature can not explain (to his satisfaction) is the origins of modern RNA/DNA. And this is where ID will succeed or fail.
By making such a concession, Dr. Meyer no longer needs to address G?nter W?chtersh?user and others who offer testable theories of organisms that can naturally form, reproduce and evolve without RNA/DNA.



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Dan

posted January 28, 2010 at 8:46 pm


Unapologetic #48 wrote:
?Is belief in the resurrection unscientific if we cannot explain it with a naturalistic mechanism??
“An unqualified ‘Yes.'”
Therein lies the disagreement. Exactly there. I agree that science can only study natural phenomena. I do not agree that science must arrive at natural conclusions exclusively. I think that is a rationalistic modern bias. Scientists prior to the Darwinian revolution made discoveries and practiced science quite well prior to the “limitation” of naturalism. It is a phony slur to say that those who believe in something beyond nature will somehow start attributing every single mystery to magic or divine intervention. Many have argued that science as we know it could never have developed in the west apart from a belief in an orderly world fashioned by an orderly mind. Could science have developed at all if the first assumption of the human mind is that all things are the product of undirected chance? I think not.
As for the illustration of weather patterns being describable as natural cause and effect, I do think there is a difference. Weather is an observation of current processes and current phenomena. The principles are sound, yet weather prediction is still a very inexact science. Considering how difficult it is for a weather man using the best tools in the present to predict whether it will rain five days from now, I remain skeptical that scientists looking at bone fragments and DNA strands can tell me precisely what happened tens of thousands or millions or billions of years ago. That is not anti-science, it is just a recognition of the limits of observation and the unverifiability of our assumptions. And the naturalistic bias that sequesters makes me doubly skeptical.
I’ll stand pat. Science need not be limited to naturalism and belief in something beyond nature is NOT a repudiation of natural law. And I do believe it is intellectually inconsistent for a Christian to believe in the miracle of the resurrection on the one hand and close his or her mind to the possibility of the miraculous in the formation of the universe.



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pds

posted January 28, 2010 at 8:48 pm


BradK #47,
Calling someone a “saint” is not name calling. Collins is held in very high regard by theistic evolutionists. I applaud the design arguments in his book. I do wish he would be more accurate in his comments on ID.



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RJS

posted January 28, 2010 at 9:00 pm


Dan,
I don’t think that virgin birth and resurrection fall into the same category. If I was a philosophical naturalist I would – but I am not, I am a theist. I believe that God interacts with his creation and he sometimes does so miraculously. If I had been alive and among the disciples I rather expect I would react like Thomas and want to see … but that is a slightly different question. But I wouldn’t want to dissect.
The issues on creation and evolution are slightly different. God could have created miraculously, but the world shows every evidence of a more gradual process – “natural” with the understanding that all is of God and through God.
With respect to the origin of life – I don’t know if we will ever have a complete “natural” explanation. Maybe, maybe not – nothing really hinges on this. If it is not an impossible problem I think it quite likely that there will be a “natural” explanation someday. It is a challenge – and if there is anything a scientist loves, it is a challenge. We are puzzle-solvers by nature. Regardless “natural” or “supernatural” – God did it.
The stakes get higher on two counts once we move past origin of life and into the questions of origin of species and common descent. The evidence for the general historicity of evolution is overwhelming. Inference to best explanation… no doubt at all in my mind here any longer. Inference to best explanation once we have a cell is genetic modification and natural selection. We understand much – but not all – of how evolution progresses and the mechanisms at work. Pds often brings up the Cambrian explosion as an anomaly, and such observations challenge ideas about the mechanism of evolution, but don’t challenge the overall historicity.
The stakes are higher here because (1) the strength of the evidence challenges the faith of Christians who study enough to understand it and (2) the anti-evolution position prevents the spread of the gospel of Jesus Christ among large segments of our population.
These last two reasons are why I am persistent on this issue – if they were not such huge problems I would not put time into this discussion.



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AHH

posted January 28, 2010 at 9:15 pm


Dan’s comment #50 where he bristles at calling belief in the Resurrection “unscientific” illustrates something important.
I think much of the ID movement assumes an Enlightenment mindset where “scientific” truth is over-emphasized. Therefore, scientific proofs of God are sought, sliding right past the question of whether that mode of inquiry is appropriate to the object.
Just because belief in the Resurrection is “unscientific” (which of course it is unless perhaps one gets into Shroud silliness, though maybe “non-scientific” would be a better term) doesn’t make it untrue. I have historical and Holy Spirit-related reasons for that belief, which I find adequate without trying to call it scientific. Similarly, belief in God as designer, or that my wife loves me, need not be established scientifically in order to be true.
And, I think most of us who are not fans of the ID movement have not “closed his or her mind to the possibility of the miraculous in the formation of the universe“. We just would say some or all of:
1) Beyond a certain point such arguments are not science (which does not mean they can’t lead to truth).
2) The Paley-like arguments so far in the area of biology are not convincing.
3) Great damage is done by insisting that God’s design must be scientifically detectable in order for theism to be viable, which is the case in much ID rhetoric (not in Meyer’s book that I am aware), especially at the popular level.



