On Deciphering the Signature

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September 12, 2011 Tags: Design

Today's entry was written by Darrel Falk. You can read more about what we believe here.

On Deciphering the Signature

Steve Meyer has responded to Dennis Venema’s review1 of his book Signature in the Cell in the September 2011 issue of Perspectives on Science and the Christian Faith (PSCF) (63:171-182). Although, Dennis has ably responded (63:183-192), I would like to address one specific aspect of Meyer’s response, especially since it relates to the final paragraph of my initial essay regarding the book and Dennis’s six part series on the BioLogos website.

BioLogos has dealt fairly extensively with what we thought was the basic premise of Signature in the Cell. I had read the book carefully and I know Dennis did as well before we responded. I sincerely thought that the heart of Meyer’s argument is summarized in the following three quotes from the book:

1. “So the discovery of the specified digital information in the DNA molecule provides strong grounds for inferring that intelligence played a role in the origin of DNA. Indeed, whenever we find specified information and we know the causal story of how that information arose, we always find that it arose from an intelligent source. It follows that the best, most causally adequate explanation for the origin of the specified, digitally encoded information in DNA is that it too had an intelligent source. Intelligent design best explains the DNA enigma” (p. 347, emphasis added).

2. “Since, as argued in Chapters 8 through 15, intelligence is the only known cause of large amounts of specified information, the presence of such information in the cell points decisively back to the action of a designing intelligence” (p. 382, emphasis added).

3. “Because we know intelligent agents can (and do) produce complex and functionally specified sequences of symbols and arrangements of matter, intelligent agency qualifies as an adequate causal explanation for the origin of this effect. Since, in addition, materialistic theories have proven universally inadequate for explaining the origin of such information, intelligent design now stands as the only entity with the causal power known to produce this feature of living systems.” (p. 386, emphasis added).

So we at BioLogos have always thought that if mainstream science demonstrated an increase in “complex specified information” (CSI) without needing to invoke supernatural intervention, Meyer’s assertion that “intelligence is the only known source of such information in the cell” will have been refuted at the scientific level. It sure seemed to me that this is what he said in the above quotes.

With that in mind, we’ve put a great deal of effort into showing a number of cases in the lab and in nature where scientific data have provided very strong evidence for increased CSI which is entirely consistent with how we scientists would define “natural explanations.” All this time, starting with my first essay almost two years ago, we sincerely thought we were engaging Meyer’s book on Meyer’s terms.

But now, in his PSCF article, Meyer states that arguments based on examples of increased CSI don’t count if they occur after life began on Earth.

Signature in the Cell argues, first that no purely undirected physical or chemical process—whether those based upon chance, law-like necessity, or the combination of the two—has provided an adequate causal explanation for the ultimate origin of the functionally specified biological information. In making that claim, I specifically stipulate that I am talking about undirected physical and chemical processes, not processes (such as random genetic mutation and natural selection) that commence only once life has begun. Clearly material processes that only commence once life has begun cannot be invoked to explain the origin of information necessary to produce life in the first place) (pp. 173-174, Perspectives on Science and Christian Faith, Sept. 2011, emphasis added).

Since I had read the book very carefully, and have gone over it many times since, I was amazed that I could have missed this stipulation. Again, he says: “I specifically stipulate that I am [not] talking about … processes (such as random genetic mutation and natural selection) that commence only once life has begun.”

Did he really specifically stipulate that? Have we been barking up the wrong tree all this time? While we knew the main focus of Meyer's book was the origin of life (not mechanisms of evolution), his argument clearly stated, we thought, that no large increase in CSI (Complex Specified Information) had ever been demonstrated without the need to invoke intelligence. Period.

I went back through my well-marked up copy of the book again, re-examining each section in which he wrote about increased CSI. Despite my best efforts, I could not find the stipulation he mentions in the PSCF article. Still, thinking I had missed it, I spent $15 for an electronic version of the book—one that would allow me to identify every time the word “mutation,” or natural selection” appeared—anything that would help me find his stipulation. I couldn’t find it.

Actually I thought Meyer was pretty clear and highly specific in his book. Consider this scientific challenge on page 429:

If, for example, someone successfully demonstrated that "large amounts of functionally specified information do arise from purely chemical and physical antecedents," then my design hypothesis, with its strong claim to be the best (clearly superior) explanation of such phenomena, would fail.

Find a case where a large amount of CSI has accumulated without needing to invoke intelligence, and his argument, Meyer said, fails. This is a strong statement, clearly worded, and there is no hint of Meyer’s stipulation that it doesn’t count if life has already begun. In Dennis Venema's BioLogos blog series, he showed many cases where there were large increases in CSI (whole genome duplication, for example) without needing to invoke that supernatural intervention was necessary to create it. Chromosomes, the cell division machinery, and nucleotides are “purely chemical and physical antecedents.” The information content in the genome, Venema showed, quadrupled early in vertebrate history through material processes that we know and understand well. Did this not meet the scientific criteria that Meyer specifically called for?

I don’t know how misunderstandings like this happen. I believe that Stephen Meyer, who I consider to be a friend and colleague, thinks the stipulation exists in his book and that he worded it clearly. I assume he thinks it was implied in some overarching statement that I have not been able to find. I also think he believes he was clear. Unfortunately, clear he was not. I’ve looked thoroughly and I have not been able to find his stipulation.

In post after post, we have set out to demonstrate the scientific case we thought Meyer called for. Then in the end, it sure seems to us, that the rules changed, even though Steve feels they were written in his book all the way along.

Still, let’s move on. Let’s play by the new rule and let’s define it carefully.

So here’s the rule as I now understand it: If large increases in CSI can be demonstrated without the need to invoke an external intelligence, “then [Meyer’s] design hypothesis with its strong claim to be the best (clearly superior) explanation of such phenomena, would fail.”

Having stated the rule, we have to make two exceptions (Meyer himself made Exception #1 clear in Chapter 13; Exception #2 is the new stipulation we've been discussing):

Exception 1. We can’t count large increases in CSI which develop as a result of computer programs because minds designthe program parameters.

