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The Origin of Biological Information, Part 6

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July 7, 2011 Tags: Genetics

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

The Origin of Biological Information, Part 6
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)

A brief recap of the series to date

This series of posts has been exploring the question of how new structures and functions arise through evolutionary mechanisms. This topic is one that is of considerable interest for Christians, since the Intelligent Design Movement claims that the generation of such features (what it terms Complex Specified Information, or “CSI”) is not possible for natural processes to produce in any significant measure. As such, it holds up examples of CSI in nature as evidence for a supernatural designer. Unfortunately, this approach has the effect that new scientific evidence that explains how CSI arises naturally diminishes the perceived evidence for God.

As we were careful to point out in the very 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. If it were so, the obvious conclusion would be that “natural mechanisms” and “God’s actions” are effectively a zero-sum game where every scientific discovery diminishes God’s activity. Indeed, the ID argument strongly tends in this direction. This is certainly not a historic Christian view of science, and one we would do well to steer the church away from.

With these theological considerations in mind, we have explored several examples of new CSI arising through evolutionary processes (the posts in this series are linked in the sidebar for those who have not yet read them). In summary, we have seen 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. For example, 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 (see Part 2). A second example we observed is how neutral mutations opened up new future possibilities during the evolution of hormone/hormone receptor complexes in vertebrates (see Part 3).

  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.

  5. The detailed examples of new CSI arising through changes to existing proteins appear to apply generally to many, many protein families across multiple organisms (see Part 4). There is nothing about protein structure that prevents proteins from acquiring new functions through evolutionary means.

  6. Comparative genomics evidence, especially evidence from synteny, strongly supports the hypothesis that large swaths of modern vertebrate genomes are the result of ancient whole-genome duplications, where some of the duplicated genes go on to acquire new functions through mutation and selection (see Part 5).

Comparative genomics and new CSI: details, details

One last way to assess the ability of natural processes to generate CSI that we will explore is based on comparing the genomes of two closely-related species that nonetheless have significant biological differences. The most detailed approach, of course, is to examine and compare the entire genomes of the species in question. Such a comparison shows us the total genetic differences that have arisen between the species since they parted ways:

It needs to be emphasized that only a subset of the observed differences will be meaningful. Put another way, many of the mutations that have occurred in the two lineages are neutral, having no discernable effect on the organisms in question. Indeed, the subset of truly meaningful differences is likely to be relatively small. Still, the subset of meaningful differences cannot exceed that of the total genetic differences. So, even if we do not, as of yet, understand all the details of how the species in question came to be biologically different, we can be sure that we know what the upper maximum is for the necessary mutations needed to bring about the differences we observe. So, while the total genetic differences between two species is an overestimation of the genetic changes needed to cause the differences, it is still a useful measure because we know that all of the meaningful changes must be accounted for within it.

Applying this test to humans and our closest (living) evolutionary relative, the chimpanzee, reveals that at a whole-genome level, we are over 95% identical. This value is even an underestimate, since it “counts” mutations that duplicate or delete sections of DNA as if they were separate mutations affecting individual DNA “letters” even though it was created by only one genetic change. Indeed if we use the same criteria to compare the diversity which exists within our own species, we humans are only 98% identical to each other. By whatever measure used, we are but a hand-breadth away from our evolutionary cousins at the DNA level (for those interested in a full treatment of how the human and chimpanzee genomes compare, please see this recent article).

Of interest for our purposes here is the simple realization that a relatively small number of subtle genetic changes undergird the large biological differences we observe between humans and chimpanzees. The increase in CSI associated with building the complex human brain and other distinctively human features in contrast to the body of our cousin, the chimpanzee does not appear to require huge changes at the genetic level. The differences we see, when examining these two genomes, are consistent with small changes,of the sort easily accessible to evolutionary mechanisms. While this observation does not rule out the possibility of God directing this stage of human evolution in a more supernatural way, the genomics evidence suggests that this stage was accomplished in gradual, incremental steps. This observation also matches what we see in the fossil record, with gradual increases in brain capacity, tool making, and other features that mark us out as distinctly human.

Evolution and new CSI: cause for fear or celebration?

So, for evangelical Christians, what is perhaps the most challenging evidence for new CSI arising through evolutionary means comes from within our own genomes. Here we see that, at the genetic level, we are but a stone’s throw from other primates such as chimpanzees. This realization leads to what may be for some an uncomfortable choice: either evolution is capable of generating significant novelty through mutation, genetic drift, and natural selection, or the differences between humans and other forms of life must be seen as insignificant. The only other option is to reject these lines of evidence altogether.

Of course, this response, for many, is one driven by fear: fear of having to re-consider the range of methods by which God creates, or perhaps how one interprets the opening chapters of Genesis. My hope is that this series, while challenging for some, would not ultimately be cause for fear. Indeed, this response plays into the false “natural versus God” dichotomy discussed above. Rather, my hope is that understanding some of the natural means God uses to bring about biodiversity on earth, including for our own species, will provide an occasion to offer thanks and praise to our Creator.


Dennis Venema is professor of biology at Trinity Western University in Langley, British Columbia. He holds a B.Sc. (with Honors) from the University of British Columbia (1996), and received his Ph.D. from the University of British Columbia in 2003. His research is focused on the genetics of pattern formation and signaling using the common fruit fly Drosophila melanogaster as a model organism. Dennis is a gifted thinker and writer on matters of science and faith, but also an award-winning biology teacher—he won the 2008 College Biology Teaching Award from the National Association of Biology Teachers. He and his family enjoy numerous outdoor activities that the Canadian Pacific coast region has to offer. Dennis writes regularly for the BioLogos Forum about the biological evidence for evolution.

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Steven Curry - #63149

July 7th 2011

The article presumes that there is a coherent definition of CSI. There is no reason to think so. Nobody has been able to apply it to even simple examples. Watch the confusion unfold as people try to actually calculate CSI: http://mark_frank.blogspot.com/2009/01/lets-calculate-some-csi.html


Steven Curry - #63151

July 7th 2011

Copy and paste URL text manually in order to follow the link above; clicking on it won’t work (presumably an anti-spam measure).