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Dan

posted January 28, 2010 at 9:54 pm


AHH wrote:
“I think much of the ID movement assumes an Enlightenment mindset where “scientific” truth is over-emphasized. Therefore, scientific proofs of God are sought, sliding right past the question of whether that mode of inquiry is appropriate to the object.”
Couldn’t disagree more. The enlightenment built a concrete wall between science and faith and compartmentalized them completely. Everything I’ve been saying today is a repudiation of that – the insistence that “natural law” explanations ALONE can be categorized as science. Not sure early scientists would have thought that way.
RJS wrote:
“the anti-evolution position prevents the spread of the gospel of Jesus Christ among large segments of our population.”
If I held your position on the science, the intellectually honest position for me would be agnosticism. You wouldn’t be advancing the Gospel in my case, and that is the honest truth. I can’t say any more and I have other things to do.



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Mike Gene

posted January 28, 2010 at 11:06 pm


RJS: “DNA is….not reactive”
Not true. Simply google something called ‘DNAzymes.’ Here is a short excerpt from just one research article using these DNA-enzymes:
“The 10?23 RNA cleaving DNAzyme is a catalytic nucleic acid composed entirely of DNA (Fig. ?(Fig.1)1Figure 1) (1). It was derived from a combinatorial library of sequences by in vitro selection. *The tremendous activity and sequence specificity* against its target RNA under simulated physiological conditions (2,3) has generated the expectation that it may function in cells as a gene suppression agent.”
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC156713/



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RJS

posted January 29, 2010 at 6:34 am


Interesting Mike, I was not aware of that research. From what I find in a quick search they are not found naturally, (i.e. only made in laboratories) but are powerful for a specific purpose (gene replication). I looked at a few articles as well but they make wikipedia: Deoxyribozyme, an easier place for someone to get a quick overview.
The limited function achieved and the reasons given for this rather confirms my overall point – although the function in gene replication is an important one to consider in thinking about the issues of origin of life.



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pds

posted January 29, 2010 at 6:55 am


http://thedesignspectrum.wordpress.com/
RJS #52,

Pds often brings up the Cambrian explosion as an anomaly, and such observations challenge ideas about the mechanism of evolution, but don’t challenge the overall historicity.

The Cambrian Explosion is actually not completely an anomaly. The whole fossil record shows a general pattern of sudden appearance and stasis, especially in the higher taxa. Also, “mechanism” is what made Darwin noteworthy. Throw out RMNS and you don’t have “evolution” as it is commonly understood.

The stakes are higher here because (1) the strength of the evidence challenges the faith of Christians who study enough to understand it and (2) the anti-evolution position prevents the spread of the gospel of Jesus Christ among large segments of our population.

I think the anti-ID position here and at Biologos prevents the spread of good science in the Church, which can hurt the gospel. When I see Christian scientists espousing and endorsing really bad logic, scientists lose credibility.
The church would be helped if all the reasonable commenters here would hold hands and agree:
1. Design arguments from nature are valid arguments. Some are stronger than others. There is a wide spectrum of acceptable views on how to use design arguments in apologetics.
2. “Evolution” has lots of different meanings. Depending on how you define it, evolution explains a lot, but does not explain everything well. There is a wide spectrum of acceptable views on evolution among orthodox Christian thinkers.



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RJS

posted January 29, 2010 at 7:10 am


pds,
I don’t actually think that any of these views on creation impact Christian orthodoxy. It is an issue on which we can disagree.
But I disagree that mechanism is what made Darwin noteworthy. He had no real clue about mechanism. He identified connections and patterns.
The question at the root here is whether these patterns have a natural mechanism and whether these mechanisms can be discovered by scientific investigation. So — a refinement of the mechanism of evolution changes nothing. Sudden appearance and stasis is data for refining our understanding – not disproof of evolution.
You said:

When I see Christian scientists espousing and endorsing really bad logic, scientists lose credibility.

Bingo! And this is the major problem with Signature in the Cell. It is really bad logic – over and over and over. But I am trying to work through it to point out to readers here why I think that is the case.