Exception 2. We can’t count large increases in CSI which develop in the history of life, because DNA was necessary to set those processes in motion.

So what can we count? Until he clarified the existence of Exception #2, I thought any general increases in CSI would count. However, it is now very hard for me to imagine any increase in information that would not be categorized within either Exception 1 or Exception 22. The only thing left that doesn’t fit into one of these two exceptions is the origin of life itself. The point of the book, I thought, was to bring other examples of increased CSI to bear on this very question.

With Meyer’s exceptions and the inability to bring general CSI increases to bear on the origin of life question, we also no longer have “positive3 experiments [which] provide causal adequacy of intelligent design” (p. 335, emphasis added).

So what are we left with? Are we not simply left with the question of whether the origin of life experiments show that information-rich molecules will arise in a test tube from chemicals off the shelf? Dr. Meyer, I think, says no, for reasons that are no longer clear to me other than that he’s given up on the science. I, on the other hand say, “Wait a while. Let the science play itself out before a scientifically based decision is made.” To be frank though, I am a little concerned that even if the right mix of materials is found to produce molecules that can spontaneously assemble in a manner that gives rise to complex specified information, Dr. Meyer or those who follow him will say, “Sorry, you can’t count that because it took a mind to create the conditions and it took a mind to mix them together in a test tube.” And with that we’ll have a new stipulation which most likely was in some manner implied in Signature in the Cell to begin with.4

The interesting thing about this is that Steve Meyer and I are probably really in almost the same exact position when it comes to our core beliefs. Obviously as fellow Christians, we both believe that there is a Mind behind the process. We both think that the history of life with its constant increase in complex specified information is a product of the activity of God. We both stand amazed at the majesty of creation and our love for the Creator who is personally involved not only in our own individual lives but those of our families and faith communities as well. We differ primarily in one regard. Steve thinks he has shown through scientific analysis that this Mind we both believe in must have been present and supernaturally active in the creation of information. I think the Mind (God) was present, but I can’t put the existence of God into a scientific experiment to demonstrate God's activity. Furthermore, unlike Steve, I have no pre-conceived ideas about whether God's,supernatural activity was necessary for creation of information. God, as I see it, may have chosen to create information bearing molecules indirectly through God’s natural activity in a manner that is analogous to the development of a baby or the growth of a tree from a seed.

In the end, our difference is simple, he thinks that the test tubes won’t ever deliver information rich molecules and I think it is too early to say. He has declared the matter more or less settled on the basis of scientific analysis. I consider the matter fully unsettled. But the most important thing of all has been settled and on this we both agree. This Mind we speak of is God’s Mind--God's Holy Spirit. That Spirit not only fills all of creation, but more specifically that Spirit fills us with his Presence and envelopes us in his love. This is cause for celebration and, with "sandals off," we each bow our heads in humble worship. Truly, we--all of us--are standing on holy ground.

Notes

1. Perspectives in Science and Christian Faith 62:276
2. Note to Steve: Does not the human brain count within Exception #2? After all, it arose in the history of life and its development depends upon DNA. If so, you might need an exception to the exception.
3. The term “positive” is used 21 times in the book. It is clearly important to the author that the evidence for intelligence associated with the origin of DNA be viewed not as absence of contrary evidence, but rather a piece of convincingly positive evidence that hinges upon the fact that CSI in general, can’t be built without a mind.
4. I’m really not trying to be facetious here. I really do think that’s what would happen. I can almost draft the stipulation now.


Darrel Falk is former president of The BioLogos Foundation. He transitioned into Christian higher education 25 years ago and has given numerous talks about the relationship between science and faith at many universities and seminaries. He is the author of Coming to Peace with Science.


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gingoro - #64638

September 10th 2011

Darrel 

I do not remember Meyer’s recent stipulation occurring the SitC so it must have been something that he assumed was obvious and did not need to be said.  Can happen to the best of us but it is very annoying.
Dave W

sy - #64641

September 10th 2011

I think it is clear that the ID concept of CSI and design is evolving (pun intended). I think we are witnessing a wondrous sign of hope. Darrel is of course completely right that the critical stipulation of CSI occurring in the absence of life is missing in Signature in the Cell. I also looked for some indication that Meyer was not conflating origin of life with biological evolution, and was frustrated to find that in fact he was in his book. But now, it appears, he is no longer. This is truly a praiseworthy development in Christian thought, and is one I think is worthy of celebration.

Darrel, I love your analysis of all that you and Meyer share in common, and I have faith that if it is really true that at least some part of the ID movement is prepared to accept evolutionary theory  without design for biological transformation (as implied by the stated stipulation), we may come to see a glorious unification of all of these ideas. Halleluljah.


athanasius - #64643

September 10th 2011

So I don’t get it. If he isn’t going to talk about information after life began, then what is the point of writing the book? Most of the information in the “signature” occurred after life began.


glsi - #64647

September 10th 2011

Well, Doctor, the only thing I can say is just get yourself a good chemistry set and some tubes and start mixing away.  The day you find something wiggling around in there you’ll actually have something to blog about.


