The Origin of Biological Information, Part 3: CSI on Steroids

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April 7, 2011 Tags: Design

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

The Origin of Biological Information, Part 3: CSI on Steroids
If your heart is right, then every creature is a mirror of life to you and a book of holy learning, for there is no creature - no matter how tiny or how lowly - that does not reveal God’s goodness.

Thomas a Kempis - Of the Imitation of Christ (c.1420)

In part 2 of this series, we explored how the Long Term Evolution Experiment (LTEE) performed by the Lenski research group on E. Coli, demonstrates some key features of how biological “complex, specified information” (i.e. “CSI” as the ID movement terms it) arises through mutation and natural selection. To briefly recap, we noted that:

  1. CSI does not need to arise all at once, but can arise piecemeal through independent mutation events.

  2. Separate mutations that later combine to form CSI do not need to confer a specific advantage on their own. In other words, mutations that are “neutral” with respect to the survival of the organism can later be co-opted into CSI that does have a distinct survival advantage.

  3. Neutral mutations may open up new future paths. In the LTEE, the brand-new ability of one bacterial population to use citrate as a food source required that a neutral mutation appear several thousand generations before it combined with other mutations to provide the CSI for using citrate.

  4. When CSI arises, it can be pretty poor at the beginning. Nascent CSI, though poor, provides a survival advantage because it is the “best game in town” at that time. Further mutation in, and natural selection on, the offspring of the original CSI-holder quickly refine the nascent information into ever-more “specified” CSI.

And, as we noted at the close of the first post in this series, understanding how natural processes create information is in no way a threat to God’s ordaining and sustaining of creation. Rather, it is an opportunity to explore some of the mechanisms by which He does so.

With these important principles in mind, we are ready to examine a second fascinating case of a novel function arising through mutation and selection: the evolutionary history of steroid hormones and their protein receptors in vertebrates.

Experimental Evolution as Textual Criticism

The elegant work by the Lenski group has one very distinct advantage that other researchers surely envy: when new structures and functions arise in the experiment, a trip to the freezer is all that is needed to resurrect and examine the relevant ancestors. For researchers who study other organisms less amenable to laboratory experimentation, or for evolutionary transitions that happened deep in the past, other methods are needed. One approach to this type of problem is to “resurrect” ancient proteins in the lab in order to study their properties.

Bringing an ancient gene back to life starts with determining what its DNA sequence was, (and thereby determining the sequence of amino acids that made its functional protein product). While researchers don’t have direct access to ancient DNA, we have the next best thing: many modern examples of genes copied from the ancestral one.

For those who are familiar with textual criticism, the principles are very similar. Textual criticism is the process of recovering the words of an ancient manuscript by comparing several very similar, but still imperfect, copies. In general, as more copies agree on a certain wording, the more likely it is that the original had that wording. Also, the more widespread and older a certain wording is, the more likely it is original. Groups of manuscripts that have similar copying errors or other variations can be grouped together as more closely related, and so on. Given enough manuscripts, it is possible to recreate a copy of an ancient text with a very high degree of accuracy. As Christians, we benefit from this type of analysis daily when we read the Bible: though no two Greek manuscripts of the New Testament are exactly alike, scholars have used these methods to recover the original text with a very high degree of confidence.

And so too, for ancient gene sequences. Consider a hypothetical amino acid sequence in six modern organisms:

Though none of the modern sequences are identical, it is easy to see that there is a “consensus” at each of the 12 amino acid positions. This consensus sequence is very likely to be the ancestral sequence: explaining the pattern in any other way requires many more changes, with many changes occurring in parallel after species separate.

Once the researchers determine the correct ancestral amino acid sequence, it’s a relatively small matter to engineer a DNA sequence that encodes it and give it to cells to make into protein. This protein can then be tested to see how it functions compared to the modern sequence.

What makes this type of analysis even more interesting is that sometimes related genes acquire new functions. In cases like these, bringing the ancestral gene back to life in the lab allows researchers to not only test its properties, but to test hypotheses about what the specific amino acid changes were that changed the protein’s function over time:

The laboratory of Joseph Thornton at the University of Oregon has used this method (with great success) to determine how certain hormone / protein receptor complexes arose during vertebrate evolution. Hormones are small molecules that act as signals by binding to a protein target, called a receptor. The receptor / hormone pair then goes on to effect a change in the target cell by regulating other genes.

In vertebrates, two hormone – receptor pairs were of interest to the Thornton group: the mineralocorticoid receptor (MR), which binds a steroid hormone called aldosterone, and the glucocorticoid receptor (GR), which binds a second steroid hormone called cortisol (see diagram above). Cortisol can also activate MRs, but an enzyme that breaks down cortisol is present in tissues where MR is used so cortisol cannot accumulate. Aldosterone, on the other hand, cannot activate GR – it is specific to its binding partner MR. Even though these two hormone / receptor pairs regulate different processes in modern organisms, the two receptors are the result of an ancient gene duplication that occurred early in vertebrate evolution, around 450 MYA (million years ago). As time has gone by, the derivatives of the original gene have picked up distinct binding partners and physiological roles. Thornton and colleagues wanted to tease out the details of these important changes.

They started out by determining the ancestral sequence of the original receptor gene, prior to the duplication, and recreating it in the lab. When they tested this lab-designed protein, they found that it, like modern MRs, (but not GR’s)could bind either cortisol or aldosterone indicating that the ancestral protein must have been able to bind both. This result suggested that somewhere along the line the GR lost its ability to bind aldosterone and became specific to cortisol. This is interesting, because at the time the ancestral receptor was present, aldosterone didn’t exist. Aldosterone is a relative newcomer on the scene: it is present only in four-limbed vertebrates (tetrapods), which arose around 390 MYA. So, the ancestral receptor present prior to 450 MYA already had the ability to bind a hormone that wouldn’t evolve for tens of millions of years. Of course, the ancestral receptor “didn’t mind” – it had its own binding partner - a steroid hormone closely related to cortisol and aldosterone. It wasn’t sitting around doing nothing in the meantime.

This finding strongly suggested that the reason aldosterone binds only to MRs is because modern GRs, in contrast to the ancestral protein, have lost the ability to bind it. By comparing the amino acid differences between MRs and GRs, the Thornton group was able to test different combinations to see what the key changes likely were. They also did the (difficult) work of determining the precise new shape of the receptor for each of the changes that had an effect. All in all, it is an impressive body of scientific work.

Through these techniques, the Thornton group demonstrated that the loss of aldosterone sensitivity in GR occurred in a series of mutational steps that progressively remodeled the portion of the GR that binds the hormone molecule:

  1. First, a mutation occurred that altered one of the amino acids near the hormone binding site. This change had no effect on its own (it was a neutral mutation).

  2. Second, a change in an amino acid outside the binding pocket bent one side of the binding site into a new shape. Now the amino acid from the first neutral mutation in step #1 was thrust up against the hormone binding site. This amino acid can interact appropriately with cortisol, but not very well with aldosterone. The receptor was now strongly biased towards cortisol.

  3. Later, several more mutations accrue that “tune” the receptor to its new specificity. Some of the mutations are neutral at first (like step #1) and then combine with later mutations to refine the receptor into its modern cortisol-specific role.

