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Evolution Basics: Assembling Vertebrate Body Plans, Part 4

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October 24, 2013 Tags: Genetics, History of Life
Evolution Basics: Assembling Vertebrate Body Plans, Part 4
(Photo credit: Davide Meloni [CC-BY-SA-2.0], via Wikimedia Commons)

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

Note: This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we discuss the origins of birds, consider one of the longest-known and most famous “transitional forms” – the stem-group bird Archaeopteryx – and examine more recent discoveries that have greatly illuminated a century-old mystery.

As a brief recap, in the last few posts in this series we have traced the origins and diversification of vertebrates from their (pre) Cambrian origins, through jawless and jawed fishes, and on to the origins and diversification of stem-group tetrapods (“fishapods”?) in the late Devonian.


Phylogeny diagram

From this amphibian-like origin, crown-group tetrapods continued to diversify and acquire new characteristics that we can mention only briefly – such as the key transition to laying eggs on land with a membrane separating the egg from the terrestrial environment (i.e. an amniotic egg), and the subsequent diversification of amniotes into reptiles, birds, and mammals (as well as a number of extinct lineages that are known only from the fossil record).


Archaeopteryx lithographica

Archaeopteryx lithographica, a stem-group bird exhibiting features transitional between non-avian theropod dinosaurs and crown-group birds. [source: Wikimedia Commons]

Just winging it

With all of this tetrapod diversity to explore, we can only hope to visit a few points of special interest along the way – transitions that will also serve to illustrate other features of evolution that we have not yet discussed in great detail.

One transition that has long fascinated scientists is the origin of birds, with their striking adaptations of feathers and powered flight. These adaptations place modern birds at a sizeable distance from other present-day tetrapods – a fact that was troublesome to Darwin. Only a few years after the publication of his On the Origin of Species, however, a stunning stem-group bird was discovered in Germany – Archaeopteryx lithographica.

Even to a casual observer, Archaeopteryx displays a mix of “reptilian” and “avian” characteristics. Like reptiles, Archaeopteryx had a long bony tail, teeth, and forelimbs with clawed digits – but combined these features with a trait that until then had been thought to be the sole hallmark of birds – feathered wings. For Darwin, Archaeopteryx was simultaneously support for his theory as well as a reminder of the paucity of the fossil record. He would express these thoughts in a letter to a colleague in 1863:

The fossil Bird with the long tail & fingers to its wings (I hear from Falconer that Owen has not done the work well) is by far the greatest prodigy of recent times. It is a grand case for me; as no group was so isolated as Birds; & it shows how little we know what lived during former times.

Later, he would include a discussion of Archaeopteryx in a revised edition of On the Origin, as well as note that it had “affinities” with a then-known theropod dinosaur, Compsognathus:

Let us now look to the mutual affinities of extinct and living species. They all fall into a few grand classes; and this fact is at once explained on the principle of descent. The more ancient any form is, the more, as a general rule, it differs from living forms. But, as Buckland long ago remarked, all extinct species can be classed either in still existing groups, or between them. That the extinct forms of life help to fill up the intervals between existing genera, families, and orders, cannot be disputed. For if we confine our attention either to the living or to the extinct alone, the series is far less perfect than if we combine both into one general system. With respect to the vertebrata, whole pages could be filled with illustrations from Owen, showing how extinct animals fall in between existing groups… Another distinguished palæontologist, M. Gaudry, shows that very many of the fossil mammals discovered by him in Attica connect in the plainest manner existing genera. Even the wide interval between birds and reptiles has been shown by Professor Huxley to be partially bridged over in the most unexpected manner, by, on the one hand, the ostrich and extinct Archeopteryx (sic), and on the other hand, the Compsognathus, one of the Dinosaurians—that group which includes the most gigantic of all terrestrial reptiles.

So, even in Darwin’s time, the evidence supported the hypothesis that Archaeopteryx was a transitional form in the sense that we have been discussing – as a stem group on the lineage leading to modern birds – with that stem rooted within theropod dinosaurs.

Theropods of a feather, group together

Despite the early discovery of Archaeopteryx, other fossil species that “fill up the interval” between crown-group birds and extinct theropods were unknown until over 100 years later. In the mid 1990s, however, the first of what would be a number of significant discoveries was made in deposits of the Yixian Formation in China – namely, a feathered, non-avian theropod dinosaur named Sinosauropteryx prima. This fossil was noteworthy not merely because it was feathered and related to Compsognathus, but also because of the nature of its feathers – this theropod possessed only relatively simple “protofeathers” – unbranched filaments that could serve as insulation. Sinosauropteryx seems to have branched off the avian lineage at a time when feathers were not (yet) even branched, let alone adapted for flight.


Sinosauropteryx prima

An artist’s interpretation of Sinosauropteryx prima, a non-avian theropod with primitive, filamentous feathers. Coloration in feathered dinosaurs can be inferred from the shape of cells (melanosomes) responsible for feather pigmentation. [source: Wikimedia Commons]

Not long after the discovery of Sinosauropteryx, an additional “transitional form” – i.e. stem group on the avian lineage displaying transitional characteristics – was found in China that revealed a progression in feather evolution towards the feathers found in modern birds. Sinornithosaurus is not only a feathered, non-avian theropod, but one with tufted and branched feathers, which up until its discovery, had only been observed in birds:


Phylogeny diagram


Feather illustrations

Examples of feather types observed in the fossil record: (a) – single filaments, (b) tufted, (c) branched, symmetrical and (d) asymmetrical (flight) feathers. Not all types known are shown here.

These discoveries (and many others – feathered dinosaurs don’t even seem to make the popular press anymore, since they are now so common) thus “fill in the space” between non-avian theropods and birds – to the point where the boundary is so blurred that some new discoveries are debated as being “true birds” or merely very close non-avian relatives.

