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Evolution Basics: Artificial Selection and the Origins of the Domestic Dog

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April 4, 2013 Tags: Genetics, History of Life
Evolution Basics: Artificial Selection and the Origins of the Domestic Dog

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 examine how artificial selection shaped the dog genome during the early domestication process.

In the last post in this series, we looked at how artificial selection played an important role in Darwin’s conception of natural selection. One example of artificial selection that Darwin drew upon was the domestication of dogs – a process that has recently been greatly informed by genomics comparisons between dogs and their closest wild relatives, wolves. 

(Slowly) becoming man’s best friend

The domestic dog has the distinction of being the only known animal to be domesticated by humans prior to the advent of agriculture. As such, dogs are not only man’s best friend in the animal kingdom, but also his oldest one. Though the precise origin of dogs was a mystery in Darwin’s day, Darwin drew on them as an example of artificial selection that would be familiar to his readers, since the practice of shaping breeds over time was familiar to his audience:

But when we compare the dray-horse and race-horse, the dromedary and camel, the various breeds of sheep fitted either for cultivated land or mountain pasture, with the wool of one breed good for one purpose, and that of another breed for another purpose; when we compare the many breeds of dogs, each good for man in very different ways… We cannot suppose that all the breeds were suddenly produced as perfect and as useful as we now see them; indeed, in several cases, we know that this has not been their history. The key is man’s power of accumulative selection: nature gives successive variations; man adds them up in certain directions useful to him. In this sense he may be said to make for himself useful breeds.

Note that Darwin is careful to point out that the variation itself is due to heredity: while humans can “add up” variation over time through selective breeding, they cannot produce the variation upon which they act. This point was important for Darwin to make, since he would later argue that natural selection also acts on that same heritable variation over time in a cumulative way.

Darwin’s use of dogs as an example was hindered, however, by his not knowing whether all dogs were descended from one ancestral species or if different breeds had been independently domesticated from different species. Darwin (erroneously, as we will soon see) suspected the latter, perhaps in part because of the dramatic morphological differences between dog breeds. He does, however, contemplate the possibility that some widely divergent dog breeds were derived from a common stock, and notes that, if demonstrated, such a finding would be significant evidence that “closely allied” species in nature were, in fact, related:

When we attempt to estimate the amount of structural difference between the domestic races of the same species, we are soon involved in doubt, from not knowing whether they have descended from one or several parent-species. This point, if it could be cleared up, would be interesting; if, for instance, it could be shown that the grey-hound, bloodhound, terrier, spaniel, and bull-dog, which we all know propagate their kind so truly, were the offspring of any single species, then such facts would have great weight in making us doubt about the immutability of the many very closely allied and natural species—for instance, of the many foxes—inhabiting different quarters of the world. I do not believe, as we shall presently see, that all our dogs have descended from any one wild species; but, in the case of some other domestic races, there is presumptive, or even strong, evidence in favour of this view…

The whole subject must, I think, remain vague; nevertheless, I may, without here entering on any details, state that, from geographical and other considerations, I think it highly probable that our domestic dogs have descended from several wild species.

As it turns out, Darwin was wrong on this point—we now know that all dog breeds are derived from only one wild species, the gray wolf (Canis lupis). Genome sequencing studies place dogs and gray wolves as extremely close relatives, which is hardly surprising, since they remain fully capable of interbreeding. Beyond establishing wolves as the closest wild relatives to dogs, genome comparisons are also beginning to reveal how human artificial selection brought dogs into being.

Teasing out the genetic basis for the domestication process has become increasingly possible now that the dog genome has been completely sequenced (published in 2005). This complete sequence allows for detailed comparisons between dogs and gray wolves, as well as comparisons between dog breeds. Both studies shed light on how artificial selection shaped dogs over their shared history with humans. Comparisons to wolves allow us to determine what selection steps took place during the early domestication process, whereas comparisons within breeds allow us to examine the selection steps that gave each breed its unique suite of characteristics.

From wolf to dog: the early domestication process

Though the wolf and dog genomes are overwhelmingly similar to one another, there are subtle differences between them. Recent research has sought to identify regions of the dog genome that were selected for during the domestication process. These regions are expected to show less variation than what is seen in the rest of the dog genome at large. Recall from our prior discussion that selection reduces the variation in a population by picking out certain variants and favoring their reproduction over others. As we scan through the dog genome, we can thus look for regions that show very little variation (i.e. all, or almost all, dogs have the same sequence in that area) in contrast to other regions where dogs, as a population, have more variation present. We can also then compare these putative selected regions with the wolf genome, to find the regions that not only have reduced variation within dogs but also differ from what we see in wolves (since we are interested in regions that contribute to the differences we see between wolves and dogs). Having found the regions of the dog genome that meet these criteria, it is then possible to examine the sorts of genes found in them, and generate hypotheses for why selection on those specific genes may contribute to the morphological and behavioral differences we observe.

The results of this analysis were striking in that the main category of genes found in such “candidate domestication regions” were genes involved in nervous system development and function. These results support the hypothesis that the primary focus of the early domestication process was selecting for behaviors, such as reduced aggression and willingness to submit to an altered, human-dominated social structure.

Image from Webster’s New Illustrated Dictionary, published 1911.

Small genetic changes add up

At both early stages of dog domestication (and as we will see, at later stages of breed creation), similar conclusions can be drawn: small changes at the genome level can have very large effects on morphology and behavior for the organism as a whole. We have discussed this point before in the context of comparing the human and chimpanzee genomes, and drawn the same conclusion—small perturbations to a complex system can effect substantial change over relatively “short” timescales. (By short, I mean short from a geological perspective.) Dogs and wolves have been in the process of separating for about 100,000 years, meaning that the dog domestication process and the subsequent creation of dog breeds occurs in a blink of an eye geologically speaking. If future paleontologists were to find a dachshund in the fossil record, it would seem to appear out of nowhere and have only a distant relationship to wolves, despite the fact that we know dogs and wolves are part of the same species (with all the inherent “fuzziness” that the term “species” entails).

Selection, artificial or natural, is selection

The power of artificial selection was a useful argument for Darwin in the 1850s, since it demonstrated the remarkable flexibility a species could have under differing selective environments, and revealed the inherent variation within populations that could be acted on to drive significant change over time. Here in the early 21st century we are beginning to see the genetic underpinnings of artificial selection at a genome-wide level, and the results are absolutely in keeping with Darwin’s ideas: that populations contain significant diversity, and that artificial selection can act on that diversity over time to promote the reproduction of certain variants over others, and thus shift average characteristics of a population. And just as Darwin drew parallels between artificial and natural selection, so to can we: the evidence we have suggests that natural selection acts in essentially the same way as artificial selection—by favoring the reproduction of certain variants over others.

In the next post in this series, we’ll examine how artificial selection shaped the creation of specific dog breeds, and examine how natural selection has also shaped the dog genome during the domestication process.  

For further reading:

Lindblad-Toh, K., et al. (2005). Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438; 803 – 818 (link).

Axelsson, E., et al. (2013). The genomic signature of dog domestication reveals adaptation to a starch-rich diet. Nature 495; 360 – 364 (link).


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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Lou Jost - #78167

April 4th 2013

Great article! Do we know much about the frequency of larger genetic changes (gene duplication, non-aligned sequences, chromosomal rearrangement, etc) in the dog genome compared to the wolf genome? Commenter Eddie and I have been having a discussion of this in


p3; see for example my #78141 and Eddie’s nearby comments.

Dennis Venema - #78177

April 4th 2013

Hi Lou,

The short answer is that they are very, very close, but I haven’t seen a specific genome-wide comparison yet. The 2005 dog genome paper has some estimates based on limited samples: in gene exons, they observe 0.04% divergence, so dogs and wolves are 99.96% identical. In introns they observe greater divergence (0.21%), so here dogs and wolves are 99.79% identical. The sequences they chose were ones that were more divergent than average, so these values are skewed downward, likely. Still, an incorporation of indels, etc, has not been done at a genome - wide level.

In layman’s terms, dogs and wolves show divergence comparable to what is seen between divergent human populations.

PNG - #78190

April 5th 2013

In the second paper linked above they found that 3 starch digestion genes were selected. One, alpha-amylase (AMY2B), had a copy number increase from 1 (haploid number) in wolves to 2-15 in dogs. Several variants that cause breed specific traits are copy number variants. In the following review, Table 2 lists a bunch of traits of morphology, hair type and behavior for which loci have been mapped, but most have not been defined to the point of knowing what type of mutation they contain. 

Genomic signature of dog domestication       http://www.ncbi.nlm.nih.gov/pubmed/22270221

Copy number variants have been mapped in dogs and wolves, but I don’t think enough wolves have been analyzed to identify CNVs that might be specific or occurring at much higher frequencies in dogs.

PNG - #78192

April 5th 2013

Got the title of the review I referenced wrong - it is Evolutionary Genomics of Dog Domestication

Lou Jost - #78204

April 5th 2013

That;s very interesting, and explains why dogs are able to eat that crappy commercial dogfood!

Dennis Venema - #78208

April 5th 2013

The next post in this series will discuss the amylase duplications.

Len Ralph - #78174

April 4th 2013

interesting article.

I have a basic question for a geneticist.

Adaptation is easy to understand, but how do you get from on species to another, in particular when the other species has a different number of chromosomes.  presumably it is possible for a creature to be born with some kind of mution that causes it to have an extra set, but what does this creature mate with produce a new species with a different chromosome number?


Lennie the Lip

Dennis Venema - #78178

April 4th 2013

Hi Lennie,

The short answer is that chromosome structure changes, like any mutation, occur in an individual and then may spread through a population. There are many examples known of mammals with different chromosome numbers in different populations that can nonetheless interbreed just fine (for example mouse populations on the same island). The mice all have the same DNA content, just arranged into different chromosome forms. They are all able to breed together just fine.


Lou Jost - #78179

April 4th 2013

I’ll add that in plants, there are rare accidents of cell division that double the total number of chromosomes. These are called “tetraploids”. When tetraploids mate with a regular plant, the progeny are triploid, which have greatly reduced fertility. So these tetraploids instantly show almost complete reproductive isolation from their parent species. It is an instant speciation event!

To reproduce and prosper, the first tetraploid to arise in a population either has to be self-pollinated, or be pollinated by a normal plant’s (or triploid plant’s) pollen grain that has accidentally gotten two sets of chromosomes instead of one. These accidents are not so rare as they might seem. Orchids, for example, have been hybridized for two centuries, and careful records of all crosses have been kept by the Royal Horticultural Society in London. During these two centuries, in almost every genus of commonly grown orchids, chance tetraploids have appeared several times. And these have managed to reproduce. Now almost all commercial orchids are tetraploids (because they often have bigger cells, bigger flowers, and more intense coloring than diploids).

When we look at wild orchid species, we sometimes find closely related species pairs, one with x chromosomes, and one with 2X chromosomes. These are probably examples of an ancestral species and a new species produced instantly by this kind of chromosome doubling.

melanogaster - #78227

April 6th 2013


I think that Dennis’s reply fails to address your fundamental misconception about the origin of species.

The speciation typically occurs when a single population starts diverging into separate populations that gradually become unable to interbreed. This usually occurs gradually, but some events can make it more abrupt.

For example, two populations of a species, if separated geographically, will tend to drift (non-Darwinian evolution) apart, with the drift creating genetic (chromosomal translocations, fusions) or inherited physical characteristics (which also are genetic, but one step downstream) that inhibit interbreeding, even if the geographical barriers are removed. If there are different selection pressures in the different environments, speciation is accelerated. Once interbreeding is inhibited, that’s inherently selective and accelerates the split even more.

So the enormous misconception that prevents you from understanding the mechanisms is this idea (not limited to creationists) that one species changes into another. What’s really going on is that one population splits into two populations that lose the ability to interbreed.

So will you let go of this misconception or cling to it?

Seenoevo - #78183

April 4th 2013

I’ve often heard the question: “If humans evolved from chimps, then why do we still have chimps?” To which I’ve often heard the rabid response: “Humans did NOT evolve from chimps! How many times must I repeat this? Don’t you know anything about evolution? Don’t you read? Humans did NOT evolve from chimps! But humans and chimps have a common ancestor.” At that point the evolutionist usually directs attention to the real holy grail: determining the identity of the common ancestor (CA) and understanding the logistics of genetic divergence from the CA to the human and the chimp.

However, in this article, I see no talk of a barking holy grail: the ancestor of dogs. [I might have said “ancestor of dogs and wolves”, but the article indicates wolves and dogs are the same species:

“…we now know that all dog breeds are derived from only one wild species, the gray wolf (Canis lupis)”

“... we know dogs and wolves are part of the same species…”

“In layman’s terms, dogs and wolves show divergence comparable to what is seen between divergent human populations.” ]


This is not very interesting to me. What would be more interesting is the evidence for the identification of the common ancestor of dogs/wolves and the how and why of genetically going from the CA to dogs/wolves.


Lastly, I could swear that I’ve read on these pages, maybe even from this author’s pen, that ‘individuals don’t evolve, populations do’. [To which I might have responded: ‘How does a population of individuals evolve if individuals don’t evolve?’ But I never get a comprehensible (to me) answer.]

Yet in this article I read:

“The short answer is that chromosome structure changes, like any mutation, occur in an individual and then may spread through a population.”

Or have I mis-read and misunderstood the basics?


I did not intend the big bold text above. I copied it in a “civil” size, but when I pasted it some of it got BIG, and I was unable to change it. And I’m not going to retype it all.

PNG - #78196

April 5th 2013

Each individual gets a new crop of mutations, some of which originated in the father in the cells that gave rise to sperm and some of which originated in the mother in cells that gave rise to eggs. The male side gives rise to several times as many mutations as the female, probably because it involves more cell divisions. A few mutations may happen after fertilization in the embryonic cells that give rise to germ cells (sperm and eggs), but of course mutations that happen in cells that give rise to the rest of the body (somatic mutations) don’t get passed on to the next generation. They contribute to cancer development and other health problems for the individual, but they aren’t inherited. Mutations that are passed on in the specific sperm and eggs that give rise to the offspring become part of the population’s gene pool. Any new mutation, even if it is neutral or advantageous, has a pretty good chance of simply being lost in the first few generations, but some do get passed on and become part of the variation in the population of the species.

So, individuals only evolve in the sense that they get a sampling of the variation that existed in their immediate ancestors plus a small number of new mutations that occurred in the germ cells that gave rise to them. They get the genetic cards that are dealt to them as embryos. But the genetic makeup of the population changes over time because the frequency of variants changes a little with each generation. Some variants are coming to fixation, while other are being lost and many are changing in the fraction of the population that has them.

melanogaster - #78502

April 13th 2013

“Any new mutation, even if it is neutral or advantageous, has a pretty good chance of simply being lost in the first few generations, but some do get passed on and become part of the variation in the population of the species.”

You are fixated (pun intended) on new mutations. Do you think that evolution stop cold if we magically stopped all new mutations? How many generations would it take to notice?

melanogaster - #78503

April 13th 2013

That should be, “Do you think that evolution WOULD stop cold…”

PNG - #78514

April 14th 2013

I said everyone gets a sampling of the pre-existing variation, plus a few new mutations. What else do you think needs to be said?

PNG - #78515

April 14th 2013

I should add that I was just trying to answer Seenoevo’s question about what it means  that individuals don’t evolve while populations do. If you think you can make it clearer than I did, have at it.

melanogaster - #78526

April 14th 2013

I think you’re overemphasizing new mutations. They just aren’t needed. 

melanogaster - #78528

April 14th 2013

Having at it:

Individuals are different.

Some of those differences are heritable.

Some of those heritable differences affect the rate at which individuals reproduce.

If all of these are true, then the frequencies of those heritable characteristics in the population will change over time. 

PNG - #78529

April 14th 2013

New mutations happen. That’s all I asserted.

Test question, if you choose to accept.

How far could evolution get if after the ancestor of chimps and humans there were no new mutations? Were all the variants that were needed to get to today’s chimps and humans already present in the population of the CA? Justify your answer.

Eddie - #78544

April 15th 2013


Thanks very much!  I’ve had the same question all along, whenever the Fruitfly has made this same claim, but I’ve judged it wise not to ask it, knowing the kind of reply such questions from me generally evoke from him.  Perhaps he will respond to you without charging you with ignorance, stupidity, not reading the scientific literature, etc.  I’ll watch for his reply.

melanogaster - #78562

April 15th 2013

Gee, Eddie, if you are reluctant to ask you could just look it up instead of hurling insults. Both mutation rates and polymorphism have been repeatedly measured and published. But then I gave you the figure for divergence between whales and other artiodactyls on a platter and you predictably ignored it.

I’m curious. Have you ever made a comment on this site that was limited to ideas and facts, without mentioning a single name or opinion in either a positive or negative manner?

Think about it carefully before replying.

melanogaster - #78561

April 15th 2013

“New mutations happen. That’s all I asserted.”

I don’t disagree with that as a simple fact. I vehemently disagree with the deemphasis of existing polymorphisms in favor of starting with new mutations. Mutation is an event. We know when particular mutations happened in very few cases, so there’s no reason to pretend that selection primarily acts on new variants—or even worse, this creates the completely false impression that selection acts only on one genotype or phenotype. It interferes with an understanding of hybrid vigor, and its corollary that populations with high polymorphism are more evolutionarily and epidemiologically resilient. It prevents people from thinking clearly about things like histoincompatibility and the evolutionary reasons for it (look up immunology research on tunicates). A good place to start might be:

Sebat et al., Science 305 (5683): 525-528
Large-Scale Copy Number Polymorphism in the Human Genome

In other words, my main concern is that it’s an enormous didactic mistake! It allows people to shut down and make the issue the source of polymorphism, when the existence of polymorphism is undeniable. I also disagree with the often improper use of the term “mutation” when “variant” is much more appropriate, as well as more considerate of those of us who are variants (IOW all!).

“How far could evolution get if after the ancestor of chimps and humans there were no new mutations?”

Almost as far as it did get.

“Were all the variants that were needed to get to today’s chimps and humans already present in the population of the CA? Justify your answer.”

All? Obviously not, because the mutation rate is >0, but I think you know that.

Most? Definitely, but the fraction of the total would depend on the size of the population of the CA. 

melanogaster - #78567

April 16th 2013

Test question for you, PNG:

If I make a database of markers distributed throughout the human genome, say more than 30,000 of them, what do you think the mean observed frequency of heterozygosity is?

And if we apply the known mutation rate to the numbers of cell divisions in the germ line, how many of the homozygous loci would become heterozygous per generation?

Feel free to only answer the first one, as the second involves some math.

PNG - #78638

April 17th 2013

I don’t know the first one - I’d have to go look it up. Probably close to the inter-individual SNP rate of ~1/1000. The human mutation rate per nucleotide per generation is ~ 10e-8. I suppose your point is that the new mutations in a generation are a tiny fraction of the variants already there in the population. The bigger the population the more variants there are. 

melanogaster - #78662

April 18th 2013

“Probably close to the inter-individual SNP rate of ~1/1000.”

That’s a different parameter. The frequency of heterozygosity would necessarily be much higher.

“The human mutation rate per nucleotide per generation is ~ 10e-8. I suppose your point is that the new mutations in a generation are a tiny fraction of the variants already there in the population. The bigger the population the more variants there are.”

Exactly. Therefore mathematically, evolution would take a very, very long time to coast to a stop.

Eddie - #78692

April 18th 2013

But of course, such a purely mathematical analysis (so typical of the geneticist’s theory-driven approach to evolution, as opposed to the molecular biologist’s more concrete “show me how you evolved that novel protein” approach) does not deal with the meat of the question.  

What is the content of the variants?  If the overwhelming majority of the variants in the population concern things like green eyes versus blue eyes, brown hair versus red hair, etc., they aren’t going to effect major changes in body plan, and aren’t likely to account even for the difference between a primitive, pre-chimpanzee ape and a human being.  So you need some serious mutations for the in-depth transformations.  And no one here will specify what those mutations would have to be.  Which is not surprising, because not enough is known about either genomics or developmental biology to say what they would have been.

And that’s fine.  I don’t blame biologists for not knowing everything.  I do blame them for overclaiming, saying that they know that existing mechanisms can explain everything, when they can’t.

Lou Jost - #78205

April 5th 2013

Seenoevo, it might also help you to note that wolves, which have not been artificially selected, are still pretty much the same as they were 100000 years ago, with some minor variation due to genetic drift and maybe some weak natural selection. So when Dennis compares the wolf genome to the dog genome, he is essentially comparing the common ancestor’s genome to the dog genome.