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pds

posted January 29, 2010 at 7:12 am


http://thedesignspectrum.wordpress.com/
AHH #53,
I think it’s too bad that you call the Resurrection “unscientific.” Unscientific means “anti-science” to a lot of people. Better to say “beyond science” if you must.
I use “inference to the best explanation” when I evaluate the truth of the Resurrection claim. I am not alone. That is pretty standard methodology for any historical question. So I don’t see how it is unscientific to conclude that Resurrection is the best explanation of the relevant events.
By the way, if you follow RJS’s thinking, you can call the Resurrection an “argument from ignorance.” Maybe science will someday figure out how to resurrect people. RJS’s “hey, you never know” methodology works to defeat any claim of a miracle.



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RickK

posted January 29, 2010 at 8:51 am


Dop @35 said: “The real “enemy of rationality” is naked ad hominem”
Ah, but my attack wasn’t ‘naked’, it was supported by Meyer’s clearly documented goal to use “design” as a wedge in public discourse to push the god of the Christian Bible into science education and science policy. If Meyer were serious about rational science, he would circulate his ideas through the scientific community and respond to and incorporate the feedback of biologists and mathematicians. He doesn’t. He puts his ideas, some quite complex, out to the public so that they can be used as scientific-sounding soundbites in policy debates.
This is a restatement of the objections that I made in the post. So there was nothing ‘naked’ about my statement. “The Wedge” demonstrates intent to deceive. Deception, and those that practice it are enemies of rationality.



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pds

posted January 29, 2010 at 9:46 am


The Design Spectrum
By the way, I am glad to see that Biologos has published a reply by Stephen Meyer on its blog:
http://biologos.org/blog/response-to-darrel-falks-review-of-signature-in-the-cell/
It would be nice to see a guest post by him here. (Hint. Hint.)



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pds

posted January 29, 2010 at 9:47 am


That may also be a good vehicle for letting Jay Richards know that RJS is a woman. :)



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RJS

posted January 29, 2010 at 10:02 am


pds,
I linked Meyer’s response in my post yesterday morning – right after I found out it was up (see above). I think that he repeats some of the bad logic from the book, but it may be a good place to focus conversation.



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dopderbeck

posted January 29, 2010 at 10:15 am


pds (#59) — the problem with using “inference to the best explanation” with respect to the Resurrection is that this buys into a mistaken epistemology. The “best explanation” for the Resurrection ultimately depends on your starting point. If I were not a Christian — that is, if the Holy Spirit had not first prompted in me the spark of faith — I would say the “best explanation” for the Resurrection is some kind of trickery, delusion and/or fraud. You could make all the arguments you like about how improbable that seems historically, but it would not matter. Only by grace can anyone truly understand and believe in the Resurrection of the Christ. Once the eyes of faith are opened by God’s grace, it’s possible to see how all the probabilities and such cohere with what faith demonstrates. The same is true for “design” in creation.



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Hrafn

posted January 29, 2010 at 10:16 am


PDS (57):
“The whole fossil record shows a general pattern of sudden appearance and stasis, especially in the higher taxa.”
This claim is demonstrably FALSE, as is evidenced by thousands of transitional fossils.
Likewise the Cambrian *Slow Fuse* did not exhibit “sudden appearance”. The period in question was 70-80 million years, and evidence of PRE-Cambrian development is also expanding.
I would challenge PDS to present evidence from the *scientific* literature (as opposed to the creationist, including ID creationist, literature) supporting his claim of “sudden appearance and stasis” (as opposed to mere non-uniform rates of evolution).



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Your Name

posted January 29, 2010 at 10:43 am


re @ #65
It really depends on what one means by “transitional”. If common descent is true, then every fossil is a transitional fossil.
However, if what one is analysing is the appearance and then disappearance of morphological forms evidenced in skeletal remains that are stable for long periods of time, then it is debatable whether there are any transitional forms given what we know from DNA. That is, the DNA tree is hopeless and cannot be related on a correspondence basis with historical morphological change. Depending on what type or location of DNA one is analysing, one comes up with different “trees”, and the DNA trees frequently do not correspond with trees based upon morphological similarities and dissimilarities.
If one assumes Darwinist gradualism, then it is apparent that there are no examples of gradualist change in skeletal morphology. And again, the Darwinist version of evolution is non-falsifiable because every form is a transitional form (including all extant forms today) and the gaps will eventually be filled in with examples of gradualist transitions.
One can construct a theory of common descent and macroevolution that is consistent with much of the data, but not with all of it, and the consistency is not in any event rationally compelling. By rationally compelling I mean that term as it is used in philosophy: one is compelled to believe it if one thinks rationally. Evolutionary theory is, to a large extent, a theory of history and an exercise in trying to prove something by arguing from the consequent (which, of course, cannot not provide a rationally compelling argument).
regards,
#John