The use of “half a wing”

So, despite decades of protests from antievolutionists that no possible intermediate forms for birds could exist, we see a group of fossil species that meets the criteria handily – and demonstrates that yes, there was a use for “partially-formed feathers and wings.” Long before birds took to the air, feathers were a common feature of terrestrial, non-flying dinosaurs with a body plan markedly similar to birds. Indeed, at this time and place in biological prehistory, the body plan of “non-avian, feathered theropod” (and later, “quasi-avian, feathered theropod”) seems to have been a remarkably successful one, as evidenced by the number of species we observe in the fossil record that fit this general description. Feathers and wings are thus examples of exaptation – the repurposing of parts through evolution. Feathers were originally selected for a non-flight function (insulation, for example) and later were co-opted for another function (flight). Likewise, the wing is a repurposed (i.e. exapted) tetrapod forelimb. Had Darwin lived to see their discovery, no doubt he would have seen feathered theropods as another “grand case” for his theory.

In the next post in this series, we’ll return to the tetrapod lineage leading to our own species – that of mammals.


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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Roger A. Sawtelle - #83176

October 24th 2013

“God moves in mysterious ways His wonders to perform.”  William Cowper

Eddie - #83247

October 26th 2013

Above we read:

“Feathers and wings are thus examples of exaptation– the repurposing of parts through evolution. Feathers were originally selected for a non-flight function (insulation, for example) and later were co-opted for another function (flight).”

This is a classic example of speculation reported with the tones of certainty appropriate only for demonstrations in Euclidean geometry.  Plausible storytelling is offered as a nailed-down truth of modern science.  Yet in fact we don’t know whether feathers were “selected” at all; and if they were selected, we don’t that it was for insulation, and we don’t know that it was for any of the other alleged uses that have been suggested for non-flight feathers.  This is an example of why evolutionary theory, as long as it remains mired in neo-Darwinian categories (as it is on BioLogos, in the ASA, etc.), will never rise to the level of rigor of experimental sciences such as physics and chemistry, or the parts of biology that are purely empirical and experimental.  The whole Darwinian scenario invites just-so stories to a degree that is unparallelled in any other area of natural science.

BioLogos expects traditional, orthodox, evangelical, Reformation Christianity to reinterpret its Bible and rewrite its theology in order to conform with evolutionary theory.  If such a religious sacrifice is being demanded in the name of science, it would be nice if that science were something more than just-so stories.

It would also be nice if that science were up-to-date.  Though some of the data presented in the columns here is relatively recent, the theoretical perspective is pretty much the perspective that Mayr and Dobzhansky had.  It is as if BioLogos is stuck in some kind of time-warp and can’t get past about 1975.  There appears to be zero awareness of the seismic shift against neo-Darwinism over the past 20 years, and zero awareness of the writings of Shapiro, Newman, Wagner, etc.  To ask Christians to alter their theology to conform to “consensus science” is already cheeky enough; to ask them to alter their theology to conform to the consensus science of yesterday shows unbelievable chutzpah. 

My comments above are not meant to be harsh toward Dennis Venema, who is a very clear expositor and deserves credit for his very positive interaction with BioLogos readers.  They are a critique of the general approach to evolution on this site, an approach which has been shared in the past by other columnists here, e.g., Falk, Ayala, Alexander.

I haven’t made a comment under the “technical” columns here in quite some time; but I wanted to make my biological point one last time before the comments are shut down under the new policy of BioLogos.  I think the evolutionary theory offered here is theoretically inadequate, and that evolution in fact happened in almost nothing like the way it is portrayed as having happened by TEs, and that over the next 20 years developments in evolutionary biology are going to put neo-Darwinism out to pasture and make the commitment of TE to neo-Darwinism a very great embarrassment to TE as such.  That’s my warning; I don’t expect anyone here to heed it, or to agree with me.  But 20 years from now we will know the truth.  I’ll check back in then; maybe comments will be allowed again by that time.

Bobsie - #83253

October 27th 2013

Just curious. Since there is actual evidence of several types of feathers on obvious flightless animals exhibiting phenotype characteristics similar to birds as we know them, why do you call that evidence a “just-so story? Is it your assumption these feathers at whatever develoment state have no benefit or use for the species? If not, what is your speculation and why is it better than any other?

Eddie - #83270

October 28th 2013

I don’t offer speculations.  I observe that feathers are found.  I don’t conjecture that they are there because they have been “selected.”  For all we know (and a good number of evolutionary biologists have suggested this, though you would never know it from reading the columns on this site), much of evolution takes place outside of the reach of “selection.”

Selection is part of the narrative that Darwinians tell themselves as they look at the data.  Narratives and data are two different things.  If you read the narratives of non-Darwinians, narratives which are never discussed or even mentioned on this site, e.g., the narrative of Shapiro, or the narrative of Newman, you will find that they make quite a different story out of the same data.  (I’m not speaking specifically of feathers in the previous statement, but of different models of evolution generally.)

Could feathers have served some purpose before they were used for flight?  Possibly they could have.  Do I have knowledge of what that purpose was?  No.  Does anyone?  No.  I’m simply asking people not to present speculations in the form of declarative sentences in the conclusion of an article or essay.  

Dennis Venema - #83276

October 28th 2013

Eddie, this very series has posts on genetic drift and the founder effect - both “non-selective” and “non-Darwinian” features of evolutionary biology. I’ve also discussed neutral evolution of DNA sequences and the presence of large amounts of DNA in mammalian genomes that is not under selection, as far as we can tell - again, a non-Darwinian, non adaptationist view of the genome. So, I can hardly be accused of ignoring such data, nor am I quick to run to “adaptationist” views in general. The widespread presence of feathers in non-avian dinosaurs is good evidence that feathers were under selection of some kind - perhaps insulative, perhaps sexual selection, etc - but certainly not for flight, and that is the main point of this post. Flight feathers were exapted later.

Bobsie - #83311

October 30th 2013

I think I understand now. You are offended by the term “selected”. How about maybe using a less caustic word such as dominates, flourishes or prevails within a sub population. Those words imply a more innate reason. “Selected” sounds so external. Would that be better?

Eddie - #83315

October 30th 2013

I’m not “offended” by anything in the realm of ideas.  I think everything should be on the table.  The term “selection” doesn’t offend me.  I just think it’s epistemologically unwarranted in this case.