Eddie - #78213

April 5th 2013


Interesting.  Artiodactyl to whale is supposed to have taken place in 9 million years or less.  That is 90 times the 100,000-year figure you give during which wolves, without the help of artificial selection, have by your own admission hardly changed at all.  So would 90 periods of “hardly changed at all” be likely to produce an astounding set of major morphological and physiological changes and a complete change of ecological venue?  Maybe.  But it’s not clear that this would be so.  (And as an amusing side remark, I can’t resist throwing in that 50 years ago, evolutionary biologists were pretty sure it was a wolflike animal (e.g., Mesonyx) that evolved into the whale.  If they were still holding that view, my question would be if anything more pertinent.)

Once again, Lou, I’m not disputing “evolution”—just wondering how the mechanisms you endorse, which have kept wolves so stable for so long, can work absolutely alchemical magic on some primitive deer over a period of time not even two degrees of magnitude greater.  :-)


Lou Jost - #78232

April 6th 2013

Eddie, you can see the answer to that by asking why today’s dogs are so different from wolves, even though they were identical not long ago. Dogs were under strong new selection pressures (both natural and artificial) because they were entering a rich, novel environment. Wolves had a niche in which they were successful, so there was little pressure to change.

The sea was a vast new environment for terrestrial mammals. There would have been strong selection pressure to adapt, if there were resources there that mammals were capable of using.

By the way, I don’t have a list of “endorsed mechanisms” for producing variation. We have a rich pallete of known mechanisms available, and surely more to be discovered. Like I said elsewhere, it’s all grist for the mill of natural selection and drift. What we do not have so far is evidence for truly teleological mechanisms, though. We also don’t have evidence that such mechanisms are needed. The dog genome shows how small genetic changes can make big differences.

I know you’ll answer by discussing macroevolution/ microevolution (you’ll bring up Prothero). Sure there are occasional very rare major genetic changes that are nonlethal. The example of polypoid speciation I just discussed is one of these. Changes in genes controlling development and body plan can be another. Prothero is right that big macro changes are possible. But the fossil record shows that lots of small transitions really do add up to big transitions over time (that’s why people argue about the likelihood of sudden big changes). The whale case is like this. The cat/dog dichotamy is another; cats and dogs seem very different now, but as you go back in time they get harder and harder to distinguish, until eventually you get to the point where there is no difference. It is very hard to point to one of these ancestors and say “Aha, here is where macroevolution happened!”

Eddie - #78235

April 6th 2013

Ah, yes, “selection pressure.”  But of course, “natural selection” is neither an entity nor a force; there is no agent called “selection” that can “exert pressure” on anything, so the term is, strictly speaking, nonsensical, but I take it you are using it as kind of shorthand, so we’ll let that pass.

What would be more helpful would be an enumeration of the “selection pressures” that the hypothetical artiodactyl ancestors of the whales were under.  Were they constantly being driven toward the water by gangs of vicious wolves, for example, so that the accidental acquisition of fins in place of hooves would have been helpful to them, to escape from the wolves?  Or did they find themselves, just by mutational accidents, slowly losing their hooves and flopping through the forests clumsily on flippers, so that there was strong incentive for them to switch to a watery environment?

These examples are facetious, but the general point is not.  “Selection pressure” is one of those big, vague, generalities which is compatible, after the fact, with almost any evolutionary result.  Unless it is nailed down more precisely how this “pressure” is exerted in specific cases (e.g. the land to sea transition), the notion provides no illumination.

I find your quasi-teleological picture—of this vast ocean resource beckoning, like a tourist pamphlet, to the land creatures to try it out—rather amusing.  Let’s try to apply it more consistently.  71% of earth’s surface is covered by ocean.  That’s a huge, inviting resource, just crawling with potential food for the right sort of enterprising land mammal.  Over millions of years, one would think that the tools for utilizing this resource would “pop up” in the mammalian population.  (After all, Dawkins tells us the camera eye is a piece of cake, having evolved, without any design or foresight, 20 or 30 times.  So why not fins, marine lactation, blowholes, hair loss, blubber, etc.?  Surely they, too, could emerge more than once, in different lines of land mammals.)  But nowhere near 71% of the mammals on the planet (whether you count by individuals or by species or by genera or families) are marine mammals.  Thus, based on “selection pressure,” one would have expected a much greater exodus to the sea than what in fact happened.

You write:  “Wolves had a niche in which they were successful, so there was little pressure to change.”  Well, so did primitive artiodactyls.  They were exploiting the land quite successfully, becoming all the different varieties of cattle and sheep and goats and deer and giraffe and so on.  The laborious route to becoming sea creatures seems to make little sense, when they already had “the right stuff” for land life, and none of “the right stuff” for sea life.

Think of “method acting”; you, the director of the film, tell the artiodactyl star to take to the sea, and it will ask you, “What’s my motivation?  I’m happy where I am.”

Note that I am not denying that artiodactyls evolved into cetaceans.  I’m saying that the transformation makes no sense, given your understanding of evolutionary mechanisms.  In a neo-Darwinian universe, primitive deer had no more reason to take to the ocean than primitive wolves did.  But if evolution is driven by something quite different than what you have presented, then the case may be otherwise.

Lou Jost - #78237

April 6th 2013

Lots of misconceptions here. I’ll deal with them one at a time, in separate posts, as my time and energy permit. First, an important one: “natural selection is, strictly speaking, nonsensical”

Natural selection is a real force acting to change gene frequencies of populations. A selection coefficient for a given gene in a given environment can be quantified exactly.

For example, suppose a gene arises in a population of hippopotamus that makes it easier for them to live in water. We could observe the reproductive success (number of offspring that go on to reproduce) of the hippos that have this gene, and we could compare it to the reproductive success of the hippos that don’t have this gene. This is enough information to calculate the selection coefficients. Then, if I also know population size, generation time, and a few other objective demographic variables, I can use the equations of population genetics (which are mathematical deductions based on the way genes are inherited) to predict with great precision the following: (1) whether the gene is likely to spread through the whole population, (2) how fast will it spread, (3) what will its equilibrium frequency be in the population.

These predictions are quantitative and testable (by observing what happens in multiple populations).

Your question about why more mammals aren’t marine is similar to creationists’ “If people evolved from apes, why are there still apes?” Kind of disappointing to hear. Will respond later, I have to go do work.

Eddie - #78240

April 6th 2013

Natural selection is not a force.  If you don’t believe me, believe Allan MacNeill, lecturer in evolutionary biology at Cornell (and no ID proponent!), who has lectured ID folks on this point over and over again.  Natural selection is a result.  It is what happens as the outcome of evolutionary changes.  Some things die, some things live.  Darwin recognized this when he admitted, in response to Spencer, that the phrase “survival of the fittest” was in some ways a better phrase than “natural selection.”

But actually, I did not say that “natural selection” was nonsensical.  I said “selective pressure”—if taken literally rather than as shorthand—was nonsensical.  There is no invisible entity called “selection” hovering over life, literally exerting “pressure” on any organism.  Rather, organisms that don’t thrive well in a particular environment lose out.

Imagine saying that someone with a degree in Sociology doesn’t have a job because of “unemployment pressure” as if there is some invisible unemployment-causing “force” out there, working against Sociology B.A.s or more probably against people generally.  In fact, Sociology B.A.s who don’t have jobs, often don’t have them because they don’t know any Pacific Rim languages, or Spanish, or computer programming, or accounting, or marketing, or law, or electronics, or can’t write a decent English sentence, or have oafish social skills (cultivated by four years of living in an ivory tower, drinking beer and yammering about fascism and sexism and racism and classism and “speciesism”), or in general lack the skills and qualities that employers want.  As a result, they are “selected” out of the job market; “unemployment” is the result; but it isn’t a spirit or force or material thing that exerts any “pressure” on anyone.

By contrast, there does appear to be a force of gravity, electromagnetic attaction, nuclear cohesion, etc. which binds bodies together.  That is what I meant by saying that “selection pressure” is a misleading expression, if taken literally.  

“Suppose a gene arises in a population ...”  Exactly.  In neo-Darwinian evolution, life has to wait around for the lucky break, and then natural selection bestows its blessing.  A crude blind search.  

I don’t deny that you can calculate how fast genes will spread through a population.  But I’m not interested in that, unless you first convince me that those particular genes can build a whale out of an artiodactyl.  Genes for blue eyes won’t do the trick.  Nor will genes for feathers.   And nothing you have said gives me the impression that you know which genes those might be, or how they might be manufactured, or how they will interact with epigenetic processes to produce new body plans, etc.

Actually, my example is not parallel to the creationist one.  I did not argue that all land mammals should have died out and only marine mammals should remain.  I argued that if—on your premise—the marine environment is such an inviting place for creatures seeking food and survival—we should expect that the ancestors of wolves would have found it just as enticing as the ancestors of hippos.  I did not say that no wolves or hippos would be left on the land.  I said that there should have been many more migrations to the sea than just the migrants from the artiodactyl group.  

What I’m trying to get you to see is that you have not consistently applied the notion of “selection pressure” to see if it explains all the data across the planet.  You have appealed to it on an ad hoc basis, to deal with an objection of mine, but that is like appealing to gravity only to explain the motion of the Moon, and not Mars as well.

You say there is no selection pressure on wolves to change.  How do you know that?  Do you have a list of all the competitors of wolves and all the environmental conditions (temperature, precipitation, volcanic ash in the air, UV penetration, types of vegetation, microbial  diseases, migrations of typical wolf prey, etc.) that have existed since the rise of wolves?  And you are equally sure that in the case of artiodactyls, the selection pressures were such as to make them (but not wolves) jump into ocean and change their way of life.  How do you know that?  Have you got a list of the competitors and environmental conditions of artiodactyls over the relevant period?  Do you know even a tenth of the species which existed tens of millions of years ago, when the proposed evolution was taking place?  Species some of which would have interacted with the transforming artiodactyls?  If not, how can you know what was putting “pressure” on the artiodactyls during that time period?

So you seem to be guilty of two things:  (1) Arbitrarily exempting some groups of mammals from “selective pressure” while insisting that other groups are under immense “selective pressure”; (2) Providing no concrete information about the evolutionary environment in the eras during which the proposed evolution was taking place—without which information you have no justification for your procedure in (1).  Once again, evolutionary theorists do too much extrapolating, projecting, speculating—and not enough demonstrating. 

Dennis Venema - #78239

April 6th 2013


I don’t have time for many comments, but are you aware that seals and sea otters, as examples, have adapted to a marine lifestyle independently of the whale lineage?

Also, we see the mammalian (cetacean) raditation into the sea after the asteroid impact wiped out the large apex sea predators like ichtyosaurs, opening up a new niche.

Dennis Venema - #78242

April 6th 2013

and of course ichtyosaurs themselves represent a separate terrestrial—> aquatic shift, from a reptile lineage. This sort of thing has happened many times in evolutionary history.

Eddie - #78243

April 6th 2013

Hi, Dennis:

Yes, I am aware that according to evolutionary theory, there were other migrants from the land.  I’m suprised that Lou didn’t pick up on that; he could have argued that perhaps a wolflike animal was the ancestor of the seals and walruses.  That would have made more credible his view that the mere presence of the sea, with all its potential for creatures that could use it, would create immense “selection pressure,” drawing not just the artiodactyl, but many branches of land mammals into the marine way of life.  But he didn’t argue in that way.  He seemed to assert a general principle, and then to apply it to only one special case.  But possibly I am reading his words with a precision he didn’t intend.  I await his clarification.

Dennis Venema - #78245

April 6th 2013

Another question, Eddie - for your choice of ~9 million years for the artiodactyl—> whale transition, you are aware that you’re not talking about a fully modern whale, right? 9 million years in they still had four limbs, for example. Kind of like large otter-like critters.

Once we have a full genome of a cetacean we’ll have a better handle on the transitions at the gene level, but whales still have the same basic mammalian body plan, with some modifications. There’s nothing about a whale that is unexpected, given its heritage.

When we compare other organisms, for which we have full genome sequences, we see that even fairly wide morphological divergences have small genetic divergences. Take humans and chimps, for example: significant morphological / behavioural differences, but very little genetic difference. There is nothing separating humans and chimps genetically that cannot be bridged by the types of mechanisms I’ve been describing here, for example.

Eddie - #78255

April 6th 2013

Hi, Dennis.

I’m willing to be corrected regarding the 9 million years.  I only took 9 million years because that has been the figure batted about in the debate, and I’ve never heard anyone from the Darwinian side challenge it.  Can you (a) tell me the current figure for the complete transition and (b) give me some sources where I can find this figure?

In your last paragraph, the key word is “genetically.”  But I don’t believe that evolution is the result solely of changes to the genome; the way the genome is interpreted by cellular processes, and hence developmental considerations, also come into play.  Even for everyday biological processes that is the case, and there is no reason it should be different for evolution.

Your writings give the impression, even if you never say it directly, and don’t mean to say it, that you think that evolution is wholly a matter of altering genes and spreading the new genes through the population.  It’s as if you are working on the traditional “one-way” model:  a gene changes, therefore a protein changes, therefore structures in the animal change, the new structures are subject to selection, and if they are selected, they rapidly become the norm in the population.  But from what I’m reading, we are now discovering a vast network of very complex activities within the cell that are not controlled by the genome, but, on the contrary, control how the genome is read, where and when its genes are turned “on” and “off” etc.  It’s as if the genome is merely the DVD, and other parts of the cell are the DVD player (without which the DVD is useless, inert information).

Further, if James Shapiro and his supporters are right, the genome can under some circumstances actually be “intentionally” altered by internal organismic activity (as opposed to being altered by “random mutations” due to radiation, chemicals, copying errors, etc.), in response to environmental challenges, and those alterations are (shades of Lamarck!) heritable.  I’m not saying that this, if true, challenges “evolution”—indeed, I think it potentially makes evolution work faster and far better!—but it challenges the old idea that life just has to “wait” for one or two or three or more mutations so that selection can then approve of them.     In fact, I would find things such as the artiodactyl-to-whale transition much more convincing if I thought that evolution proceeded in Shapiro’s way, than if I thought it proceeded in the way the old guys (Dobzhansky, Mayr, Dawkins, etc.) have supposed that it did.  In fact, if Shapiro is right, much of the ID criticism of “Darwinian evolution” is largely beside the point, since many of the most important evolutionary changes are owed to “non-Darwinian” capabilities of the organism rather than to “random mutations plus natural selection.”

Dennis Venema - #78261

April 6th 2013

“But from what I’m reading, we are now discovering a vast network of very complex activities within the cell that are not controlled by the genome, but, on the contrary, control how the genome is read, where and when its genes are turned “on” and “off” etc.”

These features are ultimately controlled by variation genome (epigenetic markers and mechanisms) even if the control is a few generations back. Biologically what would you claim is not controlled by the genome ultimately?

Eddie - #78270

April 7th 2013


You are right, but only in a rather pedantic way.  Yes, genomic change is central and necessary and there must be a genomic base even for the other parts of the cell that interpret the genome.  I grant it entirely.  But we have a massive chicken-and-egg problem in the dance between the DNA and the protein apparatus that interprets it.

And yes, I’m aware of the attempts of origin-of-life theorists to transcend the problem, e.g., by postulating primitive replicative molecules that did double duty as both databank and apparatus for expression, but so far these attempts have seemed very far-fetched, have little empirical support, and seem driven by the premise that there must be a non-teleological origin for the DNA-protein system.  But why must there be?  Because most origin-of-life theorists are atheists and agnostics who dislike the idea of a designer?  Is that a good reason for assuming the very thing that needs to be proved?

Once again, tacit metaphysics comes into all these debates, and I find that scientists who investigate biological origins are generally not very good at identifying their own possible metaphysical prejudices.






Dennis Venema - #78320

April 8th 2013

Eddie, how did we suddenly go from the origin of whales to the origin of life? You’re saying you doubt the sufficiency of evolutionary mechanisms for whale evolution because the origin of life is not explained?

Eddie - #78323

April 9th 2013


First of all, I have not said that I doubt the sufficiency of “evolutionary mechanisms.”  I doubt the sufficiency of your proposed evolutionary mechanisms.  And I’m not alone in that.  So do some very illustrious biologists, including many whose lifetime specialization has been evolutionary theory:  Margulis, Shapiro, Newman, etc.  Yet neither you nor nor any other life scientist on BioLogos has in five years even mentioned criticisms of neo-Darwinian theory coming from these people—who are neither ID proponents nor fundamentalists, but people who have researched and taught in significant secular academic institutions. 

Second, my point was not to complain that the origin of life has not been explained.  I did drift into talking about the origin of life, but that was because I was anticipating an objection you might raise, and I got carried too far in that direction.  My apologies for any confusion.  My point was that the mutually reinforcing DNA-protein complex (which also poses a problem for origin-of-life theorists) makes it difficult to say that evolution can be explained simply by changes in genes, filtered by natural selection.  It is the dance of DNA with protein, not either alone, which makes life possible.  And I think that insight needs to be applied to evolutionary theory also.

If you read Shapiro’s new book, you will see that he has a discussion on the limitations of the gene concept, and that his discussion bears on evolutionary theory.  I’m not asking you to agree with him, but it seems to me that he speaks for a growing minority of biologists who are no longer satisfied with the old orthodoxy (represented by Mayr, Dobzhansky, Dawkins, etc.) which imagined (haunted by the ghost of Weissman, and cajoled by Crick) purely one-way causality between genome and organism.

In fact, if you and other TEs could get past the traditional orthodoxy regarding evolution, you could neutralize most of the ID criticism, since the ID criticism is centered on neo-Darwinian mechanisms.  Shapiro’s account of evolution doesn’t rely upon “randomness” to any great extent (compare with the number of columns on BioLogos explicitly dedicated to talking up randomness!), and therefore ID arguments don’t really damage him.

In fact, as you know, there are a number of ID proponents who accept evolution but don’t like the Darwinian explanation—and many of them are quite interested in Shapiro’s thinking.  Shapiro could be a sort of dialogical meeting-ground between ID and TE.  But I’ve found in the past that TEs, despite their protests that they want love, not war, between Christians over evolution, have shown no interest in any of the evolutionary theorists that ID people like.  Denton, Sternberg, Shapiro—all are evolutionists, and all naturalistic—but TEs turn up their nose at all of them.  So it’s not just “evolution” that TE wants to defend, but a particular set of mechanisms, a particular way of looking at evolution.  That programmatic narrowness is a big part of the problem in bringing ID and TE people together.

Lou Jost - #78337

April 9th 2013

Eddie, have you read about any evidence showing that these “natural genetic engineering” mechanisms are not produced by the genome itself? If they are produced by the genome (and certainly the best example, the immune system, is produced by the genome) then your whole argument falls apart. If they are produced by the genome, then these mechanisms did arise by blind, random genetic changes.

Eddie - #78360

April 9th 2013


Shapiro is (whether you like it or not) one of the leading evolutionary biologists in the world today.  (I did not say “most correct”; I said “leading”; there is a difference.)  If you think he is seriously misleading the biological community, you have the duty to expose him by challenging his views in the scientific arena.  You will do zero good by challenging me, a non-biologist, on a blog site like this, frequented largely by people with only a minimal knowledge of evolutionary biology.

I am no longer going to defend Shapiro.  In fact, I never set out to defend him.  I merely wanted his existence acknowledged.  He is (apparently) agnostic and therefore cannot be accused of religious motivations for his criticism of Darwinian mechanisms; he believes wholeheartedly in evolution and therefore cannot be called a creationist; and he believes in natural causes only and therefore cannot be accused of supporting “God of the gaps” or violating the sacred tenet of “methodological naturalism” preached by the philosophy-challenged scientists of the NCSE.  So he cannot be dismissed on the grounds of alleged motivations, in the way that so many others have dismissed the critics of Darwinism.  

Nor can he be dismissed on the grounds of incompetence.  His theory may be wrong, but he is certainly not incompetent.  He is a smart guy who works specifically in evolutionary theory, has many articles in the field, and has produced a book which world-class theorist Carl Woese calls a “game-changer.”  He has a massive knowledge of the literature in the area of evolutionary theory, and in related biological sciences (as his notes and discussions prove).  He is neither stupid nor ignorant nor insane nor wicked, to use Dawkins’s phrase.

If you or Dennis or anyone else has the detailed knowledge of evolutionary mechanisms, or of biology generally, to show that Shapiro’s position is untenable, then do so in proper scientific venues.  Not here, by using me as a Shapiro-substitute.

It’s easy for you to score points against a non-biologist who can only summarize the main points of Shapiro’s argument, not adequately defend it in detail; but as the saying goes:  “Try picking on someone your own size.”  You can easily (a) publish a refutation of Shapiro in some peer-reviewed venue; (b) write to Shapiro and have a personal conversation to address your differences; (c) comment on his Huffington Post articles and try to get his replies.  That would be far more profitable than arguing with me.  And more enlightening to anyone who views the exchange.  I am sure that anyone on the planet would rather see Shapiro defended by himself than by me. 