As the GR and MR lineages were becoming functionally distinct, other changes in other genes accumulated that refined their ability to regulate different processes (such as the enzyme that breaks down cortisol where MR is present, or the target genes that the two hormones regulate). While many of those details remain to be worked out, this work is an elegant demonstration of how a new function arose: gene duplication; sequence divergence with a neutral mutation that opened up a new possible trajectory; a second mutation that altered function in one of the gene copies; further mutations that refined this nascent difference; and the final result of new structures and functions that act as key regulators of important physiological processes in tetrapods, including humans.

In other words, new CSI.

Over and against these lines of evidence, however, the Intelligent Design Movement claims that such novelty is inaccessible to random mutation and natural selection. Rather, they claim that functional protein shapes are incredibly rare and therefore so isolated from each other that random mutation and natural selection cannot bridge the vast gulfs between them. Though Thornton’s work (and the work of Lenski that we examined previously) refutes this claim with detailed, concrete examples, new comparative genomics tools have addressed this issue with greater power and breadth than ever before. In the next post in this series, we’ll explore the question: are these examples rare, isolated cases, or indicative of a wider pattern?

Further reading:

Harms, M.J. and Thornton, J.W. (2010). Analyzing protein structure and function using ancestral gene reconstruction. Current Opinion in Structural Biology 20: 360-366.

Bridgham, J.T., Carrol, S.M., and Thornton, J.W. (2006). Evolution of hormone-receptor complexity by molecular exploitation. Science 312: 97-100.

Thornton, J.W. (2004). Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Reviews Genetics 5: 366-375.


Dennis Venema is Fellow of Biology for The BioLogos Foundation and associate professor of biology at Trinity Western University in Langley, British Columbia. His research is focused on the genetics of pattern formation and signalling.

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Rich - #57643

April 10th 2011

Mike Gene (57504):

You wrote:

“A truly clever designer doesn’t need to cheat to bring about a result.  A truly clever designer would know that stochastic events will reliably happen so they can then be exploited by setting them in a context that will  nudge things along particular trajectories.  From this design perspective, stochastic events are fuel, not obstacles.”

I agree with this as far as it goes, but I wonder if it goes far enough.  Stochastic events can yield predictable outcomes (as in your example of the casino), and we can imagine that this would give some broad general tendencies to evolution, e.g., that eventually arthropods *of some sort* would be produced, or that vertebrates *of some sort* would be produced, but this does not mean that the existence of nine-banded armadillos or venus flytraps or platypuses was guaranteed from the outset.  Are you willing to go so far as to say that man was the predictable outcome of the original biological setup?

In asking this question, I stress that I want a scientific answer, not a theological answer.  I already understand your belief that man (and in fact every individual human being) was guaranteed “because God loved us” or something of that sort.  I want to know what there is about the mechanics of the evolutionary process, as you conceive it, that guaranteed—not merely made possible, not even made 75% likely, or 90% likely, but *guaranteed* that evolution would eventually (not on a particular target date, but eventually) arrive at man, or something very much like man.  Is there any *biological* basis for thinking this?


Mike Gene - #57674

April 10th 2011

Hi Rich,

You write, “I agree with this as far as it goes, but I wonder if it goes far enough.”

Does it need to go further?  My hypothesis of front-loading was never intended to do any metaphysical heavy-lifting.  I simply explore how one might go about designing evolution.  

I want to know what there is about the mechanics of the evolutionary process, as you conceive it, that guaranteed—not merely made possible, not even made 75% likely, or 90% likely, but *guaranteed* that evolution would eventually (not on a particular target date, but eventually) arrive at man, or something very much like man.  Is there any *biological* basis for thinking this?

No.  Front-loading is not determinism or predestination.  Just as there is no *biological* basis for thinking your existence or my existence was *guaranteed*. As you note, my own theological understanding makes such a concern superfluous.  It thus frees me to look at the data without feeling the need to force it into a particular, preconceived teleological or non-teleological template.


Argon - #57745

April 12th 2011

“Front-loading” is a bit of a loaded term… ;^)

For example Mike Gene’s conception of this is slightly different from Michael Denton’s. Denton proposes that the physics of the universe itself is front-loaded not only to produce life but also to produce organisms very much like humans. So, his is a highly-constrained front-loading. Behe descrfibes front-loading as well but perhaps mostly in the sense that it still takes ‘special sauce’ from a designer to bridge most systems. Thus Behe may look at a large family of G-protein coupled receptors and suggest that evolution of their involvement in multiple signalling pathways would require special interventions of some form, but perhaps less so (???) such that relatively small-scale changes (???) would be required.

Jon Garvey - #57747

April 12th 2011

From my (limited) reading of Behe, as opposed to his detractors, I suspect that if it were shown that the genetic code were loaded so that it could produce simultaneous mutations resulting in de novo complex structures, he’d say, “I told you so.” The question would then be, who gave the genetic code its capacity for intelligent planning.

His argument, as I understand it, is that purely stochastic individual gene mutations won’t wiggle the flagellum, not that God nust do it by miraculous intervention.


John - #57751

April 12th 2011

Jon,


The term “genetic code” refers to the correspondence between codons in mRNA and the amino-acid residues in proteins, not the genome or its sequence.

You’re missing a testable hypothesis here—that evolution beyond Behe’s “edge” involves new complex structures. You’re just assuming that it is correct because you desperately wish that Behe is correct.

Rich stumbled upon this hypothesis and ran away. Do you have so little faith in Behe as well?

Jon Garvey - #57753

April 12th 2011

I have no faith in Behe at all - you’re just assuming I do because you desperately want to label me as an ID enthusiast.

Or quite possibly you don’t, but if you’re going to keep telling people what they think you deserve to have your own views misrepresented.


Argon - #57757

April 12th 2011

From my (limited) reading of Behe, as opposed to his detractors, I suspect that if it were shown that the genetic code were loaded so that it could produce simultaneous mutations resulting in de novo complex structures, he’d say, “I told you so.” “

Hi John, 
I don’t see that. After all, this is Behe who claimed that the evolution of IC systems, like the blood clotting cascade, have the odds stacked against them (Ergo “design!”). No, what Behe has said & written is that if it turns out natural mechanisms are found sufficient to account for the evolution of such systems & life in general it wouldn’t shake his faith in God (and why would it?). However, it would knock his hypothesis into the garbage bin and so I’d argue that he would probably be surprised.

His argument, as I understand it, is that purely stochastic individual gene mutations won’t wiggle the flagellum, not that God nust do it by miraculous intervention.”

The first part sounds correct. The second half is borderline. Behe argues: “Ergo, design!”. Personally, he thinks the designer is God and so I think a good case could be made that he thinks some ‘super’-natural (ultra-natural?) intervention was involved.


Jon Garvey - #57765

April 12th 2011

“No, what Behe has said & written is that if it turns out natural mechanisms are found sufficient to account for the evolution of such systems & life in general it wouldn’t shake his faith in God (and why would it?). However, it would knock his hypothesis into the garbage bin and so I’d argue that he would probably be surprised.”

Would it knock his hypothesis of intelligent design out? Someone would have to explain how the genetic code got thus loaded first.