Glen Davidson - #64651

September 11th 2011

Meyer:


<blockquote> In making that claim, I specifically stipulate that I am talking about undirected physical and chemical processes, not processes (such as random genetic mutation and natural selection) that commence only once life has begun. </blockquote>
br>
To be fair to Meyer, he did at times make such a stipulation.  On page 420 of his book he writes this:
br>
<blockquote>Advocates of intelligent design use a law (“Complex specified information always arises from an intelligent source in a nonbiological context”) to infer a past causal event, the act of a designing mind.</blockquote>
br>
I would object to the designation of “law” to their presupposition, as well as any meaningful “causal event” even being illegitimately inferred, but the “law” does stipulate that outside of biology (abiogenesis) “CSI” can’t arise.  
br>
Even the quote from p.429 seems to be leaving out the biological in its “challenge.”  
br>
Of course Meyer often confuses the abiogenesis and evolution in his book, hence at times he resorts to a conventional ID denial that large amounts of CSI can arise without intelligence either within or without the biological realm.  Yet it’s fair to say that his strongest claim is always that CSI can’t arise outside of biology, even though he often conflates that with the claim that it can’t arise within biology either.
br>
I have occasionally been slightly bothered when blogposts have not made the distinction between the two, even though I always understood the importance of showing that large amounts of information comes from evolution, since at the end of the book he’s attacking evolution about as energetically as he is abiogenesis.  
br>
For Meyer’s strongest claim, it wouldn’t matter much if he ever stipulated the difference, nor that his terms and claims are often equivocal and ambiguous.  This is because it’s still the strongest claim that can be made.
br>
<a href=“http://tinyurl.com/mxaa3p”>Glen Davidson</a>

beaglelady - #64653

September 11th 2011

Glen, note that you can’t use tags in this stinking editor.


Darrel Falk - #64654

September 11th 2011

Glen,

The quote from p. 420 does not  directly (or indirectly) imply a stipulation that only “non-biological” CSI would count as a valid rebuttal to Meyer’s hypothesis.  All it states is that non-biological CSI is always associated with an intelligence. 

With regard to the quote on p. 429, Meyer spoke in terms of “large amounts of information arising from physical and chemical antecedents….”   You don’t think that free nucleotides are chemical antecedents? 

Regardless, my point is that the stipulation was not clearly laid out.  Since I believe that  Steve is honest, I know he considered the stipulation to be implied in some fashion.  We just didn’t catch it.

However, as I’ve said, now that I know his rule excludes all increased CSI after  the origin of DNA, then I’m not sure where that leaves us.  Not only does this stipulation exclude the increased information resulting from duplicated chromosomes (because DNA built the cells in which this occurred), but  I assume that that it also excludes the increased information that results from the brain, (since DNA also is also responsible for building brains).  Once you exclude the brain and increased CSI derived from it, it seems to me that this leaves us back at square one.   With his exceptions in place, I don’t see that Meyer’s hypothesis has any meaning. 

So with that, we’re back to the simple question.  Has the science of origin of life research reached a dead end or not? 

 


Glen Davidson - #64657

September 11th 2011

Pages 293-294 also have a formulation of the “law of conservation of information” that excludes the biological. Whatever one thinks of it, passages like that and the one on p. 420 would be to what Meyer would likely refer to back up his claim.  But on to more fertile matters:


Regardless, my point is that the stipulation was not clearly laid out.”
br>
No question.  There is a constant conflation of standard ID claims about evolution with Meyer’s claims with respect to abiogenesis.  On p. 293 he deliberately leaves out the biological realm, then from p. 351 to around 372 he’s using Dembski’s “design detection” which doesn’t in the slightest refer only to abiogenesis, but is normally used against evolution.  On pp. 434-438 he complains about the Dover decision, which involved evolution almost completely.  In the Conclusion, prior to the Epilogue and appendices, he states, “We now find, however, that orthodox evolutionary thinking—with its reliance upon these twin pillars of materialistic thought—has failed to explain the origin of the central feature of living things:  information.” (p. 451)
br>
I mean, he ends with an attack on evolutionary theory altogether based on his “information argument,” so there’s hardly much scope to complain that anyone responded by showing how information evolves.  There are too many things wrong with that quote for me to even begin stating them.
br>
“Since I believe that Steve is honest,”br>
br>
That is fine with me, but surely I can at least ask why he began his book by acting as if he were in this for the science, then on p. 450 revealing his early motivations to find meaning in a personal God to which he claims ID leads.  Was that an honest way of dealing with these matters, intellectually honest anyway?
br>
In later material aimed at religious audiences Meyer’s interest in holding to literal “Biblical truth” becomes apparent.  See:  http://www.youtube.com/watch?v=BmXn7bfhE2w  He is every bit as much opposed to philological scholarship involving the Bible as he is to the Dover decision.  Is that lacuna in “Signature” within accepted practices of scholarship, or somewhat less than that?  I don’t make claims here about Meyer himself, but it seems fair to question a good deal of his output.

Glen Davidson
http://tinyurl.com/mxaa3p

Jon Garvey - #64661

September 12th 2011

Darrell, it seems to me you’re concluding there are two broad hypotheses being offered on origins of life.

#1 is actually in two parts:
(a) Can information rich molecules be produced by pure chemistry?
(b) Can information rich molecules be produced under natural conditions?

#2 is also in two parts:
(a) Can information rich molecules be produced by design?
(b) Were information rich molecules originally produced by design?

What matters most is which is true. But scientifically, what matters currently is which has more supporting evidence. If it is not yet possible to offer a #1 pathway to such molecules even in theory, still less produce them in a plausible natural scenario (and surely Meyer et al would not be unreasonable in stipulating real-world conditions before #1 is proven), then it’s hard to see what the substance of the hypothesis is, beyond “Maybe something happened naturally once.”

You suggest science should be given sufficient time to come up with the necessary evidence. I think that’s questionable, because science isn’t supposed to operate on evidential credit, is it? It maintains alternative hypotheses or no hypotheses until the point where there actually is evidence. That’s no problem because science is, I was taught, happy to change at any time when new evidence comes in.

Regarding #2, (a) is already demonstrated, and (b) is an inference which, as least, seems a valid hypothesis. The problem comes (as many have pointed out) in whether it could ever be possible to demonstrate (b). That might well be its Achilles heel.

Naturalism would, of course, rule it out a priori, but that’s a sociological issue, not a matter of truth. But excluding that, is not the current position that #2 has at least evidence for its first proposition, whereas #1 does not?

So what is the scientific problem with preferring option #2 (with the understanding that #2(b) might be hard or impossible to prove), until there is sufficient evidence for #1 to replace it (with the understanding that it might be hard or impossible to move from #1(a) to #1(b))?