Lou Jost - #78265

April 7th 2013

Eddie, you say “we are now discovering a vast network of very complex activities within the cell that are not controlled by the genome”  That’s not a valid conclusion to draw from Shapiro. Think about the immune system that is one of Shapiro’s main examples. The cells of the immune system have all these “natural genetic engineers” floating around working on the cell’s DNA. Where did those engineering elements come from? The immune system cells, and those elements, did not exist when the animal was concieved. The specialized immune system cells, and the genetic engineering elements they contain, were produced by following instructions on the genome of the mother cell. Activation and deactivation of segments of the genome control the type of cell that is made. So ultimately all those genetic engineering mechanisms are, as Dennis says, produced by natural selection acting on the genome. They aren’t something extra. IDer Casey Luskin, in his review of Shapiro’s book, also mentions this point.

You say “it challenges the old idea that life just has to “wait” for one or two or three or more mutations so that selection can then approve of them.” Maybe we can agree on that, in part. But the “old idea"of everything coming down to point mutations is much more powerful than you give it credit for, and anyway that is not the current idea. Many of the things Shapiro mentions, by the way, have been known and widely accepted for a long time. Shapiro does not even cite some of the major prior work on the evolution of “evolvability” (see Moran’s review for details).

“I’m not saying that this, if true, challenges “evolution”—indeed, I think it potentially makes evolution work faster and far better!” Exactly! In fact it doesn’t even challenge “Darwinian” evolution. Darwin didn’t know any details of how variation is generated, and he would have liked Shapiro’s summary. He only would have objected to Shapiro’s dissing natural selection….


Eddie - #78271

April 7th 2013


Re your first sentence in your first paragraph, I did not draw that conclusion only from Shapiro.  I read other things besides Shapiro, you know.  I have read other biologists who have written about the extra-genomic controls on what happens in development, etc.  

I grant your point about how immune systems come to be in the individual organism.  I would have thought that was obvious and needed no debate.  But if you ask why organisms have provisions for immune systems built into them, very far back, possibly as far back as the very first cells, you will find the question is much harder to answer.  Shapiro himself does not even try to answer it.  He pleads the fifth regarding the ultimate origin of any of these rock-bottom capacities.  He is interested in explaining evolutionary change given that these amazing capacities (for self-engineering, etc.) exist.  So he stops short of becoming an ID proponent.  The ID folks, on their part, keep pressing Shapiro, without success, to say where he thinks those early cells got this great ensemble of talents.  But mum’s the word.

I may have missed it, but I didn’t see a huge criticism of natural selection in Shapiro’s book; at least, not huge in comparison with his criticism of random and unplanned variations as the big factor in generating biological novelty.  In fact, his whole premise seems to assume that some sort of selection is operating; that’s the whole reason why organisms self-engineer, to make themselves more fit in relation to environmental challenges; and if they are more fit they will survive, i.e., be selected, in preference to the less fit.  But if you point me to passages where he “disses” natural selection, I’ll reread them.  I don’t claim complete understanding of his thought.

melanogaster - #78290

April 8th 2013

“I’m willing to be corrected regarding the 9 million years.”

Ethically, if you can’t support it with evidence, you should retract it and apologise for pretending to be certain about it.

“I only took 9 million years because that has been the figure batted about in the debate, and I’ve never heard anyone from the Darwinian side challenge it.”

You don’t hear a lot of things, but ethically, that is a pathetic excuse for a fabrication. That’s almost as bad as claiming person X never does Y when you know full well that he did Y.

“Can you (a) tell me the current figure for the complete transition and (b) give me some sources where I can find this figure?”

Couldn’t a competent academic learn this for himself? I’m guessing that a bright 8-year-old would have no problem doing it.

Eddie - #78325

April 9th 2013


Are you incapable of communicating with other human beings who disagree with you without sneering, jabbing, making insulting comparisons, accusing people of deliberate dishonesty, etc.?  Have you not perceived that virtually every person posting here (except beaglelady) is repelled by your manner of conversation?  Where did you learn the habit of treating your fellow human beings in this way?  From your science teachers?

melanogaster - #78504

April 13th 2013

“Where did you learn the habit of treating your fellow human beings in this way? From your science teachers?”

Of always pushing for a return to the evidence instead of hearsay? Obviously, any real scientist would learn that from teachers, followed by long apprenticeships.

So why are you unable to find evidence for yourself, and why do reject evidence that is provided on a platter? I’ve already given you a direct link to the answer in graphical form.

You’re off by more than an order of magnitude, and that matters.

Lou Jost - #78247

April 6th 2013

In my comment above I was explaining that  natural selection is a precise concept yielding testable predictions. So yes, I was arguing a general principle. As I said in my second sentence, I only have time to deal with one of your misconceptions at a time. See my 78241 below for more on this particular case. In that comment, I am not claiming to be able to provide every detail of the transition  to whales. I am explaining general principles. We have these known processes, tested many times, and they seem to be sufficient to explain the evolution of whales. You are the one making the specific claim that known processes are insufficient. The burden is on you to show that, not just to argue from your own incredulity.

Eddie - #78256

April 6th 2013


Actually, I am not making the claim that “known processes are insufficient” because, as I explained on another thread, I don’t understand “known processes” in the same way that you do.  

But even supposing that I agreed with you about the “known processes,” I reject the epistemological burden you are placing on me.  It is not up to the doubters of any theory or hypothesis to show that the theory or hypothesis is impossible.  It is up to the supporters of that theory to show that it is credible.

If I tell you that it is possible for a human being to fly by flapping his arms, and give you some complicated equations that “prove” that this is possible, and you don’t trust that those equations prove the alleged possibility, I cannot attack you for 
“arguing from your own incredulity.”  Rather, I have to give you an example—show you someone who can fly by flapping his arms.  Similarly, I’ve asked you to give me a sample set of changes for any major evolutionary transition—organ, body plan, organism.  It’s up to you to provide concrete demonstration—not general conceptual or mathematical arguments based on “drift” or “selection” or the like, not conjectures based on genome differences—a demonstration  by example that all your proposed morphological and physiological transitions in between are physically possible and also selectable.

I’m sorry, but the burden is on you to become much less theoretical and much more empirical.  Don’t tell me how similar the genomes of artiodactyls and whales are.  Build me a whale from an artiodactyl, stepwise, employing the mechanisms that you think were used to do so.  I want to examine each proposed step for soundness.  

melanogaster - #78289

April 8th 2013

“Yes, I am aware that according to evolutionary theory, there were other migrants from the land.”

No, Eddie, not according to evolutionary theory. According to evidence. Your allergy to evidence is poisoning your mind.

Lou Jost - #78241

April 6th 2013

You answered your own question about why there are not many more marine mammals. You often stress the improbability of the necessary genetic changes arising by chance. Precisely because they do arise by chance and are improbable, they have not arisen in every group. In addition, some groups of mammals have developmental or other constraints that would make it difficult for such genetic changes to confer advantages. Finally, mammals originally arose on land, and most individual mammals never have contact with the sea, so saltwater-friendly mutations would never convey advantages to them, hence would not spread in the population. Note that a very large fraction of coastal mammals are at least partially aquatic.

You ask “Over millions of years, one would think that the tools for utilizing this resource would “pop up” in the mammalian population…So why not fins, marine lactation, blowholes, hair loss, blubber, etc.?”

We see many of those things in other mammal groups. Fins, hair loss, and something like blubber on walrus and on manatees. Hippos can nurse under water and have many other adaptations. We see rudimentary flippers or toe webbing on many other mammals, such as otters (including both marine and freshwater members), beaver, and platypus.

Your “exodus to the sea” is a misrepresentation of how evolution happens. Groups as a whole don’t all suddenly decide to become aquatic. Changes in fitness are environment-dependent and begin with individuals. A change that favors an aquatic life might involve some fitness cost during terrestrial life. So such a change would spread if it arose in populations near the sea, but would tend to disappear if it arose in individuals inland. Population genetics can tell us at what point a subdivided population would be likely to split into two or more species, depending on the relative sizes and fitnesses and interchange-rate of the subpopulations. Once the species attain reproductive isolation, the inland one is free to move on a different evolutionary path than the seacoast one.

Why did primitive deer take to the water, and not wolves? I don’t know. But we do see many deer species today spending lots of time in water, and we don’t see wolves doing that so much. Moose spend lots of time in water because there are lots of edible plants there which are higher in sodium (which may limit moose populations) than terrestrial plants. Moose already show some adaptations to aquatic life (most notably, big unusual closable nostrils—will future moose have blowholes?)

Eddie - #78244

April 6th 2013


I see the reasonableness of much of this answer.  But note how frustrating it is for ID folks.  Here you are, granting me that the element of chance makes repetitions of major changes unlikely, but on other occasions, I’ve seen exactly the opposite argument from Darwinians:  helpful mutations are much more common than supposed, and so are nearly neutral mutations, which can be saved up and later combined with others, etc.; Dawkins says the eye has evolved 20 or 30 times—piece of cake!  So who represents good Darwinian theory, you or Dawkins or someone else?  Hard to know!

I get your point about different artiodactyl groups going in different evolutionary directions, depending on proximity to the ocean, etc.  That is fine with me.  It was never my view that it had to be “all or nothing.”

I would still maintain my point that calculating “selection pressure” on species that lived 40 million years ago, in an environment about which our information is very imperfect, involves a great deal of extrapolation and just plain guesswork.

I would also say that there often seems to be a degree of circularity in pronouncing on selection pressure.  If wolves have not changed much in 100,000 years, it is easy to say:  “The reason for this is that they did not experience much selection pressure.”  But unless some sort of objective method of calculating “selection pressure” on wolves in 50,000 B.C. is offered, I don’t see that such a statement has any confirmation that does not involve circular reasoning.

If we first infer that, since the wolves haven’t changed much, they haven’t experienced much selection pressure; and then, when someone asks why the wolves haven’t changed much, we offer the “fact” that they didn’t experience much selection pressure, our explanation is bogus.  For if the “fact” of low selection pressure was inferred from the outcome, and not determined independently, that “fact” can’t be used as the explanation for the outcome.  Such an argument is circular.

Dennis Venema - #78246

April 6th 2013

Eddie, do you beleive that erosion happens at a uniform rate, everywhere on the planet, or that local situations can influence the rate such that it is faster in some locations and slower in others?

Eddie - #78257

April 6th 2013


Of course the rate can be different; but the onus is on the geologists to provide mechanisms that explain the various rates, and to show that these mechanisms were actually operating (not “might have been operating”) at certain specific times in the past (the times relevant to whatever phenomenon is being interpreted).  If all they say is that rates of erosion sometimes differ, and can’t apply that in specific cases, they haven’t explained anything, but have only offered a big generality to cover their theoretical rear ends when the data don’t match what they first predicted.  

The same is true if someone say that mutation rates have varied, or that selection pressures have varied.  Easy to say, but useless from an explanatory view unless spelled out exactly for specific situations.

So, for example, suppose (for the sake of argument; I’m just making it up, not asserting anything actual) that someone argues that the transition between reptiles and mammals took 80 million years, based on proposed mutation rates, reproductive rates, fixation speed, etc..  And suppose that at first the fossil record supports this theory-driven calculation.  But then suppose that new paleontological finds show that the transition had to take place in only 20 million years.  If the theorists simply resort to “well, the mutation rates must have been faster back then than we thought”—they are simply offering an ad hoc patch to cover their flawed prediction.  If they can’t provide empirical evidence that the mutation rates were faster back then, they are simply arguing circularly, making the data fit the theory and vice versa.  Unless a reason can be given why mutation rates should have been faster during a particular period (e.g., maybe it has recently been discovered that there was more UV radiation or the like) such explanations are mere dodges, attempts to rescue the proposed mechanism with a deus ex machina.  And historical sciences such as evolutionary biology and cosmology are much more prone to invoke a deus ex machina than experimental sciences such as normal physics and chemistry.  That’s why I take their claims with a larger grain of salt than the claims of other sciences.

Lou Jost - #78248

April 6th 2013

Eddie, we do have skeletons of ancient wolves (for example from the La Brea tar pits). They are virtually identical to those of today. So my statement to Seenoevo that wolves today are much like the common ancestor is empirical. My statement that dogs were under strong artificial selection, and changed dramatically, is also empirical. Why might it be that the same genome in the human-selected population changed dramatically, but the wild genome did not? It is reasonable to infer a difference in the strength and direction of selection in the two populations, because this is the known cause of genetic change in large populations today.  The larger population size of wolves vs dogs also comes into play to insulate the wild population from any rapid fluctuations in the selection coefficient.

In fact there were many changes in the habitat and competitors of the wolf during the last twenty thousand years, so in some ways it is curious that it stayed so stable. I’d say the reasons for this is still not fully understood; it is not clear if there is something interesting behind it. This is part of the “punctuated equilibrium” debate.

I understand the frustration of IDers, but trying to fit ID mechanisms into the gaps of our knowledge is not very objective or scientific. It is being done purely for ideological reasons. As I’ve said before, I think it would be possible to detect strong enough ID if people could really do the math and show, for example, that the number of mutations and other genetic differences between a chimp genome and a human genome is too great to have arisen given known rates for these things, or that the selection coefficents involved would have to be unreasonably high. No one has convincingly done this yet (we’ll see what Sternberg comes up with in his book). Also, if someone does do it, most scientists will look for a naturalistic explanation, as they should, since this has proven to be the most productive approach to science in the past.

Eddie - #78258

April 6th 2013


Thanks for your concession regarding the curious stability of wolves.

I’m not trying to fit ID explanations into gaps in our knowledge.  I’m trying to point out where evolutionary theorists cover up gaps in our knowledge by speaking in a facile manner of “changes in selection pressures”—changes that they can’t even specify, let alone document, for periods 50 million years in the past.

I’m not trying to “prove” that design is real; I’m trying to show the incompetence of existing explanations that bend over backwards to avoid design and make use of chance, randomness, drift, selection, or anything they can get their hands on to keep the design foot out of the door.  And since you have changed your mode of argument to ad hominem, by speaking of “ideological reasons,” I will respond in kind:  Coyne, Dawkins, Myers, Scott, etc., have “ideological reasons” for not wanting design to be real, just as strong as any such reasons that ID people have for wanting it to be real.  Two can play at the “motivations” game.  I’d rather speak of the evidence:  what random mutations etc. have been proved capable of doing.  And what they have been proved capable of doing isn’t very much.

You know perfectly well that whenever any ID person comes out with a new mathematical argument for design—such as you say that you might in principle accept—the critics of ID have already decided—before reading the book—that the argument is rubbish.  I’ve seen book reviews on Amazon.com less than 24 hours after the book has gone on sale, demolishing the ID book (with no clear proof that the person has even read the book).  You couldn’t read the book through carefully and write a thoughtful critical review in such a short time.  There is a will not to believe in design among Darwinians, and that will goes straight back to Darwin, as anyone who has read his writings carefully can attest.  This debate is about metaphysics far more than biology.


Dennis Venema - #78260

April 6th 2013


Lou has already provided you with some of the evidence for why wolves are likely to have remained fairly stable over the last 100K years. Selection can stabilize a population within a niche, as well as be directional for a population exploiting a new niche. None of this is controversial, and I think even someone like Behe would accept these basic principles. We have good evidence for selection acting in both ways, depending on the circumstances.

I have another question for you, though, and it’s one of honest curiosity: when you say “there is a will not to believe in design among Darwinians” what exactly do you mean by “design”? Do you mean divine intervention, or something else?

Eddie - #78268

April 7th 2013


No, I mean design—which could be instituted through divine intervention, but need not be.  But Darwinians have always been against teleological explanations (and I mean teleological, not teleonomic as, say, Gaylord Simpson means the latter term), whether they involve interventions or not.  Interventions aren’t the issue.  

Ayala—who is on your side—has expressed the classical Darwinian and neo-Darwinian opposition to teleology extremely well.  Nobody has planned anything that happens in evolution, he says.  It may sometimes simulate the results of planning, but there is no planner and no plan.  And if there is anything that looks as if it must have been planned, the first duty of the evolutionary biologist, on Ayala’s view, is to show that the appearance of planning is just that—appearance only.

Look at people like Michael Denton and Mike Gene.  Both deny the need for interventions.  Yet both are widely reviled by the evolutionary biology community.  The cause can’t be appeal to interventions, because they make no such appeal.  The cause is appeal to design.  That’s the prime heresy for any Darwinian or neo-Darwinian, and indeed for all but a few evolutionary theorists.  They are almost all looking for an explanation that does not require design.  

On your other point:  I don’t deny that selection can, in principle, act “both ways”—but in each case, evolutionary theorists should be able to explain why it acted in a conservative or a revolutionary way.  And explanation requires providing a list of at least some of the factors (competitors, climate, geological upheavals, whatever) which led to either stability or change in each case.

If I ask an engineer why a particular building fell down during an earthquake, while another one stayed up during the same earthquake, he will not say:  “The first building lacked stability, whereas the other one had stability.”  That is a virtual tautology, and tautologies explain nothing.  The engineer will specify the factors that led to stability or instability in each case.  That’s all I’m asking for—far fewer big generalizations such as:  “drift, natural selection and gene duplication could have done it” and far more detailed explanations describing the exact parts of the gene that are supposed to have been duplicated, the alleged changes accomplished by “drift” between 50 and 45 million years ago, and the specific factors that should have made one phenotype more “selectable” than another.  I distrust sciences that rest in big generalities.  

One of the reasons I always liked chemistry and physics better than biology is that my chemistry and physics teachers, in both high school and university, were always much more precise in their explanations, much less likely to explain phenomena solely in terms of big general causes and much more likely to pinpoint the precise form those big general causes took in particular cases.

Lou Jost - #78272

April 7th 2013

It’s not biology’s fault that it is less precise than physics. We are dealing with a vastly complex system, which arose through chance accidents along paths that were winding and chaotic. We’ll never be able to give a detailed explanation of every detail (some of which were completely random) of an evolutionary process taking place 50 million years ago, and neither can you. We can, however, make testable predictions based on things we have been able to observe. Evolutionary theory does have its big general causes and general laws, but just as physicists need to know the initial conditions to solve their differential equation, biologists also need a lot of detail in order to apply these laws, especially in the distant past. These laws, however, have been tested and confirmed in cases when we know the initial conditions. If you claim they don’t work, the burden really is on you to show some evidence of that.

You are right that real teleology is heresy to scientists, because it violates even the sciences you appreciate, such as physics. We will demand a great deal of evidence before we accept teleological explanations, and this is completely reasonable. You have an unsubstantiated hunch that non-teleological processes are not enough to explain evolution. The genomes we have sequenced show no striking excess of mutations or rearrangements compared to what we’d expect from known processes. The dog genome discussed here is a good example. Even the chimp/human genomes are strikingly close. As I said above, if you look at the whale fossil sequence, there is no point where someone would say “Wow, that was macroevolution!”

The world is still waiting for good evidence that ordinary evolutionary theory is not enough to explain what we see. You said somewhere that biologists rejected Behe’s evidence for design  because of his lack of credentials. No, we rejected them because his arguments were bad. He might have noticed this himself if he knew more population genetics, and in that sense his background may have contributed to his making bad arguments, but it was the arguments that were rejected, not him. Sternberg’s arguments, which you also brought up before, fell flat as well (at least, the popular version presented in his YouTube video ), because (as you agreed) he neglected natural selection. I hope we will discuss Sternberg’s more detailed version of his arguments when his book comes out.

Eddie - #78274

April 7th 2013


Here is an example of where we differ in how scientists should write.  You have:

a vastly complex system, which arose through chance accidents along paths that were winding and chaotic.”

I find this formulation both speculative and dogmatic.  Here is how I would rewrite it:

“a vastly complex system, which, if neo-Darwinian theory is correct, arose through chance accidents along paths that were winding and chaotic.”

Do you see my point?  Your reply “refutes” what I said by assuming the very thing that is at issue between us.  It is therefore dogmatic.  And I find much writing in evolutionary biology and cosmology  to be dogmatic in this sense.  I’d like to see much more tentativeness of assertion, more sentences in the subjunctive and fewer in the indicative, etc.

You also wrote:

“We’ll never be able to give a detailed explanation of every detail”

But I’ve repeatedly said that I’d be happy with a set of hypothetical, physically possible steps, given that the actual steps are certainly beyond full recovery.  And no one is willing to provide even that.

The view that teleology “violates” science is a modern view.  Aristotle, the medievals, and even people like Newton accepted at least some degree of teleological thinking regarding nature.  

“The world is still waiting for good evidence that ordinary evolutionary theory is not enough to explain what we see.”