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pds

posted January 29, 2010 at 10:48 am


The Design Spectrum
Hrafn #65,
Please show a transitional series from one phylum to another phylum.
The pre-Cambrian fossils show the same pattern of sudden appearance and stasis. The pre-Cambrian fossils are not the expected Cambrian ancestors. Why do we see soft-bodied creatures persist in the fossil record right up to the Cambrian, but we have no evidence of any hard-bodied ancestors of trilobites or any of the other Cambrian animals?
Scientific lit.: This link refers to an article in Science:
http://www.vtnews.vt.edu/story.php?relyear=2008&itemno=1

“These Ediacara organisms do not have an ancestor-descendant relationship with the Cambrian animals, and most of them went extinct before the Cambrian Explosion,” said Shen. ?And this group of organisms ? most species ? seems to be distinct from the Cambrian animals.?



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pds

posted January 29, 2010 at 10:54 am


dop #64,
What you describe does not account for how I came to faith, how my faith was strengthened or the accounts of many, many other people. The body of Christ is full of apologetic diversity and faith journey diversity that corresponds to 1 Cor. 12.



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Hrafn

posted January 29, 2010 at 11:31 am


PDS (67):
1) As far as I know, current palaeontological thinking does not posit “a transitional series from one phylum to another phylum”. See ‘A critical reappraisal of the fossil record of the bilaterian phyla’ http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=623 for some current thought on the subject.
2) We see a number of early arthropod-like creatures bearing some resemblance to the trilobites in the pre-Cambrian, e.g. Spriggina & Parvancorina.
3) Virginia Tech News, being the newsletter of Virginia Polytechnic Institute and State University, IS NOT “scientific literature”.
4) The research in question does not show “stasis” but rather “more than 200 Ediacara species … [which] cover three evolutionary stages of the entire Ediacara history across 33 million years”. Given the paucity of pre-Ediacara fossils, we cannot (as yet) know the extent to which this radiation occured solely in the Ediacara period or not.



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Mike Gene

posted January 29, 2010 at 11:36 am


Hi RJS,
I?m not sure how an argument gets confirmed when one of its premises is found to be false. What you present is the classic, foundational argument for the RNA world:
*DNA is inert, but is passes on information across time.
*Proteins don?t pass on information across time, but are reactive.
*RNA is both reactive and passes on information across time.
*Since life requires both reactivity and the ability to transmit information, life must have started with RNA.
But DNA is not inert. Yes, the reactivity is limited and man-made, but that is just an observation of our current understanding. I would also add that proteins can pass on information ? simply research prions and evolution.
In reality, all three biomolecules (RNA, DNA, and proteins) are reactive and transmit information. One can make arguments about degree, that are a function of our current understanding, but the forceful beauty and simplicity of the argument for the RNA world is gone.
Look, I don?t agree with Meyer?s denial of the RNA world nor do I buy into the whole information argument. But I would remind people that the RNA world is neither a fact nor a well supported theory ? it is a hypothesis/speculation supported by strands of circumstantial evidence with a mixed bag of predictive success. While I cannot deny the RNA world once existed (it sounds plausible and would fit well within a teleological explanation), neither can I cheerlead for the RNA world because of some serious, fundamental problems.



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dopderbeck

posted January 29, 2010 at 11:38 am


pds (#68) — I understand that many people have journeys in which various rational arguments have played an important part. However, I want to suggest that, in fact, your appreciation of those arguments was only made possible by the prior gracious work of the Holy Spirit, even if you don’t fully recognize that. I think this is a basic principle of the doctrine of grace. God’s action is always prior to ours.
I think this also can help us understand why it seems to be the case that people sometimes come to faith in Christ after hearing apologetic arguments that simply are plainly false, such as young earth creationism; or that are misapplications of the Bible, such as “proofs” of Bible prophecies coming true in the Middle East; or that are “harmonizations” of conflicts in the Bible that are strained to the point of silliness; or that are misrepresentations of their inherited family religious traditions, such as claims that Catholicism teaches salvation by good works. (Please note that I’m not necessarily equating all ID arguments with these categories — this is just by way of illustration).
Truth be told, this phenomenon has troubled me over the years. Why do some really bad apologetic arguments persuade some people to become Christians, and what is really the status of a faith built on bad arguments? The theological answer, I think, is that arguments ultimately don’t persuade people to accept Christ; the openness to faith in Christ and faith itself are gifts of the Holy Spirit — even if the person’s own perception is that some rational argument or another cinched the deal.
“Apologetics” is really the art of explaining the coherence of faith in Christ with all of reality — or rather, explaining what reality actually is once the Triune God revealed in Christ is understood to be the font of reality. There is then room for the fact that our explanations often are amiss in some ways, without eroding the true foundation of faith.