The point is that in Darwinian thinking, “selection” provides a reason why something happens.  We are told that birds retained their feathers, once they appeared, due to “selection.”  How do we know that?  How do we know the feathers didn’t just appear, and, having once appeared, did neither harm nor good to the animal, were about equally as useful as reptile scales, and just “went along for the ride”?  Dennis has just admitted that he isn’t an extreme selectionist and that much genetic and morphological change may not be under selection at all.  So how does he know feathers were “selected”?

And the same could be said about “exapted.”  “Exapted” implies a narrative of many steps.  You don’t just go from feathers on a body to a fully working feathered wing.  How do we know that the transition was a simple case of “exaptation”?  Again, the vocabulary of neo-Darwinism is laced with hypothetical explanations, broad terms used in an almost incantantional way to stand in for detailed transitions about which we have almost zero historical or experimental knowledge.

I don’t say it’s “false” to say that feathers were “selected” or later “exapted”; I say it’s not logically compelling.  But it’s being presented as though it is logically compelling.  And I don’t single out Dennis in this regard—who by the way is a very clear writer and a very constructive columnist for his interactions with critics.  I’m really criticizing the whole tendency of neo-Darwinism (and all the later adjustments which evolutionary theorists have tried to harmonize with it, e.g., “drift”) to solve complex problems by appealing to a few broad concepts that are superficially plausible but often not so impressive when one asks for detailed steps.  And sure, I appreciate that Dennis is doing a popular summary here, but I have the right to point out where the popular summary may conceal some difficulties beneath the apparently smooth surface.

If it’s not already clear, I’m not insisting on a historical reading of Genesis 1 and I’m not rejecting common descent or the idea that God could use an evolutionary process.  I’m simply playing the role of skeptic, trying to sharpen and improve both scientific and theological claims by demanding more rigor and clarity.  And just as I find many of the theological claims on this site to be very weakly defended, so I find some of the proposed evolutionary mechanisms to be sketchy and speculative.  I have nothing more to say on this topic, so I’ll exit now.


Hanan D - #83351

October 31st 2013

>How do we know the feathers didn’t just appear, and, having once appeared, did neither harm nor good to the animal, were about equally as useful as reptile scales, and just “went along for the ride”?

Well, isn’t that what evolution is? As Dawkins said, “an ear doesn’t know it’s an ear.” So ya, it appeared, lets say, it didn’t harm the animal and it has been here ever since. 

Bobsie - #83567

November 19th 2013

Oh, I understand. You’re an “eyewitness” guy. Forensics just won’t do it. Good thing you’re not in police work. Wouldn’t you agree?

Roger A. Sawtelle - #83252

October 27th 2013


Thank you for an interesting comment.

You claim that BioLogos is asking evangelicals to accept “just so” Darwinian theory that is out of date. 

Fierst of all from what I understand Darwinian theory at least the brand of Dawkins and Dennett is against “just so” stories of this kind, because it goes against Dawkins’ gene’s eye view of evolution.  Just so stories indicate that evolution is designed through ecology. 

You say that you believe in design, so what do you have against just so stories, or does your understanding and support of Dawkins extend to criticism of just so stories backed up by science? 

You mention some names but leave out Dawkins, who is the best known evolutionary biologist of our time.  You say that there has been a seismic shift against neoDarwinism  over the last 20 years, but not what the change entails.  How about other thinkers such as Wilson, Gould, and Margulis?  Where do they stand in this shift?       

Eddie - #83271

October 28th 2013


All of Dawkins’s thought on evolution is one long just-so story, overwhelmingly speculative.  Indeed, even evolutionary biologists are frequently critical of Dawkins as too qualitative and philosophical rather than quantitative and scientific in his approach.  But he is very persuasive because he is a great science writer.  That’s why everyone, after reading The Blind Watchmaker (a great exposition of evolution), should read Behe’s Darwin’s Black Box (a great way of stripping away the just-so stories that Dawkins offers).  Have you read Darwin’s Black Box, Roger?  

If you want to know what the shift in evolutionary theory entails, you can read about it.  Get Suzan Mazur’s book on the Altenberg 16 for a popular account of the Altenberg conference, then get the actual conference proceedings for a more accurate scientific account.  And get the new book Evolution by James Shapiro.

As you know, Roger, comments are going to be closed down soon.  You probably won’t hear from me again.  Thanks for all your conversations and best wishes.



beaglelady - #83259

October 28th 2013

If God controls everything and there are no random things happening out there, how can we do things like calculating genetic outcomes?  That’s what genetic counseling, at least in part, is all about.

Eddie - #83272

October 28th 2013

It’s well-known, beaglelady, that you don’t believe that God controls everything.  Indeed, it is not clear that you believe that God controls anything.

It’s amazing, the level of agreement one finds among Episcopalians, Methodists, Mennonites, Nazarenes, and others around here, that for God to actually do anything in evolution would constitute a sort of theological embarrassment.  One wonders if any of these people have ever actually picked up a Bible and noted the description of God’s creative activity found therein.  But then, why should Protestant evangelical Christians care about what the Bible says?

beaglelady - #83304

October 30th 2013

I was wondering why we can calculate genetic outcomes using probability.   Mendel wasn’t exactly evil, since he was a monk.

Eddie - #83310

October 30th 2013

There can be evil monks, as well as evil priests, and evil professors of theology.  The logic of your “since” does not hold up.  However, I grant you that Mendel was not an evil man.  

You cannot predict actual genetic outcomes.  You can only give a list of the mathematically possible outcomes, and calculate their relative likelihood.  That’s what Mendel did.

Mendel did not advocate evolution, by the way.  And note that Neo-Darwinism requires Mendel’s results in order to be true, but Mendel’s results do not require neo-Darwinism in order for them to be true.

As usual, you dodge the theological question of whether or not God actually does anything in evolution.  And as usual, I can think of only one possible reason why you would do this.  If you believed that God was in control of any part of the process you would not have any motivation to remain silent.  You would gladly specify where you think the control is exercised.

beaglelady - #83323

October 30th 2013

Yes, you can predict genetic outcomes in Mendelian genetics.   The larger the sample size, the more accurate the predictions will be.   Mendel had studied mathematics, and his sample sizes were pretty large.   