As I said elsewhere, I reject this “burden of disproof.”  From my point of view, “the world is still waiting” for a plausible, relatively detailed causal account of the evolution of any major organ, body plan, or organism.  The onus is on Coyne, Dawkins, Myers, Shallit, etc. to provide it; they have failed to do so.  They of course have every right to believe what they believe, even if I think they have insufficient grounds.  But they have no right to my intellectual assent, or to society’s.  If they want society to assent to Darwinism as readily as it assents to “atoms” or “four fundamental forces,” they had better start providing causal explanations as good as those of the physicists and chemists.

Lou Jost - #78285

April 8th 2013

Point taken about my phrasing, but the scientific world rightly regards that part of the theory as confirmed. Always open to evidence for the contrary, but until then, confirmed.

You didn’t address my comment that even physics would be unable to make specific predictions from, say gravitational theory unless they knew the actual distribution of matter in the area they were interested in. Evolutionary theory is like that. The general laws have indeed been confirmed when we know the initial conditions. In nature, and especially in the distant past, we don’t know the initial conditions so it is very hard to make precise predictions. This is not the fault of the laws but of our knowledge of the context (initial conditions). This happens also in physics, even with precise deterministic differential equations. In evolutionary theory it is even harder because there is an important random element.

Eddie - #78299

April 8th 2013


If physicists can’t make responsible predictions because they are lacking empirical data, then they should refrain from making predictions.  (That would stop a lot of the irresponsible conjecture that comes out of cosmology these days, conjecture which gets reversed every two or three years, as new evidence appears—evidence which should have been waited for before any conjecture was offered.)  And the same applies to biologists who explain, e.g., that the titanotheres died out due to “selective pressures” when they don’t know enough about the environmental conditions of the period to specify what those selective pressures were.

Modern scientists need to be much more modest in their claims of what they know.  That is why I like chemistry and physics better than cosmology and evolutionary theory.  The proportion of “strongly supported claims” to “speculations, conjectures, and mathematical extrapolations built upon questionable theoretical foundations” is much higher in laboratory sciences than in historical sciences.  There is less speculative room for scientists to overclaim and showboat in “materials science” or “organic chemistry” than in “evolutionary mechanisms” or “string theory.”

Lou Jost - #78266

April 7th 2013

Eddie, sorry if you interpreted that as ad hominem.

You are right that any scientist, presented with evidence for design, would try to find a naturalistic, causal explanation. Not because we rule out design, but because it has always failed in the past and is extremely improbable, based on what we know about the world. Give us real evidence and we would change our mind, but it would have to be very clear evidence.

Your complaints about the quality of evolutinary explanations are sometimes valid. But we really do have a rich palette of known mechanisms for generating variation (including the ones mentioned by Shapiro) and these show no evidence of design. Even Shapiro’s prime case, the immune system, does not produce just the antibody that is appropriate to fight an invader; it operates in shotgun fashion spewing out many random attempts, a tiny fraction of which will stick.

Eddie - #78269

April 7th 2013

Lou, you have no “very clear evidence” that random mutations plus drift plus selection can turn an artiodactyl into a whale on the order of 10 million years (you have no ancient genomes to confirm your inferences what they would have been like, you can’t give anything near a complete list of selection pressures from 50 million years ago, you don’t have anywhere near a full account of the interrelationship of genomic and extra-genomic factors even in everyday reproduction, let alone in evolution, etc.),  yet you believe it happened that way, on the strength of a straight extrapolation from microevolution to macroevolution—an extrapolation which not all evolutionary theorists grant is legitimate.

On the other hand, there is plenty of “evidence”—not proof, to be sure, but evidence, for design in nature; it’s all over the place.  But, given the choice of two explanations, neither of which can be proved, you choose the non-design explanation every time.  You have a preference for a non-design explanation.  And if you do some deep soul-searching, I think you will find that this preference is not merely because “methodological naturalism on the whole works better”; I think you will find other grounds for your preference.  The thousands of words you have written about religion on this site indicates what some of the those grounds might be.

As Ted Davis says, none of us are “neutral” in discussing these things.  None of does “pure science, no metaphysics”—even when we think we do.  We always have interpretive preferences, and, as every decent philosopher and historian of science knows, these preferences are shaped by non-scientific factors, including aesthetic and metaphysical notions and beliefs.

I agree with you about Shapiro.  He has never claimed to be a design theorist, and I never said that he was.  But he does provide an account of evolution that is quite different from classical neo-Darwinism (and I explained at great length how I’m using that term on the other thread we’re involved in).  And as I’ve already said, I find his notion more intrinsically plausible than the accounts of Dawkins, Mayr, etc.  Whether it holds up empirically is another matter.  But it’s logically sensible that evolution could move faster and more effectively if the old genome/organism barrier erected by Weissman is erroneous.  That’s what I find exciting in Shapiro’s proposal.  (And yes, he had some predecessors for the idea, but no one has put it so clearly front and center as he has.)  

melanogaster - #78565

April 16th 2013

“Another question, Eddie - for your choice of ~9 million years for the artiodactyl—> whale transition, you are aware that you’re not talking about a fully modern whale, right? 9 million years in they still had four limbs, for example. Kind of like large otter-like critters.”

Eddie, April 6:
“I’m willing to be corrected regarding the 9 million years.”

Eddie, April 7:
“Lou, you have no “very clear evidence” that random mutations plus drift plus selection can turn an artiodactyl into a whale on the order of 10 million years…”

Why would you repeat that as a fact when the day before you had admitted that you had nothing to support it?

“… (you have no ancient genomes to confirm your inferences what they would have been like…”

Dennis’s point, which you ignored, was that we don’t need the ancient genomes.

We can use a modern whale (which should be done soon) to compare and contrast with modern cattle to confirm predictions. We already have some studies on the differences that are consistent with what Dennis wrote.

Dennis and I are excited about the prospect of getting new data that have the capability to falsify or alter our hypotheses. What do you predict, Eddie?

Why aren’t “ID theorists” excited about real scientists sequencing a whole whale genome? Better yet, why aren’t they doing it themselves?

Eddie - #78273

April 7th 2013


Don’t worry.  By “ad hominem” I did not mean that you had personally insulted me.  I meant the term in its full and proper Latin meaning:  “directed to the person.”  An argument doesn’t have to be insulting or malicious to be ad hominem.  If one argues on the basis of someone’s alleged motives, that is formally ad hominem.  I was merely saying that if your side can speak of motives, so can my side.  If Dembski, Meyer, Nelson, etc. are said to be motivated by particular religious beliefs (which they are), the same can be said of the motives of Dawkins, Coyne, Scott, Myers, Rosenhouse, etc.  In both cases one might suspect that the pre-established religious commitments (and atheism is ultimately a religious commitment) are guiding the selection of evidence, the suppression of evidence, the estimation of relevance, the estimation of probabilities, etc.

Of course that does not mean that all atheists’ arguments are tainted by bad motives or that their arguments should not be replied to with evidence and counterargument.  It just means that “nobody’s neutral”—and we should be the most suspicious of those to pretend to absolute neutrality, who say they are doing “just the science”—as if science as a human activity is not influenced by extra-scientific considerations—especially when we are dealing with an existentially significant area of science—the question of origins.

I don’t know about you, but I cannot think of any evidence that in practice would convince Dawkins, Myers,  etc.  If Dembski “corrected” every alleged math error in his works, and even had his new work checked by a couple of Harvard agnostics, the same people who are attacking him now would attack his new math.  They would find some flaw, because they have to. Dembski’s “design” threatens not just the scientific opinions of these people, but a number of personal commitments they have made about how to live.  They think that if a designer exists, it is probably God; and God is not an idea they like.

The same goes for Behe.  If he recalculated his “edge of evolution,” and in doing so “corrected” every alleged error from his last book, and got some math help from some good population geneticists at Chicago and Yale, and still came up with an improbability of certain evolutionary changes happening by “Darwinian” means that was unacceptably low, the atheists would try to find new flaws in his math, even if there weren’t any obvious ones, motivated by their revulsion against his conclusion. 

Lou Jost - #78275

April 7th 2013

You are right about that. We’d try very hard to find flaws in those calculations. But that is what scientists should do. We do that all the time to our peers even when their results are purely naturalistic and do not violate well-established laws. (In fact I am doing it right now in the paper I am trying to write between posts here.) But if Dembski’s or Behe’s or Sternberg’s calculations were right, they would eventually win out. Even if the calculations prove to be too complex to do, it could happen that the ID viewpoint which generated them would prove to be productive at making new predictions about the structure of genomes and the pace of evolution. The moment scientists saw that the ID viewpoint was actually productive, they would flock to it. But IDers have had 160 yrs to show that this viewpoint is productive, and they haven’t yet come through with interesting results that can compete with the detailed results generated by the Darwinian, naturalistic paradigm.

Science is conservative by nature, but also competitive. We want to find out new things, and we want to be the first ones to do it. This hunger for discovery eventually trumps ideology. So I don’t think it is only our ideological distaste for design that keeps us from taking it seriously. Design is just not helpful in understanding reality. Indeed when you look closely at biological systems, they shout out their sloppy, random, un-designed pedigree.

melanogaster - #78288

April 8th 2013

“We’d try very hard to find flaws in those calculations. But that is what scientists should do. We do that all the time to our peers even when their results are purely naturalistic and do not violate well-established laws.”

And even more so when they don’t produce any empirical results and depend entirely on rhetoric, as Behe and Shapiro do.

“But if Dembski’s or Behe’s or Sternberg’s calculations were right, they would eventually win out.”

But people have to understand the only scientific way they can be shown to be right and win out is with new data. Desperate spinning of cherry-picked existing data (see ID blogs) and testing of silly misrepresentations of evolutionary hypotheses (Axe, Geiger) just shows how little faith they have.

“Even if the calculations prove to be too complex to do, it could happen that the ID viewpoint which generated them would prove to be productive at making new predictions about the structure of genomes and the pace of evolution.”

Correct, but they have to make said predictions before, not after, the data are produced. Rhetoric is never enough.

“The moment scientists saw that the ID viewpoint was actually productive, they would flock to it.”

Exactly. This is what Eddie fails/refuses to grasp. We are dogmatic about predicting new data, not against design. The question Eddie should be asking himself and Behe is why they so dogmatically oppose the fundamental requirement of predicting and producing new data. In doing so they oppose science itself.

He desperately pretends that it’s about having “proper debates” and rhetoric instead. The most damning aspect of the ID movement is the fact that its own promoters have no interest in demonstrating the productivity of any ID hypothesis. IOW, all of the data indicate that they have no faith.

“But IDers have had 160 yrs to show that this viewpoint is productive, and they haven’t yet come through with interesting results that can compete with the detailed results generated by the Darwinian, naturalistic paradigm.”

And there’s no sign that they have any intention of trying. Eddie could go do a PhD or postdoc with either Behe or Shapiro—even pure theoreticians have grad students and postdocs. If Eddie’s too old to do so, he should be talking others into doing something.

“Science is conservative by nature, but also competitive. We want to find out new things, and we want to be the first ones to do it. This hunger for discovery eventually trumps ideology.”

And there’s absolutely zero hunger to find out new things in the ID movement. It’s pseudoscience, and all the qualifications in the world can never trump productivity and predictive value.

“So I don’t think it is only our ideological distaste for design that keeps us from taking it seriously. Design is just not helpful in understanding reality. Indeed when you look closely at biological systems, they shout out their sloppy, random, un-designed pedigree.”

And that’s why I hypothesise that people like Eddie are afraid to look closely. That’s why Behe doesn’t do exhaustive searches of the primary literature before foolishly making global claims of empirical fact. That’s why creationists and IDers alike try to blow off the massive amount of sequence data as mere “similarity” if they talk about it at all.

Jon Garvey - #78292

April 8th 2013


Eddie - #78295

April 8th 2013

Thanks, Jon, for doing the research that disproves Fruitfly’s irresponsible charges against Shapiro.

Interestingly enough, in one of the articles given in the c.v., Shapiro rebuts Larry Moran’s review of his book.  One of his complaints is that Moran, by his own admission, has not read a good chunk of the central argument of the book.  It would not surprise me if Fruitfly has read even less of that book, like, maybe, none of it.  And it would not surprise me if Fruitfly has not read anything by Shapiro at all.  After all, since Shapiro is critical of mainstream evolutionary theory, he must be wrong, so there is no need to read his actual arguments before declaring him wrong.  Just as that famous Aristotelian, according to legend, did not need to look through Galileo’s telescope at the moons of Jupiter, because he knew in advance that Galileo, being critical of mainstream Aristotelian/Ptolemaic physics and astronomy, must be wrong.

It’s ironic that Fruitfly charges everyone within sight of refusing to look at the evidence, but he makes a statement about the quantity and quality of Shapiro’s work without looking at the evidence of Shapiro’s productivity that is easily available on the web.

Note to Lou Jost:

Please read Shapiro’s Reply to Moran:

http://shapiro.bsd.uchicago.edu/Reply to Larry Moran.pdf

It is interesting that Shapiro’s remarks on Moran parallel the complaint of Stuart Newman (another cutting-edge evolutionary theorist):  many of the loud voices in these debates are rather hidebound, with a fierce attachment to old ideas and a resistance to the new.

Lou Jost - #78309

April 8th 2013

Eddie, I had read Shapiro’s response long ago. As I mentioned to Jon above, I participated heavily in the Moran post on biologists and physicists which Shapiro cites in his rebuttal. You can go back and see that I defended Shapiro against Moran.

Lou Jost - #78310

April 8th 2013

“As I mentioned to Jon above” should read “As I mentioned to Jon below”

Eddie - #78324

April 9th 2013

OK, good.  Thanks for that.

melanogaster - #78313

April 8th 2013

“Thanks, Jon, for doing the research that disproves Fruitfly’s irresponsible charges against Shapiro.”

In what way, exactly? That’s your first false claim.

“It’s ironic that Fruitfly charges everyone within sight of refusing to look at the evidence,…”

That’s false and you know it. For example, I’m not charging Shapiro with refusing to look at the evidence, I’m charging him with merely relabelling the existing body of evidence in a way that is scientifically meaningless if it doesn’t produce an empirically testable hypothesis. Put another way, I’m accusing him of refusing to produce new evidence from an empirical test of his pet hypothesis. Are you claiming that such evidence exists in one of these papers post-1999?

“… but he makes a statement about the quantity and quality of Shapiro’s work without looking at the evidence of Shapiro’s productivity that is easily available on the web.”

Again, that is completely false. I did look at it. That’s why I asked you to show me a new datum that he has published since 1999. That’s why I asked you to tell me the differences between papers he has published since 1999 and his book.

Three false claims in one comment, Eddie. That’s pretty dense even for you.

Lou Jost - #78308

April 8th 2013

Jon, take a look at the blog post that Shapiro (at the link provided by Eddie below) cites in his (Shapiro’s) rejoinder to Larry Moran’s review. Moran’s post is here:


You’ll see I defended Shapiro there, and was very eager to get his book. My criticisms of his book are not due to pre-existing bias against it.

Jon Garvey - #78322

April 9th 2013


I have no suspicion that you were criticising Shapiro from prejudice. I just linked to his publication history for those who wished to see it. Reading the Moran thread you were a breath of fresh air in both your clarity and charity.

It’s interesting how your reasoned examples actually poured cold water on others’ ad hominems and prompted some actual discussion in between the smug put-downs.

There was surprisingly little general engagement with your critique of the maths used in biology, though. Larry’s only reply to your raising the issue appears to have been to say that David Berlinski is not a mathematician… or the right sort, anyway.

Your position in contrast actually said something, but came close, it seems, to getting you censured as a fellow-traveller with heretics. As we all know, seeing a grain of truth in Shapiro is as good as endorsing David Berlinski and proving yourself a Creationist like them!

My only disagreement with you was your suggestion that Shapiro says complete ignorance about a subject is useful. I’ve never read any such sentiment from him, though Moran seems to make a similar boast in his OP.

Lou Jost - #78344

April 9th 2013

Hi Jon, thanks for this comment. And yes, I was probably influenced by Moran’s original post and should not have read Shapiro to be saying that complete ignorance is useful.

melanogaster - #78312

April 8th 2013

So where are the new data since Shapiro started riding this horse in 1999, Jon?

Eddie - #78326

April 9th 2013

There is tons of it, in the book that you haven’t read.

melanogaster - #78349

April 9th 2013

Then it’s simple enough for you to point me to 10 examples.

Eddie - #78357

April 9th 2013

I don’t deal with biologists who are too lazy to read books by other biologists but still think they have the right to criticize them.

It must be nice to be able to tell that a book is wrong without having read it.  It would save a lot of research time.  I take it that this has been your normal procedure throughout your scientific career—to pass judgment on things you haven’t read.

Eddie - #78297

April 8th 2013


This comment is shocking:

“You are right about that. We’d try very hard to find flaws in those calculations. But that is what scientists should do. We do that all the time to our peers even when their results are purely naturalistic and do not violate well-established laws.”

Why should scientists try to find a flaw in calculations merely because they don’t like the conclusion that the calculations seem to establish?  Remember, I am not arguing that scientists should not be critical of new scientific work.  Of course they should be.  But they should not be out with their axes, ready to cut down any view not congenial to their own theoretical commitments.  If something in the scientific argument being presented makes them suspect sloppy work, or incomplete analysis, then fine.  But as I made clear, I’m not talking about that.

I’m talking about Amazon reviewers who can produce a review of a 300-page book within 24 hours after the book goes on sale on Amazon, faster than the book could be shipped to a customer.  And I’m talking about reviews in newspapers and on the internet which run like:  “On Page 1, Behe is stupid.  On Page 2, he is dishonest.  On Page 3, he makes a sophomore error in biology.  On Page 4, he shows he knows no math.  And by the way, did you know that all his colleagues at his school disagree with him, and that he hangs out with creationists?  On Page 5…”  

Well, you get the picture.  Nothing like:  “Behe makes an intriguing argument in Chapter 2 which, while not well-supported in its current form, could be productive of useful research” or “Behe is right to point out a weakness in current evolutionary theory on this point, even if his own analysis is not adequate.”  You could scour the reviews of Coyne, Miller, Scott, Dawkins, Myers, etc. and you would not find moderate, scholarly sentences like that.

If a scientist is ready and eager to respond negatively to a new book or article like a racehorse surging against the gate, the scientist is not in an objective frame of mind, but a prejudiced one.  And there is an active prejudice against ID which tends to prevent moderate, balanced responses from its critics.

I do not think you can possibly have followed the anti-ID literature as closely as I have.  Otherwise, you would have seen how often both atheist and TE writers (Miller, Scott, etc.) have invoked “methodological naturalism” to rule design inferences out of science in principle.  And if they are ruled out in principle, then no calculations, however good, could ever establish that anything in nature is designed.

It is certainly not true that design is not helpful in understanding “reality.”  Do you think your car or house or computer sprang into existence without design?  But if by “reality” you meant to say “nature”—you are making a dogmatic statement.  There are many people who have “looked closely at biological systems” and have seen strong evidence for design, including, e.g., Ivy League professors with a score of genetic patents to their name.  They just happen to disagree with you.

If you want to see research along ID lines, I would suggest that you follow the journal BioComplexity. More has been done than you think.

Lou Jost - #78306

April 8th 2013

“This comment is shocking”

Why? If someone proposes something that contradicts an established and well-tested theory, of course he or she is going to get grilled, and the grillers will do it with gusto. That is science. Even if someone just proposes a boring detail on some subject, if someone else has a hunch that it is wrong, he or she will go after it and try to disprove it. And if someone proposes a nice solution that elegantly resolves a bothersome problem, even people who like the solution will try to see if they can prove it wrong, because we don’t want to fool ourselves. My own contribution to population genetics spawned at least four attack articles in high-impact journals trying to tear my idea apart. That’s good! Science is always vigorously probing itself. Guess what? Good ideas survive this trial by fire.

I’m not defending people who don’t examine the claims before rejecting them.

I am well aware that people often invoke methodological naturalism as an a priori reason for rejecting an idea. I have repeatedly said elsewhere on this site that it is philosophically and scientifically wrong for Scott or anyone else to build that kind of wall between the claims of science and those of religion. I am not the only atheist who says that either; Coyne and Moran, among others, have also publicly criticizes Scott for this.

If you could suggest just one or two of the best articles in that journal for me to read, I’ll look at them. But as I said above, the design viewpoint has not been a fruitful one to date. The Discovery Institute is constantly trumpeting that the big break is right around the corner, but we keep waiting.

Eddie - #78328

April 9th 2013


We aren’t going to agree on this one.  Yes, I can grant that it’s healthy in science or in any academic field to have a “loyal opposition” which critically assesses new proposals.  And I have no problem with the criticism being thorough.  But deep down, you know that is not what I am talking about.  You know that, when it comes to origins questions, there are, in addition to that healthy motivation, unhealthy motivations for attacking certain views.