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pds

posted January 29, 2010 at 12:52 pm


Hrafn #69,
1. Universal common descent requires transitions from phylum to phylum and from body plan to body plan at some point.
2. “some resemblance”? I have seen them. Highly speculative.
3. As I said in my comment, the linked article discusses an article in Science.
4. Like I said, I am talking about the higher taxa. Species are not higher taxa.
Bottom line: you seem desperate to impose a framework on the evidence. The “best explanation” should explain the evidence, not explain it away.



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R Hampton

posted January 29, 2010 at 4:30 pm


pds & Your Name (#66),
Let’s get to the chase. From the dog to wolf to fox to leptocyon and back, when does this transitions from phylum to phylum occur and what does ID predict? Furthermore, what is the irreducibly complex structure that separates the dog phylum from its ancestor, and again, what does ID predict?



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RJS

posted January 29, 2010 at 5:03 pm


Mike (#70),
Fair enough – I don’t disagree on your points. But remember that this post was intended to be a very brief overview to introduce a non-science audience to the subject, not really an attempt to explore all the nuance. RNA world is not a fact – or even a well supported theory – it is a hypothesis being tested. (I was careful in the post in fact to use “hypothesis” and “candidate” – and not to indicate any degree of certainty for this reason).



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pds

posted January 29, 2010 at 5:19 pm


R Hampton #73,
These animals are all in the same family, so there is no change here from phylum to phylum. There is no “dog phylum.”
I think macroevolution from species to species and genus to genus is pretty plausible.



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Paul Burnett

posted January 29, 2010 at 7:27 pm


“pds” correctly noted: “There is no “dog phylum.”
The phylum that dogs belong to is chordates – humans are in the same phylum as doga, as are all other vertabrates. Maybe somebody was thinking “kind”?



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R Hampton

posted January 29, 2010 at 7:31 pm


pds,
I used the label “dog phylum” to reference the set of animals that all belong to the same family as dogs –the point being that ID needs to determine which animals belong to the same phylum. Why? Because Meyers, Dembski, et. al. make the bold claim that “phylum to phylum” transitions are impossible without an Intelligent Designer (GOD). But then these same fellows – and ID “theory” itself – refuse to identify the phyla of life or the specific intelligently designed parts that prohibited said (natural) transition. That makes ID not just a disingenuous model, but deliberately deceitful.



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Hrafn

posted January 29, 2010 at 11:02 pm


PDS (72):
1) Your first point is COMPLETELY WRONG! Universal common descent DOES NOT entail that current phyla are descended from other known phyla, only that they share ancestors (which may well be of unknown or ambiguous phyla). The fossil record for such distant events is very sparse, so there is insufficient data to build up much in the way of a ‘family tree’ linking the phyla (genetics may tell us something more however). Lack of sufficient data to work up a *detailed* hypothesis is not however, in any way, evidence that natural forces could not have caused this radiation.
2) See last two sentences of (1).
3) Summarisation in the non-scientific press frequently leads to loss of accuracy & detail.
4) Again, per last two sentences of (1), expecting detailed evidence of ‘higher taxa’ transitions in the sparse fossil record of the pre-cambrian periods is unreasonable. Evidence of ‘higher taxa’ transitions becomes increasingly more common and more detailed after the Cambrian (as we get more fossils, and the fossils become more complex, allowing a greater level of comparison of fossil details).
Bottom-line: lacking a large body of detailed facts in the pre-cambrian for evolution to explain, and to constrain these explanations, it is not a flaw in the evolutionary explanation that it is “speculative” and lacking in detail.
Postscript: given my posts in (#3 & #4 above) I find that you are still harping on about “best explanation” to be absolutely ludicrous.
As I pointed out, ID IS ARGUABLY THE WORST EXPLANATION, as it provides little or no “understanding”, and no “precision” or “information about underlying mechanisms”.
Further, the only ‘evidence’ you purport it to explain is a very weak and heavily disputed analogy (@8). Even were the analogy strong and undisputed, analogies are not scientific evidence. So we have a non-explanation of non-evidence — worst squared.