Argon - #63156

July 7th 2011

I agree with you, Steve. At this point in time CSI is a presumed conclusion looking for a real-world, biological application. “I just know it when I see it” seems to be the current operational criterion for determining CSI.


Dennis Venema - #63164

July 7th 2011

Hi Argon / Steven, 


Yes, “CSI” is not defined, and its lack of definition is indeed a problem for the ID movement. I’m using the concept here aguendo - for the sake of argument. Argon’s “special sauce” placeholder is amusing, and serves the same point. If folks who take an ID view want to argue that none of my examples are “genuine CSI” I would love to see the math, as it were. Thanks for the comments. 

Dennis Venema - #63165

July 7th 2011

sorry, “arguendo”. Time for more coffee. 


Jon Garvey - #63157

July 7th 2011

“Of course, this response, for many, is one driven by fear: fear of having to re-consider the range of methods by which God creates, or perhaps how one interprets the opening chapters of Genesis.”

If one were certain that natural mechanisms were the only way that God creates, might not the suggestion that this might not be the case also lead to fear, or even to rejecting any evidence for the suggestion? One would, after all, still be having to reconsider the range of methods by which God creates.


Dennis Venema - #63166

July 7th 2011

Hi Jon, 


I doubt you’d find anyone who simultaneously claims Christ as Lord and that God creates / acts only through natural mechanisms. Do you know of examples?

Jon Garvey - #63367

July 16th 2011

Hi Dennis. I missed this response in the nested heirarchy - sorry. The answer is, “Yes”, but I’d no doubt be accused of ad hominem attacks if I named any.

But it depends, maybe, on how one defines words like “create” and “natural”. Leave aside “acts” because your article is about creation, not resurrection or miracle. How do you define them, since you raided the matter in the article? What non-natural methods would you attribute to God in the creation of life?


Jon Garvey - #63158

July 7th 2011

Dennis, on another thread you suggested that the majority of changes between the chimp and human genomes involve control mechanisms (switches in the EvoDevo jargon). You talked about the issue of small changes in an already complex orgnaism leading to large effects.

That being the case, the issue of new information is surely irrelevant. It only takes 1 bit of new information to turn a switch from “off” to “on”, and the simplicity of the input says nothing about whether the event was random or planned. But if the switch were connected to an automated car assembly line, it would be a brave, or foolish, man who said that 1 bit of randomly introduced information was sufficient to create a car from raw materials: it’s the vast amount of information already in the system that does that.


Argon - #63159

July 7th 2011

Good notes, Jon. I think Dennis’ point is that things like mammalian evolution (and broader) aren’t much of a stretch in terms of ‘new information’. And generally, his argument is a counter to those who propose that transitions among primates and most particularly, the evolution of humans require more ‘special sauce*’ than natural mechanisms can provide. I would add something that Dennis doesn’t mention: If one can accept that a fair number of species transitions via natural mechanisms have occurred then even if one assumes that many ‘larger’ steps couldn’t, it’s wickedly hard to differentiate those ‘acceptable’ changes from those found in the human/ape transition.


*I’m using ‘special sauce’ as a placeholder for ‘some kind of information metric that remains poorly defined’.

Jon Garvey - #63162

July 7th 2011

It is indeed notoriously hard to define prescriptive information in biology, so I’m happy with your “special sauce.”

But it’s also hard to define “random mutation” after the event. My example needed 1 bit of information to build a car - but if one had a panel of many buttons rather than 1, to push the right button successfully would decrease the probability of achieving it by chance. Noting that the right button had, in fact, been pressed would say nothing about whether the choice was unguided in any way.

If a coordinated sequence of, say, 10 buttons was required, each operating long sequences of events at different levels of a control heirarchy, the small number of changes made is irrelevant - a very complex task has been achieved. You also, of course, have the challenge of explaining the existence of a sophisticated system that can be transformed by a just few keystrokes.

I’m not aware of anyone saying that the genetic change from ape to human is harder than any other species transition: but on the other thread Dennis suggested this one because it’s one of the only clear examples where sequencing has been done.


Dennis Venema - #63170

July 7th 2011

i>If one can accept that a fair number of species transitions via natural mechanisms have occurred then even if one assumes that many ‘larger’ steps couldn’t, it’s wickedly hard to differentiate those ‘acceptable’ changes from those found in the human/ape transition.

i>
Indeed. Hence why baraminology has abandoned using DNA differences as a metric for distinguishing separate “kinds.” Any metric that returns a reasonable number of kinds (so as not not overload the ark) simultaneously lumps humans and chimpanzees into the same baramin. 

Jon Garvey - #63185

July 8th 2011

Dennis - one intriguing thing from your post is that the 2% difference in genome within our species isn’t even sufficient to separate us into separate biological races or subspecies. So what is it about the <5% difference between us and chimps that makes for such large phenotypic differences? And also, presumably, allows room for the Australapithecines and all the past Homo species?

Mutations would appear to differ widely in the amount of clout they exercise.


John - #63189

July 8th 2011

Jon,


Differences between entire genomes are metrics that add more to confusion than to understanding.

As for phenotypic differences, how much mutational clout would you predict would be required to add a vertebra to a human?

You are working from a cartoonish view of biology in which you are assuming that the genome acts as a blueprint. An understanding of the absurdity of that view, metaphors meant for the masses aside, would aid you in understanding why ID depends on ignoring most of biology and lying about much of the rest.

Hence my question. One would think that a curious physician would find it to be interesting…

Jon Garvey - #63193

July 8th 2011

“Differences between entire genomes are metrics that add more to confusion than to understanding.”

Better take that up with Dennis, then, hadn’t you?


Jon Garvey - #63195

July 9th 2011

John, one of the annoying things about you is that you set people tasks of your own device with no clear relationship to the issue in hand and then criticise them (in advance) for lack of curiosity.