I would argue that philosophical and metaphysical considerations, rather than the state of evidence, is the deciding factor in practice.

If it were concluded that the inference from #2(a) to #2(b) would be invalid, because (for example) lack of knowledge of the designer necessarily precludes a design argument, then the only valid conclusion is that, currently, there is no currently valid OOL hypothesis, and science should hold its tongue and let theology, philosophy and speculation rule the day.


Darrel Falk - #64666

September 12th 2011

Hi Jon, 


In your final sentence you said:
”... science should hold its tongue and let theology, philosophy and speculation rule the day.”

As Christians, we all believe that in Him all things were created—that all things were created by Him and for Him—and that through him all things hold together.  This means that we all believe in design.   So, for the Christian, the answer to questions #2 a and b, is yes.

Many Christians (including myself) do not consider #1 inconsistent with Scripture.  The natural laws are, after all, a manifestation of God’s minute by minute activity.  (Take divine activity out of the universe and all creation ceases to exist [Colossians 1:16,17]).  Supernatural activity does not somehow make it more God’s activity.  God can work any way God chooses.  So pitting number 1 against 2 is, at least for me, a false dichotomy.  (Perhaps though, I am misunderstanding you.)

The purpose of Meyer’s book is to take the origin of life question out of the theological and philosophical realm and engage it scientifically.  He reaches a conclusion which he thinks is the best scientific explanation, and he thinks it is based upon positive evidence.  I have tried to show that once you factor in his exceptions (including the new one which I didn’t know about), all positive evidence is removed.  

With that, all we’re left with is negative evidence: Since science hasn’t yet explained how it could have occurred naturally, this means that a non-natural explanation (what he calls “intelligence”) is now the best explanation.

As a scientist, I don’t find this compelling.  Furthermore, since #1 and #2 are not mutually exclusive, there is nothing beyond our intellectual curiosity at stake—it is God’s design no matter what.



Jon Garvey - #64692

September 13th 2011

Darrell, you’re misunderstanding me to the extent that, in this context, I was trying to compare things on the level of scientific hypothesis. If #2 is true, but undetectable scientifically, then it’s a faith statement (and one that I too agree with) rather than a hypothesis.

Theologically, from a Reformed position especially, #1 need not be incompatible with #2, but to formulate it as “#1 is not inconsistent with Scripture” is also a faith statement, and also one I agree with, but that’s not a hypothesis, either. #1 becomes a scientific hypothesis only when the evidence is presented, whether or not it is theologically acceptable.

Glen Davidson restates the design hypothesis in a way that suggests it to be too vague to be useful. I would argue that the same can is true of the abiogenesis hypothesis - it is too general to be scientific, which is what I meant by saying science should therefore be silent on the matter until it has a specific hypothesis based on actual evidence, rather than on evidence that is hoped will emerge at some future date.

Of course, all of us are meanwhile at liberty to base our opinions on speculation or faith statements such as:
(a) “Sufficient material causes seem to have been generally accepted for most natural phenomena, apart from the origin of the Universe, and maybe human consciousness and morality, so one might expect some such so-far unspecified material process to account for life.”
(b) “God seems to have used secondary material causes for most natural phenomena, apart from… [continue as (a)].”
(c) “The origin of the Universe, human consciousness and morality, and miracles in the Bible have not been sufficiently explained by material causes, so one might expect some such so-far unspecified non-material process to account for life.”
(d) “As (c), but such an unspecified process might have left  its mark in, say, the sudden appearance of CSI, which can be seen today, just as the Universe, human consciousness and morality, and Biblical miracles have left varying degrees of detectable evidence.”

All of those non-scientific positions (possibly excepting (c)), might provide the opportunity of lines of research that could make for specific testable hypotheses, but until then they are variations of metaphysical explanation only.

To quote part of your sentence: “Since science
hasn’t yet explained how it could have occurred naturally, this means…” Well, as far as I can see it means no more than “We know that we don’t know.” Profound philosophically, I guess, but what we don’t know is not scientia (ie knowledge).


John - #64693

September 13th 2011

Jon:

“Darrell, you’re misunderstanding me to the extent that, in this context, I was trying to compare things on the level of scientific hypothesis.”

Jon, he’s not misunderstanding you. You misunderstand and repeatedly misrepresent science and the functions of hypotheses within science. You are doing nothing “on the level of scientific hypothesis,” you’re just throwing terms around as a pretense of understanding them.

“If #2 is true, but undetectable scientifically, then it’s a faith statement (and one that I too agree with) rather than a hypothesis.”

We detect things empirically, not “scientifically.” This is a smokescreen you’re using to cover up the absence of faith on the IDCreationist side—they lack the faith to do what science does, which is test hypotheses.

”...#1 becomes a scientific hypothesis only when the evidence is presented, whether or not it is theologically acceptable.”

This is utter baloney.

“Glen Davidson restates the design hypothesis in a way that suggests it to be too vague to be useful.”

If those who promote design hypotheses had sufficient faith to test design hypotheses empirically, how one states them would be irrelevant.

“I would argue that the same can is true of the abiogenesis hypothesis - it is too general to be scientific,...”

More baloney. Abiogenesis hypotheses make empirical predictions and real scientists test them empirically.

Pseudoscientists pretend that real scientists don’t do this.

”... which is what I meant by saying science should therefore be silent on the matter until it has a specific hypothesis based on actual evidence, rather than on evidence that is hoped will emerge at some future date.”

One needs zero evidence to advance and test a hypothesis. “Science” as a discipline doesn’t need to have “a specific hypothesis.” The history of science is full of competing hypotheses that gain or lose favor because of new evidence. Those who care the most about a particular hypothesis are usually those who produce this new evidence. Not so with the IDCreationists, who lack faith.