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Hrafn

posted January 29, 2010 at 11:11 pm


R Hampton (77):
Your ‘dog phylum’ is Chordata — which includes all vertebrates and a number of closely-related invertebrates.



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Hrafn

posted January 29, 2010 at 11:35 pm


Taking Chordata as an example, it is a member of the Superphylum Deuterostomia, whose members also include sea stars, sea urchins, sea cucumbers (Phylum Echinodermata) and acorn worms (Phylum Hemichordata). Chordates first appear in the fossil record in the Cambrian, but such fossils are rare, and there appears to be some degree of difficulty in distinguishing fossils of primitive chordates from fossil hemichordates (although modern genetics have proven that the two phyla are less closely related than was once thought).
Deuterostomia in turn is believed to have split from Protostomia in the Ediacaran.
Bottom line: common descent, but no “transitional series from one phylum to another phylum” postulated.



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R Hampton

posted January 30, 2010 at 1:36 am


Hrafn,
Yes, Chordata (which includes mammals, birds, reptiles, amphibians, fish, lancelets, et al.) is the phylum as defined by the “pro-evolution” sciences. However the ID folk deliberately speak of in terms of “body plans.” Thus the impression they give is that Man and Sea Squirts could not possibly share a common ancestor because their bodies are so different (from the lay person’s perspective). Therefore it’s reasonable to conclude that the ID folk believe in a very different system of phyla. Furthermore, I believe this to be a deliberately strategy on the part of the ID movement. By refusing to specify how ID would redefine Evolutionary tree, they provide a pseudo-scientific justification for Christians who want to believe that each and every species was created by God.
By referring to the “dog phylum” I was prodding PDS to hunt for the ID definition of phyla and the irreducible complex structure that necessitate a designer – that is, I was sending him on a wild goose chase.



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Hrafn

posted January 30, 2010 at 2:20 am


R Hampton (81):
From your description, ‘body plan’ seems to be another ID-created concept (similar to ‘specified information’) of vague definition and questionable scientific utility, created for the apparent sole reason of claiming that evolution can’t explain it.
The scientific concept of ‘phyla’ seems to be fairly fluid, with a number of previous phyla relegated to sub-phyla status based on further information, and some questioning the utility of such a fixed level of radiation (as opposed to more free-form cladistic trees).



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pds

posted January 30, 2010 at 7:49 am


Hrafn #82,
You said,

‘Body plan’ seems to be another ID-created concept . . . of vague definition and questionable scientific utility, created for the apparent sole reason of claiming that evolution can’t explain it.

LOL. Thanks for the good laugh this morning.
I don’t have time to educate you on basic science. You may want to do a little more reading about “body plans,” “bauplans,” and how they relate to phyla classification.



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Hrafn

posted January 30, 2010 at 9:43 am


Hrafn DID NOT say what PDS (83) said Hrafn said. Hrafn further suggests that PDS not start his quotes mid-sentence, particularly without explicit ellipsis, as such misquotation gives rise to the accusation of contextonomy and lying by omission.
I made it quite clear that I was basing my comment on R Hampton’s description (“From your description”). If PDS wants to claim that this description, or my interpretation of it is inaccurate, then he is welcome to do so. Misquotation and hollow mockery is simply a waste of bandwidth.



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Hrafn

posted January 30, 2010 at 9:45 am


(Addendum: “welcome to do so” above should in fact read “welcome to do so WITH EVIDENCE”)



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Paul Burnett

posted January 30, 2010 at 9:48 am


R Hampton wrote: “Yes, Chordata…is the phylum as defined by the “pro-evolution” sciences. However the ID folk deliberately speak of in terms of “body plans.” Thus the impression they give is that Man and Sea Squirts could not possibly share a common ancestor because their bodies are so different (from the lay person’s perspective).”
“(from the lay person’s perspective)” says it all. The pseudoscience of intelligent design creationism is deliberately constructed to appeal to the “lay person” – not to the scientist or to anybody with any understanding of science. This appeal to the scientifically illiterate (if not willfully ignorant) “lay person” reveals intelligent design creationism for the demagoguery it truly is.