Eddie - #83326

October 30th 2013

Mendel did not predict the outcome in his initial experiments with the peas.  He discovered that certain ratios of characteristics were found in the second crossed generation.  He then was able to show that these results were consistent with a mathematical theory of genes involving dominant and recessive traits.

Of course, we live after Mendel, and have the benefit of his insight.  If you know in advance the genetic makeup of your sample, you can make certain predictions.  If I know that I have purebred green peas crossing with purebred yellow peas, and I know that green is dominant, I can predict the offspring will be all green.  But if I’m working with crossbred offspring of green and yellow peas, and I crossbreed any two individual plants, how can I predict what trait any single individual offspring will have?  I can’t, because it’s probablistic.  I can predict that 1/4 of such offspring, over the long haul, will be yellow, and 3/4 green (if green is dominant), but I can’t predict the individual case.

So the question is, beaglelady, when God created the earth, did he create it such that the probability of the emergence of man upon it was something like the probability of the emergence of a yellow pea in the second generation?  Something with only a minor probability, as opposed to a certainty, of appearing?  Or did he do something to make the appearance of man a sure bet, like the probability of a green pea appearing in the first generation cross?

If the former, how could God say, “Let us make man” with a straight face?  He would have to say:  “Let us roll the dice and see if man emerges.”  Is that orthodox Christian teaching about creation?

Dennis Venema - #83344

October 31st 2013

So, Eddie - when our son was born with a life-long, serious medical condition caused by a single allele (one dominant to the wild-type allele), and it was a 50:50 chance of him being affected or not affected, is it your position that God “didn’t roll the dice” as it were, but determined in advance that he would inherit the disease?

Hanan D - #83349

October 31st 2013

but determined in advance that he would inherit the disease?

As personal as this comment is, I will just throw my hat in to play devils-advocate. Why is it theologically problematic that it was in fact determined? Don’t think for one second, that just because you may believe God had nothing to do with it personally, that he is not to blame. This is where Ayala is totally wrong in thinking that it is a slap to God’s face to suggest he personally did X to a person. It is irrelevant if God specifically did it, or did not. The reason being, that God created the system at some point. He made it to be random (under your theology) so He is still implicated by the fact that he made it that innocent people will get a disease. 

Dennis Venema - #83352

October 31st 2013

Thanks, Hanan. I realize it is a personal comment, but it was an issue that came to mind once “Mendelism” was the topic of discussion.

I don’t follow Ayala’s thinking, no. I’m more interested in what Eddie thinks - does he allow for anything “natural” to be non-determined? If no, why? If yes, why?

My personal opinion is that God ordains and sustains everything we perceive as “natural”, but that He doesn’t necessarily determine things at a micromanagement level. So, our son’s disease is part of the fabric of a real world, with real cause and effect, just like a world with gravity means that sometimes people will fall to their deaths. But I’m not a theologian, and I try to stick with my own areas of expertise.

To this day, however, no student has ever complained about the randmonness of chromosome segregation at meiosis that is absolutely necessary to get probabilities we observe. Bring up Darwin, and randomness is a problem; Mendel, not so much. (Note, I’m using random in the scientific sense, not as a synonym for “ateleological.”

Hanan D - #83350

October 31st 2013


I have come to the conclusion that trying to get an answer out of beaglelady for anything to do with theology is pointless and a waste of time.  Better to leave her alone and simply deal with issues of science and that is it. 

Yes, I know this is Bio"Logos” and you want to deal with theology, but sometimes you need to make some exceptions in who you are dealing with. 

beaglelady - #83355

October 31st 2013

And you are incredibly rude, and you have a strange fixation on randomness.  

Hanan D - #83360

October 31st 2013

a) nothing rude in what I said. It is better to not discuss anything related with God with you. You have a habit of a) never answering any questions b) when you attempt to answer, you simply answer with another question c) ignoring the essense of the question. That is why things go on in circles. So it is better not get into theology with you.

And yes, I am fixetated with randomness. so? Some people come here just to learn dry evolution. Other people come here to ask the tough questions as how randomness can work with a theistic God. In my book, and probably the vast majority of theistis, a God that simply rolled the dice and had no idea of what was going to happen or had no vision in his “head” is not a theistic God. That is deism.  You can kvetch Christ all you want into that. But in the end of the day, it is deism.

Hanan D - #83361

October 31st 2013

BTW beaglelady, this is for your own well being as well. Aren’t YOU sick of us always going around in circles? You have a right to whatever theology you want even though I don’t find it to make any sense. Therefore, it is simply easier to let you be and not annoy you with the same questions which ends up annoying us. 

Obviously, Eddie is free to do as he wishes. 

beaglelady - #83354

October 31st 2013

Mendel did not predict the outcome in his initial experiments with the peas.

Obviously.  The dominant theory at the time was blending.   He would discover his famous laws of segregation and independent assortment. 

While we can’t predict single outcomes, we can predict ratios of genotypes and phenotypes. 

beaglelady - #83356

October 31st 2013

If God had very specific goals in breeding us and our appearance is of paramount importance, how did he accomplish that?  Forced matings?  Genetic engineering?  It makes you wonder why so many sperm are released at one time, since he’s apparently got his money on only one of them for any human coupling. 

Richard W - #83266

October 28th 2013


While I still can let me thank you for your contributions to this site.  I’m sure that you have to stay up late in your busy life to spend the time to write such informative, clearly written and (relatlively) easy to understand articles, and friendly responses to comments that aren’t all the time that friendly.  I’ve been silent fan of yours since I’ve been on here and always look forward to your newest piece.  I’ve learned so much about biological evolution from you and I’ll even go so far as to say that if your work were to dissappear along with comments, I might not come back.  Keep up the good work and I look forward to your next article.

Dennis Venema - #83275

October 28th 2013

Richard, I’m glad that these posts were useful to you. Thanks for the encouragement. And yes, most of them are written in the wee hours of the night! I prefer to do my research and write when I have long stretches where I won’t be interupted.

Roger A. Sawtelle - #83278

October 29th 2013


Thank you for the referral to the book Evolution by Shapiro.