Gregory - #57784

April 12th 2011

Related to the behaviour of ‘telling people what they think,’ which has obviously happened to me by the same person too, I’ve been picking up on a theme via that same person’s messages here in recent weeks. Rich included him as one of the reasons he gave for leaving BioLogos (suggesting the person plays dirty & ‘throw elbows’). It may account for the impunity that this certain person thinks he has *just because he is a biologist*

There is an exclusivity of value given toward biology at BioLogos. For some people this should be obvious & welcome. For others, it is deserved, ‘natural’ and ‘proper.’ A third perspective, it is a dangerous privileging of one academic field at the cost of several others that at times & in their own respective ways in ‘this conversation’, are much more important than biology.

If that person is outside his comfort zone with questions that go beyond biology, he simply says: “Go study more biology,” & assumes this will ‘win’ an argument. The idea of a ‘biology trump card’ is taken for granted by this person. To me it’s a simple discipinary insult to many people, coupled by the fact that this happily-deviant likes to taunt people by saying they ‘lack faith’ to enter his realm & do tests there.

His is like a ‘leave your family & follow me’ approach that over-elevates the value of biologists, thinking that we will respect his for this. Wrong.

I find it pretty much the most narrow-minded, attempt at condescending possible at BioLogos & everyone here who has come up against this tactic has seen through it & rejected it. I suggest BioLogos make something clear to this ignorant & haughty person, otherwise the term ‘BioLogos biologism’ is easily applicable & appropriate.

To me, biologists are SERVANTS in this conversation, not leaders. This is an observation, not an accusation. Would appreciate comments to this effect if anyone hears this message. I do not reject the person in question as a person, but refuse to participate with such a bad-mannered person who claims in the name of Biology to be a Christian. Thanks.


John - #57845

April 12th 2011

Jon Garvey:

“I have no faith in Behe at all…”

Obviously, and I didn’t claim that you did. The evidence indicates that Rich doesn’t, and that even Behe himself doesn’t—otherwise Behe would be working in his lab instead of bamboozling laypeople.

” - you’re just assuming I do because you desperately want to label me as an ID enthusiast.”

No, I’m not assuming that at all. Clearly, the failure to act is far more consistent with a lack of faith.

“Or quite possibly you don’t, but if you’re going to keep telling people what they think…”

That was an overstatement. I apologize for it and retract it. What I should have said was that the failure to see a testable hypothesis suggests wishful thinking trumping logic. I do not conflate wishful thinking with faith, so I’m curious as to why you did.

”… you deserve to have your own views misrepresented.”

Interesting. I don’t think that anyone ever deserves to have her or his views represented. How do you derive such a sentiment from a Christian perspective?

John - #57855

April 13th 2011

I don’t think that anyone ever deserves to have her or his views MISrepresented.


Jon Garvey - #57877

April 13th 2011

“That was an overstatement. I apologize for it and retract it.”

And I apologise for, apparently, misrepresenting your assessment of my motivations. Which closes it, as far as I’m concerned, on the Scriptural principle that love keeps no record of wrongs.

It does seem you have difficulty understanding irony (perhaps it’s a cultural thing). But if I had to justify, as per your last point, replying to misrepresentation of my views by misrepresenting the other, it would be on the basis of  “Answer a fool according to his folly.”

On the matter of “testablre hypotheses”...


Jon Garvey - #57883

April 13th 2011

... or “testable” hypotheses, even.

It is hard for me to understand how a suggestion from me that a writer’s position was misunderstood by Argon should in any sense obligate me to undertake research.

This is a suggestion you appear to have made (not to put words in your mouth) as a criticism of several who have expressed an opinion here, including myself (I knew it would come eventually - one reason for avoiding dialogue with you, I’m afraid), Nedbrek, Gregory and Rich.

Nedbrek works in IT, Gregory and Rich in academic social science and theology respectively. I myself have retired from a long career of treating sick people. Just suppose I had indeed spotted a testable hypothesis arising from my exchange with Argon, and burned with the urge to avoid all hearsay and actually do the research.

The last biological research lab I worked in was in 1970, but I remember enough to know that had I suggested that they divert their resources from pest control to molecular biology I would not have succeeded.

As it is I live on a pension ouside a small village of 400 people. Opportunities for 59 year olds to retrain in cutting edge science, obtain employment and gain enough respect and funding to check out Behe. And unlike others, I don’t have a mortgage to pay (...).


Jon Garvey - #57885

April 13th 2011

(...)
These real constraints are obvious to most people, but not, it seems, to you. Biologos does not exist as a reference exchange for working biologists, but as a means of sharing insights across a wide range of disciplines, and in particular increasing understanding for those in none of them.

That means bearing with the weaknesses of others’ opinions (a Scriptural principle), welcoming all who come without unnecessary disputing (a Scriptural principle), bearing with one another in gentleness (a Scriptural principle), not thinking of ourselves more highly than we ought because of superior knowledge (a Scriptural principle), and being always ready to give an answer with gentleness and respect (a Scriptural principle).


“A gentle answer turns away anger.” One last Scriptural principle - today’s meditation.


Mike Gene - #57898

April 13th 2011

Hi Argon,

Can you find for me where Denton refers to his views as front-loading?  Can you find for me where Behe refers to his views as front-loading? 


Argon - #57937

April 13th 2011

Hello Mike.
Denton doesn’t call it “front-loading” but it’s the same thing, Mike, and Denton believes loading occurred at the moment of the universe’s birth (cosmological front-loading <> ultra-fine tuning???). In his earlier writing (Darwins’ Black Box) Michael Behe presented a hypothetical scenario of the designer creating a first cell with all the IC systems already present but perhaps not expressed or turned-on (reserved to later use or possibly modifiable at later events). He also believes in common descent though doesn’t accept that all evolutionary steps can be bridged with ‘natural’ mechanisms. “Front-loading” is not a trademark, so call it as you wish but both men really have proposed front-loaded scenarios.




Argon - #57942

April 13th 2011

Jon Garvey - #57765
(regarding my comment#57757)
Would it knock his hypothesis of intelligent design out? Someone would have to explain how the genetic code got thus loaded first.

Behe specifically discusses IC systems and limitations to the evolution (from earlier organisms) of biochemical systems. His claim is that ‘natural’ mechanisms are not sufficient to account for the evolutionary steps involved and has proposed an ‘edge of evolution’ that lies somewhere around the level of the genus (perhaps… systematics being a bit sketchy sometimes). Given that *his scientific hypothesis* of intelligent design revolves around the porposed inability of ‘nature’ to give rise to IC systems, then absolutely, his hypothesis would be trashed if it was demonstrated that these systems could arise from previously existing organisms (i.e. if you’ve read Behe, you might recall what he believes his hypothesis indicates about the evolvabilty of the blood clotting cascade).

Would that rule out intelligent design of the first cell? No, but that’s an orthogonal argument. Behe’s scientific claims relate to how living organisms evolve, not how the first ones came about. So, it would blow the core “IC = unevolvable”, “edge of evolution near the level of genus” arguments of Behe out of the water.


John - #57968

April 13th 2011

Jon Garvey:“It is hard for me to understand how a suggestion from me that a writer’s position was misunderstood by Argon should in any sense obligate me to undertake research.“Curiosity and humility should drive you to do so.