When two scientists are arguing about, say, whether or not the head of a comet contains nitrogen gas, they may thoroughly criticize each other’s position, but there is nothing like the tension in the air that there is when the notion of “design” is mentioned, or when someone criticizes evolutionary theory.  And that’s because in the case of the comet, the two scientists have no existential stake in the truth of either answer.  The answer couldn’t possibly have any effect on the way those scientists lead their lives.  But origins questions have deep associations with scientists’ existential commitments.  You must know this.  

One of the reasons I despised Creation Science as a youth (when I was a flaming Darwinist) was that I could see that, underneath the formal appearance of scientific criticism, there was a deep wish on the part of Gish, Morris, etc. to believe that evolution was not true.  This “will to disbelieve” generated arguments that were so poor that, in their heart of hearts, these people must have known they were not entirely legitimate.  They would not have used such weak and faulty reasoning in any area of life—except for origins questions.  And I found that intellectual dishonesty far more objectionable than the actual conclusions they were drawing.

Similarly, in the people I’ve been criticizing here—Scott, Myers, Coyne, Shallit, etc.—there is a deep personal will to believe that there is no design in nature.  Even if Coyne and Moran do, as you say, avoid formally excluding design arguments, they will never personally accept any argument for design presented during their lifetimes.  There is a mental barrier of an extra-scientific kind operating.  So I can give them points for not adopting the intellectually primitive epistemology of science adopted by Miller, Scott, and the NCSE, but I don’t believe for a minute that they will ever assess any present or future ID argument fairly.

Jon Garvey - #78332

April 9th 2013


Even-handedness is the issue here. On the Moran thread, Lou pointed to mathematical misconceptions that commonly affect biological papers. He seemed to suggest they’re not corrected often enough, but in any case such errors are certainly not used to marginalise their perpetrators, and rightly so. The right thing is to point out the error and move the discussion forward. “You know zilch about maths” is not helpful - still less, “you know zilch about maths because you’re just a stupid microbiologist.”

Occasionally in my profession, sadly, managers have taken a dislike to a doctor, perhaps for whistle-blowing on dangerous policies. A common ploy is to suspend him and investigate his work closely (and slowly) - and surprise, surprise, there are always concerns to justify ending his contract. And the reason is that nobody’s error-free over a career.

The wrong is that only the grit in the oyster gets investigated, not to improve standards, but to maintain the status quo. The motive is betrayed by both the selectivity and the lack of respect of the critique.

So true science will see errors called out on work supporting the paradigm as often as that questioning it, and will criticise the error, not the worker.

Eddie - #78358

April 9th 2013

Good points, Jon.

melanogaster - #78505

April 13th 2013

Perhaps you should try to put them in practice? A scientific discussion will focus on ideas and evidence, not people and hearsay.

melanogaster - #78314

April 8th 2013

“If something in the scientific argument being presented makes them suspect sloppy work, or incomplete analysis, then fine.”

Shall I list the sloppiness of Behe’s work that easily justifies hardened skepticism?

“I do not think you can possibly have followed the anti-ID literature as closely as I have.”

That’s insane, Eddie. The anti-ID literature is primarily the primary literature that you are afraid to examine for yourself. If you had faith that it would support your position, you would be eagerly devouring it. Did you already forget that you said that you didn’t know how to search it?

“If you want to see research along ID lines, I would suggest that you follow the journal BioComplexity. More has been done than you think.”


There’s no empirical test of any ID hypothesis there. It’s a joke!

Dennis Venema - #78318

April 8th 2013

Eddie, have you seen YEC Todd Wood’s take on



Lou Jost - #78345

April 9th 2013

Eddie,  you said “I would suggest that you follow the journal BioComplexity. More has been done than you think”  From your comment, I imagined a normal journal, reporting a vigorous research program, like we would expect in any real science. I thought I wouldn’t have time to go through all the articles and choose a couple of good ones, so  I asked you to suggest a few of the best. Since you didn’t, I went to look myself. It turns out there are only two or three articles published per year! And mostly by the same people as always—Dembski, Axe, Gauger, to name a few. So I’ll be able to find a couple interesting ones on my own, and will get back to you in a week or so when I have had time to read them.

Lou Jost - #78346

April 9th 2013

Eddie, you wrote “I would suggest that you follow the journal BioComplexity. More has been done than you think.” From this comment of yours, I naturally imagined a normal journal with lots of research. I asked you to pick two of the best articles so I could look at them. You didn’t do that, so I browsed the journal myself. To my surprise, I found only two or three articles per year! Hardly a vigorous research program. And the articles are mostly written by the usual authors, Dembski and Marks, Gauger, Axe. One article is written by the journal’s editor. The laughably tiny number of articles per year speaks for itself about the unproductive nature of the design hypothesis, and suggests that maybe there is not as much out there as you think.

Anyway I picked an article to look at, and will report back in a week or so when I have time to read and analyze it.

(An earlier version of this comment got lost somewhere here; maybe it will show up later? If so, apologies for the duplication.)

Seenoevo - #78249

April 6th 2013

Three questions: 1) Dennis Venema (DV) wrote: “are you aware that seals and sea otters, as examples, have adapted to a marine lifestyle independently of the whale lineage?” What did seals allegedly evolve from, or who are the leading candidates?   2) DV: “we see the mammalian (cetacean) raditation into the sea after the asteroid impact wiped out the large apex sea predators like ichtyosaurs, opening up a new niche.” I had never heard of the idea that an asteroid wiped out big sea creatures. I heard of the flight of fancy that an asteroid expunged dinosaurs, but these were always presented, to my knowledge, as land lubbers. And the hypothesizers pointed to what might be the remnants of a crater on land, I think in Mexico. Not that it would resolve or prove anything, but just out of curiosity, how confident are you that an “asteroid impact wiped out the large apex sea predators like ichtyosaurs”?  

3) DV: “Eddie, do you beleive that erosion happens at a uniform rate, everywhere on the planet, or that local situations can influence the rate such that it is faster in some locations and slower in others?”

I won’t speak for Eddie, but I’d say erosion happens at different rates, but that it always results in the same thing: detritus.

Dennis, do you believe erosion could have caused something like Mount Rushmore?



Unfortunately, this website offers no way to change font. The big bold above was not intended.


Seenoevo - #78250

April 6th 2013

Lou Jost (LJ) wrote: “The sea was a vast new environment for terrestrial mammals. There would have been strong selection pressure to adapt.” I think life is tough all over. Survival stress on land, sea and sky. But I would think the “selection pressure” would be abnormally intense for an animal that was no longer as “fit” for land as it used to be but was not yet as fleet of fin as it might yet become. And this animal would be in these sub-optimal transitional phases for eons. If anything is going to be on the menu for surf and turf, this is it. I see no reasonable chance of such a thing surviving, reproducing, flourishing for eons until the time it becomes a whale.    LJ: “Moose spend lots of time in water … Moose already show some adaptations to aquatic life (most notably, big unusual closable nostrils—will future moose have blowholes?)” Now, this is a serious question. So you can withhold any response accusing me of being sarcastic and un-serious. Lou Jost, do you think Michael Phelps could develop closable nostrils or a blow hole before his Olympic career ends (or ever in this life)?
Lou Jost - #78254

April 6th 2013

Sorry, I actually don’t believe your second question was serious.

But I’ll answer your first comment. There are lots of plants that grow underwater, and lots of fish. It is easy to see how the ancestors of whales might have gotten started, just by looking around us. We can see many of todays terrestrial animals dabbling in aquatic environments, and we can see a great range in their degree of adaptation for aquatic environments, from barely adapted moose (the only deer with nostrils that close tight underwater) and nutria to highly adapted manatee and seals. It should not puzzle you that the terrestrial ancestors of whales did exactly the same things. Furthermore, we have many actual fossils of intermediate forms of the transition to whales. There is no question that this really happened. Even Eddie, who has been arguing here about the mechanisms, will tell you that the transitions happened. The only way to “See no Evo” is to stick your head in the sand.

Seenoevo - #78251

April 6th 2013


Was my memory playing tricks on me when I wrote above that “I could swear that I’ve read on these pages, maybe even from this author’s pen, that ‘individuals don’t evolve, populations do’?   [Which was in response to Dennis Venema’s statement that ““The short answer is that chromosome structure changes, like any mutation, occur in an individual and then may spread through a population.”]

Dennis Venema - #78253

April 6th 2013

Populations evolve as average characteristics change over time. Mutations occur in individuals, and if they become more frequent in a population over time, may contribute to changing average characteristics of the population as a whole.

Dennis Venema - #78252

April 6th 2013

Sorry, seems I was a bit off. Ichtyosaurs go extint prior to the K-T impact, but mammals radiate afterwards. So,  apex sea predator niches were open at the time of the mammalian radiation, but not directly because of the K-T asteroid impact.

Seenoevo - #78276

April 7th 2013

Lou Jest wrote: “Design is just not helpful in understanding reality. Indeed when you look closely at biological systems, they shout out their sloppy, random, un-designed pedigree.” Are you serious? If you are, that is one very remarkable statement. I’ll remark only that I thought biomimetics was one of the hottest, most useful areas of science today. Here are just four recent examples: 1) Mini-helicopter that tries to emulate the design of the dragonfly. (Neat video.) http://www.festo.com/cms/en_corp/13165.htm 2) A new iPhone app “inspired by biology and replicates the complexities of the human ear.” [What they meant to say is “design of the human ear”. Complexity by itself doesn’t get you anything. A knotted, tangle of fishing line is complex, It’s almost impossible to figure out and untangle. But it’s not very useful.]   http://medicalxpress.com/news/2013-03-mobile-app-iphone-biologically-aid.html 3) Medical device designs based on the architecture of squid: http://phys.org/news/2013-04-bioinspired-material-mimics-squid-beak.html 4) Robots relying on the propulsion systems of jellyfish: http://www.livescience.com/28286-jellyfish-robot-cyro.html   Research just a little bit and you can find countless other examples of scientists and technologists trying to understand and emulate the designs they see in nature. If my car breaks down, does that mean it wasn’t designed? Remarkable.
Lou Jost - #78277

April 7th 2013

For the flip side of that, look up “genetic algorithms” in Wikipedia. Computer scientists can solve complex problems by imitating blind evolution.

Nature is indeed amazing and inspiring, but if you look closely at the things you mentioned, you’d find recycled, repurposed parts being used for new functions that they are not optimal for, and you’ll find partial solutions that are constrained by the organism’s ancestral history, etc. These wonderful adaptations, when you look at them closely, reveal their chaotic, opportunistic, accidental past.

Seenoevo - #78282

April 8th 2013

Lou Jest responded:

“Nature is indeed amazing and inspiring, but if you look closely at the things you mentioned, you’d find recycled, repurposed parts being used for new functions that they are not optimal for, and you’ll find partial solutions that are constrained by the organism’s ancestral history, etc. These wonderful adaptations, when you look at them closely, reveal their chaotic, opportunistic, accidental past.”

Another remarkable statement. And very quizzical. Here are some quizzical remarks: That first example above involved the dragonfly. The dragonfly has remained unchanged for 300 million years, according to evolutionary scientists. 1) Which parts of the dragonfly are “recycled, repurposed”? 2) What were these parts used for prior to over 300 million years ago? 3) Which parts of the dragonfly have been “not optimal” for the last 300 million years? 4) If these parts have been “not optimal” for the last 300 million years, why are these parts still being used by the dragonfly? 5) What suggestions would you have (or natural selection/mother nature have) to optimize or make better the 300 million year old dragonfly? 6) In answer to 5), maybe accidentally add some sonar, like the bats have? 7) Why don’t dragonflies, and other flying creatures, have sonar like the bats? I’m fairly certain some of them must get hungry for a midnight snack from time to time. The sonar could enable them to satisfy the urge. And they’d have no competition from the parts of the population which hadn’t yet experienced the serendipity of sonar snacking. [Conversely, why can’t bats fly backwards like dragonflies? Isn’t it always more optimal to have an extra gear?] Hopefully, you can adequately address these questions, because I have many more, about the other three examples above (e.g. the chaotic history and sub-optimal state of ears, and of the 500 million year-old squids).  

The title of this series is “Evolution Basics”. I despair that I’ll never be able to digest any advanced courses. Because I’m having great difficulty just swallowing the “basics” dish.

Lou Jost - #78284

April 8th 2013

So many mistakes, so little time…dragonflies have changed and diversified enormously over the last 300 million years, they can’t fly backwards as far as I know (though damselflies might be able to) and you yourself have just answered your own question about suboptimality by naming some possible features that dragonflies could have had, but didn’t, either because the required mutations never arose by chance or because of developmental constraints.

Seenoevo - #78287

April 8th 2013

Lou Jest responded:

“So many mistakes, so little time…dragonflies have changed and diversified enormously over the last 300 million years, they can’t fly backwards as far as I know… and you yourself have just answered your own question about suboptimality …”

So, dragonflies have changed enormously in 300 million years? I know they used to be bigger, we have fossils to prove it. But other than in size, how have they changed, and changed greatly? Maybe you’re right. Note how very different the old dragonflies looked. I wouldn’t recognize them in a million years. No, even in 155-300 million. http://www.naturenorth.com/dragonfly/DOM/Page03_Palaeobiology.html http://www.flickr.com/photos/junesbugs/802046031/


Regarding your claim that dragonflies “can’t fly backwards”, look and see time 1:39-1:56: http://www.youtube.com/watch?v=41OD5NEV-Kw   “…you yourself have just answered your own question” If this is another true statement of yours, I wish I’d listen better. Because I’m still not hearing these answers you say I’m giving myself. But I think I can do two things at once. So, while I’m endeavoring to listen and learn better from my own wisdom and insight, I’ll also be looking for your answers to questions 1-5 & 7 (you can skip # 6). And I’m not looking for more generalities like “required mutations” and “developmental constraints”. Specifics and step-by-steps, please.
Lou Jost - #78307

April 8th 2013

You are right about the dragonflies flying backwards! Apologies for doubting you.

The rest of what you wrote is still wrong, though. For example, the dominant dragonfly genus of Africa, with forty-some species, is just about 6 million years old:


Ancient fossil dragonflies might look similar to today’s, but if you look closely, you will see that most of the old fossil dragonflies aren’t even in the same suborders as today’s dragonflies, much less in today’s genera or species. To see the tremendous radiation of dragonflies in the last 100 million years, see the phylogeny in Fig 6.31 of  Grimaldi and Engel, “Evolution of the insects”, Cambridge Press, 2005, available online if you search “dragonfly phylogenies”.

I’ll leave you to research the answers to your other questions. You  don’t really seem to care about the answers anyway.

Seenoevo - #78348

April 9th 2013

Lou Jest responded:

“The rest of what you wrote is still wrong… see the tremendous radiation of dragonflies in the last 100 million years, see the phylogeny in Fig 6.31 of  Grimaldi and Engel, “Evolution of the insects”…”

Per your direction, I found several links, some with pretty pictures and all with lots of words. But I didn’t see anything that would answer my questions.

And are you saying that if one of these fossils (http://www.naturenorth.com/dragonfly/DOM/Page03_Palaeobiology.html) somehow came back to life, and started flying around, that a normal human being would NOT identify it as a type of dragonfly? Even an evolutionary biologist?


“I’ll leave you to research the answers to your other questions.”

That’s quite a convenient avoidance tactic. But it won’t work. I HAVE researched and I’ve NEVER found any logical and/or empirical basis for someone to claim what you did (“Nature is indeed amazing and inspiring, but if you look closely at the things you mentioned, you’d find recycled, repurposed parts being used for new functions that they are not optimal for, and you’ll find partial solutions that are constrained by the organism’s ancestral history, etc. These wonderful adaptations, when you look at them closely, reveal their chaotic, opportunistic, accidental past.”)

Apparently, YOUR research HAS found what mine didn’t. So, I’m just asking for the details, which again, exclude the fuzzy generalities like “required mutations” and “developmental constraints”. I’d like to see the specifics your research has produced.


“You  don’t really seem to care about the answers anyway.”

You’re wrong once again. I DO care.

And I’m waiting for your answers (to 1-5 & 7 above).

Lou Jost - #78351

April 9th 2013

Here’s what you said to my last answer: “Per your direction, I found several links, some with pretty pictures and all with lots of words. But I didn’t see anything that would answer my questions.” No engagement or coherent thought. Bye.

melanogaster - #78501

April 13th 2013

“And are you saying that if one of these fossils (http://www.naturenorth.com/dragonfly/DOM/Page03_Palaeobiology.html) somehow came back to life, and started flying around, that a normal human being would NOT identify it as a type of dragonfly?”

That’s not the issue. The issue is whether that dragonfly could mate with today’s dragonflies and produce fertile offspring.

“Type of dragonfly” is analogous to “mammal” as both are orders. Would you expect any mammalian fossil that came back to life to mate with any other mammal, or can you see that those are very different species within an order?

You’re making this mistake for two reasons: we are better at discriminating between organisms more similar to ourselves, and (despite the larval stages and metamorphosis) insects develop from fertilized egg to adult in a very different way than we mammals do, making them less plastic evolutionarily.

Lou Jost - #78352

April 9th 2013

Eddie, in earlier comments on this thread you recommended I look at the journal Bio-Complexity to see how much ID research was being done. I looked through every article published in 2012. All four of them! Two research articles, and two critiques/reviews. Some may have merit, I haven’t read all of them yet. But the one that was written by the journal’s editor was amusing. He claimed that since lignin is really hard to break down, it must have been designed by some unnamed intelligence (we all know who that must be). Eddie, you recommended this journal to me as a showcase of ID research. How can you be so tough on real science yet give this crap a pass?

Eddie - #78355

April 9th 2013


I actually have read that article closely—did you do any more than a quick skim of it?—and the article is much richer in contents and argument than you are indicating.  I’m not saying I endorse the conclusions, but your snap rejection is crude.  

I was not endorsing any particular article in the journal.  My point was not that any article in the journal had yet proved anything; my point was that the journal is trying to present research that is done from within a design perspective.  I was responding to your charge that all that ID people do is attack Darwinism, and never try to shed any light on the way nature works.  Whether the articles in BioComplexity are yet of the highest quality—it is a relatively new venture and needs to be given a chance—the point is that ID is trying to move from the negative to the positive.  

BioComplexity is not the only place where this is happening.  Articles trying to employ design in the understanding of nature are starting to appear in journals of computer science, engineering, etc., and occasionally even journals of biology.  You can get lists of such articles from the Discovery web site.  Kirk Durston, who has posted comments here, has been doing post-doctoral work in bioinformatics and is very interested in looking at biological systems as expressions of information.  (No doubt you will look up Durston’s publications, give them a quick skim, and dismiss them as “crap,” but nonetheless, he is getting published in peer-reviewed venues.)  ID is slowly passing out of the negative phase and turning into a positive research program.  That was the only point I was trying to make.  I leave the qualitative judgments to the readers of future ID research. 

Lou Jost - #78359

April 9th 2013

“No doubt you will look up Durston’s publications, give them a quick skim, and dismiss them as “crap,” but nonetheless, he is getting published in peer-reviewed venues.” That is an unfair assumption.

Do you think that the lignin article is any better than the “just-so” stories you  accuse evolutionists of making? Just maybe, you have a double set of standards, one for evolution (which you and Berlinski demand to reach the level of exactness of physics or chemistry) and one for design research.

Eddie - #78361

April 9th 2013


Is it an unfair assumption?  You dismissed the work of an active researcher in evolutionary theory as “crap” without giving any arguments to show why it was “crap.”  You’ve already made clear that you think Berlinski’s criticisms are “crap.”  What is the point of my continuing to point out people—whether Axe or Gauger or Sanford or Denton—who have degrees just as good as yours, from universities just as prestigious as the ones you graduated from, have publications in mainstream journals, etc., if that is going to be the uniform response?  You haven’t paid a substantive compliment to an ID person, or even to an atheist Darwin critic, since we started engaging.  You seem to focus only on how wrong they all are.  

I say neither yea or nay to the lignin article.  But your characterization of it suggests a lack of sympathetic engagement.  You don’t appear to have made any effort to give a balanced judgment of the article, pointing out good things in addition to bad things.  And that’s par for the course on both atheist and TE websites.  The name of the game is always:  let’s show that ID is not merely wrong, not merely inadequate, not merely still immature as science, but that it’s rubbish, nonsense, trash, etc.

I weary of these conflicts.  You are one of the more polite and reasonable anti-ID people I’ve engaged with, and I praise you for that, but still you are starting to sound doctrinaire and one-sided in your comments, and I don’t think I have the patience for further dialogue which is mainly nay-saying on your part, no matter what I suggest.  