Below is a critical quote from a review by Anthony Dean that was taken from the Amazon website: (emphasis added) 

In Part III Shapiro seriously overreaches. He argues that horizontal gene transfer, symbiogenesis, whole genome doubling, and the modular and duplicative nature of protein evolution are non-Darwinian because they do not conform to strict vertical inheritance and Darwin’s advocacy of “numerous, successive, slight variations.”

Comment 1:  Shapiro is saying that ecological biology advocated by Lynn Margulis and myself is overtaking traditional evolutionary explanations of genetic change.  Of course I would tend to agree.  Thus if you agree with Shapiro than you are agreeing with Margulis, and the ecological view of evolution, which is part of what I have been saying all along.

Comment 2:  The problem with Shapiro and his critics is that they they confuse evolution with Variation or genetics.  Evolution is not primarily about how life forms change (Variation), although this is an important part of evolution. 

Evolution is primarily about why life forms survive and flourish, which is the story of Natural Selection.  Life forms survive and flourish because they adapt to their environment, their ecological niche which is constantly changing in one way or another. 

Darwinian Malthusian theory which has not been updated bases Natural Selection not on adaption, but competition.  The only adaption which Malthus suggested to avoid catastrophe was population limitation.  The irony of this is that population limitation by part of the world population means that they are “less fit” than those who allow their population to grow geometrically.  

The adaptionist, ecological view is to both limit population while increasing production in a ecological responsible manner working together for the good of everyone.  

Comment 3:  My point has always been that we need a better understanding of evolution which is not based on an atomist, competitive understanding of Nature, which is the view of Darwin and the Selfish Gene.  Ecological evolution offers such a scientific view, which is compatible with the Christian point of view that Jesus Christ is the Logos. 

The question is not “Is God in control?”  The question is “Does God reign and rule through Love?”  The answer to this question is YES.          

Hanan D - #83284

October 29th 2013


I am curious to as the jist of your disagreement with Eddie about the mechanism of evolution. I’m trying to narrow it down, but honestly I don’t get it. 

Eddie - #83285

October 29th 2013

Roger, if you have scholarly or scientific training, you should know that one can’t form a reliable opinion of the value of a book, or even an understanding of the contents of a book, based on a third party’s opinion of the book.  Especially not some reviewer on Amazon.com, which is not a venue where scientific criticism is properly aired.

You haven’t read Shapiro’s book.  You therefore have no business offering an opinion on his arguments or overall conclusions.  I have read Shapiro’s book.  It’s clear to me that you don’t understand what Shapiro is about.  Please do everyone here the courtesy of refraining from further speech about Shapiro until you have acquired such understanding.

Contrary to your view, the theological question regarding evolution is very much, “Is God in control?”  And by the way, where in the various Biblical accounts of creation do you find the word “love” employed?  I must have missed it.

Roger A. Sawtelle - #83286

October 29th 2013

Hanan D

Thank you for your question. 

There are two aspects to our disagreement.  First is based on my disagreement with all or almost all persons about the primary role of ecology in Natural Selection and evolution.  You have not responded to my comment in the last thread on this topic (at least not at my last view:)

The other aspect is based on his philosophical and theological stance which makes him an advocate of Intelligent Design.  His position is that God, not Natural Selection, determines evolution.  My position is that God uses ecologically driven natural selection to guide and determine evolution.

I can understand your confusion.   

Eddie - #83289

October 29th 2013


In your comment above to Hanan, you have mischaracterized my views.

First of all, I have never for a moment denied the importance of ecology.  Indeed, I can’t think of any evolutionary biologist who does.  In some universities, there are even departments with names like “Evolutionary Biology and Ecology.”  Certainly the idea of natural selection itself implies an ecological view of nature.  I don’t think Darwin knew the word “ecology,” but if he were introduced to it, he would say that it was central to understanding evolution.

Second, I have never said that God instead of natural selection determines evolution.  I have never ruled out the possibility that God works through natural selection, mutations, or other things.  Nothing in my view requires that God directly creates new species by a wave of the divine hand.  The point is that whether God creates directly or indirectly, he is in control of the results.  That is a conclusion required by any truly Biblical Christianity.  It is also a conclusion required by any historically orthodox Christianity.

Finally, you say that that it is my “philosophical and theological stance” which makes me an advocate of intelligent design.  That is not the case.  I am an advocate of intelligent design based on my reasoning from the data provided by nature.  And the fact that ID numbers among its advocates Catholics, Anglicans, Orthodox, Reformed, Baptists, Methodists, Jews, Muslims, Hindus, Deists, and agnostics indicates pretty clearly that it is not any particular theology that drives ID.  

Of course, any truly Biblical or orthodox Christian will believe that nature is intelligently designed, even without making inferences from the scientific data, because both the Bible and the Christian tradition are crystal-clear in their position that God designed and made nature.  But the point of ID is that one can reason to an intelligent designer of some kind without relying on the Bible or tradition.  If you would take the time to actually read books by ID writers, e.g., Darwin’s Black Box or The Design of Life, you would see how such reasoning works.  You won’t find any appeals to revelation in either of those works.  You’ll find appeals only to the data provided by nature.

It helps, Roger, to understand the position of others before you express disagreement with it.  And understanding the position of others sometimes requires careful listening to them, and careful reading of the sources which inform them.  You haven’t been particularly good at listening to me, and you’ve been neglectful in not consulting my sources.  These have been the problems in our communication all along.  Best wishes.


Roger A. Sawtelle - #83296

October 30th 2013

Eddie wrote:

It’s clear to me that you don’t understand what Shapiro is about.  Please do everyone here the courtesy of refraining from further speech about Shapiro until you have acquired such understanding.

I was clear in saying that I have not read Shapiro’s book which is why I used the quote from the review.  Maybe the reviewer did not understand the book. 

I do not agree with the conclusions of the reviewer, but as far as I can tell his synopsis is accurate.  The problem with your response is that you did not criticize the statement from the review, only that it was a statement from a review.  By the same measure you have rejected my book without reading it.  

And by the way, where in the various Biblical accounts of creation do you find the word “love” employed?  I must have missed it.