“This is a suggestion you appear to have made (not to put words in your mouth) as a criticism of several who have expressed an opinion here, including myself (I knew it would come eventually - one reason for avoiding dialogue with you, I’m afraid), Nedbrek, Gregory and Rich.“Here’s an example. Rich stumbled onto a testable hypothesis that Behe hasn’t bothered to test, stating, 

“Now, to get from an artiodactyl to a whale, you’ve got to have many [of Behe’s] CCCs.”


That’s true IF Behe is right about variation not being up to the job BECAUSE it can’t provide the raw material for selection to act upon to create these CCCs.

But what if there aren’t many (or even any) different CCCs between modern artiodactyls and modern whales? Behe’s hypothesis is dead meat.

“Nedbrek works in IT, Gregory and Rich in academic social science and theology respectively. I myself have retired from a long career of treating sick people. Just suppose I had indeed spotted a testable hypothesis arising from my exchange with Argon, and burned with the urge to avoid all hearsay and actually do the research.”

Rich’s hypothesis, deceptively presented as fact, can easily be tested from your keyboard. Ned has run away from examining the most IT-friendly evidence for evolution.

“The last biological research lab I worked in was in 1970…”

I’m not telling you to go work in a lab, Jon, although it is telling that Behe has quit working in his.

“As it is I live on a pension ouside a small village of 400 people.”

But you have internet access.

“Opportunities for 59 year olds to retrain in cutting edge science,…”

I’m not expecting Rich or you to do cutting edge science, Jon, I’m expecting Rich and Behe to be curious about whether Behe’s assumption (actually a testable hypothesis) has any evidentiary support. Rich isn’t—are you?

“These real constraints are obvious to most people, but not, it seems, to you.”

I don’t see any constraint that prevents you or Rich from doing a PubMed search on the molecular basis of whale morphology.

Here’s a big one:
www.pnas.org/content/103/22/8414.long
 
“Biologos does not exist as a reference exchange for working biologists, but as a means of sharing insights across a wide range of disciplines, and in particular increasing understanding for those in none of them.”

Yes, so I’m sharing the insights that real scientists have produced on the loss of hindlimbs in cetaceans, with not a single CCC to be found. Do you think they will find any associated with the relocation of the nostrils to the top of the head?

The next step will be to “knock-in” the whale sequence differences into the mouse genome. What do you predict the results will be?

”...not thinking of ourselves more highly than we ought because of superior knowledge (a Scriptural principle),…”

I’m not making any arguments from authority, Jon. I’m challenging you to test hypotheses and grapple with the evidence for yourself. That’s very scary to those with an authoritarian bent and who have little faith in what they reflexively claim to be true.

Mike Gene - #57989

April 14th 2011

Hi Argon,

You originally said, ““Front-loading” is a bit of a loaded term…”  That’s what I was responding to and the subject of consideration was the term.  As such, it seems very significant to me that neither Denton nor Behe have appropriated the term to describe their views on evolution.  The term is being put in their mouths.  

You describe Denton’s views as follows, “Denton proposes that the physics of the universe itself is front-loaded not only to produce life but also to produce organisms very much like humans.”  Okay, now that also sounds like Simon Conway Morris.  Does he propose front-loading evolution?  And Ken Miller and Christian DeDuve seem to agree with Morris.  Are they advocates of front-loading?  This is the problem you run into when trying to put terms in other people’s mouths.

Denton’s book was entitled “Nature’s Destiny.”  Destiny does not sound like front-loading.  It sounds more like predestination or determinism than mere front-loading.  This is the emphasis on laws as opposed to chance.  Behe’s book was about the Edge of Evolution.   That sounds like a limit to evolution and a place to stick the designer.  That sounds more like evolutionary interventionism, where the emphasis is placed on intelligent intervention as opposed to chance.  Front-loading is not about determinism or about the failure of evolution/need for intervention.  It is about recruiting and exploiting chance to carry out a design objective.  It is about increasing the odds to facilitate the success of evolution.  


Argon - #58018

April 14th 2011

Mike, I understand where you’re coming from but to me, it’s “six” vs. “half a dozen”. I don’t expect a “wrong” or “right” answer to a precise definition of ‘front-loading’. “Front loading”, to me and as a generic term says nothing about determinism or how many intervention events are involved. It’s about where & when the information / “special sauce” from a designer goes in that provides the building blocks for future lifeforms. Denton places this at the start of the universe. You place this with the first cells. Behe starts with the first cells but also expects subsequent tweaking to help guide much of subsequent evolution and setting up for the future systems. And it’s not exclusively what you, Behe and Dembski say is ‘front-loading’: It’s also how others talk and think about it.


Rich - #57646

April 10th 2011

I don’t know where the appropriate place for this announcement would be, but since this is a technical thread about the mechanisms of evolution, perhaps it is as good as any.

There is an interesting new interview with Lynn Margulis in the latest issue of Discover magazine:

http://discover.coverleaf.com/discovermagazine/201104?pg=68#pg68

At one point in the interview, Margulis is asked about the similarity between her criticism of the Modern Synthesis and that of others, such as ID proponents.  While denying that ID counts as science, she says something interesting about ID and creationist critics of natural selection:

“The critics, including the creationist critics, are right about their criticism.” 

Since at least one commenter posting on this thread has on a past thread denied that this is Margulis’s view, I thought I would throw out that sentence, but I recommend reading the whole article.  Here is a secular, humanist, ID-rejecting, creationist-rejecting, recognized authority on evolutionary biology making a pretty blunt criticism of the main stream of 20th-century evolutionary theory.  She certainly has no hidden agenda for a Christian theocracy, and she certainly cannot be accused of ignorance of biological science in general or of evolutionary theory in particular.  I for one find that interesting.  I think her views on evolution should be discussed on Biologos more often than they are, since, if she is right, the particular synthesis of evolutionary theory with Christian theology that many writers here have championed is based on an outdated and faulty understanding of the mechanism of evolution, and hence is insupportable.


John - #57660

April 10th 2011

“ While denying that ID counts as science, she says something interesting about ID and creationist critics of natural selection: “The critics, including the creationist critics, are right about their criticism.””

How does that sentence apply to ID critics?

“I think her views on evolution should be discussed on Biologos…”

Anything but those posts about evidence on which Rich never comments in any substantive way. Yes, it has to be all hearsay all the time!


Jon Garvey - #57698

April 12th 2011

Let me get this right - an article on Thornton’s work is “evidence”.

An article on Margulis’ work would be “hearsay”?

John, the role you give to hearsay in human interaction is almost as all-encompassing as the role given to stochastic events in the Modern Synthesis.


Argon - #57746

April 12th 2011

What ‘work’ has Margulis done on the topic of evolutionary mechanisms and genetics? I’ve read the same arguments about evolutionary problems in creationist literature. She’s a bit of a one-trick pony: “It’s all symbiosis!” And like a stopped clock, she’s right once in a while but she’s terrible at describing evidence contrary to what she wants to see. Her descriptions of evolutionary science are no more respected among the biological community than her ideas about HIV and AIDS. meh.