In fact, real scientists can sometimes test two specific (or vague) hypotheses with a single experiment! You can’t admit this simple fact or your house of cards comes tumbling down.

beaglelady - #64667

September 12th 2011

“With that, all we’re left with is negative
evidence: Since science hasn’t yet explained how it could have occurred
naturally, this means that a non-natural explanation (what he calls
“intelligence”) is now the best explanation.


In other words, a god-of-the-gaps argument, where God is a placeholder for human ignorance.


Glen Davidson - #64669

September 12th 2011

”#2 is also in two parts:
”(a) Can information rich molecules be produced by design?
”(b) Were information rich molecules originally produced by design?”

br>
That’s where Meyer uses terms equivocally, and in two ways, no less.  
br>
First, the actual question is can life be produced de novo by design.  The answer right now is, no.  But what will it mean to life’s beginning even if we get to the stage that we can make life de novo by design?  The question doesn’t change because humans evolved and developed culture, science, and technology.  10 million years ago, the fact that “information rich molecules” had not been produced “by design” doesn’t conceptually mean that the science answer then would be different from the science answer now when they have been produced “by design.”  
br>
Meyer’s reliance on Lyell’s notions of uniformitarianism is convenient for Meyer’s ID apologetics, not current nor good science practice.
br>
Second, the idea that design is design is design, and intelligence is intelligence is intelligence isn’t close to what science thinks.  Philosophically, many theists would strongly object that God’s design and intelligence wouldn’t be something to which human design and intelligence would compare.  Above all, what human endeavor compares in the least to a 4 billion year evolutionary project to, what?, produce humanity?
br>
What actual aspects of design have ever been found in life, anyway?  Something not based on negativity, but actual findings of rationality and forethought, which are what investigators actually look for when trying to detect human action (not demons, etc.)?
br>
ID blithely compares extremely different processes and results, using the excuse that there are some aspects that can be classed with human achievements.  Doing so certainly is not science.
br>
The mountains of Antarctica are an enigma to geology at the present time.  Since we don’t know how they got there, despite their looking “natural,” and intelligence can design rock shapes, should we suppose that God sculpted them?  But we know nothing scientifically about God’s capabilities or predilections, so how could we meaningfully connect the effect—Antarctica’s mountains—with God as a proximal cause?  And could we scientifically do anything with the conclusion that God designed Antarctica’s mountains, or with ID?  No one has made the case for either, in spite of Meyer purporting to do so with respect to ID in his book.
br>
Glen Davidson
http://tinyurl.com/mxaa3p

 


Glen Davidson - #64670

September 12th 2011

The above was supposed to go after Jon Garvey’s post, and I have no idea why it didn’t end up there.  I had clicked “Reply to this comment.”  Apparently a cut and paste causes a hard return to show with html tags, too.


Anyhow, continuing the post above:

No, science never just says, “intelligence can do it,” so it happened.  That’s meaningless.  Glen Davidson could kill Caylee Anthony, so he did it?  Even if all other “suspects” could be eliminated (not that the main one was)?  It doesn’t word that way, classical science matches up known causes to known effects, which is why it sticks with abiogenesis as an investigative program.  
br>
Science looks for identifiable causes, which is why it continues to try to identify one.  Meyer never has identified a cause.
br>
Glen Davidson
http://tinyurl.com/mxaa3p

RBH - #64677

September 12th 2011

Glen Davidson wrote “Science looks for identifiable causes, which is why it continues to try to identify one.  Meyer never has identified a cause.”

br>
Which is why in the absence of any hypotheses about how the putative designer(s) of life on earth actually did it, in the absence of hypotheses about the manufacturing process by which the putative designer(s) pushed atoms and molecules around to produce the purported molecular CSI, ID offers no explanation at all.  ID remains a claim that can be summarized in a single sentence:  “Sometime or other, something(s) or other designed some molecules (or body plans, or species, or “kinds”), and then somehow instantiated—manufactured—those designs in matter and energy, all the while leaving no independent evidence of the design process, no independent evidence of the manufacturing process, and no independent evidence of the presence, or even the existence, of the designing and manufacturing entity(ies).”



Bilbo - #64679

September 12th 2011

Hi Darrel,

I haven’t tried to find and read Meyer’s response—is it online?  But I have a few responses for you and Dennis:

1)  I agree that Dennis did present a stiff challenge to Douglas Axe’s view that proteins cannot evolve and gain new functions (and I even put that in a comment on his post).  So yes, it seems to me that Darwinian evolution can add new CSI.

2)  But can it add a “large amount” of new CSI?  Dennis’s example was the duplication of genomes.  But I asked him if this is really new CSI?  I don’t remember getting a response.  Perhaps you could explain why it would be new CSI.

2)  But can it add a “large amount” of new CSI?  Dennis’s example was
the duplication of genomes.  But I asked him if this is really new CSI? 
I don’t remember getting a response.  Perhaps you could explain why it
would be new CSI.

3)  See my point?

4)  Those were very nice theological sentiments you expressed at the end, but I’m not sure you really believe them.  If I recall, you agree with Ard Louis that it would be theologically unacceptable to believe that God used supernatural activity to create life or guide its evolution.  If my memory is correct, then you have theological objections to Meyer’s position, and your call for unity is problematic. 

5)  I myself see no sound theological objections to ID or to Darwinian evolution, so I can honestly call for unity.  I suggest that you revisit your theological arguments against ID, so we can thoroughly thrash them out.  Once we dispose of them, then you can also honestly call for unity.


Open Circle - #64683

September 12th 2011

Bilbo,

To respond to whether evolution can add a “large amount” of “new” CSI, consider two mechanisms: 1) nucleotide insertions and 2) duplication followed by mutation. If nucleotide insertions are not large enough for you, then simply by mutating your genome duplications can you easily get a lot of new CSI. I have to say that from the point of view of genomics, the notion that new CSI cannot be generated by evolutionary processes (as opposed to being generated by abiogenesis, which I will not comment on here) honestly seems to be a very odd idea.

Cheers,
-Open Circle


Darrel Falk - #64687

September 12th 2011

Bilbo,


With regard to #2 and #3, see Open Circle’s response.    