Where in the Bible is the word Trinity?  “In the Beginning was the Word, and the Word was with God and the Word was God.”  “God is Love.”  1 John 4:8

When Darwin accepted Malthusian population theory, survival of the fitest, as the basis for natural selection, he denied the crucial importance of Ecology and Love.  To be clear that is not your mistake.  That is almost everyone’s error.  

Finally I do not think that anyone, believer or nonbeliever should apologize for his or her world view and acknowledge that it does influence how we see the world.  I have made it clear that my Trinitarian understanding of life and the universe does guide my understanding of science.  

This has guided my critique of Darwinism and it seems that we agree in many respects, certainly that God is guiding evolution and traditional Darwinism is passe. 

I does seem a shame that you for whatever reason are unwilling to consider my solution to this problem.   

Eddie - #83297

October 30th 2013


Of course love is important in Christianity and it is an important subject in the Bible as well.  My point was not that love was unimportant, but that “love” does not figure largely in the passages of the Bible that are about the creation of the world.

I have not “rejected” your book in the sense of rejecting its arguments, because I have not read the book.  Therefore, I make no comment on the contents of your book at all.  However, I have read your comments here, and therefore I have the intellectual right to comment on them.  And since we have interacted extensively, I think I have enough knowledge of your overall approach to religion and science questions to judge that your book, whatever its merits, would not be of enough interest to me to invest the time required to read it.

I’m certainly not asking you to apologize for your world view.  However, I don’t know why you keep pretending that a “Trinitarian” world view is something special or rare, and that you are introducing something striking to the world by advocating Trinitarianism.  Trinitarianism is standard Christian teaching and nobody here has spoken against it.  Why do you continue to stress that you accept the standard Christian teaching?  That is simply expected of a Methodist clergyman, and is nothing surprising.

You are in some way trying to relate Trinitarianism to theology/science discussions, but your way of doing so is murky and unclear.  And you seem to fail to perceive that the people you are debating with, e.g., Jon Garvey, are completely onside with the Trinity, and that their disagreement with you is not over the Trinity but over other theological matters, over scientific matters, and over how you connect theology and science.

Trinitarianism is a doctrine of the relationship between the three Persons in the Godhead.  It is not specifically connected with ideas of the natural world, evolution, etc.  If you think there is a connection, you need to show it, not merely assert it.  And the best way to show it, to people like myself and Jon Garvey who are well-trained in Biblical studies, is to take us through Biblical passages in a connected way and show how Trinitarian doctrine has implications for the creation of the physical world, for discussions of evolution, ecology, etc.  I don’t see any firm Biblical basis for your speculations.  Isolated passages like “God is love” won’t do the trick.  They have to be connected in a larger theological picture.  I’m not saying it can’t be done; I’m saying you haven’t done it.  At least, not in this forum.

Roger A. Sawtelle - #83298

October 30th 2013


You indicate that you feel that you understand my views well enough that you have little interest in them.

In the rest of your comments you indicate that that you do not really understand them, but you know that they are different from yours so they cannot be worthwhile. 

Even though this kind of give and take is frustrating I hope that others benefit from it and I do think that it would be a shame if BioLogos does cut it off.

Best Wishes,




Eddie - #83312

October 30th 2013


Regarding your comment in your second paragraph, on my alleged motivation, Roger, I would have you know that I have graded thousands of university papers and exams, and have never once failed or downgraded a student for disagreeing with my position.  In fact, I rather like students who disagree with my position, provided that they do so based on evidence and logical argument.  The easiest way to get an “A” with me is to disagree with me, but to do so intelligently.  So your charge that I reject your ideas because they disagree with mine is simply false.  You do not know me personally and you should not be imputing such motivations.

Roger, the reason that I do not read your book is not that you disagree with me.  The reason is that I doubt that it would be much different from the material you have presented here.  I have a good sampling of your factual knowledge (regarding history, philosophy, theology, and science) from what you have written here, and I have a good sampling of your reasoning and of your personal theological biases from what you have written here, and based on these samples, I extrapolate to what your book will be like, and decide that it is not the sort of book I would benefit from reading.  It’s like going to free food sample displays at a Costco store.  You taste the free samples, assume that a larger package of the food will taste much like the sample, and decide whether or not to buy the larger package based on the taste of the sample.  And just as you wouldn’t purchase a whole package of frozen shrimp after tasting a sample you didn’t like, so I don’t intend to read 100+ pages of writing with style and contents similar to what you have presented here.  I don’t say that to attack you personally.  I’m saying that you have had more than ample time and space to make your strongest “sales pitch” for your book, and that I’m not sold.  Best wishes.

Hanan D - #83305

October 30th 2013


In an interview with the late lynn margulis, she made the remark: “There is no gradualism in the fossil record.” What would you say to her? Are fossils like Archaeopteryx evidence that she is simply overlooking?

Dennis Venema - #83338

October 31st 2013

Magulis is claiming that we don’t see species-to-species transitions in the fossil record. For the most part this is true, as I have discussed already (since for most species the sampling frequency of fossilization is too infrequent to document a species-to-species transition). She overstates her case, though - for species where the fossil record is very good (say for example, microscopic marine organisms that are constantly deposited in sediment) we can observe gradualism that slowly morphs one species to new forms over time.

Hanan D - #83340

October 31st 2013

we can observe gradualism that slowly morphs one species to new forms over time.

And she didn’t know this?

Hanan D - #83341

October 31st 2013

But again, wouldn’t Archaeopteryx a sample of a species-to-species transition?

Dennis Venema - #83343

October 31st 2013

No, not unless we could find a species so very, very close in morphology to Archaeopteryx that we would suspect it was a very, very close relative. Even then, there is no way to determine with certainty that this new fossil was a descendant or antecedent of Archaeopteryx, or just a very close relative.

If you think back to our discussion of “species” as a fuzzy concept, you’ll see the issue - once you’re talking about “species-to-species” transitions, you’re up against the issue that there is no clean dividing line between species as they form (think: dogs and wolves, for example). The fossil record is just not suited to that level of fine detail - we have a diffcult enough time on the species question when we have access to full populations!