Jon Garvey - #57748

April 12th 2011

Isn’t her work on the mitochondrium of some slight relevance to evolution? But maybe that’s just hearsay…


Argon - #57755

April 12th 2011

And that’s about it. Others nailed down the relationships with the essential sequence and biochemical analyses. Margulis doesn’t delve deeply in population genetics, selection, core biochemistry or reasonable descriptions of proposed mechanisms but does favor denial that variation and selection might have had something to do with the symbiosis of the plastid and mitochondrion. Nope, instead it was all warm and fluffy cooperation with and little to do with the ‘capitalistic’ Darwinian paradigm. She can’t see that mutualism and current evolutionary thought can be compatible. Now, if she only had data for her more outré claims, yes, then other biologists would take her more seriously. 


John - #57771

April 12th 2011

Jon Garvey wrote:
“Let me get this right - an article on Thornton’s work is “evidence”. “

No, Jon, the article on which you are ostensibly commenting is ABOUT evidence. The article points you to the evidence. I predict that you won’t admit to your misrepresentation.


Rich spews comments on such articles, but they don’t relate to the evidence. Rich’s avoidance suggests that he fears evidence. Many of Rich’s evidentiary claims are total fabrications, clearly derived from wishful thinking and/or deceptive hearsay.

“An article on Margulis’ work would be “hearsay”?”

An interview on Margulis’s opinions is hearsay. Are you claiming that Margulis is introducing relevant evidence in the interview?

“John, the role you give to hearsay in human interaction is almost as all-encompassing as the role given to stochastic events in the Modern Synthesis.”

Jon, you don’t know what you’re talking about. But that’s expected from someone whose concern for accuracy is so low that he can flatly deny addressing any comments to me mere hours after specifically addressing two comments to me.

Jon Garvey - #57880

April 13th 2011

Sigh.

The article on Thornton, if I can still read, did not say “Thornton presents evidence in the following references. Go look.” It says, “Here is an abstract of the evidence found in Thornton’s work, references at the end so you can check the detail.”

An article on Margulis’ views might well, I imagine, present a similar précis of her research, either with approbation or with disapproval. At the very least, an account of her work on the mitochondrium would be instructive and demonstrate one of the lesser-known mechanisms of evolution.

But were an article simply to be a statement of her views, or an interview, it would not, actually, be hearsay. That term ought to be reserved, in my opinion, for
(a) inadmissible evidence in a court of law
(b) Malicious gossip

If one uses it of everything one hears, but does not know to be true (OED) then it would apply to nearly every conversation, utterance or thought - and certainly to every scientific hypothesis not yet dignified as theory, currently untestable speculations about multiverses and other unknowable phenomena, extrapolations from the particular to the general - in fact, most of life.


John - #57955

April 13th 2011

Jon Garvey:

“The article on Thornton, if I can still read, did not say “Thornton presents evidence in the following references. Go look.” It says, “Here is an abstract of the evidence found in Thornton’s work, references at the end so you can check the detail.”

What’s the difference between those two summaries, Jon?

“An article on Margulis’ views might well, I imagine, present a similar précis of her research, either with approbation or with disapproval.”

It’s an interview.

“At the very least, an account of her work on the mitochondrium would be instructive and demonstrate one of the lesser-known mechanisms of evolution.”

Any credible account of her endosymbiosis hypothesis would cite the evidence supporting it, which IIRC did not come from Margulis.

“But were an article simply to be a statement of her views, or an interview, it would not, actually, be hearsay.”

Jon, any interview, by definition, is hearsay. It is someone telling you what someone else said. 

“That term ought to be reserved, in my opinion, for
(a) inadmissible evidence in a court of law
(b) Malicious gossip”

Then maybe you should publish a dictionary.

“If one uses it of everything one hears, but does not know to be true (OED) then it would apply to nearly every conversation, utterance or thought - and certainly to every scientific hypothesis not yet dignified as theory,…” 

No, Jon, the essence of science is flying over your head. Testable hypotheses exist independently of those who advance them. They are tools for approaching the truth and have value when tested, even when they are shown to be false. Tribalism is only rarely associated with competing hypotheses, and even then the tribes almost always agree on the experiments or observations that will distinguish between them; they even make jokes. Alternative hypotheses about the primacy of beta-amyloid vs. tau in Alzheimer disease is a fine example of this.

IMO, this is precisely why people like Rich are so adamant about promoting hearsay over evidence. It’s all about pretending that science is anything but hypothesis testing.

My primary job as a scientist is to figure out what would be true if a hypothesis is false, and to actively obtain that evidence. Do you see anything like that happening on the ID side?

Jon Garvey - #58001

April 14th 2011

I had no real knowledge of Margulis at all until Rich’s post, regarding her as the most kooky of the Darwinist fringe.

But someone guided me to this link today: http://www.sciencedaily.com/releases/2011/04/110407141328.htm. This would seem as much an example of evolution as the E. Coli in the work of Thornton, and it would seem to depend in some significant way upon the Rickettsiae. On the face of it, potentially corroborative of Margulis’ hypothesis about symbiosis as a significant mechanism in evolution.

One thing that strikes me is that such ecologically-determined mechanisms are only ever likely to be observed in the field rather than the lab, which is going to affect the amount of research done to test it.

Proponents of new ideas are prone to bang their drum loudly to get anyone to listen, but I have the impression babies sometimes get thrown out with bathwater. McClintock took the opposite line about contol genes by stopping publication, but it still took 30 years or so for her ideas to be incorporated into the mainstream.


Argon - #58014

April 14th 2011

Hi Jon. Yes, symbiosis (mutualism) is a known factor of evolution. Darwin discussed this with flower evolution. Interactions between organisms in nature run the gamut from ‘indifference’ to parasitism, to mutualism. Part of the several controversial aspects of Margulis’ notion is not that mutualistic interactions have shaped evolution but that mutualism is the key driver even for speciation, and not say, selection. She makes a binary argument (symbiosis vs. neo-Darwinian mechanisms) out of what most others see as a continuum (symbiosis is an expression of neo-Darwinian mechanisms, not a replacement).


Jon Garvey - #58020

April 14th 2011

Apparently becoming increasingly recognised as important, despite Margulis’ fixation with it. So worth discussing here. And can one discuss it without significant reference to her, as its major proponent  - which was the original point?


Argon - #58024

April 14th 2011

Jon, everything is this subthread and immediately after Rich’s introduction pertained to Margulis and her views. Mutualism *wasn’t* the point of Rich’s presentation and subsequent discussion—It was her dispute with other parts of evolutionary theory.

Mutualism is part of evolutionary theory. Horizontal transfer is a well-documented mechanism that has been discussed quite actively in the literature since gene transduction via viruses were discovered (> half a century or so ago). DNA sequencing & analysis over the past decades has proved additional information about the the relative level of horizontal transfer. Is something getting swept under the rug here? The news, info and reviews section of Science and Nature magazines are a great place to start one’s investigation about subjects like horizontal genetic transfer and how interactions between organisms affect their evolution.

What precisely do you want discussed without reference to Margulis? It’s *her* package.