I now have another deadline coming up, so it will be a few days before I can engage again.  Best wishes.

Lou Jost - #78373

April 10th 2013

Yes, that is unfair. I did not say Shapiro was all bad, and in fact I have defended him on some points. (And in his case, you criticised me for NOT saying he was wrong!) But some of the stuff you steered me to really was crap. I’ve given you specific reasons when it seemed worthwhile, and you eventually seemed to accept that I was right about those reasons, though you would not directly say so. You praised Sternberg; his video presentation (admittedly not an adequate forum) ignored natural selection, which invalidated his conclusions. You agreed with me and said we should wait for his book. Fine, I’m waiting. Behe too made serious mistakes in his probability calculations. Eventually you said you weren’t qualified to judge them, which was admirable.

Now you sent me to  journal whose editor wrote a “just-so” story. If it was an article on evolution of lignin, and the design language were replaced by talk about selection pressures on plants to make a non-decomposable substance like lignin, complete with hypothetical pathways and ancestors, you would have criticized it (as you did with whale material). You should have criticised this lignin article with the same rigor, but you only hedge and say you neither endorse nor reject it. Why is that?

You say I never said something positive about any of those guys. I did several times endorse their approach to checking if known mechanisms could produce what we see today. But their particular methods, so far, have been wrong. If these are the best you have, then your position is in trouble. 

It is laughable that you say I never criticize a supporter of evolution. I guess you didn’t bother to read my Sandwalk blog comments referred to above, and you have obviously never looked at my published papers, which are highly critical of some mathematical misconceptions regarding the evolution of genetic divergence between populations (the process that underlies speciation).

I will look at Kirk Durston’s work which you recommended, and I will examine it with the same rigor I apply to the arguments of my geneticist colleagues. I may report back in a week or so, as I also have many deadlines.



Eddie - #78376

April 10th 2013


I did not undertake to evaluate the lignin paper or any other paper in BioComplexity.  I indicated the existence of the journal only to point out that some ID people are now trying to move away from culture-war activity and publish interpretations of nature based on an ID rather than Darwinian perspective.  

You have every right to disagree with the conclusions of the lignin paper or any other paper you find in BioComplexity.  However, I would prefer to see statements such as:  “While the author shows sound knowledge of features X and Y of plant physiology, he has mistakenly inferred Z” to statements such as:  “this is crap.”

Indeed, one of the things that led me to take the ID side of the culture wars (aside from the fact that I’m persuaded there is a good case to be made for design in nature) is the fact that the other side kept trying to shout down ID with language like that.  The scientists who taught me in undergrad, in a genteel world that apparently no longer exists except in my memory, were not like that.  They were gentlemen.  They criticized moderately and in a balanced way.  And they did not try to win scientific battles in popular media.  But apparently universities are now turning out a new breed of scientist—the scientist who attempts to influence popular opinion by getting down and dirty in popular debates.  Normally you have risen above that.  I praise you for not being like Moran, Coyne, Myers, Shallit, etc., all of whom I consider puerile rather than adult.  But your “crap” remark seems to put you into their category.  I would like to believe that it was just a moment of intemperance and impatience.  I have a higher opinion of you than I do of the others I mentioned.

Let’s take a break from this now, a cooling-off period, if you will.  

Lou Jost - #78377

April 10th 2013

Thanks for the compliment I guess. I still think the best one-word summary of the lignin paper is the word I used….once in a while it might be appropriate. But anyway, yes, let’s take a break. Meanwhile I will look at Kurt Durston’s work if you think it is really good. Pleae, if you think it is not good and were just mentioning it to show that people are doing work in the field, tell me now so I don’t waste my time. I would really prefer to analyze the articles that you and other ID people regard as the best, articles that they believe make the strongest case for their position. Please just let me know that, and then, see you in a week or so.

Eddie - #78379

April 10th 2013


I understand.  I never meant you to go chasing after every name I mentioned as if I thought that these people had “proved” ID or “disproved” Darwinism.  My point all along has been that there are qualified scientists who are not stupid, ignorant, insane or wicked who have some doubts about the standard account of evolution (based primarily on mutation, selection, and drift) and who have sympathy with or at least openness to the idea of intelligent design.  I was only protesting your assumption/assertion that it’s lack of biological knowledge that causes people to doubt Darwinian mechanisms and/or believe in design.

I am not competent to assess Durston’s work, which is highly technical.  I can tell you he has a fairly recent Ph.D. (no more than 10 years ago and I think maybe about 3-5 years ago), so that his science in his area is recent, not dated, and that he works in the area of bioinformatics, so his criticisms of Darwinian mechanisms and/or anything he says about design will be couched in a bioinformatic analysis.  I cannot guarantee you that everything Durston says is right, but he appears to be very precise and careful and to have done his homework.  His scientific articles (as opposed to any popular writing he may do on religion and science) steer clear of religious issues.

Kirk had a lengthy exchange with Dennis Venema here several months ago (I don’t know if it is still up, since they no longer preserve the comments indefinitely).  The discussion was good, and polite—a model of how ID and TE proponents should speak to each other about science.  (This can be compared with another exchange, between Fruitfly and Kirk Durston, in which the tone on Fruitfly’s part was aggressive and edgy.  But Kirk did not lose his composure, and Fruitfly, unlike Dennis who is a gentleman, came off looking very bad.)   If you look up Dennis Venema under authors here, you should get a list of the titles of his columns for the past six months and even further back.  I think the title of the column where Durston was involved may have had something to do with biological information or with Stephen Meyer.

Best wishes.

Lou Jost - #78381

April 10th 2013

Eddie, I’ll try to look up that exchange. However I’d really prefer that you directed me to an article or two (by any author) that you and the ID community feel has made a very strong technical case for ID or against undirected evolution. I’d like to focus on the best, since time is limited.

Thanks, Lou

Eddie - #78386

April 10th 2013


I can’t claim to represent the ID community.  I have read lots of ID literature, both the heavy-duty books and the more popular presentations, and I think I have a pretty good idea of what ID people argue and what they are opposing.  But none of them have appointed me as an authorized ID teacher!

Another difficulty, I think, is that, no matter how much ID scientists improve their arguments—“correct” all the alleged errors etc.—their arguments will always be interpreted by ID critics as “God of the gaps” arguments.  That is, no matter how striking the appearance of design, and no matter how much that appearance is reinforced by some serious numbers, serious biochemistry, etc., I expect that both atheists and TEs will continue to argue:  “ID is nothing but an attempt to use “design” to fill in where current chance-and-natural-law explanations are not yet adequate.  Thus, it is doomed to fail when chance-and-natural-law explanations are eventually given; and even if chance-and-natural-law explanations on some points just don’t seem to be available, it is too dangerous, methodologically, to allow design inferences in the door.  They are a recipe for laziness and science-stopping.”

So tell me, Lou, is there anything you would count as positive evidence for design—that you would not simply explain away in the above manner?  What sort of thing, if you saw it in a scientific book or article, might convince you that design is the best explanation for the origin of anything?  (The origin of life, the origin of the flagellum, the origin of winged flight, etc.)  What would it take?  I’m not asking you to do IDers’ detail work for them; I’m just asking you what form a convincing ID argument would have to have.

If I don’t know this, there is little point in my continuing to tell you to read X or Y or Z.  I will always suspect that, no matter whose arguments I recommend—Durston or Sanford or Axe or Denton or anyone else— they will all be labelled “designer of the gaps” arguments—unless you give me reason to believe otherwise.

Lou Jost - #78403

April 11th 2013

You’re partially right Eddie; our experience throughout the history of science tells us not to close doors to naturalistic explanations. Articles showing that some feature could not be explained by our current understanding of evolution would not prove ID; there would be other options.

So if I were an IDer, I would not look to “prove” design, but rather to show that the design viewpoint is a fruitful tool for making unexpected new predictions that would not have been made by naturalistic evolutionists.

However, for now, I’d be interested to know if you think there are articles that really show that evolution as we currently understand it is inadequate to explain some feature, or could not be fast enough to produce the observed diversity. If so, and if the reasoning is valid, this would at least show that naturalistic evolution has a problem. Unless IDers can show that current evolutionary theory has a problem, no one will ever look to ID for a solution. So it would be reasonable to ask IDers not an article proving ID but rather for one that meets a more modest goal, one that shows that evolution as currently understood has some problem that needs a solution.

Origin of life is a separate issue. We have so little information about the subject that it is difficult to say anything meaningful.

Lou Jost - #78404

April 11th 2013

Eddie, I do use a filter to avoid wasting time. Authors who deny common descent, or who are YECs, are not worth reading. You might say I am prejudiced, but would you read an article by a flat-earther who claimed to overturn all of modern navigational theory based on his flat-earth theory? I think you wouldn’t (unless you had a lot of free time on your hands).  YECs demonstrate that they are not good judges of scientific evidence.

Eddie - #78408

April 11th 2013


Your request for flaws in “Evolution as we currently understand it” is hard to meet, because your very usage of “we” presupposes a situation in evolutionary theory that I would stoutly deny, i.e., it presupposes much more consensus in evolutionary theory than—in my view—exists.  When evolutionary theorists aren’t presenting a fake show of unity in front of media cameras and recorders, in order to thwart creationism and ID, they quite often strongly disagree with each other.  These disagreements have even been discussed on BioLogos—though only in the comments sections, never in the columns (which always try to present the fraudulent unity).  Some of the commenters here in the past appear to have been profs or grad students in the life sciences, and these people have apprised readers here of major differences in thought, with Dawkins, Gould, the evo-devo people, Conway Morris and others each occupying a position that is in some tension with other positions—not over religion or design, but over mechanisms.

And I’m not going just by this site.  I’ve read or heard enough of Ayala, Dawkins, Miller, Prothero, etc. in books, articles, blogs, news snippets, podcasts, etc. to see that there is a wide variety of views.  Sure, there is agreement on some points, but the disagreements are just as great on other points.

I think the ID criticisms of what I’m calling the “old guard” evolutionary synthesis of neo-Darwinism—the Mayr-Dobzhansky-Simpson version which, slightly updated, has been defended by Dawkins, Ayala, Ken Miller, Francis Collins, BioLogos, probably Lewontin, and others—is pretty sound criticism.

I think that ID criticism of evo-devo, Conway Morris, some of the Altenberg group, Shapiro, etc. is less strong.

Now you may say:  ID is attacking an outdated form of evolutionary theory.  Probably true, to an extent.  But that outdated form is the one that the lay public still thinks of as evolutionary theory—random mutations filtered by selection.  It’s the form that the NCSE pushes in its legal actions against school boards; it’s the form you see on NOVA TV specials; it’s the form pushed in bestselling popular books by Dawkins, Collins, Miller, etc.  The public conception of evolutionary mechanisms is still very much 1960s/1970s.  Most of the public hasn’t even heard of the very old criticisms of Darwinism levelled by Gould and Margulis, let alone the new work of Sean Carroll, the Altenberg group, Shapiro, etc.

So, if you want ID writings, or pre-ID or extra-ID writings, that allege serious problems with the old meat-and-potatoes neo-Darwinism, I can give you lots.  You’ve already said you aren’t impressed by a very small snapshot of the work of Sternberg and Axe, so I’ll leave them out.  But there is Sanford (former Cornell geneticist, widely known for his “gene gun”) with his argument for genetic entropy, there is Minnich with his knockout experiments in Minnesota, there is Denton, there is Kirk Durston up and coming, not yet hitting his stride; you can also look up some of the writings of the Altenberg group (whose allegiance to the old synthesis covers a very wide range, from “let’s keep it but modify it” to “it’s pretty well useless”)—none of whom are ID supporters and most of whom, as far as I can tell, are agnostic/atheist.

I haven’t read any of the Altenberg people’s actual scientific arguments—though they have a conference volume out which I may buy soon—but all of their members (unlike Miller, Scott, Dawkins, Collins, etc.) are still very active in research, at conferences, etc.  There is a long interview—about 45 minutes with Stuart Newman which can be found on the web, in which he gives a popular overview of new directions in evolutionary theory.

All of these people have argued in one way or another “that evolution as currently understood has some problem that needs a solution.”  And many of them—the Altenberg group and Shapiro, anyway—share your atheist/agnostic world view, and your conception of naturalistic explanation. I’m not asking you to agree with their biology, but they exist.  And many of their criticisms of current evolutionary theory are similar to those offered by Behe, Dembski, Meyer, etc.  (E.g. many members of the Altenberg group seriously doubt that the modern synthesis can explain the rise of major new organismal forms.)

That’s the best this non-biologist can do for you at the moment.

Lou Jost - #78409

April 11th 2013

Eddie, thanks. as you know, most of the disagreements about evolution among mainstream biologists are about the importance of one naturalistic process versus another. I was not asking for examples of that; I am well aware of most of those. They do not attack the core of the modern theory. IDers do claim to attack the very core, the idea that modern naturalistic evolution is capable of producing the diversity and degree of adaptation that we see today. This seems to be your position too. I really just wanted you to name a couple of the best articles  supporting the position that naturalistic evolution is not sufficient, and that something like ID is needed. Could you give me just a couple of article citations? The one or two or three articles that were the most convincing to you? I don’t want to look at some article by X, only to find that you never endorsed it’s view, or that you didn’t put much weight on it. Please, if you can, give me the best you have, not a long list of authors who have probably each written scores of articles of varying quality.

Eddie - #78415

April 11th 2013


1.  A qualification.  Not all ID people fit your characterization regarding naturalistic mechanisms.

Denton insists on naturalistic mechanisms, but also believes that biological nature pretty much shouts aloud about its designed origin.

Sternberg seems to be fine with purely naturalistic mechanisms.  He just thinks neo-Darwinism is washed up.

Behe has said that design could, in principle, be delivered through naturalistic mechanisms.  Similar statements can be found in Dembski and Jay Richards as well.  (Though Dembski doesn’t personally think that naturalistic evolution is what actually happened.)

So for many ID people, the criticism is not against naturalistic mechanisms per se; the focus of ID criticism is on naturalistic mechanisms that heavily weight chance and blind searching.  And as I said, that criticism is shared by some non-ID people who are generally recognized as competent evolutionary theorists.

2.  Readings.  I think Nature’s Destiny by Denton is a great book—an attempt to extend the fine tuning argument all the way from the origin of the universe up to the evolution of the human brain.  Do I claim that Denton has “proved” his case?  No.  (Denton himself acknowledges that much in the second half of his book is speculative and needs more work.)  Do I think he has made a good case?  Yes.  Will the book interest you?  If you are looking for a standard professional handling of evolutionary theory:  No.  Denton’s background is molecular biology/biochemistry, not population genetics, selection, etc.  But he certainly knows something about genes and proteins.  You will like Denton if you are in the mood to read something off the beaten track, expand your mind a bit, consider how evolution looks from the point of view of someone with scientific training different from yours.    

3.  A procedural suggestion.  I get the sense that you think that anyone who is not convinced by what you consider overwhelming evidence for the adequacy of your mechanisms must somehow be a less competent scientist than you are, does not have enough math, does not understand enough about the genome, etc.  And against such an argument I’m helpless.  I don’t have the qualifications to make such judgments.

I know, however, that there are people who, as the world generally judges qualifications and expertise (based on training in excellent institutions, holding chairs in prestigious institutions, having many peer-reviewed publications, grants, patents, etc.), are your peers or superiors, who do not share your conclusions.  And it bothers me that you want to spend your time arguing with me, a non-biologist, instead of with these peers whose views you reject.

I would far rather see you engage at length with Sternberg, Axe, Shapiro, Sanford, Denton, etc.  so that I could see the arguments back and forth.  I would learn far more about evolutionary theory from such a discussion than I could learn by giving you my layman’s translation of these guys, and then have you knock it down, leaving me in the position of not knowing whether your knock-downs are valid, because I can’t know what they would reply.  So why don’t you move your discussion from this place to other other venues?  You can comment on Shapiro’s Huffington Post site, and the Biologic Institute has a discussion site as well, where you can engage Gauger and Axe directly.  Then you can drop a note here, telling us where to follow your quest to slay the dragons.  

This is an uneven combat.  If you are Godzilla, I am King Kong’s baby brother.  Godzilla would have no problem crushing King Kong’s baby brother.  But King Kong himself is another matter.  I wish you would engage with King Kong directly without using me as a go-between.

Lou Jost - #78416

April 11th 2013

Your point #3 is very unfair, again. You keep framing things in terms of qualifications, status. etc. It is about the quality of arguments, Eddie. I am looking for good arguments about the inadequacy of undirected evolution. All I am asking is that you give me one or two or three strong articles.

I don’t have access to Denton’s book, but it sounds like if even he says it is highly speculative, it is probably not what I am looking for. I’m looking for things along the lines of Behe or Dembski or Sternberg, who actually try to show that random searching is not adequate to explain what we see. (But I’d like to see it done without the big mistakes we’ve seen in at least Behe and Sternberg.) Without such a demonstration, or at least a plausibility argument, there is no purely scientific reason to reject unguided evolution.

If you can come up with a strong article, and if I find flaws in it, I will be happy to try to engage the author and share the results with you. But I can’t get there unless you give me a couple of the articles (sorry, no books for now) that you think really make a strong case, articles that were influential for you.

Eddie - #78419

April 11th 2013


Fine:  read Stephen Meyer’s original article on the Cambrian Explosion.  It’s reprinted on the Discovery website.  Then, if you don’t like it, write to Meyer and start a conversation with him.  Then get back to us here.

Frankly, though, I would rather you chose someone who engages publically, whose responses we can see.  That’s why I suggested Shapiro or the Biologic Institute site.  And I would suggest you engage Shapiro specifically on his book, which I have read, and would like to understand better, by hearing him debate it with a critic.  Or Axe on the lignin article.

However, I reject the premise of your question.  I reject the idea that ID people should have to prove that random searching is not adequate.  I insist that you have to prove it’s adequate.  And you haven’t even come close to doing that here.  Nor has anyone else, since this site began.  What we’ve had on this site is five years of sheer assertion, with popular articles on genome comparisons of closely related animals, e.g. humans and chimps, or dogs and other dogs.  No one has shown any understanding at all of how a major morphological change could occur via Darwinian mechanisms.  Other than to blandly assert that macroevolution is just microevolution repeated more times.  Which of course is to assume the very thing that is under debate.

Lou Jost - #78420

April 11th 2013

“I insist that you have to prove it’s adequate. ” But Eddie, we have an existing mechanism which we know is capable of making small changes. We can see via the fossil record and the genomes themselves that evolution does seem to proceed via small changes (see for example the transition from an ancestral cat/dog to cats and dogs, or from reptiles to mammals). So the onus is on someone to show why our known mechanisms, which seems to work, aren’t adequate. Even creatures that are vastly different from each other today can be traced back to common ancestors, and we often have enoough fossil records to show how the transition proceeded in small steps. There is nothing blind about the assertion that microevolution repeated over and over for billions of years can make big transformations. I do not want to exclude the occurence of rare major changes, such as the events that doubled the genome of ancestral vertebrates. These events surely played a major role in vertebrate evolution, as Dennis and everyone else agrees. However, there is nothing particularly mysterious about these either. As I mentioned earlier in this thread, my orchids have made this same transition (gene duplication) during my lifetime. It is not a big deal. Some day, a million years from now, maybe these orchids will diversify in unexpected ways because of the extra freedom afforded by the duplicated set of genes. Then scientists will look back on this duplication event as a major “macroevolutionary event”. But for now it doesn’t look like much, and certainly doesn’t require design. It is a consequence of meiosis being an imperfect process. The miracle would be if chromosome duplications never ever happened.

But leave that aside for now, as you seem set on that opinion. I am disappointed you think the lignin article is one of the strongest in the ID portfolio, whereas a few comments ago you would not even endorse it. It is sooo bad!!! Can you not see the double standard you have regarding judging mainstream science and this ID stuff?

I was hoping you had in mind a more quantitative demonstration that evolution was inadequate, so there would be something concrete to argue about (and this is where I have some expertise). Verbal arguments with Meyer about the Cambrian explosion will surely be inconclusive. But if that is what you think is best, I’ll keep my word. I’ll look at it and see what Meyer says. This is not something I know a heck of a lot about, though.

Dialogue with Shapiro depends on what he decides to post about. I’ll try to keep watch, and if he says something fundamental that I disagree with, I’ll comment on it. Help me out please; if you see him comment on something appropriate, let me know.

Lou Jost - #78421

April 11th 2013

By the way, regarding public comments, I was somewhat intimidated by Bio-Complexity’s unusual comment policy. They require  a prospective commenter to have an institutional or corporate email address, and they require that he write an application, complete with areas of interest, etc. And then, the comments are so well hidden that I could not find them.