And as for Margulis, she wasn’t exactly an expert on the fossil record. She either wasn’t aware of counterexamples or she was intentionally overstating her case - perhaps not maliciously - it would depend on the context of the conversation. She may have been engaging in hyperbole.

Hanan D - #83346

October 31st 2013

I understand that “species” is a fuzzy concept, but how can it be that no transitional fossil been found? Maybe I am oversimplifiing things, but why is dinosaur—>archaepteryx—>bird wrong? With archaepterix being the transitional form from dino to bird? Simple as that no?


She was replying to this question from here:

What kind of evidence turned you against neo-Darwinism?

What you’d like to see is a good case for gradual change from one species to another in the field, in the laboratory, or in the fossil record—and preferably in all three. Darwin’s big mystery was why there was no record at all before a specific point [dated to 542 million years ago by modern researchers], and then all of a sudden in the fossil record you get nearly all the major types of animals. The paleontologists Niles Eldredge and Stephen Jay Gould studied lakes in East Africa and on Caribbean islands looking for Darwin’s gradual change from one species of trilobite or snail to another. What they found was lots of back-and-forth variation in the population and then—whoop—a whole new species. There is no gradualism in the fossil record. 

Hanan D - #83348

October 31st 2013

And BTW, I often hear biologists defending evolution saying there are many transitions in the fossil record. Are they over stating it as well, or am I misunderstanding them?

beaglelady - #83357

October 31st 2013

There are many posts on this site about transitional forms.  Also, have you visited a natural history museum and looked at fossils?    

Hanan D - #83359

October 31st 2013

I was asking Dennis, but thank you beaglelady

Dennis Venema - #83362

October 31st 2013

Look again at Margulis’ quote - she’s interested in transitions from one species to another. Dino >> archaeopteryx >> birds is not a likely path (archeopteryx is a stem-group species on the avian lineage), but even if it was, there would be many more species in between those three groups. The fossil record samples too infreuently in most cases to capture the fine detail of species - to - species gradualism.

Hanan D - #83371

November 1st 2013

but even if it was, there would be many more species in between those three groups.

Ok, but it would still mean that it was a transitional fossil. Yes, there would be more in between, but it would be one of those. So then am I to understand that none of the hominid fossils are transitional? That they too are stem group species? So again, what do I make out of the fact that many scientists always claim there are plenty of transitional fossils to disprove the critics.

melanogaster - #83444

November 5th 2013

“Ok, but it would still mean that it was a transitional fossil.”

Transitional between what and what?

“Yes, there would be more in between, but it would be one of those.”

One of what?

“So then am I to understand that none of the hominid fossils are transitional?”

Transitional between what and what? Did you not read what Dennis wrote to you?

“That they too are stem group species? So again, what do I make out of the fact that many scientists always claim there are plenty of transitional fossils to disprove the critics.”

I’m pretty sure that NO scientist would do so. How would a mere claim disprove anything? Why are you obsessed with discussing what people claim (including gross misrepresentations of what people claim) instead of examining the evidence for yourself? Beaglelady’s question, and your avoidance of it, was very revealing.

And I still don’t know if you’ve bothered to retract your implicit claim of intellectual superiority over God, since you clearly know the outcome (immunity after vaccination) of a biological process involving a huge random component (the adaptive immune response) while your God is somehow too mentally feeble to know the outcome (man) of a biological process involving a huge random component (evolution).

beaglelady - #83306

October 30th 2013


Thank you for the excellent post.

Here’s a very interesting video by Mark Norell, a paleontologist at the American Museum of Natural History. He discusses his discovery that a dino had iridescent black feathers, much like modern crows. He also had a paper in Science about it.   Some time ago he also did a webcast on feathered dinosaurs which was very cool.  (I like Mark Norell, but his hair always looks like he just got out of bed—talk about ruffled feathers!)  

Roger A. Sawtelle - #83318

October 30th 2013

OK Eddie,

Now you are saying that I am and my ideas are stupid.  I think that you should have quit while you were still ahead.

Eddie - #83327

October 30th 2013

No, Roger, I didn’t say that at all.  I said that I could not benefit from reading your book, if your posts here give a fair sample of what is in your book.  That merely indicates that our methods and conclusions and appraisals of the facts are so different that we cannot have a profitable discussion.  It may be that I am the one who is “stupid”; or it may be that both of us are confused and wrong.  The point is that, whoever is right or wrong, further conversation is a dead end.

If I were to read your book and comment on it, we would be back on the treadmill, rehashing the same inconclusive arguments all over again.  So why would you want me to read your book?  If you were Karl Marx, would you, after a month of barroom arguments with Donald Trump, urge him to read your Communist Manifesto?  Why would you bother, when it was clear from your conversations that Trump was opposed to your most fundamental premises and convictions?  Would you actually think that the book might convert him, when none of your oral arguments could?  

You are being about as practical as a Christian missionary who goes to Saudi Arabia and knocks on the doors of the Muslims there.  You need to find the right target audience, and it isn’t me.  Best wishes.

Roger A. Sawtelle - #83329

October 31st 2013


Now you are saying that we are as different as a Christian and a Muslim.  Which are you?  As for me my fundamental premises and convictions are based on a belief in Jesus Christ as Logos.   

Even Christians and Muslims need to come together to find a modus vivendi if we are going to have any peace in this world.  So I should say especially Christians and Muslims. 

And as I noted before the schism between Christians on the right and on the left in the US is scary.  You might not be concerned about this, but I am. 

Christ called Christians not to divisiveness, but to a Ministry of Reconciliation.  If you are convinced that we cannot come to a meeting of the minds, so be it, but I am going to try, even if you do not.      

Eddie - #83336

October 31st 2013

Stunning.  Absolutely stunning.  Entirely missing the point of my analogy (the uselessness of a Christian missionary knocking on a Muslim’s door in Arabia) and you launch into talking about actual Christians and Muslims!