Jon Garvey - #58030

April 14th 2011

Maybe it’s the sub-threading that causes confusion…
*Rich points to article about Margulis - says it would be interesting to have something about her work here.
*John says it would be hearsay.
*I say it could be about her work, which is of interest.
*You say she’s a one-trick pony and that no serious biologists take any notice of her.
*I would have said it’s a significant trick anyway, having pointed to mitochondrial and chloroplast origins way before anyone believed her (but John at that point starts accusing me of deception, lack of faith, denying science etc).
*Next day, lo and behold - a news article apparently about the very endosymbiosis she’s pushing: rare maybe but worth us amateurs learning about.
*You say it’s well known (but for Margulis the be-all-and-end-all).
* I say it’s still interesting, and since she is the name associated with the field, Rich’s original suggestion is not as silly as all that.
Is that all soreted now?

But it doesn’t matter - we can have another article about E. coli instead. I’ve used antibiotics on enough of the critters.


John - #58033

April 14th 2011

Jon Garvey:

”*Rich points to article about Margulis - says it would be interesting to have something about her work here.*John says it would be hearsay.”

Nope. Rich wanted to discuss her VIEWS. I didn’t say that her views were hearsay, but that the interview Rich cited is hearsay.

”*I say it could be about her work, which is of interest.”

But Rich only wanted to discuss what she said in an interview about ID.

”... (but John at that point starts accusing me of deception, lack of faith, denying science etc).”

Nothing of the sort in my comment above, but that explains how you could deny having addressed me hours after directly addressing me.

”...Rich’s original suggestion is not as silly as all that.”

It’s still silly, because you substituted “views” with “work” to make it look less silly.

Argon - #58071

April 15th 2011

Jon Garvey - #58030: I say it’s still interesting, and since she is the name associated with the field, Rich’s original suggestion is not as silly as all that Is that all soreted now?

The evolution and impact of mutualistic interactions is indeed fascinating. For more info, Google “symbiosis, evolution, mutualism”. “Game theory evolution” is another avenue to pursue. Here are some starting places:

Nancy Moran’s lab is particularly a good place to start for microbial symbiosis. Recent paper: “Symbiosis as an adaptive process and source of phenotypic complexity”, PNAS May 15, 2007 vol. 104 no. Suppl 1, p8627-8633 (http://www.pnas.org/content/104/suppl.1/8627.full)

The Pierce lab at Harvard is studying mutualism from multiple angles including microeconomic and game theory. http://www.oeb.harvard.edu/faculty/pierce/index.shtml

Jon Garvey - #58073

April 15th 2011

Now that’s probably the most helpful reply I’ve had on Biologos in a long time!

I actually read the Wiki overview myself, but will chase up the others when I have a moment.

Thanks a lot.


Jon Garvey - #58116

April 16th 2011

Argon - have read the links now. Definitely interesting, and much of it new to me. I think I’ve sorted out the difference between Nancy Moran and Lynn Margulis now, though I’m not 100 % certain.

Moran says : “Although symbiosis was once discounted as an important evolutionary phenomenon, the evidence is now overwhelming that obligate associations among microorganisms and between microorganisms and multicellular hosts have been crucial in many landmark events in evolution, in the generation of phenotypic diversity, and in the origin of complex phenotypes able to colonize new environments.”

So she says symbiosis has been grossly underrated, though natural selection is important.

Whereas Margulis says the opposite: ie that “natural selection is of critical importance to the evolutionary process” but that symbiosis has been underrated. No wonder she’s not taken as seriously.


Argon - #58581

April 24th 2011

Moran and Pierce recognize like many other biologists that mutualistic relationships and horizontal transfer play a role in evolution. Certainly among bacteria, we know a great deal of horizontal transfer goes on (thought much, much less so in metazoans like us). Moran’s husband, Howard Ochman has papers withing the last couple decades describing the extent of transfer in bacteria.


Overall, the are two differences with the work of those I’ve mentioned and Margulis. First is that the former biologists investigate symbiosis/mutualism as one of many mechanisms at work in evolution and see connections between the mechanisms. This is in contrast to Margulis, who believes mutualistic interaction is the *main ‘driver’* in evolution.

Second, the former groups tend to be less dogmatic or narrow and consequently are more open to evaluating multiple mechanisms. One can see this difference reflected in Margulis’ attempts to confront the current synthesis along two fronts: 1) Denial that other mechanisms contribute much to evolution, and 2) Trying to explain everything as a product of mutualistic explanations. The problem with Margulis as most other biologists see it, is that her attempts at denying the roles of other possible evolutionary mechanisms flies in the face of rather decent data. In other words, her arguments in many cases seem quite forced and not well supported. Also, many of her claims about symbiotic origins of many later metazoan features don’t hold much water. Basically her case for the predominate and universal role of mutualism across all life is quite weak and in many cases, apparently wrong. This, sadly (IMHO), has been her MO over the course of much of her career and appears again in her more recent forays into the debate about the causal role of HIV in AIDS wherein she brings up contrarian positions that were addressed long ago and apparently hasn’t read much of the literature before making claims.

Rich - #57691

April 11th 2011

Mike Gene (57674):

Thanks for your answer.  So you are saying that there is no initial position of the elementary particles of the universe (or, if you wish to take it further down the line, of the first living cells and nutrients on the earth) which could have guaranteed the arrival of man? 

Does it not follow that, if God created *exactly the same* initial position—right down to the position of every last electrical charge and atom— a million times, in some cases man would evolve, in other cases no intelligent being would evolve, in other cases mammals would not evolve, in other cases, nothing would evolve beyond various types of bacteria?

And if that *is* what follows, do you see that as compatible with the understanding of Creation presented in Genesis?  (I don’t mean six-day literalism; I mean the correspondence between God’s design and the set of outcomes.)  Is it compatible with Augustine’s understanding?  With Aquinas’s?  With Calvin’s?  Or are you indifferent to whether it is compatible with any of those understandings?  That is, are you indifferent to whether or not your own understanding of Creation is compatible with what the tradition has taught?


Alan Fox - #57699

April 12th 2011

OT: anyone else experiencing problems in connecting to Biologos over the last couple of days?


Jon Garvey - #57708

April 12th 2011

Yes - probably a spontaneous mutation on the Internet. But it’s OK now.


Alan Fox - #57706

April 12th 2011

Mike Gene:

It has credence in the sense that yes, the receptor is complex, and yes, its ability to bind these ligands is dependent on specific amino acids being in certain positions. But is that a metric that delivers a design inference?  I think not and Dennis does a nice job of explaining one reason for this.

<a href=“http://pandasthumb.org/archives/2011/03/uncommon-dissen-3.html”>Joe Felsenstein</a>makes this point too. I’m not convinced there is a metric that will tell us what the functionality of a particular run of nucleotides (gene) might be before running it other than post hoc observation. If someone comes up with a way of reliably predicting the functionality of of some theoretical DNA sequence so that synthesis confirms prediction, the possibilities would be pretty mind-blowing, considering the tiny fraction of possible proteins that are involved in life “as we know it”.



Alan Fox - #57710

April 12th 2011

Do casinos have to load their die to make a profit?  

A truly clever designer doesn’t need to cheat to bring about a result.