Eddie - #78453

April 12th 2013


The first point I’ve already covered.  I’ve indicated that there is disagreement between full-time evolutionary theorists on whether macroevolution is simply microevolution writ large, or whether other mechanisms are needed for major structural changes, e.g., radically new body plans.  You and Dennis apparently take the side of the first group.  That’s legitimate, but so is the other side.  You’re not representing the full range of views in the field.  Sometime you should get the conference volume from the Altenberg group, or read some articles on organismal form by some of its members.

You wrote:

“evolution does seem to proceed via small changes (see for example the transition from an ancestral cat/dog to cats and dogs, or from reptiles to mammals).”

Spoken like a true neo-Darwinist.  You are aware, I trust, of the “dirty little trade secret of paleontology” published by Gould and Eldredge?  Would you care to qualify the above remark, or do you dismiss Gould and Eldredge as incompetents?

I’m not “set in my opinion.”  I’m merely trying to make sure that you don’t pass off your opinion as the consensus of evolutionary biologists, because it isn’t.

I never said that the lignin article was “one of the strongest in the ID portfolio”!  I never even said that it was good.  I said that you dismissed it based on a crude oversimplification of its contents.  If you want to show that it is weak, I might agree after reading your arguments.  But you gave no argument, just a blanket dismissal of pages of detailed analysis and argument.

I have no double standard.  Whether it is ID stuff or mainstream science, I dislike, among other things:  (1) historical speculation based on mere possibilities; (2) extrapolations based primarily on theoretical assumptions, rather than a strong empirical base; (3) over-confidence regarding conclusions; (4) omission or misrepresentation of contrary positions; (5) the importation of metaphysical assertions (e.g., “this must have happened due to chance, because God wouldn’t have designed something that way”); (6) the use of strained reasoning—which one would never employ in any other walk of life—to  avoid certain conclusions (e.g., the conclusion of design).

I don’t follow Shapiro’s blog with any regularity.  I’ve hardly ever looked at it, except when someone has linked to it.  If you decide to engage with him over his main hypothesis—that organisms can reengineer their own genomes in a quasi-Lamarckian way, and that this view is a marked departure from mainstream 20th-century evolutionary biology—let me know and I will look up the dialogue you have with Shapiro.

Lou Jost - #78455

April 12th 2013

I never said that the lignin article was “one of the strongest in the ID portfolio”!  I never even said that it was good. ” I asked you repeatedly to choose two or three of the best articles supporting ID. In your 78419 you finally did. One of them was the lignin article.

You misunderstand my take on micro/macro evolution. If there are occasional big changes, fine. My point is that small changes seem sufficient most of the time. Tell me, where did “macroevolution” happen in the divegence of dogs and cats from their common ancestor?

You do have a double standard, Eddie. Most of the ID things you  have cited over these last few weeks are poorly reasoned; you would have recognized that if they had been supporting unguided evolution.

Regarding Shapiro, I would argue with him if he claims real teleology. I would not argue with him when he claims that cells can alter their genomes. I know they can. I would argue with him, though, if he says that this ability did not itself arise by random variation and natural selection.

Eddie - #78460

April 12th 2013


Sorry for the miscommunication over the lignin article.  When you said you might engage in public debate with some of these people, I suggested it because (a) I know they have some discussions somewhere on the Biologic Institute site; (b) I happened to have read the lignin article fairly slowly and carefully, so I would have a hope of following what you and the author(s) said about it.  I didn’t think, when I suggested it after your repeated pressure for specific articles, that you might count it as one of the “all-time best.”  

Anyhow, I’m not interested in endorsing a list of all-time best ID articles.  Even if each ID article has only 10% worthwhile material in it, that is still a contribution to science, and it’s the overall direction of ID that I’m endorsing, not any particular ID achievement in its entirety.  (For example, I have some problems with some arguments of Meyer and Sewell.)

What you, like all ID critics, seem to be constitutionally unable to do, is to give a qualified verdict.  ID is always “crap” or “all wrong” or “filled with sophomoric errors” or written by people who “are not real scientists” etc.  How often do you see a review of any ID work that says, e.g.,:  “Behe has a point here, and he makes a reasonable argument; however, he starts to fumble the ball when he says ...  If he could avoid such errors, he might be able to strengthen his case in the following manner ...”  In other words, critics don’t approach ID writing with an open mind; they approach it with their hatchets out, ready for mayhem.

If you put together the best insights of Behe, Dembski, Meyer, Nelson, Wells, etc., and if you combine that with the parallel criticisms of Darwinism and the alternative evolutionary mechanisms that one finds in Denton, the Altenberg group, Shapiro, Mike Gene, etc., it seems to me that you have a substantial body of criticism of “chance plus natural selection” and a substantial case that nature looks a heck of a lot as if it it’s designed, from the fundamental constants of nature right up to human beings.  And with the rise of information science, and the increased influx of people from physics, engineering and computer programming into biology (people like Newman, Marks, Durston, etc.), I foresee more and more biological research taking place along de facto “design” lines (even though, for cultural and political reasons, it will not be identified as such for a few decades yet).

I play the long game.  What I’ve recommended to you does not signify that I think that ID has won, or that I expect it to win any day now.  I’m looking at a much broader tapestry of history of science, history of evolutionary theory, history of ideas, sociology of knowledge, the rise of information science, the fine-tuning argument in physics/cosmology, etc., and I’m projecting that the trajectory of evolutionary theory, in the long run, is headed far away from neo-Darwinian and similar “chance” approaches, and moving toward quasi-teleological approaches and ultimately maybe even straight-out teleological versions (as are already championed by, say, Denton). 

I’ve made no claims specifically about dogs and cats, etc.  But if you are certain that microevolution repeated produces macroevolution, I’m not the one qualified to refute your certainty.  You should be looking up those evolutionary biologists who disagree with you, and meeting their arguments, not mine.  Theirs will be much more precisely formulated in the professional language of biologists.  

Lou Jost - #78461

April 12th 2013

Eddie, you said “What you, like all ID critics, seem to be constitutionally unable to do, is to give a qualified verdict.” That is not true, as you have seen with my comments on Shapiro.

I am disappointed that you can’t name two or three really good ID articles to read. 

Eddie - #78473

April 12th 2013


Shapiro is not an ID proponent.  I was referring to your response to ID articles and books.  I haven’t seen much that’s very positive in your responses.  You are much more polite in your negativity than certain belligerent people around here, of course; but it seems that you think that ID literature is pretty nearly 100% worthless.

And that’s a general pattern I’ve noticed; that people who are against ID are entirely against ID, to the point where they will not acknowledge anything of value in any publication by an ID person.  As a well-trained academic, I’m very suspicious when I see such a pattern.  Such blanket judgments would not be tolerated in the fields where I work; criticism is expected to be balanced and constructive.

I can’t always remember the exact wording of titles of journal articles offhand, because they tend to be long and bloated, as opposed to book titles, which tend to be short and punchy.  But Meyer’s article on the higher taxonomic categories and the Cambrian explosion is on the Discovery web site; you can search there under Meyer or Cambrian and I’m sure you will find it.

[It was one of the very first ID articles, and Eugenie Scott was so incensed at its publication (which meant that she could no longer say that ID had no peer-reviewed publications) that she launched a witch-hunt against the editor, Sternberg (who at the time had no affiliation with ID), which disrupted Sternberg’s professional life.  A full statement of the affair can be found on Sternberg’s web site.]   

If look on the Discovery website, you will find an article celebrating ID’s 50th peer-reviewed publication, and a list of all 50+ peer-reviewed publications ID now has accumulated.  If they are peer-reviewed, then presumably they are among the best writing that ID has to offer, so I would suggest you have a look at that list, if you want to know what IDers are publishing in real scientific (as opposed to popular) venues.

But I don’t want to debate you article by article; this is for information only.  In any case, many of them I have not read, and some I probablly never will read, because they involve highly technical discussion of evolutionary algorithms and computer programming.

I’d be willing to respond to you about Meyer’s article, but my response will be of the same quality of thoughtful engagement as your criticism.  A one-sided verdict of “crap” or the like will produce an equally non-nuanced reply on my side.  But in the end, even if you and I have a dialogue, it will likely be unsatisfying, because I suspect you will argue that Meyer has underestimated the power of Darwinian mechanisms, which you regard as proved, and I regard as not proved, and we will be back at square one.  But have a look at it, and if you can think of even one sincere, positive thing to say about it, then maybe we have some sort of basis for dialogue.

melanogaster - #78506

April 13th 2013

“I can’t always remember the exact wording of titles of journal articles offhand, because they tend to be long and bloated, as opposed to book titles, which tend to be short and punchy.”

You don’t need to remember any titles, as there are plenty of computer applications that will remember for you.

Also, the bodies of the journal articles are short and punchy contrasted with books. Do you realize that real scientists tend to use the text only when the figures and tables are unclear? That one does a journal club presentation by presenting the figures, not the text?

Lou Jost - #78463

April 12th 2013

Want to see your double standard? You say “Even if each ID article has only 10% worthwhile material in it, that is still a contribution to science, and it’s the overall direction of ID that I’m endorsing, not any particular ID achievement in its entirety.”

So articles that have maybe 10% worthwhile material are just fine by you when they have an ID theme, but when it comes to mainstream evolutionary science, you demanded that we produce every tiny detail of the whale transition, and you supported Berlinski’s demand that biology needs to have a rigor comparable to that of physics in its precision. You regularly dismiss insightful biologists like Coyne because you don’t like their personality and philosophy, but if I so much as use a strong word to criticize a specific poorly-argued ID article, you are all over me.

That is a double standard, my friend.

Eddie - #78476

April 13th 2013


There’s no double standard.  If a Darwinist produces an article arguing for a Darwinian explanation for the Cambrian explosion, and 10 out of the 100 points made in the article are reasonable, I would admit that they were reasonable.  I would say:  “I have to admit, these 10 points do count in favor of the Darwinian explanation.”

I’ll be interested to see if you grant that even 1 point out of 100 in Meyer’s article on the Cambrian explosion is reasonable.  

Note that Behe goes out of his way, in his second book, to grant value to Darwinian explanations.  He doesn’t sweepingly condemn Darwinian theory as wrong, or rubbish, or lies, or religious apostasy.  He offers a nuanced critique of it, granting Darwinian mechanisms a place in evolutionary theory, but arguing that their role is more limited than people such as Dawkins and Miller and Scott suppose.  Whereas for Behe, Darwinian theory is only partly wrong, not all wrong, for ID critics, ID is all wrong, not just partly wrong.

It’s Behe’s balanced approach I’d like to see in critics of ID theory.  I haven’t seen that.  I’ve seen nothing but knee-jerk rejection, coupled with scorn and hostility and superciliousness.  (And in saying this, I’m thinking of the tone, not of yourself, but of Myers, Moran, Coyne, Dawkins, etc.).

I don’t “dismiss” Coyne—Behe himself says that Coyne has done good work on speciation.  I have no reason to disagree.  I do reject Coyne’s narrowness and dogmatism.

Lou Jost - #78414

April 11th 2013

If that is not possible, it would still be interesting to see if there are reasonable demonstrations that simple mutations, gene duplications, etc are insufficient. I’d be very surprised.

Seenoevo - #78395

April 11th 2013

Since the word “crap” appears fashionable and allowable in this forum, I was wondering if this would meet its definition:

Someone claims that the dragonfly utilizes

a) “recycled, repurposed parts” in a

b) “not optimal” way, which

c) reveals “a chaotic, opportunistic, accidental past”.

Then, despite repeated requests for the identity of these “recycled, repurposed parts” and for more details on their performance and history, the claimant is unwilling or unable to answer.   

No answer at all, other than a smoke and mirrors dismissal (“No engagement or coherent thought. Bye.”)


I think this qualifies as “crap”.

Lou Jost - #78407

April 11th 2013

Here’s how YOU (and all other vertrebrates) contain repurposed parts in your genome:


Seenoevo - #78397

April 11th 2013

Here are some unarguable facts for reflection:

1) Evolution is true or it is false. There is no in-between.

2) Promoting falsehood undermines the telling of the truth. To do so unknowingly is, at a minimum, unfortunate. To do so knowingly is more dire. It is deliberate deception. Some would declare it diabolical.

3) It is written:

“You are of your father the devil, and your will is to do your father’s desires. He was a murderer from the beginning, and has nothing to do with the truth, because there is no truth in him. When he lies, he speaks according to his own nature, for he is a liar and the father of lies.”

Lou Jost - #78405

April 11th 2013

Here in Ecuador, when my then-girlfriend introduced me to her mother, a very simple country woman, the mother asked my religion. I said I was an atheist. The mother immediately got all excited and  told me that this meant I was the devil (and Jewish!!!?) and that soon, hairs would grow out from all of my body and etc etc.

beaglelady - #78410

April 11th 2013

Well, did the hairs hide your horns, hooves, and tail?

Lou Jost - #78413

April 11th 2013

I’m still relatively hairless, so I have to cover up the horns and hooves….

beaglelady - #78422

April 11th 2013

I wondered why you always wear a hat and those funny shoes….

Seenoevo - #78411

April 11th 2013

To Lou Jest: I looked at the article you linked. It’s by Dennis Venema! This is supposed to be your answer? I not only looked at it, I read it. And I give myself credit for patience, too. Because virtually every sentence provoked head-scratching. My skull is raw. Herewith are ten spots needing some salve: 1)     “… two huge increases (doublings) in information content likely occurred in the evolution of vertebrates (organisms with a backbone) about 450 million years ago. Indeed it is likely that these doublings served as a key prelude to the huge array of vertebrate organisms (including ourselves) that subsequently arose in the history of creation.” How likely is “likely”? Does this mean virtually certain? Like 99% probability? How would the likely scientists ever know if they bet right? 2)   “Biologists have known for a long time that genes exist in families where … It is known that each member of the family arose through a series of duplication events all of which trace back to a single ancestral gene.” “Known” means what? A certainty beyond any reasonable or scientific doubt? More certain than the “likely” above? How does something “new” arise from a “duplication” event, an event which by definition propagates the “old”?   3)   “After each duplication event different mutations accumulate in opposing members of the duplicate pair…” Don’t mutations occur and accumulate all the time, regardless of whether a grand “duplication event” is occurring? Why this focus on the WGD? 4)   “Every time a gene duplicates it provides an opportunity for new information (complex specified information, to use Meyer’s term). This has happened routinely in the history of life and it occurs through natural mechanisms that are well understood.” How does “well understood” compare to the “likely” and “known” above? 5)   “… there has long been speculation that early in vertebrate evolution there was a time when the entire genome (the complete collection of genes) was doubled in a vertebrate ancestor. This is called a whole-genome duplication (WGD) event.” Does “speculation” equal science? Even if it’s scientists doing the speculating? How did the duplication capability arise? [A Canon copying machine can make perfect copies. But who makes the Canon copier?] 6)   “WGD events provide a wealth of raw material for evolutionary innovation, since genes dedicated to one function now have a copy that is not constrained by natural selection to perform that role any longer (since the other copy can do that function).” Maybe this is like how, when you backup/copy your computer’s hard drive, you do so with the hope and intent that the copy not be an accurate duplication of what you’re copying. Surprises are more fun than dull copies. Or like when fish have a million babies. They really just want a couple like them. The multitude of others are meant to go to “school” to become something different. 7)   “Two key pieces of information were needed: first, the complete genome sequence of an organism closely related to vertebrates, and secondly, knowledge of the precise arrangement of the genes thought to be involved in the WGD events.” Does “thought to be” mean not as absolutely certain as “It is known…”? 8)   “Darrel Falk and I have previously discussed synteny when examining human – chimpanzee common ancestry, and readers who have not read that post might find it helpful.” What I think would be helpful is if evolutionists would stop presuming as true the very thing they’re supposed to be proving (e.g. “human – chimpanzee common ancestry”). Going in circles makes one dizzy. 9)   “As before, rapid gene loss (of redundant copies) and some neofunctionalization (to produce paralogs) would be expected.” Isn’t “redundant copies” redundant? In other words, aren’t copies meant to be “redundant”? Or is this supposed to mean that only one copy is necessary and the second, third and beyond copies are disposable? Who’s to say the extra copies aren’t needed or meant to be? Reminds me of the “treasures” being found in what was formerly considered “junk” DNA. 10) “Significantly, a large percentage of these modern paralogs are still present in four-fold syntenty groups that span about 25% of the human genome (and thus have persisted as blocks of synteny for approximately 450 million years).” Twenty-five percent preservation after 450 million years? I think about 100% of the synteny block of the Coelacanth has remained unchanged. The fish that swam an alleged 400 million years ago is indistinguishable from the Coelacanth caught today. Why is that?                                                         But let’s not get too lost in the weeds, or genes. Genes are means. Genes are just means to an end, just as instructions are not meaningful in themselves. They’re meaningful for what they enable to be accomplished, for the end result. Which brings me back to the end result of the dragonfly. Which parts of the dragonfly are “recycled, repurposed”? Is it the eyes? Or the legs? Or the two sets of wings (redundant?!?)? And what were they before they got involved in the recycling program?


Lou Jost - #78412

April 11th 2013

Thanks for reading it! You said “How does something “new” arise from a “duplication” event, an event which by definition propagates the “old”?”

That is why I sent you there. Once the genes were duplicated, mutations accumulated on some of the extra copies, and eventually these acquired new functions. “Recycled, repurposed parts”, as promised.

“The fish that swam an alleged 400 million years ago is indistinguishable from the Coelacanth caught today”

Nope, they are very different species. Read about this fascinating fish on Wikipedia, which includes this line with many citations for you to explore: “recent studies pointed out that coelacanth morphological conservatism is a belief that is not based on data”


melanogaster - #78507

April 13th 2013

“But let’s not get too lost in the weeds, or genes.”

Why not? That’s where the best and most comprehensive evidence is!

Seenoevo - #78468

April 12th 2013

To Lou Jest:

Are you saying that if one of the allegedly 400 million year-old coelacanth fossils miraculously came to life and began swimming around that a normal human being (or maybe an evolutionary ichthyologist) would NOT identify it as a type of coelacanth?

Would it appear so much different from the one that was thought to have met extinction 70 million years ago, until one was caught off the coast of Africa in 1938?

“Rare and extremely endangered coelacanths are animals that have not fundamentally changed for 400 million years.” http://www.astrobio.net/pressrelease/4840/why-coelacanths-are-living-fossils   “Once the genes were duplicated, mutations accumulated on some of the extra copies, and eventually these acquired new functions. “Recycled, repurposed parts”, as promised.” Well, I guess that’s that. Evolution must be true then. Very compelling.  It’s a wonder that 150+ years after The Origin of Species, and after many decades of evolution lessons such as you just provided, that about half of Americans still disbelieve evolution. Shocking.   “No engagement or coherent thought. Bye.”
Lou Jost - #78480

April 13th 2013

“....About half of Americans still disbelieve evolution. Shocking.” Shocking indeed. The US ranks second-last (above only Turkey) in acceptance of evolution, among western democracies. Religious fervor (whether Christian or Muslim) is strongly correlated with non-acceptance of evolution:


Eddie - #78475

April 12th 2013


Regarding my earlier reference to Kirk Durston here on BioLogos, under this column by Dennis Venema:


Kirk has a constructive exchange with an anti-ID person named “Ashe”.  Then Fruitfly (who was then known as “John”) jumps in and lowers the tone with his belligerence.  

Later in that series, or perhaps it was in a later series written by Dennis, there is a civil exchange between Dennis and Kirk that sticks to the science (no charges of religious motivations, etc.).  If only all ID/TE/atheist/YEC exchanges could be like those between Kirk and Dennis, as far as decorum goes!

If you type in “Durston” on the search line here, you will find a number of BioLogos articles that mention his name.  All of them, I think will be later in date than the one I’ve started you with.  

I think you might like Durston better than most ID proponents, because his research is, like yours, technical and nitty-gritty.  I’m not saying you will accept his conclusions, but you will probably see him as scientific in his methods.  And I think this is going to be the new norm for the next generation of ID people.

Lou Jost - #78478

April 13th 2013

That’s what IDers would need if they want to convince anyone. Can you give me a specific citation to an article of his that argues for ID, and that you think is really strong? Please, not his papers that just calculate functional complexity; everyone agrees that fully modern functional proteins could not possibly have arisen by chance out of nothing, so we can take that as a given. What is needed is a Dembski- or Behe-like demonstration that evolution can’t get to the modern proteins in the time available (but doing the calculations correctly).

Regarding Meyer and the Cambrian, all biologists recognize that something exceptional happened during those forty or fifty million years, and that most would have predicted more intermediate fossils between the little shelly things  and the trilobites, etc. I haven’t read his article yet so can’t say more. Discovery Inst. is hyping his new book on the Cambrian as a “game changer” for ID, so maybe I’ll wait to see that. 