In this case, an extra vertebra, most likely has its genetic basis in the slight shifting of Hox expression backwards in the spine - a small matter of switching in EvoDevo speak.

In humans it’s commonest in the lumbar spine, and is very common, seldom of any clinical significance and - perhaps more to the point - has a doubtful pattern of inheritance. This probably explains why it persists in the population at apparently unchanging rates, and has been observed as far back as Neanderthal man. Not much evolutionary significance there, but a textbook developmental biology case.

Even more suggestive is that hemivertebrae are actually more common and can coincide with extra vertebrae, which would suggest there is also, or alternatively, an environmental factor affecting the development of growth centres around 6 weeks gestation. The fact that isolated hemivertebrae are seldom found in siblings (only one of 245 siblings of 101 infants in one study) may support this idea - I doubt that anyone has done detailed genetic studies on it in humans.

However, such abnormalities have a tendency to occur with multi-system abnormalities in genetic syndromes, which suggests that changes in control genes can have massively deleterious effects.

So an individual modification in genetic switching can easily produce an extra vertabra, and this may be the mechanism (if it is not environmental) for its frequent occurrence in humans, and therefore form the basis for its becoming fixed in the population and subject to selection.

And that affects my question to Dennis how?


Jon Garvey - #63340

July 14th 2011

All that work and John wasn’t really interested. Duly noted. But curiosity aroused, let’s build on that simple vertebral addition between chimp and man. It has to mesh with a few other changes, which I’ll put in teleological terms - but you have to realise they actually happen from chance and mesh only by their effect on selectable function.

1 Change of 1 vertebra from thoracic to lumbar form.
2  Introduction of thoracic, lumbar and sacral curves for upright gait.
3 Redesign of intervertebral discs for greater compression forces.
4 Sexually differentiated redesign of pelvis and hip joint (whilst allowing large circular birth canal for coincidentally enlarging braincase.)
5 Shape and dimensions of femur.
6 Redesign of knee joint to allow greater cushioning and neat locking arrangement when standing.
7 Shape and dimensions of tibia/fibula.
8 Change of skull orientation and foramen
magnum moved inferiorly.
9 Redesigned ankle joint and foot.
10 Sexually differentiated changes to elbow joint to clear hips on walking.
11 Coordinated new developments to fore, mid and hind brains and spinal cord to handle entirely new upright gaits (walking, running, kneeling, hopping, tiptoe).
12 Changes to multiple musculature of spine, limbs, abdomen, pelvic floor accounting for gradual increase in weight of head.
13 Coordination of last two to balance system.
14 Development of valves in saphenous veins to prevent pooling when upright.
15 Redesign of blood pressure homeostasis to maintain pressure whether standing or not.
16 Coordination of all above to fetal and infant development program.
17 All to be done without interfering at any level from genetic to structural with parallel developments in intelligence, hand manipulation, hand-eye coordination, accommodations to new diet (bowel, skull, jaw, dentition).
18 All to be done without compromising existing function (eg spliced genes must retain multiple functional expression as before).
19 All to be done with <5% change to genome by means of stachastic mutations, most of which will be neutral and not subject to selection for many generations… or in classic Modern Synthesis terms, most to be achieved by selection of existing variation within the ape genome.

But no panic, guys! All this represents a mere stone’s throw. Be thankful you haven’t got to make the thing fly as well.


Steven Curry - #63344

July 15th 2011

Jon—judging by the way you misunderstand essential concepts in the same way the intelligent design community misunderstands them, it would seem that you support intelligent design. Do you?


Jon Garvey - #63368

July 16th 2011

Steven, I started my biology and medical sciences studies some three decades before ID was a gleam in its mother’s eyes. I’ve read 2 ID books in the last 20 years. So if I misunderstand any essential concepts it’s down to Cambridge science education.

I note from the internet, however, that ID proponents include representatives of many life sciences from many academic institutions in many countries. Does this mean that supporting ID actually effaces prior understandings? If so maybe those two books did for me.

Or do you really mean “have a different viewpoint” rather than “misunderstand essential concepts.” I say this because non-ID people like Arlin Stoltzfus (http://www.molevol.org/cdblog) seem to understand population genetics quite well and yet dissent from its concepts.


Steven Curry - #63370

July 16th 2011

Do you support intelligent design?


Jon Garvey - #63386

July 16th 2011

If I were in a tenured academic post in the US, I’d have reason to resent that question. But I’m not, so since you ask so politely…

Though my main interest in BioLogos is in unifying my understanding of science and faith, I support much of the critique of the Neodarwinian synthesis that ID shares with many non-ID biologists. But I began to question its adequacy for myself years before ID existed. ID has not significantly informed that critique. I have to date never posted on an ID website.

I see no scientific or theological reason to preclude non-naturalistic elements to evolution, but neither, as a Christian, do I consider them necessary in order for God to be fully responsible for it. On balance, I think that when the more recently discovered mechanisms of variation and cell organisation are more fully integrated into the mainstream, and better understood, many of ID’s objections to evolution will be answered - to the satisfaction of as many of them, I would add, as to anybody else.

But I think that integration will necessarily change the character of evolutionary theory considerably.

The ID case on OOL is quite distinct from the question of evolution, and interests me considerably. Evolutionary theory has, by definition, nothing to say on the matter, which is I guess why this series has, sadly, not tried to address it. I await a more complete theory of information before committing myself on the matter, but the fact that a high number of software engineers are attracted to ID is, at least, intriguing.

I believe that the views of ID workers, like those of any other group, should be represented fairly and respectfully, which from this side of the Atlantic does not always appear to be the case. Which is one reason I find the constant attempts here to pigeonhole people safely into manageable categories rather childish.

So, then, now that I’ve answered your question as fully as I can, what’s your own position in the Biologos vision of integrating science and faith?


John - #63348

July 15th 2011

Jon wrote:
“John, one of the annoying things about you is…”


Ad hominem duly noted.