Who mentioned cheating? Mutations arise from copying errors. When genes are passed on to progeny, the overwhelmingly likely result for any DNA sequence is that it is reproduced exactly. For the simplest type of mutation, it can happen that the correct nucleotide is replaced by one of the other three bases, resulting in a different amino acid in the resultant protein. I am just musing whether God could direct the process without any apparent discontinuity to the fabric of the universe. The non-theist sees a stochastic event; the theist knows better. This could also be an argument as to why there are parasites, bad backs and unwanted body hair. If God chooses to work through “natural” processes, the bad has to be there for the good to be created.

Jon Garvey - #57715

April 12th 2011

Alan, if you have a strong doctrine of providence, then whatever mechanisms are involved, stochastic, interventionary or completely understood, are all completely capable of delivering God’s purposes.

You’re then free to consider the merits of any proposal without either fearing God will get excluded or (as seems more common) fearing that he might cheat and show his hand somehow.

It does seem to me that frontloading is a proposal that, as Rich suggests, would produce a result in general, rather than in particular. In other words, it would provide an explanation for the trajectory of evolution, but not its individual results. 

It’s going to be unsatisfying to many because it suggests purpose and complexity at the horizon of our ability to investigate. But it seems to me that’s already inherent in the degree of organisation of the earliest life we know, and for which there is no explanation.


Alan Fox - #57786

April 12th 2011

I’m not sure I follow what you are saying here, Jon, but “front loading” fails as an idea for me because organisms always fit their particular environment, their niche. Evolutionary theory attempts to explain diversity by suggesting that organisms are designed by the process of natural selection. You find alpine swifts in the sky, Riftia tube worms at thermal vents, golden moles in the Namib desert. With “front loading”, the required “information” is supposed to be already there and then, I guess, somehow knows when to switch on at the appropriate moment. Doesn’t seem very convincing.


Alan Fox - #57711

April 12th 2011

Alan Fox - #57712

April 12th 2011

OT; is there neat a way of doing links?


Ashe - #57744

April 12th 2011

Mutations do not just arise from copying errors. 


Alan Fox - #57781

April 12th 2011

Apologies. What I should have said was mutations are copying errors. If DNA replication were perfect, there would be no evolution.


Ashe - #57783

April 12th 2011

Mutations are caused by a variety of processes, radiation, transposons, copying errors, etc.


Alan Fox - #57787

April 12th 2011

No…


There may be various triggers for mutations to occur; Cosmic rays and other mutagens. I was referring to single nucleotide substitutions and there are other sources of genetic variety (though I would call all genetic variation mutation). Allen MacNeill covers the issue in a blog post.


Ashe - #57812

April 12th 2011

I would say that there is a actually a mutational spectrum.  Each mutagen acts by a certain mechanism. It can be as simple as occasional structural changes in bases during DNA synthesis, resulting in a wrong base inserted, or a common chemical change in a base (e.g. deamination). Radiation causes certain types of damage. Exposure to UV light results in rather typical chemical damage, while ionizing radiation results in more different kinds of damage (is more like a sledgehammer, compared to UV). Chemicals such as alkylating agents can attach themselves to bases.  Small chemical adducts usually result in transition mutations (like GC to AT), while large adducts mostly give transversion mutations (like GC to TA  or GC to CG). So, a large compound like benzo[a]pyrene in smoke, or aflatoxin in moldy peanuts give transversions, while small alkylating agents like MMS result in transitions. 

Different mutagens have different preferences for different bases. UV light damages T or C when they are next to each other, but not A or G. Many chemicals like to attach them selves to Guanine, and to a lesser extent to Adenine. Some chemicals like a G, but like it much better if that G is preceded by another G. 

As you can see, the distribution of the damage along the DNA depends on the type of chemical agent or radiation, and also on the DNA sequence. You could say that each nucleotide has a certain probability of being ‘hit’, and that this probability is different for each nucleotide along the DNA sequence, depends on the surrounding nucleotides, and depends on the mutagen.

Once there is damage, it has to be repaired. In the vast majority of cases that repair is perfect. Otherwise we wouldn’t be alive. But repair efficiency is also different for each nucleotide in the DNA. This means that positions that are infrequently damaged, but are very inefficiently repaired may still more often result in a mutation, than sites that are often damaged, but are very efficiently repaired. This has been shown to be the case. I think this gets into some of the examples of a “house edge” that Mike refers to in his analogy .

This is where the term mutatonal spectrum come in. Each mutagen (or “spontaneous” type of event) results in a distribution of changes, like 70% transitions, 15% transversions, 5% deletions, etc. Sometimes these changes are found preferentially at certain sequence types (e.g. UV light likes adjacent CC or TT or TC bases), or small deletions may happen in sequences that are repeated. 


Alan Fox - #57870

April 13th 2011

Are we at a tangent here? I suggest that God can direct evolution by directing the result of apparently stochastic events and thus this would be invisible to a scientific observer. Are you agreeing or disagreeing with the premise?


Jon Garvey - #57886

April 13th 2011

Can you clarify for me, Ashe: can transposons be said to result in “damage”? Changes, yes, but meiosis also results in changes, and we don’t call that “damage.”


Paul D. - #57894

April 13th 2011

Isaac Newton suggested that God directed the motions of the planets through constant nudges to keep their orbits stable, which accounted for the discrepancy between Newton’s equations and the actual observed motion of the planets.


Of course, we now know that Newton’s equations simply weren’t good enough, and Einstein’s explained the actual motion we observe without positing a God of the gaps.

Jon Garvey - #57899

April 13th 2011

Paul, I’m not sure whose post you’re replying to, but Alan Fox at #57870 is in a different area from Newton.

Newton was wrong to posit special divine action to correct his anomolies, but his search was to find how God acted in the world. So his perfect circles did not enable him to tick orbits off the list of things that God did, and if he’d known about (and accepted) elliptical orbits, he’d have attributed them to God even as he understood the maths and physics. Or at least, an orthodox Christian would, Newton following an odd kind of Deism that might have limited God to the initial “Push”, though I’m not sure.

So the activity Alan is dealing with is to do with God’s overall sustaining of the Universe, not special interventions.


Ashe - #57930

April 13th 2011

Perhaps “damage” is a bit subjective. It’s probably correct to say that transposons are yet another class of mutagen, and leave it at that. 


Argon - #57972

April 13th 2011

Maybe “anything that alters the linear order of a sequence” is the category that covers this. This would include point mutations, insertions, duplications, inversions, transpositions and recombination mechanisms, as opposed to, say, methylation or changes in histone binding patterns.


Jon Garvey - #57997

April 14th 2011

This seems to be how “mutation” is sometimes used - confusingly, at other times it is used differently.

But this meaning covers a multitude of possibilities, does it not? From purely stochastic letter changes to (in principle) functionally organised re-arrangement of whole groups of genes along the lines James Shapiro suggests happen all the time. It would even include Lynn Margulis’ symbiosis, I would think.

That makes for quite a wide range of different understandings from “pure chance” to “highly specified”, all under the banner of “mutation random with regard to fitness.” That may be good for maintaining the integrity of the Modern Synthesis, but is actually a big menagerie of ideas.