#4?  You are not remembering Dr. Louis’s views correctly.  

#5?  Scripture calls for unity, not uniformity.  

Warm Regards, Bilbo.

Darrel

Bilbo - #64696

September 13th 2011

Hi Open and Darrel,

I think one could argue that insertions aren’t really creating new CSI, just passing it on.  As for randomly mutating duplicated genes or genomes, yes, that certainly seems possible, and I’m sure it has resulted in some increase in CSI.  But are we sure that the bulk of new CSI is the result of random mutations, as opposed to non-random (such as purposely caused) mutations? 

As for understanding Ard Louis’s views, I’m pretty sure I did understand him.  Correct me if I’m wrong, but I thought he said that it would be inappropriate to attribute historical events to God’s supernatural activity, unless God (through the Bible) specifically said that was how He did it.  Thus events such as the resurrection of  our Lord are confirmed by Scripture to be supernatural acts, but events such as the origin and evolution of life are not confirmed by Scripture to be supernatural acts.  Therefore we should not attribute the origin and evolution of life to supernatural acts.  

If I understood Ard’s views correctly, then I would say that he has offered a theological objection to ID.  I think it is a very poor objection.  There is no Scriptural teaching that says we must not attribute specific events to supernatural activity unless Scripture itself says so.  That seems to mean that we are free to use our own rational minds to try to determine for ourselves how God has brought about events in the past.  Since our knowledge is always imperfect, whatever conclusions we come up with should be considered tentative, whether they favor supernatural or natural activity.  So I reject Ard’s argument and see no theological reason to reject ID. 

Darrel, since you accept Ard’s argument, you really do see a theological objection to ID.  So you calls for unity ring rather hollow.


Open Circle - #64698

September 13th 2011

Hi Bilbo,

To address the CSI portion of your post:

1) What do you mean by insertions aren’t really “creating” new CSI, just “passing it on”? That sentence actually does not make sense to me. You have your original sequence (e.g., ATTAGACC), new bases are inserted into it (resulting in say, ATCTATGACC) - if that is not “creating” new CSI, I really don’t know what is. Would you please clarify what you mean?

2) Who do you propose as the agent of these “purposely caused” mutations? Extraterrestrial aliens? That was intended as a tongue-in-cheek response (please do not take offense), but the point still stands - mutations are generated by natural processes (e.g., mutagenic compounds such as EMS, ionizing radiation, endogenous oxidation, intrinsic instability of DNA, errors by DNA polymerase during replication, etc). If you want to propose God, theistic evolution is already fully compatible with God as the ultimate agent. After all, natural law is simply the regular action of the Creator.

Cheers,
-Open Circle


Darrel Falk - #64699

September 13th 2011

Bilbo,


You are not correctly summarizing Dr. Louis’s views.  One of his two major series on our site begins here http://biologos.org/blog/addressing-christian-concerns-on-the-implications-of-biologos-science-1


Darrel

Kirk Durston - #64721

September 14th 2011

I have read neither Stephen Meyer’s nor Dennis Venema’s work. However, from reading here, if Meyer’s CSI corresponds to what the mainstream literature defines as functional information and if Venema is, indeed, under the impression that duplication and/or mutation actually increases functional information, then I think Venema is mistaken.

 

From comments made here, it does appear that Meyer’s CSI corresponds to the concept of functional information found in mainstream literature. For further clarification of functional information, see the following:

 

Szostak, J.W. 2003, Functional information: Molecular messages, Nature, 423, (6941) 689.

Hazen, R.M.;
Griffin, P.L.; Carothers, J.M.; Szostak, J.W. 2007, Functional information and
the emergence of biocomplexity, Proc Natl
Acad Sci U S A
, 104 Suppl 1, 8574-81.

Durston, K.K.; Chiu, D.K.; Abel, D.L.; Trevors, J.T. 2007, Measuring the functional sequence complexity of proteins, Theor Biol Med Model, 4, 47.

 

Szostak’s article is the shortest and simplest and will do for my purpose here. The amount of functional information required to code for, say, a protein family is simply the ratio of the set of all unique sequences that will do the job over the set of all possible sequences. Note the word ‘unique’; duplication of an already extant functional sequence increases the functional information by exactly zero. I suspect that Venema is considering a more classical approach to information, say, Shannon information or Kolmogorov information. However, Szostak, Hazen et al. have already shown that the classical notion of information is inadequate for the kind of information we see encoded in the genomes of life.

 

Second,  from the equations for functional information or functional complexity published in those papers, mutations are irrelevant to any change in functional information unless there is either a loss of function or a gain of a novel function (with loss of function being more probable). The change in functional information can be measured and a mathematical method is provided in the paper by Durston et al. (we use the term functional complexity, but state that it is equivalent to functional information). A gain in functional information only occurs if a novel function is discovered. If a novel function can be achieved by only 2 or 3 mutations, then by using the Durston et al. equations, the gain in functional information can be seen to be trivial and not statistically significant in a random process.  The question is whether small, statistically insignificant increases in functional information by mutation can occur for functions that require, for example, a completely novel protein family. If the objective is to discover a novel protein family, then a large number of mutations are required (including deletions and insertions) and one can again see from the method offered by Durston et al. and the ratios seen in both Szostack’s paper and the paper by Hazen et al. that discovering a novel protein family rapidly becomes statistically impossible via mutations.

 

 


Bilbo - #64722

September 14th 2011

Open:  “1) What do you mean by insertions aren’t really “creating” new CSI, just
“passing it on”? That sentence actually does not make sense to me. You
have your original sequence (e.g., ATTAGACC), new bases are inserted
into it (resulting in say, ATCTATGACC) - if that is not
“creating” new CSI, I really don’t know what is. Would you please
clarify what you mean?”