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Hrafn

posted January 30, 2010 at 10:21 am


Given PDS decided to make a big issue about body plans, and their relationship to phyla, I decided to read up a bit on the subject. In doing so, I came across the following in ‘Anthropod Relationships’, Fortey & Thomas, 1998 (p2):
“1.2.5 CLADE ANCESTOR
The last common ancestor of two clades, such as sister phyla, is the species that gave rise to daughter species from which each of the phyla has respectively descended (Figure 1.1). As each of the daughter species founded a clade, they are termed clade ancestors here; in effect they are the first members of taxa. The parental last common ancestral species stem will share a body plan with these sisters. The sisters themselves are not likely to be much more different than any two average sister species today — and indeed the sisters might even be sibling species. furthermore, any morphological differences that the sisters do display may well have nothing to do with morphological changes that eventually occur to create the distinctive body plans of their descendants — and this is probably by far the usual case. Thus the descendant body plans are derived with respect to both their clade ancestors and their last common ancestor (except in the special case where one body plan remains essentially unchanged, probably a rare case with a phyla). If taxa are construed as being founded by a clade ancestor, the morphological concepts of taxa are lost. Phyla construed in this way can no longer be defined or identified morphologically, since a clade ancestor will not usually possess the body plan that characterizes the Linnean phylum that descends from it, but will have the body plan of some members of its ancestral lineage and of its sister phylum.”
From which I can conclude:
1) That ‘body plans’ do in fact have a well-defined scientific meaning. I therefore retract any previous statements to the contrary.
2) That the relationship between body plan, phyla and ancestral relationships is perhaps more complex and ambiguous than some might infer.



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pds

posted January 30, 2010 at 10:48 am


The Design Spectrum
Hrafn #84,
I note that your full comment was directly above my comment. I quoted your conclusion. Anyone can see what your conclusion was based on.
Delighted to give the full context.
R Hampton #81:

However the ID folk deliberately speak of in terms of “body plans.” Thus the impression they give is that Man and Sea Squirts could not possibly share a common ancestor because their bodies are so different (from the lay person’s perspective). Therefore it’s reasonable to conclude that the ID folk believe in a very different system of phyla. Furthermore, I believe this to be a deliberately strategy on the part of the ID movement.

Hrafn #82:

From your description, ‘body plan’ seems to be another ID-created concept (similar to ‘specified information’) of vague definition and questionable scientific utility, created for the apparent sole reason of claiming that evolution can’t explain it.

It is even better when you read the full one-two punch.
I think that this an excellent example of how anti-ID hysteria feeds on mutual sharing of misinformation.
And then Paul Burnett jumps in with accusations of “pseudoscience.”



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Hrafn

posted January 30, 2010 at 11:48 am


PDS (88):
It is not atypical for non-explanations (in that it provides little or no “understanding”, and no “precision” or “information about underlying mechanisms”) of non-evidence (see my post #78) to garner accusations of “pseudoscience”.



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Paul Burnett

posted January 30, 2010 at 1:33 pm


“pds” wrote: “And then Paul Burnett jumps in with accusations of “pseudoscience.””
Goodness, I didn’t make that up all by myself. The National Academy of Sciences, the American Association for the Advancement of Science and essentially every other actual science organization in the US have issued position statements that intelligent design design creationism is not science, but pseudoscience. See http://en.wikipedia.org/wiki/List_of_scientific_societies_explicitly_rejecting_intelligent_design and http://ncse.com/media/voices/science



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pds

posted January 31, 2010 at 8:17 am


http://thedesignspectrum.wordpress.com/
RJS,
I wanted to follow up on this claim by you:
“4. He misunderstands scientific method and thinking.”
Did you defend this or explain it? What are your reasons for claiming this? Do you disagree with “inference to the best explanation” as a sound methodology for the historical sciences? What is your alternative?



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RJS

posted January 31, 2010 at 11:11 am


pds,
Fair question. This thread is old – so I don’t want to enter into a lengthy discussion here. It will come up again in later threads.
He appears to misunderstand method in the way he deals with data and experiments. He often dismisses bite-size steps looking a pieces of complex problems because they don’t solve the whole problem. But we build up a body of knowledge that permits the solution of complex problems through a divide and conquer method. I would agree with him that the problems are not yet solved – but his criticisms of the intermediate steps are unjustified.



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pds

posted January 31, 2010 at 1:04 pm


http://thedesignspectrum.wordpress.com/
RJS #92,
I see where you disagree with him, but I don’t think it is fair to say “He misunderstands scientific method and thinking.”
You view the bite size steps as getting us closer to solving the whole problem. I think he sees the ideas and proposals showing the same intractable problem and not getting us any closer.
He points to strong positive evidence for design based on analogy, together with no plausible non-design alternatives. Your response seems to be “I think we will find a non-design alternative eventually.”
His methodology seems sound and based on actual evidence. Yours seems to be based on a personal prediction.
Happy to wait till later to discuss it. By the way, thanks for doing this review series. I think it is very helpful to all.