“In this case, an extra vertebra, most likely has its genetic basis in the slight shifting of Hox expression backwards in the spine - a small matter of switching in EvoDevo speak.”

Nope. As you contradict yourself by noting below, there’s no evidence that suggests that it “most likely” has any genetic basis whatsoever! 

“In humans it’s commonest in the lumbar spine, and is very common, seldom of any clinical significance and - perhaps more to the point - has a doubtful pattern of inheritance.”

So why did you just claim that it “most likely” has a genetic basis? 

“This probably explains why it persists in the population at apparently unchanging rates, and has been observed as far back as Neanderthal man. Not much evolutionary significance there, but a textbook developmental biology case.”

So the simple answer I was trying to get you to discover for yourself is “Zero.”

“So an individual modification in genetic switching can easily produce an extra vertabra,...”

But my question wasn’t about CAN. My question was how much mutational clout would be REQUIRED. The answer is none whatsoever. That clobbers the faulty extension of the blueprint metaphor by the ID movement pretty solidly, does it not?

”... form the basis for its becoming fixed in the population and subject to selection.”

There’s no basis for something that is not inherited to be subject to selection, Jon.

“And that affects my question to Dennis how?”

You don’t need mutations at all to change things in a system with no real blueprint. That is predicted by the way that evolution is constrained and by the way that any intelligent designer is not constrained.

Steven Curry’s question is an excellent one. You can see the same shallow thinking on yours on the Uncommon Descent blog—just search for “golfer.”

Jon Garvey - #63356

July 15th 2011

“You don’t need mutations at all (my emphasis)to change things in a system with no real blueprint. That is predicted by the way that evolution is constrained and by the way that any intelligent designer is not constrained.”

And that affects my question to Dennis how?

“You don’t need mutations at all to change things in a system with no real blueprint. ” Explain what this means with reference to an article about the ape-chimp transition that mentions mutation 14 times, 9 in its introduction. Dennis’s conclusion: “either evolution is capable of generating significant novelty through mutation, genetic drift, and natural selection, or the differences between humans and other forms of life must be seen as insignificant.”

I ask the author why a similar scale of genetic differences produces such different results within the human species and between human and ape, and get no response except the rotweilers barking their customary “You no understand basic science. You ID. You English spy.”

Still, one can even learn from rotweilers. I can conclude from your post that evolutionary theory (or at least the hyperconservative population genetics variant of it) teaches that the transition from ape to human could have been achieved without a single mutation, because there’s no real blueprint. The mutations catalogued so carefully by Dennis in his article on the Lenski work were, in fact, of no relevance to the ability to metabolise citrate. By extension mutation has no importance in the descent from the Cambrian and before, because blueprints have never existed - the gene pool contained all the information needed right back then… you’ve been reading Dembski, right?

Your vaguely worded and annoying question (not an ad hominem, but a criticism - look up the difference) led me to answer on the situation in humans, where extra vertebrae are produced by genetic anomalies, by environmental factors and so on. But the chimp consistently has 1-2 more vertebrae than the human. Direct evidence, please, that this has no basis in a mutation.


John - #63361

July 15th 2011

“And that affects my question to Dennis how?”


Well, your question was:
So what is it about the <5% difference between us and chimps that makes for such large phenotypic differences? And also, presumably, allows room for the Australapithecines and all the past Homo species?

I’m trying to explain to you how we can get fairly large phenotypic differences without any mutations, which is addressing your question. In a system that regulates in this way, large differences come from small genetic changes. You find this reality to be annoying.

“Explain what this means with reference to an article about the ape-chimp transition that mentions mutation 14 times, 9 in its introduction.”

This means that the underlying system is very plastic, so that small numbers of genetic differences can have relatively large effects.

“I ask the author why a similar scale of genetic differences produces such different results within the human species and between human and ape,...”

Well, there aren’t different results between human and ape, as humans are apes.

”... and get no response except the rotweilers barking their customary “You no understand basic science….”

Well, your list of changes clearly assumes some underlying blueprint. I’m trying to explain that the blueprint only exists in your fevered mind.

“Still, one can even learn from rotweilers. I can conclude from your post that evolutionary theory (or at least the hyperconservative population genetics variant of it) teaches…”

Straw man alert! Theories don’t teach anything, Jon. Scientific ones make empirically testable predictions.

”... that the transition from ape to human could have been achieved without a single mutation, because there’s no real blueprint.”

Right answer, wrong reason. Humans are apes, so there’s no “transition from ape to human.”

“The mutations catalogued so carefully by Dennis in his article on the Lenski work were, in fact, of no relevance to the ability to metabolise citrate. By extension mutation has no importance in the descent from the Cambrian and before, because blueprints have never existed…”

Nope. You really don’t have a clue, Jon. I’m talking about the fundamental ways in which biological systems are known to work in the real world, completely independent of whether they were designed directly by God or by evolutionary mechanisms. You just don’t understand how biology (particularly morphogenesis) works, as evidenced by your silly list. Hundreds of years ago, you would have insisted that sperm contained homunculi.

” - the gene pool contained all the information needed right back then…”

Nope. You’re a one-trick pony, said trick being gross misrepresentation.

“Your vaguely worded and annoying question (not an ad hominem, but a criticism - look up the difference)...”

Your comment was not that my question was annoying, Jon, but that I was annoying. That’s ad hominem. Look it up. Your ability to rewrite what both you and others say is nothing short of amazing.

“But the chimp consistently has 1-2 more vertebrae than the human. Direct evidence, please, that this has no basis in a mutation.”

Why? It clearly does. My point is that no mutations are required in a regulative system. And by the way, you’re still stuck on the ID misframing of evolutionary theory, in which selection is waiting around for mutations instead of acting on existing polymorphisms.

Jon, can you do anything other than misrepresent the positions of yourself and of others?

Jon Garvey - #63366

July 16th 2011

John, can you do anything other than misrepresent the positions of yourself and of others?


John - #63345

July 15th 2011

Why would I object to what Dennis wrote? He is politely explaining why you are confused about basic concepts.