The point is nothing to do with Christian vs. Muslims, Roger!  The point is that you and I are like night and day, fire and ice, and are never going to get along regarding philosophical/theological matters.  Our fundamental premises are almost entirely different.  Not just our religious and philosophical premises, our study and research habits, our educational backgrounds, our cultural attitudes, etc.  We don’t think alike, and we don’t feel alike.  It is not a question of disagreement over this or that passage of the Bible.  It’s a question of existential incompatibility between two persons.  I don’t want to make war with you over these differences.  I just want to stop talking to you, because I find it an unprofitable use of my time.  Best wishes.  

Roger A. Sawtelle - #83345

October 31st 2013

Eddie wrote:

It’s a question of existential incompatibility between two persons.

What an interesting idea.  Some people are existentially incompatible.  That explains everything, racism, intolerance, homophobia, etc.  We are just existentially incompatible with others.  That would funny if it weren’t so serious.

Jesus came into the world in large part to break down these existential barriers that made people incompatible, the barriers between Jew and Gentile, between Greek and Barbarian.  It is sad that many Christians do not know or care about what Jesus Christ stands for.  


Eddie - #83370

November 1st 2013


What is “sad” is that many ordained Protestant clergyman promote a Jesus Christ who is a simpering, touchy-feely, oh-so-sensitive social worker, instead of a fiery prophet who upsets the tablers of moneychangers and harshly condemns religious leaders who promote bad theological teachings.

As for your suggestion that I would justify racism or intolerance merely because I acknowledge the empirical fact some people’s views and habits and tastes are incompatible with others’—it is offensive, even despicable.  If I said that, since you would never marry a woman who was a practicing Roman Catholic and intended to remain one, you hate Catholics and want all of them to be destroyed or enslaved or forcibly converted, you would quite rightly protest my inference.  Yet you’ve just made an inference of that kind about me.  

I said, in essence, that some people just don’t on very well with each other—they have too many differences, and hardly anything in common.  And I’ve said that in such cases, they should go their separate ways, and not keep arguing with each other or trying to convert each other.  I never said, or implied, that such differences warrant the mistreatment of some human beings by others.    

Roger, I weary of your constant displays of wounded amour propre when people will not read your book.  I wish you would take your marketing campaign elsewhere.  But in the end, it doesn’t matter, because I’m not going to be posting here much longer anyway.  I leave the others here to deal with you in whatever way they see fit.  Best wishes.

Roger A. Sawtelle - #83347

October 31st 2013

Hanan D,

For some reason the “Reply to this comment” does not work for me.

Concerning your question about Lynn Margulis, these are my observations.

1) The quote is taken out of context so I have little idea what it means.

2) When a person thinks “out of the box” and is generally proven right it seems that often this encourages “contrarian” ideas, which are not always correct.

3) Her work was in the lab where she saw how life forms often developed symbiotically in a nonlinear manner rather in a traditional gradual Darwinian linear manner.

4) Her work was bitterly attacked by Darwinians which might explain her blunt push back.

5) This does not mean that there are no intermediate life forms, but they are not produced by Darwinian trial and error, but by symbiotic sharing and development. 

I hope that this helps to explain her views.    

Roger A. Sawtelle - #83366

November 1st 2013


The reason why I think that ecological evolution is right is because it accepts the indeterminate side of Darwinian Variation, while meeting the concerns of Theistic determinism through ecological Natural Selection in a sound scientifically acceptable manner.

It satisfies the need for intellectual integrity of both sides if each side has the honesty to admit that it was partially mistaken.  This seems to be the rub. 

Roger A. Sawtelle - #83369

November 1st 2013


Another point concerning Lynn Margulis. 

She gave her reference study for being against linear gradualism.  You gave your counter example.

People caught up in Western dualism, (if something is A, it cannot be not-A) are destined to think that one example of the nature of evolution is enough to determine the nature of all of evolution. 

That is they assume that evolution cannot be linear in some respects and non-linear in others.   

The advantage of non-dualistic Trinitarian thinking which Eddie refuses to understand is that it is able to reconcile linear and non-linear views as well as other real paradoxes.  

Roger A. Sawtelle - #83376

November 1st 2013

Eddie wrote:

What is “sad” is that many ordained Protestant clergyman promote a Jesus Christ who is a simpering, touchy-feely, oh-so-sensitive social worker, instead of a fiery prophet who upsets the tablers of moneychangers and harshly condemns religious leaders who promote bad theological teachings.

Eddie, because of the context of this discussion and the wild, baseless charges you have made against me, you are indicating that I represent this strawman streotype that you love to bash.  You are absolutely wrong and I hope that some day you will awaken from whatever dream world you are in and smell the coffee.

You are wrong also about Jesus.  Yes, Jesus did drive the moneychangers out of the Temple, but his attack on the Pharisees and Saduccees was on their failure as leaders, rather than their “bad theology.”  We all aerd subject to the anger of Jesus if we as leaders do not face the real problems of our time and address then in God’s Spirit.

Jesus might not have been a social worker, like I have been, but Jesus did work for and with the poor as social workers do.  No, Jesus was not weak because He cared about ordinary people as many people think. 

The problem with many conservative Christians who love to bash liberal theology like you do is that their theology is just as legalistic, if not more than liberal theology.      

Now I do not know what the world looks like from your perspective.  I don’t even know who you are and where you live.  You know who I am and where I live, but do you know any other AME ministers?  Have you attended an AME Church?  

Where I stand those who talk like you, liberals are weak social workers and they are bold prophets attacking the “bad” theology of those who think everyone should have access to medical care, which all Christians know is a “socialist plot against the USA.”

Eddie, I have tried to deal with you in the realm of ideas.  That is why I asked to read ny book.  Is that so hard to understand without trying to give me some dark ulterior motive.   

This would seem most appropriate way to realate with someone who claims to be a professor of philosophy.  However all I have gotten is evasive, bogus arguments.

First you say that I did not defend my ideas “intelligently.”  Then you said the ideals of two Christians were incompatible, even though before you indicated our differences would not have prevented you from giving me a good grade if I were your student. 

Now you give me this whole ad hominem argument about being a liberal Protestant minister, which by most standards I am not.

If you have a problem with liberal Protestant theology, so do I.  Let’s talk about it.  I also have a problem with your theology and see nothing wrong about talking about that too.      



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