Bilbo - #57809

April 12th 2011

Alan: “You find alpine swifts in the sky, Riftiatube worms at thermal vents, golden moles in the Namib desert. With “front loading”, the required “information” is supposed to be already there and then, I guess, somehow knows when to switch on at the appropriate moment. Doesn’t seem very convincing.”


It amazes me how often you can misunderstand what Mike says, Alan.  Front-loading says that the first cells were designed so that eventually it would be more probable that there would be swifts, worms and moles.  It does not say that the required information is supposed to be already there, and it does not say that it somehow knows when to switch on at the appropriate moment.  

R Hampton - #57839

April 12th 2011

Alan,
Just read your comment (#57486). Given limits of Science in regards to First Cause, I’m comfortable with the notion of “apparently” stochastic events (referring to the supernatural) and “deterministically” stochastic events (referring to the natural).


Alan Fox - #57868

April 13th 2011

So do we agree there really needs to be no issue between theologians and scientists?


Jon Garvey - #57890

April 13th 2011

At that level there need not be any conflict. That was the point of my “strong doctrine of providence” higher up the thread. God as creator is primarily the one through whom everything exists moment by moment. An unbeliever’s worldview is always able to posit the absence of such a creator/sustainer, and science cannot legitimately choose either way.

However, that doesn’t preclude the possibility that at some point the scientific worldview might lose effective explanatory power. For example, supposing that evidence could be found that a freak combination of circumstances and materials had brought cellular life into existence, complete with all the trimmings of the genetic code, in one instant.

It would be fundamentally fortuitous, and incapable of any reasonable scientific explanation. Any explanation would have to be at a metaphysical level, ie “Stuff happens” or “So God (or alien superintelligence) does exist then.” Both answers would be available, neither would be more scientific, but (to my mind at least) the first would be less plausible.

There seems no a priori reason to be able to predict that some such situation might not arise in the real world, for example if it could be proved that no scientific explanation could be sought for a phenomenon (like, say, multiverses) and yet scientists continued to look because a non-scientific explanation (or scientific non-explanation) was unacceptable. That would be a conflict of science with reason, more than with religion.


R Hampton - #57987

April 13th 2011

Yes, you and I agree, but there is another school of thought (Rich is an prime example) that can not reconcile “deterministically” stochastic events with divine providence. For them, it’s one or the other, but not both. In my opinion, this either/or presumption was essential in the founding of the Discovery Institute and their promotion of ID.


Jon Garvey - #58022

April 14th 2011

Funnily enough I read Rich as arguing for both-and rather than either-or! Perhaps you were arguing with each other from the same position. We shall never know…


R Hampton - #58053

April 14th 2011

Jon G.
Oh no, you read Rich wrong. He has made it clear on any number of occasions that God simply can not guarantee the evolution of Man (opposed to a sentient otter, for example) if there was true contingency (randomness) in the Universe.

If you care to indulge/punish yourself with long threads of such discussions, I can dig up a few links for you tomorrow.


Jon Garvey - #58059

April 15th 2011

Don’t worry - I doubt anyone’s life will be changed by my lack of preception!


Alan Fox - #57866

April 13th 2011

It amazes me how often you can misunderstand what Mike says, Alan.


It shouldn’t. Getting Mike to explain anything clearly is like pulling teeth. I don’t know anyone who uses notmore often in his comments.

Front-loading says that the first cells were designed…

“Designed” means what exactly, in this context? By what, when, how? Try to be specific and remember others, like me, have not grasped the subtleties.

...so that eventually it would be more probable that there would be swifts, worms and moles.

So the “front loading” takes place before the organism appears. Isn’t that what I said?


Alan Fox - #57867

April 13th 2011

It does not say that the required information is supposed to be already there, and it does not
say that it somehow knows when to switch on at the appropriate moment.  

Verily I say, a true student of Mike Gene!

Mike Gene - #57903

April 13th 2011

Alan,

It shouldn’t. Getting Mike to explain anything clearly is like pulling teeth.

Getting Alan to listen without relying on preconceptions or the template of stereotype is like pulling teeth.  And I have been able to document that you often don’t bother to read my responses.  For example, remember the time on my blog when you asked me to explain the Duck/Rabbit metaphor after I provided a link to explain it?

 I don’t know anyone who uses notmore often in his comments.

That’s because you have a track record of misrepresenting my position, as people often prefer tearing down straw men.  Bilbo was correct in noting your misrepresentation and your response is to mock him.  Why can’t you just accept the fact that you misrepresented my position?


Alan Fox - #57909

April 13th 2011

Mike Gene writes:


Bilbo was correct in noting your misrepresentation and your response is to mock him.

Gentle mockery, I hope, as that was all that was intended. But it is not directed at Bilbo. I like Bilbo and I would never do such a thing. It was you I was mocking. This stems from my inability to take “front loading” seriously.

Why can’t you just accept the fact that you misrepresented my position?

I think I have spent quite a bit of effort trying to establish where the meat in your “front loading” sandwich might be. For goodness sake, I even bought your book! This being a free and open environment for the exchange of ideas, tell me where I misrepresent you. My only point has been that I can’t make sense of your concept. It would help if you spent a little time explaining what it is rather than telling me I am wrong. I pointed out before that (I live in SW France, where the Occitan dialect is strong) I try to clarify if I have understood someone by asking them, “did you mean this?” which hopefully elicits a yes or no answer. So far I have been half-way successful with you.

Bilbo - #57961

April 13th 2011

Alan:  “

“Designed” means what
exactly, in this context? By what, when, how? Try to be specific and
remember others, like me, have not grasped the subtleties.”

Designed by a human-like mind.  At least as early as their appearance on earth.  By bio-nano-technology.


“So the “front loading” takes
place before the organism appears. Isn’t that what I said?”

You haven’t asked me to define “front-loading.”  It doesn’t mean what you apparently take it to mean.



Alan Fox - #57971

April 13th 2011

Bilbo:

You haven’t asked me to define “front-loading”.

Don’t wait to be asked. Jump right in. Please define “front loading”. As a bonus, could you say if you believe there is a consensus among “front loaders” as to definitions.

 It doesn’t mean what you apparently take it to mean.

But I don’t know what it means. I think it is wishful thinking but please correct my misapprehension. Let’s have some positive input. Tell me about “front loading”. Come on, Bilbo. No-one is censoring here. yo can post freely.


Alan Fox - #57973

April 13th 2011

Designed by a human-like mind.  At least as early as their appearance on earth.  By bio-nano-technology.

But what do you mean by designed? And when you say “designed” there is an implication of “design and build”. And the time line? I guess it would be difficult to design something after their appearance. What does “by nano-technology” mean?

Ashe - #58031

April 14th 2011

Uh, no, you’re completely wrong. The problem with Mike’s rush to judgment is that the BLAST only picked up the Arm repeats. They are found in many different proteins with many different functions.


Um, how is what I said completely wrong when that was exactly my point? And I don’t really have a dog in the Volvox fight, I wouldn’t be surprised at all if beta-catenin isn’t found in Volvox. It’s just an interesting sideshow, and irrelevant to my discussion. 

Ashe - #58034

April 14th 2011

Woops, posted this here by accident, mods feel free to delete


Ashe - #58035

April 14th 2011

Does that suggest a major flaw in Behe’s claims about “CCCs”?


Correct.

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