Jon Garvey - #63357

July 15th 2011

He wrote the article for ME???? And yet I’ve never met him, and he never answered any of my questions. John, since you’re so much in his confidence, would you just get him to contact me personally?


John - #63360

July 15th 2011

Jon:
“He wrote the article for ME????”


And others.

You see, in standard English, there’s ambiguity because the singular and plural second person pronouns are identical. Some regional dialects, like Texan, lack this ambiguity and use “y’all” for the plural. Would you prefer that?

“And yet I’ve never met him, and he never answered any of my questions.”

But he did, as have I! I realize that you are petulant because they are not the answers that you want.

Jon Garvey - #63339

July 14th 2011

A week later, I conclude we don’t know why some stones travel so much further than others.


Jon Garvey - #63372

July 16th 2011

Hi Dennis - you can skip answering this one, as I’ve found a pretty good reply to the very same question from Allen MacNeill, who cites the chromosomal differences as the marcator between intra- and inter-species variation. Later in the same very informative, interactive and pretty good natured thread he gives the kind of hints I was after about why the same degree of genetic variation produces such different degrees of phenotypic variation. He didn’t even think the question stupid.

He also goes a good way towards explaining what the dozens of more recently discovered non-point-mutational causes of variation are, and how they can produce such dramatic changes with such minor genomic changes. Probably one of the most educational discussions I’ve read in a long time. Just a pity it turned out to be on Uncommon Descent.


Bilbo - #63160

July 7th 2011

Dennis: “ Here we see that,  at the genetic level, we are but a stone’s throw from other primates such as chimpanzees.”

Do we know how far a stone’s throw it is? 


Jon Garvey - #63163

July 7th 2011

Maybe about as far as you’d have to walk to find a chimp writing about evolution?


Dennis Venema - #63169

July 7th 2011

Hi Bilbo - get thee to a genome browser and have a look for yourself.  :)  Fully one third of our protein-coding sequences are 100% identical at the amino acid level. The average difference is 2 amino acid differences per protein (one substitution per lineage). As for the genome as a whole, the value is 95% identical even when counting indels as individual mutation events for each affected nucleotide. 


No matter how you slice it, our genomes, as Todd Wood puts it, are “nearly identical.”

John - #63173

July 7th 2011

Dennis wrote,
“Hi Bilbo - get thee to a genome browser and have a look for yourself.  :)”

Are you kidding? Bilbo looking at data for himself? Without guidance from “Mike Gene”?


Mike Gene - #63174

July 7th 2011

Okay, “I’ll” bite.  

Bilbo, accept my guidance here – listen to Dennis.  His argument is solid.  Note that he wrote:

Applying this test to humans and our closest (living) evolutionary relative, the chimpanzee, reveals that at a whole-genome level, we are over 95% identical….. Indeed if we use the same criteria to compare the diversity which exists within our own species, we humans are only 98% identical to each other.

But there is something you need to consider, “John.”  Bilbo tends to be an independent thinker.  He agrees with me on some things and argues with me about other things.  Almost as if he was a…....human being.





Steven Curry - #63175

July 7th 2011

One stone’s throw is equal to fourteen lizard lobs.


Mike Gene - #63177

July 7th 2011

Dennis: While this observation does not rule out the possibility of God directing this stage of human evolution in a more supernatural way, the genomics evidence suggests that this stage was accomplished in gradual, incremental steps.

True.  Yet human evolution was dependent on the existence of the eukaryotic cell plan (there is no reason or evidence to think a human-like entity could be constructed from bacterial cells).  So, did the eukaryotic cell emerge from nothing more than a series of gradual, incremental steps?


G8torBrent - #63184

July 8th 2011

Good grief. Humans and chimps and lizards and inert gases and trolls and hobbits, oh my. 


I love this board.

Bilbo - #63187

July 8th 2011

Hi Dennis and Mike,

Here’s the problem I see with your argument:  Douglas Axe provided a hypothetical protein where they calculated that it would take Darwinian evolution 1.5 billion years to get from one homologous form to another.  I assume that if we compared sequences that we would find them to be rather similar.  So either

a) Axe is wrong about his hypothetical example

or

b) close sequence similarity does not necessarily translate into a short “stone’s throw.” 

Now I think Steve Matheson argued persuasively against Axe, by pointing out that Axe’s example is only hypothetical, and there may never have been the need to evolve along a similar line in natural history.  On the other hand, maybe there was such a need.  Is there a way for us to tell?  Or are we stuck with mere guesses or assumed premises?

See here:

http://biologicinstitute.org/2011/04/16/when-theory-and-experiment-collide/


Dennis Venema - #63191

July 8th 2011

Hi Bilbo,


Axe’s model makes assumptions that aren’t realistic. For example, his model requires that mutations needed for a given transition be successively fixed in a population, and that such variation be neutral or slightly deleterious. If you look at the E. Coli / LTEE work in the previous blogs in this series you’ll see that fixation of alleles in the population was not needed for the multi-step pathway to citrate metabolism - (and that the lack of fixation was demonstrated by the frozen down samples covering the entire experiment). Even after citrate metabolism is reached, the population doesn’t fix the alleles for it - a minority population persists as glucose specialists. 

The requirement for alleles to go to fixation greatly increases the length of time estimated by Axe - but we know this assumption is unwarranted from direct experimental evidence. 

Mike Gene - #63192

July 8th 2011

Bilbo,

I prefer specific, concrete examples.  What you would need to do is pick a human protein and its chimp homolog and then make the case that something like 1.5 billion years would be needed to get from one homologous form to another. Or, just find any human protein and make the case that its chimp homolog could not be related by descent.   AFAIK, no one in the ID movement has ever attempted such a demonstration. 


sfmatheson - #63337

July 14th 2011

Hi Bilbo,


That’s not quite what I argued. The problem with the analysis by Axe and Gauger is not merely that the transition is hypothetical or that there was no “need” for it. You are right that the transition is hypothetical if by that you mean that it has not been postulated to have occurred, and that is the most important reason why their experiment was uninformative regarding evolutionary transitions.