I guess it depends upon what is being inserted and where.  To use English language examples, we might have the sentence, “He created life.”  Then we might have another sentence, “And he removed his rook.”  One insertion might be the letters “re” from the second sentence, which are inserted in the first sentence, “He recreated life.”  I would take that as the creation of new information, since we have changed the meaning of the first sentence.  But notice that in order to obtain this new meaning, “re” must be inserted in the correct location.  How likely is that to happen randomly?  Something to consider when determining whether the insertion happened on purpose or not.

But now, what if we inserted the entire second sentence and obtained the new sentence, “He created life and he removed his rook.”  It is no longer clear that we have created new information, since the meanings of both sentences remains the same.  This is what I meant by “just passing it on”.

“2) Who do you propose as the agent of
these “purposely caused” mutations? Extraterrestrial aliens? That was
intended as a tongue-in-cheek response (please do not take offense), but
the point still stands - mutations are generated by natural processes
(e.g., mutagenic compounds such as EMS, ionizing radiation, endogenous
oxidation, intrinsic instability of DNA, errors by DNA polymerase during
replication, etc). If you want to propose God, theistic evolution is
already fully compatible with God as the ultimate agent. After all,
natural law is simply the regular action of the Creator.”

When you say that “mutations are generated by natural processes,” that has two possible meanings:
(1)  At least some mutations are generated by natural processes.
(2)  All mutations are generated by natural processes.

If you meant (1), then I agree with you.  If you meant (2), then either you are making a metaphysical assumption, which I challenge, or you have surveyed each and every mutation that has ever happened, which I find difficult to believe.

By the way, the atheist physicist Fred Hoyle seemed to believe that ETs created the original cells that panspermed (I think I just coined a new verb) to Earth.  I prefer to believe that God did it, and probably not by means of natural laws.


Open Circle - #64727

September 14th 2011

Hi Bilbo,

1) Okay, so this unlikeliness argument keeps getting brought up but I think the frequency at which mutations occur is being significantly underestimated. The error rate of DNA polymerase III, if I recall correctly, is around 10^-9 - which means that the expected number of mutations upon a single cell division is 3 (in a human-sized genome). And that’s just from a single source. Of course, we can only count germline cells, but the point here is that mutations are much more common than many people seem to think. A 2010 Science paper (DOI: 10.1126/science.1186802) showed that about 60 new mutations (30 from each parent) get passed per human generation. And that’s keeping in mind that we possess robust DNA repair and correction mechanisms that did not always exist.

Your example isn’t what I mean when I talk about insertions. “Insertion” does not refer to segments being taken from elsewhere in the genome and getting inserted in a different location (even though that certainly happens with transposable elements). We have pools of free nucleotides (existing in the precursor form of nucleotide triphosphates) in our cells that the replication machinery draws upon during replication. These nucleotide triphosphates (abbreviated as NTPs) don’t just serve as the building blocks for genetic material - they are also the primary molecules that the cell uses to power the majority of its biochemical processes. So, it is quite possible to generate novel information because these free nucleotides become incorporated in the genome and get passed on.

(As a side note, the genome is quite unlike English, computer code, or any human invented language for that matter because it does not have direct semantic meaning. Using human language analogies can be a flaky practice - it does not significantly impact your argument here, but it can introduce hidden incorrect assumptions in other such arguments, so be careful.)

2) Occam’s Razor. There is absolutely no evidence that these mutations occurred by non-natural processes (unless you want to posit millions of miracles that just happen to fit the natural explanation), so it is the second explanation is in fact the better explanation. Also, do realize that methodological naturalism is the operating principle of science - not a priori, but because of Occam’s Razor.

Francis Crick (of Watson and Crick fame) also believed in panspermia at one point of his career. My point is, a lot of famous, successful scientists all have their quirky beliefs in all sorts of things, but honestly no one really cares, especially if those beliefs do not pertain directly to their field of expertise.

Cheers,
-Open Circle


Bilbo - #64723

September 14th 2011

Hi Darrel,

Yes, I believe that you had two series by Ard.  I was referring to the second.  But I’ll go back and read them both, even though I offered critiques in comments at the time they both came out.  But once I read them, how do we continue this conversation?


Bilbo - #64724

September 14th 2011

OK, I read part I of Ard’s essay.  How do I get to the rest of it?


Bilbo - #64759

September 15th 2011

Open:  “A 2010 Science paper (DOI: 10.1126/science.1186802) showed that about
60 new mutations (30 from each parent) get passed per human generation.”

Okay.  How many of them result in new functions or new proteins?

 “And that’s keeping in mind that we possess robust DNA repair and
correction mechanisms that did not always exist.”

Do we know this, or do we assume it to be true? 

“So, it is quite possible to generate novel information
because these free nucleotides become incorporated in the genome and get
passed on.”

So by insertions you mean the addition of extra nucleotides?  I’m sure it is possible to generate new information, but how likely is it to do so?

“As a side note, the genome is quite unlike English,
computer code, or any human invented language for that matter because it
does not have direct semantic meaning.”

How about we equate meaning with functionality?

“2) Occam’s Razor. There is absolutely
no evidence that these mutations occurred by non-natural processes
(unless you want to posit millions of miracles that just happen to fit
the natural explanation), so it is the second explanation is in fact the
better explanation. Also, do realize that methodological naturalism is
the operating principle of science - not a priori, but because of
Occam’s Razor.”

If the probability of producing a large amount of information by random mutations is small enough as to be unrealistic by natural means, then I would count that as evidence for a non-natural process.  If methodological naturalism does not present us with a realistic explanation, then I would take that as grounds for rejecting it.

“Francis Crick (of Watson and Crick fame) also
believed in panspermia at one point of his career. My point is, a lot of
famous, successful scientists all have their quirky beliefs in all
sorts of things, but honestly no one really cares, especially if those
beliefs do not pertain directly to their field of expertise.”

I was just letting you know that I was not insulted by your suggestion of extra-terrestrials.  I certainly don’t object to being given the same status as Hoyle.