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Hrafn

posted January 31, 2010 at 10:33 pm


PDS (93):
I take leave to contradict the majority of your claims:
1) An analogy, even a strong one, is not scientific evidence at all, let alone strong evidence. an analogy is an inference (and generally a subjective one), not evidence.
2) In any case, the analogy is a very weak one — taking evidence of the artifice of human intelligences that were known to exist at the relevant times using known methods and for generally known purposes to infer the existence of a superhuman intelligence, not otherwise known to have existed, using unknown methods for unknown purposes at unknown times.
3) Meyer’s claims of implausibility are entirely self-serving, and untested in the (legitimately) peer-reviewed literature. Given this, plus the fact that Meyer is not an acknowledged expert in this field, his claims have negligible weight.
4) In any case any scientific hypothesis, based upon known and or/explicitly hypothesised mechanisms, and explaining details of known observations (and making specific, relevant and detailed predictions of future observations) will (by Lipton’s definition cited above) be an orders of magnitude better explanation than ‘I believe it resembles something designed, therefore it was designed’ (which in fact is little more than a paraphrase of Paley’s Natural Theology, which was rejected in favour of even Darwin’s original, more limited explanation — let alone the much expanded and refined explanation we have today).
5) I therefore conclude that I agree with RJS, that Meyer’s claims are methodologically completely unsound and that, contrary to your assertion, has no basis whatsoever in “actual evidence”.



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Hrafn

posted January 31, 2010 at 10:50 pm


I would note that John C. Avise, Distinguished Professor, Ecology & Evolutionary Biology at UC Irvine has recently published ‘Inside the Human Genome: A Case for Non-Intelligent Design’ (Oxford University Press).
It would appear that at least one acknowledged expert draws a rather different conclusion from Meyer.



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R Hampton

posted January 31, 2010 at 11:33 pm


Like phyla, ID has it’s own definition for “body plans”. Don’t believe me? Find one example of a phylum or body plan based clade originating from IDs evolutionary gaps. Are mammals within a group, a group by themselves, or comprises of many groups? For ID to have a scientific value, it must be able to answer this question either as a prediction or as an evidentiary argument. So go ahead, find the ID tree of life and prove me wrong



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Hrafn

posted February 1, 2010 at 5:26 am


I draw readers attention to GW Dawes’ article, ‘What is wrong with intelligent design?’ (International Journal for Philosophy of Religion, 2007), available at http://commonsenseatheism.com/wp-content/uploads/2009/09/Dawes-What-is-Wrong-With-Intelligent-Design.pdf
Although I disagree with Dawes’ unquestioning acceptance of ‘Specified Complexity’ as a legitimate phenomenon, requiring an explanation, this otherwise appears to be a fairly good discussion of the arguments underlying ID.



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A Logical Theist

posted May 25, 2010 at 4:46 pm


“There appears to be no chemical reason why GCU codes for alanine and UCG codes for serine any more than there is a fundamental reason why 109 is the ascii code for m and 230 is the ascii code for ?. But once the code is established, specified sequences carry information.”
Information theory is one of A.E. Wilder-Smiths topics. he says the fact that the code is arbitrary and dependent on what the sender and receiver agree on. how does the code AND the ability to decipher the code evolve simultaneously?. just as a PC program will not run on a MAC because the message is not understood by the receiver unless programed to do so
As the author said “But once the code is established, specified sequences carry information.”
How does the code and the meaning of the code get established between the sender and receiver from a completely non-intelligent random process.
This fact alone blatantly suggest Intelligent design



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Derwood

posted October 6, 2010 at 9:50 am


“Information theory is one of A.E. Wilder-Smiths topics. he says the fact that the code is arbitrary and dependent on what the sender and receiver agree on. how does the code AND the ability to decipher the code evolve simultaneously?. just as a PC program will not run on a MAC because the message is not understood by the receiver unless programed to do so ”
First, Wilder-Smith is a pharamcologist, not an information theorist or geneticist. he is also a young earth creationist.
Second, there is no ‘sender’ or ‘receiver’ in molecular biology, there are simply chemicaql systems that interact. This is a classic argument via analogy. Yes, we know that in human-contrived coding systems and commuication, there is a ‘sender’ and a ‘receiver’, and yes, some have attempted to append such monikers to parts of the protein synthesis apparatus. But doing so is merely metaphorical. The genome is nore the ‘sender’ than the ribosome is the ‘receiver’. They do not need to ‘agree’ on anything, they merely need to be able to bind with certain other molecules and/or catalyze reactions.
From an evolutionary standpoint, the system in place now, which appears to those predisposed to consider analogies as facts, is in place because it provided those possessing it (and its precursors) to survive.



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