And I also discussed another major weakness of their approach, which is their failure to look for transitional functions. This failure is not an oversight on their part; it would be very difficult to know which functions to look for. But the analysis they did—which was to look only at the two known functions at either end of the postulated trajectory—implicitly assumed that the only selectable activities were those at the beginning and end of the trajectory. Perhaps you’ll agree that this is a significant weakness in the experiment.

And we are certainly not stuck with “mere guesses.” We could refer to extensive analyses of the protein universe, including some very interesting new work from Dan Tawfik’s lab, and look for some part of the protein pedigree that suggests an evolutionary transition that could be reconstructed to some reasonable extent. I would think that there are hundreds of possibilities right now (depending on what the investigators consider to be “reasonable”), and there will be thousands more as genomic data accumulate.

My post:
http://sfmatheson.blogspot.com/2011/05/exploring-protein-universe-response-to.html
Tawfik lab publications:
http://www.weizmann.ac.il/Biological_Chemistry/scientist/Tawfik/publications.html

Bilbo - #63188

July 8th 2011

Hi John,

If I knew what and how to use a genome browser, I might try using one.  By we armchair philosophers often need depend upon the authority of others, which is why I frequently ask even you for information.


John - #63190

July 8th 2011

Bilbo, I doubt it. If you were at all curious, you would Google “genome browser,” and Google anticipates your need by offering “genome browser tutorial” before you can finish typing “browser.”


I don’t have a problem browsing genomes from my armchair. Why do you?

Steven Curry - #63196

July 9th 2011

Dennis,

Would you please clarify Biologos’ position with regard to intelligent design? Though my initial understanding was that Biologos opposed ID, it would appear that the relationship is more closely characterized as a “big tent” strategy.

The recent piece called “A Leap of Truth” could easily be mistaken for ID propaganda from the Discovery Institute. Indeed it features a former DI senior fellow. What was once called “intelligent design” or “CSI” is now being called “mystery”, with little change in the underlying arguments. Here was my reaction: http://biologos.org/blog/a-leap-of-truth/CP1/#comment-63036

The “Questions” section of this site states that Biologos holds the position of theistic evolution: “evolution by natural selection is the process God used to create.” So which is it? Are the gaps in our knowledge evidence that God intervened with a miracle, or did God use evolution to create?

Rather than a show of full support for theistic evolution, we see “escape clauses” such as this one in your piece: “While this observation does not rule out the possibility of God directing this stage of human evolution in a more supernatural way, the genomics evidence suggests that this stage was accomplished in gradual, incremental steps.”

On a superficial level what you said seems reasonable because nobody can really know for sure. But when you consider that the same could be said of *any* statement about biology, the implication is closer to intelligent design than to theistic evolution.

The significance is not in what you said, but in what you didn’t say: that such intervening miracles, though possible, are theologically unnecessary. That, as I understand it, is what separates Biologos from the Discovery Institute. And while I don’t fault you for not making that qualification, it does contribute to the observation that a “big tent” strategy may be in effect.

So, does Biologos oppose ID or tolerate ID?

There is a moral statement to be made here. Before poliovirus was understood, it would have been immoral to suggest that poliovirus worked miraculously via an intervening God to destroy its host. Instead, thankfully, scientists investigated poliovirus using the scientific method and consequently found a cure.

Once the poliovirus example is admitted, the proper stance with regard to any question in biology should be clear. We don’t know what breakthroughs or what human suffering may be alleviated through filling in our knowledge gaps. What applies to poliovirus applies to any unknown.


Dennis Venema - #63203

July 9th 2011

Hi Steven, 


The ID position is that God’s actions ( i.e. “designs”) are detectable through science. That’s a very different position from the epistemologically humble one that states science does not eliminate the possibility of divine action even as we use science to understand natural cause and effect. You are correct, this applies equally to everything in science. 

Trust me, I’m not exactly on the DI’s christmas card list.

Best, 

Dennis

Steven Curry - #63206

July 9th 2011

“...science does not eliminate the possibility of divine action even as we use science to understand natural cause and effect.”

And I submit that this is not theistic evolution as Francis Collins envisioned it for Biologos. What you are suggesting is very similar to ID: that evolution is insufficient in itself and that an unknown number of miraculous interventions happened in the past. Thus the only difference between Biologos and the Discovery Institute lies in whether the interventions are detectable.

Let me clarify that the moral aspect of this. There is a conflict of interest between these two positions:

(1) Such-and-such knowledge gap suggests divine action. Praise God! We were right all along. This evidence may help convince people to turn to Christ.

(2) Such-and-such knowledge gap means that we have more work ahead of us. We do not know whether it will be filled or not. It would be immoral to declare it unfillable because that would preclude the alleviation of human suffering which might result in having it filled.

If we agree that it would have been immoral to declare the poliovirus gap to be miraculous and unfillable, how can it be moral to suggest that any current gap is miraculous and unfillable?


Dennis Venema - #63207

July 9th 2011

Steven, 


I’m not sure where the confusion is coming from. 

I don’t see evolution as “insufficient”. I don’t see gaps in evidence as pointing to divine action. I have certainly not said that gaps are unfillable. I see gaps in science as an opportunity to do more work and close the gaps. And, as the article above points out, the evidence we have points to the sufficiency of evolutionary mechanisms. 

What I am saying is that even a full understanding of a process in mechanistic terms cannot rule out divine activity. No more, no less. 



Gregory - #63209

July 9th 2011

“a full understanding of a process in mechanistic terms” - Dennis Venema

Could you please give an example or two where ‘we’ (speaking of human beings) currently have such a thing as “a full understanding of a process in mechanistic terms”?

Iow, what do we have ‘full mechanistic understanding’ or even ‘full mechanistic knowledge’ of? You do not mean ‘a full mathematical X,’ but rather ‘a full mechanistic (not just mechanical) X’ of some object or entity, biological or social, etc. right?!