Open Circle - #64763

September 16th 2011

Hi Bilbo,

Since your primary argument seems to center on the notion that it is unlikely to for new functions to evolve, perhaps I could point you to the Long Term Evolution Experiment that saw an E. coli strain evolve the ability to utilize citrate as an energy source. BioLogos has an article by Dennis Venema on it. (http://biologos.org/blog/evolution-and-the-origin-of-biological-information-part-2-e-coli-vs-id)

Compared to bacteria, organisms such as humans have much longer generation times and much lower population sizes, but that 2010 study clearly showed that mutations are passed to successive generations even in complex, multicellular, eukaryotic organisms. I think you can put two and two together and very reasonably conclude that in fact, evolution is quite capable of generating novel functions over the long time periods of evolution.

To address your other points:

1) Yes, by insertions I mean the addition of extra nucleotides from the cell’s pool of nucleotide triphosphates.

2) The basic DNA repair mechanisms are fairly well-conserved, but distinct differences exist in their implementation and incorporation as part of large-scale, systematic responses. Contrast the SOS response in prokaryotes to the cell cycle checkpoint system in eukaryotes. In particular, consider the ATM kinase, which activates the DNA damage checkpoint in response to DNA double strand breaks (which are also repaired in prokaryotes) and disruptions in chromatin structure (which only eukaryotes possess - prokaryotes do not package their genomes in chromatin).

Cheers,
-Open Circle


beaglelady - #64769

September 16th 2011

We know that intelligence can produce functional information. Computer code is an example.

A computer programmer can go back to the drawing board and start from scratch. For example Microsoft’s asp.net was a total rewrite; no classic ASP was recycled.  After a point, a rewrite is often the most efficient way to proceed if one really understands what is needed.  Sure, programmers hack up existing code up to a point, but only for so many years.  They  might comment out some code thinking they might need it in the future, but eventually clean it up if they are any good.  


Glen Davidson - #64770

September 16th 2011

Even the revision of existing code is treated far differently by intelligent designers than what we see in biological evolution.  A section of code from an entirely different program can be inserted (or used as a module or some such thing), while we don’t see that in, say, vertebrates, which don’t normally undergo horizontal transfers.


That’s why all vertebrates have wings that are merely modifications of their ancestors forelimbs, rather than bats reusing pterosaur or bird wings.

The analogies always break down, because evolution simply evinces no evidence of intelligence working, instead it is limited as we’d expect from known evolutionary mechanisms.

Just thought I’d add to your disanalogy to emphasize the importance of evolution as an explanation for facts that ID generally ignores—for good reason.

Glen Davidson
http://tinyurl.com/mxaa3p

beaglelady - #64776

September 16th 2011

True. jQuery is a javascript library that is VERY popular right now and is used in many, many web-based applications. But no developer in his right mind will be messing with it years and years from now. 


Bilbo - #64773

September 16th 2011

Hi Open,

I thought you might like to read Behe’s view on Lenski’s work:

http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/


span>The major point Lenski
emphasizes in the paper is the historical contingency of the new
ability. It took trillions of cells and 30,000 generations to develop
it, and only one of a dozen lines of cells did so. What’s more, Lenski
carefully went back to cells from the same line he had frozen away after
evolving for fewer generations and showed that, for the most part, only
cells that had evolved at least 20,000 generations could give rise to
the citrate-using mutation. From this he deduced that a previous, lucky
mutation had arisen in the one line, a mutation which was needed before a
second mutation could give rise to the new ability. The other lines of
cells hadn’t acquired the first, necessary, lucky, “potentiating” (1)
mutation, so they couldn’t go on to develop the second mutation that
allows citrate use. Lenski argues this supports the view of the late
Steven Jay Gould that evolution is quirky and full of contingency.
Chance mutations can push the path of evolution one way or another, and
if the “tape of life” on earth were re-wound, it’s very likely evolution
would take a completely different path than it has.

span>I think the results fit a lot
more easily into the viewpoint of The Edge of Evolution.
One of the major points of the book was that if only one mutation is
needed to confer some ability, then Darwinian evolution has little
problem finding it. But if more than one is needed, the probability of
getting all the right ones grows exponentially worse. “If two mutations
have to occur before there is a net beneficial effect — if an
intermediate state is harmful, or less fit than the starting state —
then there is already a big evolutionary problem.” (4) And what if more
than two are needed? The task quickly gets out of reach of random
mutation.

span>To get a feel for the clumsy
ineffectiveness of random mutation and selection, consider that the
workers in Lenski’s lab had routinely been growing E.
coli all these years in a soup that contained a small
amount of the sugar glucose (which they digest easily), plus about ten
times as much citrate. Like so many cellular versions of Tantalus, for
tens of thousands of generations trillions of cells were bathed in a
solution with an abundance of food — citrate — that was just beyond
their reach, outside the cell. Instead of using the unreachable food,
however, the cells were condemned to starve after metabolizing the tiny
bit of glucose in the medium — until an improbable series of mutations
apparently occurred. As Lenski and co-workers observe: (1)

span>Such a low rate suggests that
the final mutation to Cit+ is not a point mutation but instead involves
some rarer class of mutation or perhaps multiple mutations. The
possibility of multiple mutations is especially relevant, given our
evidence that the emergence of Cit+ colonies on MC plates involved
events both during the growth of cultures before plating and during
prolonged incubation on the plates.

span>In The Edge of
Evolution I had argued that the extreme rarity of the
development of chloroquine resistance in malaria was likely the result
of the need for several mutations to occur before the trait appeared.
Even though the evolutionary literature contains discussions of multiple
mutations (5), Darwinian reviewers drew back in horror, acted as if I
had blasphemed, and argued desperately that a series of single
beneficial mutations certainly could do the trick. Now here we have
Richard Lenski affirming that the evolution of some pretty simple
cellular features likely requires multiple mutations.

span>If the development of many of
the features of the cell required multiple mutations during the course
of evolution, then the cell is beyond Darwinian explanation. I show in
The Edge of Evolution that it is very
reasonable to conclude they did.

 


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