We must establish a hierarchy or orbit then, with the organic - as in Orga/Mecha - distinction applied more carefully in the mosaic, mustn’t we?

The negative ‘cannots’ are duly noted & compared with the frequency of positive ‘cans’ (e.g. think outside of the neo-Darwinian paradigm: a 21st century rite of passage) to observe the current BioLogosian balance.

Thanks, 
Gregory 


Dennis Venema - #63210

July 9th 2011

Or put another way, would you argue for the opposite of my statement as a necessary part of an EC / Biologos position?


this observation does not rule out the possibility of God directing this stage of human evolution in a more supernatural way”
br>
That would seem to overreach into territory that science cannot speak on. Thoughts?

Dennis Venema - #63211

July 9th 2011

seems the comment system isn’t working properly. the above quote was supposed to have the “not” as a strikethrough to alter the quote to read “this observation does rule out ...”


Bilbo - #63197

July 9th 2011

Dennis: “The requirement for alleles to go to fixation
greatly increases the length of time estimated by Axe - but we know this
assumption is unwarranted from direct experimental evidence.”

How much would the length of time decrease?  And would the number of nucleotide changes be relevant?  How many nucleotide changes were required in the E. Coli case?

From Axe’s work: “We infer from the mutants examined that successful functional conversion
would in this case require seven or more nucleotide substitutions. But
evolutionary innovations requiring that many changes would be
extraordinarily rare, becoming probable only on timescales much longer
than the age of life on earth.”

I was mistaken when I said they estimated 1.5 billion years.  They estimated more than 15 billion years. 


Dennis Venema - #63204

July 9th 2011

Bilbo, 


Go read the blog on the Lenski work again. That transition, allowing the bacteria to metabolize citrate, requires at least three nucelotide substitutions (probably more, but we won’t know for sure until the Lenski group sequences everything). That experiment was started in the late 1980s. At least three nucleotide substitutions have already happened. Do you seriously think Axe’s model is correct if he says you can’t get seven in 15 billion years?

Bilbo - #63198

July 9th 2011

Mike: “I prefer specific, concrete examples.  What you would need to do is pick
a human protein and its chimp homolog and then make the case that
something like 1.5 billion years would be needed to get from one
homologous form to another. Or, just find any human protein and
make the case that its chimp homolog could not be related by descent.  
AFAIK, no one in the ID movement has ever attempted such a
demonstration.”

Yes, that would seem to be a useful area of research by those who want to prove that Darwinian evolution can’t work.  But it would also be a useful area of research by those who want to prove that Darwinian evolution can work, wouldn’t it?  Otherwise, we are just assuming one or the other, aren’t we?


Mike Gene - #63201

July 9th 2011

Bilbo,

Okay, I’ll pick three genes off the top of my head. 

Human beta globin.  When we compare its amino acid sequence to chimp beta globin, it is 100% identical.  They are the same proteins.

Human insulin.  When we compare its amino acid sequence to chimp insulin, 108/110 positions have the same amino acid.  The two differences?  At one position, humans have alanine and chimps have valine. At the other position, humans have alanine and chimps have serine.  And guess what?  It takes a single point mutation (a change in one nucleotide of the gene) to get from alanine to valine or alanine to serine.

Human forkhead box protein B2.  When we compare its sequence to chimp forkhead box protein B2, 428 out of 432 positions are identical.  The four differences:

human amino acid – chimp amino acid



Serine-glycine
Glutamine – histidine
Phenylalanine – valine
Serine-alanine

And once again, all four differences can be bridged with a point mutation.


Bilbo - #63199

July 9th 2011

I might be mistaken about Axe’s estimate on the time needed, again.  In the research paper, they estimate 10^30 generations.  In their blog they estimate more than 10^15Gyr.  Not sure how they got that second number.


Darrel F - #63213

July 9th 2011

Steve (#63206) “Thus the only difference between Biologos and the Discovery Institute lies in whether the interventions are detectable.”

I would probably word this a little differently, how about, “BioLogos and the Discovery Institute differ on whether the

activity of the Creator is scientifically testable

.”  We,unlike D.I., have significant reservations about whether this will ever be possible.  Perhaps of greater concern though is that the examples that the D.I. leaders have put forward so far have, we think, been shown to be scientifically weak.  So that’s difference #1 and #2.

BioLogos does not rule out the possibility of supernatural activity by the Creator in life’s history, but  we also do not assert that it would have been necessary.  We see no biblical, theological, or scientific  reason for making an assertion one way or the other.  If good sound reasons become apparent from any of these three perspectives, then we’ll want to re-examine this, but right now it seems premature to take a position.

I would strongly encourage those interested in exploring this question further to read Ard Louis’ article, available for download here:“http://biologos.org/uploads/projects/louis_white_paper.pdf”


Steven Curry - #63224

July 10th 2011

Darrel and Dennis,

Of course, scientific conclusions are by definition tentative. They are always subject to revision or replacement when new evidence and/or better theories demand it.

And there have always been insoluble epistemological issues in science. Can we be certain that God does not fool our instruments every time we measure? Can we be certain that the universe was not created last Thursday, complete with fabricated memories of every human being and photons apparently arriving from distant stars? We can never be absolutely sure.

Imagine reading a textbook which said, “While we cannot rule out the possibility of divine action taking place in gravitational forces, the evidence indicates an inverse square law.” It is already understood that scientific theories are tentative, so we don’t need to constantly make that qualification. If there is evidence supporting divine action in gravity (I’m not sure what that would even be), then gravity can be revised. In the meantime, we stick with the tried-and-true gravitational laws (actually general relativity).

Acceptance of evolution, like acceptance of gravity, implies a level of confidence sufficient to disfavor backtracking to divine explanations. It is _always_ true, all the time and everywhere, that divine explanations can never be ruled out. (God himself could have just now pushed a key on my keyboard, causing the typo that I just corrected.) But accepting a scientific theory means that such explanations are placed on the back burner along with Last Thursdayism.

The stated position of Biologos is that “evolution by natural selection is the process God used to create.” That sure sounds like acceptance of evolution to me.

But now we have productions like “A Leap of Truth” suggesting that evolution may not be sufficient after all. A former Discovery Institute fellow is shown making ID-like God-of-the-gaps arguments, with ID terms being replaced with the word “mystery”.

And we now have the president of Biologos saying that “it seems premature to take a position” on whether supernatural activity occurred at some point in life’s history. In other words, it may _not_ be the case that “evolution by natural selection is the process God used to create.”

So is it Biologos’ position that “evolution by natural selection is the process God used to create,” or not?


Darrel F - #63226

July 10th 2011

Steven (63224),

Yes, the BioLogos position is that “evolution by natural selection is the process God used to create.”    We would add sexual selection and genetic drift to the mechanism as well.   Furthermore, given that the God of the Bible, the God in whom we believe, worked through natural and supernatural means, it is possible that He may have worked in creation through supernatural means as well.  As Christians, this other form of “data” (the Bible) informs us and unless there is good scientific, theological, or biblical reason to think otherwise, we’ll want to keep that possibility open. 

I would like to emphasize again the significance of Ard Louis’ articles on miracles and divine action.   

I would also like to make a comment regarding any former affiliation of BioLogos contributors with I.D.  Dennis Venema was an ID supporter until several years ago.  Although, I have always been extremely concerned about the quality of the scientific work by Philip Johnson, Michael Behe, and Bill Dembski, I was invited to be an ISCID Fellow by Bill and, given that he assured me that diversity and constructive criticism would be welcomed, I accepted and held that position until 2006.  I resigned largely because I had never been asked to do anything and I continued to be concerned about the quality of the scientific conclusions.


Steven Curry - #63231

July 10th 2011

Darrel, you say that the position of Biologos is “evolution by natural
selection is the process God used to create,” but then you add
qualifications to that. So that’s _not_ the position of Biologos in
its entirety, which was my point.

I _hope_ you mean the following:

“While divine action can never be ruled out, no evidence of it has
been found in the history of life, and until such evidence is found
our position is that evolution by natural selection is the process God
used to create.”

Does that accurately reflect the position of Biologos?


Darrel F - #63236

July 10th 2011

Steven (63231),

I appreciate your desire for clarification.   Dr. Collins book, “The Language of God,” emphasized his concerns about whether The Moral Law could be explained by purely natural mechanisms.  Also, my book stressed that God may influence the direction of life’s history in a  supernatural manner, but one so subtle that it is beyond the realm of  detectability…somewhat akin to how many of us believe the Holy Spirit works in the lives of believers.   I also suggested that God may have intervened by carrying out pronounced miracles in life’s historyjust like God intervened from time to time in the history of the nation of Israel.   

However, we are all strong supporters of the science of evolutionary biology, and many biologos supporters would hold the view that the natural laws are simply a reflection of the regular ongoing activity of God and that alone is sufficient explanation for the creation of all living organisms.  Take God’s activity away, and everything ceases to exist at that very instant, but that regular activity of God is both  necessary and sufficient to explain all that has happened.

Other biologos supporters are hesitant about being that dogmatic, hence you see the caution exemplified in Dr. Collins first book and my own (albeit in a different way).

When it comes right down to it, the issue becomes a theological question rather than a scientific one.  I think it is very important that the theologians, philosophers, and biblical scholars give much careful thought to this.   I also hope that  BioLogos can aid in facillitating this conversation in the coming days.  As a non-theologian, I don’t want to pre-judge how it will turn out, but I really look forward to watching.


Steven Curry - #63238

July 11th 2011

Well, I tried to get a straight answer.

In closing I will say that scientists should categorically regard Biologos’ newfound acceptance of God-of-the-gaps arguments to be deplorable. It is as if Biologos is campaigning to be the next incarnation of intelligent design, with ID terms like “irreducibly complex” being strategically replaced with “mystery”.

This may be an unintentional result of having members who are former ID supporters, or it may reflect a new strategy to attract ID enthusiasts and sympathizers. Whatever the case my be, it is another interesting example of how quickly an organization can diverge from its original vision once its founders have departed.


Bilbo - #63247

July 11th 2011

Dennis:  “Go read the blog on the Lenski work again. That transition, allowing the
bacteria to metabolize citrate, requires at least three nucelotide
substitutions (probably more, but we won’t know for sure until the
Lenski group sequences everything). That experiment was started in the
late 1980s. At least three nucleotide substitutions have already
happened. Do you seriously think Axe’s model is correct if he says you
can’t get seven in 15 billion years?”

I don’t remember if all three of those nucleotide substitutions were non-selective.  Were they?  Are you saying that the protein example that Axe uses did not really need 7 non-selective substitutions?  Or are you saying that even if they did need 7 it wouldn’t have taken 10^30 generations? 


Bilbo - #63248

July 11th 2011

Mike: “Okay, I’ll pick three genes off the top of my head….”

A good start.  How many more to go?  Are you at least willing to concede Axe’s point that being homologous proteins does not necessarily mean an ability for one to evolve by Darwinian means into the other?  If so, then observing that there is 95% sequence similarity does not necessarily entail that Darwinian processes can account for it.


Bilbo - #63294

July 13th 2011

Dennis?  Mike?  Are you there?


Gregory - #63296

July 13th 2011

Somehow I doubt Mike Gene is out there basking in apophatic superlatives…that would be unconvincing for an ID-promoter.


Steven Curry - #63299

July 13th 2011

Gregory, you should add “[Gold Member]” to your screen name.


Jon Garvey - #63314

July 14th 2011

The interesting thing about gold stars is that they make you wonder why certain people haven’t got them!


Steven Curry - #63342

July 15th 2011

Quite true. For instance you should have been awarded a Gold Plus™membership for this comment http://biologos.org/blog/a-response-to-coyne-and-contemporary-atheists-generally-part-2/CP1#comment-62981


Bilbo - #63331

July 14th 2011

I need to look up “apophatic.”


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