Eddie - #78486

April 13th 2013

Sorry, Lou; while I think that Durston has published at least one paper in the past two years, and maybe two or three, I don’t know what journal(s) the paper(s) found their way into.  But I think he has a website at the University of Guelph; perhaps more information on his publications is found there.  

I mentioned him not because I had read any of his papers (I haven’t), but because I found his discussions in a few columns here to be very solid academically—at least in appearance.  They made no use of culture-war rhetoric, and they gave the impression of rigor both in calculation and in theoretical analysis.  But I don’t claim the ability to judge.  It is possible, however, that you would find him superior to either Behe or Dembski.  I leave that judgment to you.

I would guess that he would argue, not that “evolution” couldn’t get to the modern proteins in the time given, but that evolution of the neo-Darwinian type couldn’t do so.  But I don’t want to put words in his mouth.  I would rather you found his papers and read them yourself.  Or better still, write to him at Guelph, tell him your field and that you noticed he had put in some comments at BioLogos and that you wanted to know more about his general orientation to evolutionary mechanisms and what he is working on.  He seems very polite and if you write to him showing curiosity I am sure he would give you a polite reply.  And I’m sure you’d have a more scientifically satisfying conversation with him, because of your common math background, than you would with me, as I would be trying to play go-between and doubtless translating his thought inaccurately.

I know nothing about Meyer’s new book.  I thought his last book had some merit but was twice the length it needed to be.  I hope the new book is shorter and more direct.  I expect that his bibliography will show a thorough study of the literature on the Cambrian Explosion; he’s like that—very assiduous.  Whether his actual arguments will satisfy you, I cannot say.  But it’s likely the book will be an expansion, with more documentation and more recent scientific material, of his much older article from the Smithsonian journal (reprinted on the Discovery site).  However, the article may give you a preview of the kind of thing he will be arguing.

And now I must break off for a few days.



Lou Jost - #78489

April 13th 2013

Thanks, I’ll check out Kirk’s website for articles. But I am somewhat disappointed that you are recommending I look at publications you have never read. I wish you would point me to papers you had actually found to contain good arguments. Still, I’ll look there, over the next few days.

Enjoy your break,


Eddie - #78493

April 13th 2013


I don’t see what’s odd about my procedure.  Let’s say that you had, for one reason or another, never read any peer-reviewed articles by Jerry Coyne, but had read his book reviews of Behe and his blog site and heard him talk at some conference, and deemed him a very intelligent evolutionary biologist and very smart individual overall, and I asked you to recommend to me a good person to make a case for Darwinian evolution, and you said that I would probably find most books and articles by Jerry Coyne helpful, I wouldn’t be upset that you hadn’t actually read any peer-reviewed articles by the guy—as long as you made clear the basis on which you were calling the man intelligent and probably worth investigating.

You’ve already indicated that you find the mathematical arguments of Behe, Dembski, Sternberg and others unconvincing, so I naturally am suggesting someone who appears to have some mathematical knowledge of biological matters that you have not yet made up your mind about.  And someone who seems to be able to argue about these things in an honest academic way, actually conceding points now and then, and arguing politely as well.    Yes, I wish I had the name of an actual article for you, but I don’t.  I would take the time to look up something, but I now face a third assignment deadline.  Maybe in a few days I will try to dig up something.

And at that I must leave it.

Lou Jost - #78494

April 13th 2013

I was asking for some argument that you personally found impressive, one that played a role in determining your own position (and/or those of other IDers). First, that would filter out the junk research (which there is a lot of, I am afraid). Second, if there are serious flaws in a core article, maybe you or IDers would reconsider the reasons for your/their position. Otherwise, if I just criticize some random article, you will say that it was not an important or central article anyway. Third, I was curious about why you take your position on evolution. I figured there would be papers which helped form that position.

Eddie - #78498

April 13th 2013


I’m not a typical ID supporter, and you are going to go on a wild goose chase if you try to fit me into some mental pigeonhole.

My position on evolution, and on design, was roughly what it is now long before I even heard of Intelligent Design.  But I’m not a scientist, and my conclusions were arrived at based on only a good generalist’s knowledge of science, plus what I had learned in philosophy, intellectual history, etc.  What ID writers—and non-ID biologists such as Shapiro, Margulis, Gould (with his critique of gradualism), Newman, etc.—taught me was that there was a minority opinion among scientists which was skeptical about Darwinian and neo-Darwinian ways of thinking about evolution.

And it wasn’t stupid scientists who held this minority view.  I found, among the people endorsing or broadly sympathetic to ID, or at least dubious about Darwinian mechanisms, Nobel Prize short-listers, inventors or co-inventors of X-ray crystallography, MRI, and lasers, NAS members, one of the team from the Manhattan project, an Ivy League geneticist with a score or two of genetic patents, biochemists with dozens of peer-reviewed articles, a Templeton award-winning mathematician, an astronomer credited with the discovery of extrasolar planets whose citation record (something you have stressed as important) was better than that of any other member of his department, a pediatric neurosurgeon and medical teacher, a distinguished professor of computer science specializing in evolutionary computer programs, physics and engineering profs from MIT and Los Alamos, a Chicago biologist whose work is regarded by the discoverer of the Archaea as a “game-changer”, a scientist who is a world leader in genetic bar-coding grudgingly admitting that the evidence central to his work seems on the surface to point to a creationist scenario, the foremost man in the world in genomic engineering openly contradicting Dawkins in a panel discussion about universal common descent, etc.

These were people who had proved by their deeds that they understood very well what was meant by “good science.”  And while some of these people had strong religious convictions, they were by no means all fundamentalists; some went to Catholic or mainstream Protestant churches.  Others were not religious at all.  So I had some scientific opinion, including informed secular scientific opinion, on the side of conclusions I had already come to on my own as a result of my own personal and academic investigations.

Does that make my views right?  Of course not.  But it shows that people who are not scientific idiots and who are not blinded by religious zeal can hold such views.

So before I first opened the cover of Darwin’s Black Box, I was already skeptical, not of evolution, but of the standard explanation that I was taught in school and by every popular science writer I had ever read.  I did not believe that complex new life-forms could arise by chance mutations and natural selection.  Variation on existing models, yes; but major structural changes, no.  ID writers (and non-ID Darwin skeptics) merely gave me more and better arguments than I had previously been able to marshal.

So how does evolution occur?  I don’t claim to know.  I don’t rule out anything.  I don’t rule out Shapiro’s self-engineering, or Denton’s front-loading, or divine intervention (crude or subtle) to steer evolution in certain prescribed directions.  What does seem clear to me is that it is not an entirely undesigned or unplanned process, even though it may include a zone of indeterminacy where chance plays a role in the details.  And there is no single article, or even set of articles, that I can point you to as the source of that conviction.  It is a synthesis of my whole intellectual and life experience.  And it’s not a synthesis that I would ever try to browbeat you or anyone else into accepting.

My position is not offensive; it’s defensive.  I can go along with evolution, but I maintain that design is in important ways “in control of” evolution, until that can be decisively disproved.  I don’t ask anyone else on earth to share my view; I do ask that others stop claiming that “science has disproved design.”  Science may have disproved 6-day fundamentalism; it certainly has not disproved design.

Lou Jost - #78484

April 13th 2013

I took a quick look at the comments you directed me to. Kirk opened with this: “we can go from a lobe-finned fish to a human, given enough time and variation” That does accurately characterize evolutionary theory (and he could even had made it stronger: we don’t need an arbitrary amount of time, it can happen in a handful of billion years).

But then he says: “Therefore, a fundamental and falsifiable prediction of Darwinian theory is,
VarPred: There are no taxonomic limits to variation” and he goes on to argue this.

Surely you can see that this misrepresents evolution, which makes no such prediction or assumption. All we require with respect to the kinds of variation is that they be sufficient to produce today’s species. We do not require an infinite number of paths to infinite non-existent species. We know that evolution is constrained by the laws of physics, by developmental constraints, and constraints of history. It might very well happen that the rate of generation of big novelties will slow down or even stop over time. Evolution is silent about that.

Lou Jost - #78485

April 13th 2013

By the way, the above does not refute his later arguments about proteins (which are hard for me to evaluate since I am not a biochemist). But it certainly raises red flags about his understanding of the theory he criticizes. That is never a good sign…

Eddie - #78487

April 13th 2013


The sort of objection you are raising is a fair one, but it is one that should be sorted out in conversation, not made the basis of a snap judgment on his understanding.  I found that Durston was extremely good about replying fairly to extended criticism—both to Ashe and to Venema.  He didn’t take it personally, and he always replied in a give-and-take way that tried to advance the discussion, not just to score points.  So instead of just giving his conversation “a quick look,” you might wish to follow it through several columns.  You might decide that he is quite smart, and quite teachable, and that might encourage you to write to him to challenge the statement you are worried about; I suspect that after batting it back and forth with you, he might adjust his wording into a form that you could accept.  It’s worth a try.  Best wishes.

Lou Jost - #78490

April 13th 2013

 I had been under the impression that Durston is a YEC who doesn’t accept common descent, so I am not sure he’d be more reasonable than, say, Behe (who is honest enought to accept an old earth and common descent, as far as I know). I could be wrong.

Eddie - #78492

April 13th 2013


I don’t know his personal religious position; however, if he bases any critique of Darwinian mechanisms that he may have on molecular biology, information theory, etc., that shouldn’t matter.  If his scientific argument is good, it’s good, and if it’s not so good, it’s not so good.

It’s hard to tell just from reading his exchanges here, where he is silent about his religious beliefs, how his beliefs might contribute to his scientific thinking, but as far as I can tell, he bases no argument on Biblical or theological assumptions.  So if his published articles display inadequate science, that should be chalked up to scientific shortcomings, not to his religion.

Lou Jost - #78512

April 14th 2013

I don’t see much written by him, except the calculation of functional information (which I have quibbles with). Do you know of something where he addresses the broader question of evolution?

I think we have spent an enormous number of column-inches trying to identify good ID articles without much success. That is significant. And now I understand that your position is more of a philosophical one, your own intuition about evolution.

Eddie - #78516

April 14th 2013


As I said, on the Discovery web site, you will find a list of 50+ proper academic publications by ID proponents.  You can look up those publications at your leisure, over the next several months, and decide for yourself which of them are “good.”  You don’t need my opinion to decide that.  In fact, wherever I’ve offered my opinion, you’ve disagreed.  So it’s better for you to just deal with the authors yourself.  I’m now done with this topic.

On your last sentence, it’s not a question of pure intuition, it’s a question of the analysis of foundational assumptions, of the kinds of argument made by biologists, etc.  Philosophical and historical training helps in understanding these things.

In pre-Darwin days evolution, where it was believed, was believed largely for philosophical and theological reasons.  Darwin added empirical reasons, but he also retained the philosophical and theological ones, which provided his deeper motivation.  (Which should be borne in mind when ID people are accused of religious motivation.)  And those philosophical and theological reasons are still operative (largely at the unconscious level) in the practice of evolutionary biology today.

Whereas a pre-Enlightenment philosopher or scientist would find evolutionary explanations implausible, and would want a detailed demonstration of how one species could turn into another, a modern biologist is satisfied that this can happen on general theoretical grounds, even though he cannot explain in detail even 1% of the molecular or physiological changes and their coordination.  Because it’s assumed that natural and non-teleological explanations are adequate, any gaps in naturalistic explanation are dealt with by promissory notes of future research.  And criticism for lack of detail is responded to by the brittle defensiveness of the professional, the specialist, the expert who does not like his judgment publically questioned.  (A phenomenon which is nothing new for anyone who knows the case of Socrates.)

The massive lack of detail in the explanations should be raising the question whether non-teleological natural causes are fully adequate to explain the phenomena.  That this latter possibility is rejected out of hand—that’s where the metaphysics comes in.  Modern biologists don’t seek “the best explanation” of origins; they seek “the best naturalistic and non-teleological explanation” of origins.  And there is no rational justification for limiting the inquiry into orgins in that way.  But there is an emotional, religious, philosophical, political justification.  That’s where critics such as Berlinski perform an invaluable role, in making clear the extra-empirical commitments of the  experts who are interpreting the data for the general public.  Philosophers—Berlinski, Nagel, Monton, Popper, Adler, Bergson—have an annoying habit of doing things like that.

I don’t apologize for looking at the evolution/design debate from the philosopher’s perspective.  It would be much more intelligent and more socially useful debate if both the biologists and the Christians involved had much more training in traditional philosophy than they do.

Lou Jost - #78519

April 14th 2013

I had sincerely hoped that someone could point me to the strongest articles, as I don’t want to read 50+ articles.

You say the massive lack of detail in evolutionary explanations should cause us to doubt its adequacy. That’s wrong, Eddie. The kind of detail you want, for microscopic events that happened tens of millions of years ago, is impossible to supply, and you know it. The  reason you set the bar so high is because you don’t like the standard explanation, for philosophical reasons. There are obvious technological reasons why we can’t supply you with the detail you demand, so the absence of such details in no way suggests problems in the theory. You can see that by doing a thought experiment. Assume the theory is exactly true. There is still no way we would ever be able to obtain the details you ask for.

You said “Darwin added empirical reasons, but he also retained the philosophical and theological ones, which provided his deeper motivation.  (Which should be borne in mind when ID people are accused of religious motivation.)” A claim that Darwin was motivated to believe in evolution for theological reasons is absurd, Eddie. He made his seminal observations on “the species question” while he was thinking he would become an Anglican clergyman. He was a believing Anglican during his Beagle trip. After he published the Origin, the conflict between the implications of his theory and the religious beliefs of his wife and friends caused him much distress.

Later in life, the death of his daughter Anna probably pushed Darwin to finally reject the idea of a caring god, but to suggest that the theory of evolution had religious motivations at its outset is wrong. Darwin saw firsthand that the distributions of species on the globe followed laws that suggested natural explanations, not special creations. That was what motivated him to understand the origin of species, not philosophical or religious motivations.

Eddie - #78527

April 14th 2013


I’ve asked for no more detail in the case of whale evolution than the physicists can give me for the birth and development of a typical star.

I don’t fault the physicists for not being able to tell me the location of every single proton throughout the star’s history.  However, I would certainly fault a physicist who uttered the vague generality:  “Heavier elements are created by the combination of gravitational attraction and intense heat,” but could not give any specifics about even one such creation (e.g., helium from hydrogen, carbon from lighter elements).  I’d wonder how the physicist knew that mass X of hydrogen would have enough gravity to overcome the resistance Y to the nuclear fusion of hydrogen into helium, and how the physicist knew that energy released by such fusion (call it Z), would be sufficient to trigger fusion into heavier elements, etc.  But as it happens, I can ask a physicist such questions, and get plausible answers for most of the steps between hydrogen and uranium.

I can’t get analogous answers for the steps between artiodactyl and cetacean.  What I get is the vague generality:  “It happened by random mutation, drift, and natural selection.”  And if I make difficulty about the details, I get:  “The population geneticists have worked out the math, and there is enough time, and there are no developmental, morphological, or selection barriers that could possibly make any difference, so we don’t actually have to describe what any of the steps might have been, and you are being unreasonable to ask for them.  The specialists are quite sure that they are right, so you should trust them.”  The public will never give evolutionary theorists that trust.  And rightly so.

On your other point, I’ve been studying Darwin for some time now, reading many of his writings (including the Origin of Species in its entirety, more than once, and his Autobiography several times, and many of his letters), and I’ve read many works about Darwin, including the massive biography by Desmond and Moore.  I’ve also, as a scholar in my field, read many primary and secondary sources regarding the development of evolutionary thought (in science, philosophy, and theology) prior to Darwin.  I was giving you the shorthand account, the bare-bones result of years of academic study.

I do not have time to prove everything I said.  However, if you want to know more about the theological roots of modern evolutionary thought, you could read a number of things, starting with Lovejoy’s Great Chain of Being.  There are also three books by Cornelius Hunter on Darwin, and, while I don’t subscribe to all that Hunter argues, he provides more than enough textual evidence, from Darwin’s own words and from the words of his contemporaries and predecessors, to show the theological ethos and motivation of Darwin’s thought.  You can also pick up information about Darwin’s theological thought, by reading some of the work produced by historian Michael Flannery, who is an expert on the work of Wallace (co-discoverer of natural selection) and has studied the theological differences between Darwin and Wallace.  (Wallace, of course, has been greatly slighted in all the Darwinmania of recent years.  There are theological reasons for that.  Most modern scientists and popularizers of science have a theology considerably to the left of even Darwin’s, whereas Wallace’s theology was to the right.)

I never denied that Darwin was able to produce empirical evidence to support an evolutionary scheme.  (He does so very elegantly in The Origin of Species—one of my favorite books.)  The point—one not well-known by the general public, because the popular science writers distort the history with their “warfare of religion and science” propaganda—is that evolutionary thought did not take its birth from science, but from philosophy and theology.  It was then ready at hand for Darwin to apply it.  Darwin’s thought is best located within the liberalization of theological thought that followed from the Enlightenment.  It’s no accident that he early on found many supporters high in the ranks of the Church.

Lou Jost - #78535

April 15th 2013

Your demand for step-by-step proof for a distant-past evolutionary scenario is not reasonable, and it is telling that you never demand anything similar from design advocates. Even in physics, where every atom of a given isotope of an element has identical properties, a physicist cannot predict or retrodict the path of  a planet unless he or she knows a lot about the planet, and also knows a lot about all the other bodies near the planet (the masses, charges, fields, state of motion, angular momentum, presence of tidal effects, etc). This kind of detail is impossible to obtain for, say, one of the new exoplanets discovered orbiting a distant star. Yet we have exact laws of physics that are tested in the lab (thog on smaller objects!) and which seem to work when applied to nearby, well-known celestial objects. It is reasonable to assume that these same laws apply to the exoplanet, even though we don’t have (and may never have) enough knowledge of the boundary conditions to solve the differential equations governing its motion.

Someone may doubt that the laws apply to the exoplanet, and indeed that person could be right, but it would shake up physics to its very core. So which is more reasonable, to assume our known laws apply until proven otherwise, or to think the laws do not apply to the exoplanet (and hence that physics as we know it is wrong to the core) unless proven otherwise?

Regarding Darwin, your second comment is more measured and accurate than your first. In your first comment, you claimed that Darwin was motivated to an important degree by theological and philosophical positions. “Darwin added empirical reasons, but he also retained the philosophical and theological ones, which provided his deeper motivation.” This is not true; he came to his theory through his field work and the insight provided by Malthus’ famous essay on population growth; philosophical and theological motivations did not play a role. The same is true for Wallace, whose work on biogeography is better than Darwin’s. Wallace came to his theory via exactly the same route as Darwin, from extensive firsthand experience of species distribution patterns around the globe, combined with the trigger of Malthus’ essay. Both men came up with essentially identical theories even though they came from wildly different theological and philosophical backgrounds. Of course, Wallace drew a line in his theory between humans and all other forms of life, and he also embraced the spiritualist mediums of the time (he was often fooled by them), much to Darwin’s dismay. I agree that this may have contributed to Wallace’s being eclipsed by Darwin in the views of the next generation of scientists, but it is not the main reason. Wallace himself always agreed that Darwin was the man who marshalled the heavy evidence and developed the theory fully. He titles one of his books “Darwinism” (and at that time this did not carry the negative connotation it has today among religious folk). He always bent over backwards to give Darwin full credit for the theory, so it is perhaps unfair to say that later scientists were wrong to agree with Wallace on that point.


Lou Jost - #78536

April 15th 2013

When I said ““Darwinism” (and at that time this did not carry the negative connotation it has today among religious folk)” I should have said Wallace didn’t mean it the derogatory way that religious folk today would use it. There were lots of religious people in Darwin’s day who used the term “Darwinism” in a derogatory way, but there were also people who used it as a purely neutral descriptive shorthand for “evolution”, as Wallace does here.  Today, by contrast, the neutral term is “evolution”, and most people who use the term “Darwinism” give it a negative connotation.

Eddie - #78540

April 15th 2013


In reply to elements from the above two posts on Darwin:

I grant the historical facts about Malthus, Wallace, etc.  They are all very familiar to me.  But you won’t understand my remarks about the theological background of Darwin until you study the history of ideas in more depth.  I gave you some suggestions for preliminary reading.  I don’t have time to say more about this at the moment.

I will make the general remark that you seem to endorse the modern, positivist notion of science as an objective, value-free inquiry; serious philosophers, historians and sociologists of science have not accepted this notion for decades now, though it is still the popular conception, and the one held by most working scientists (whose training does not normally include serious study in the history, philosophy, or sociology of science, not even of their own discipline).  The general consensus of people who study these things is that:

(1) terms found in the self-conception of modern science—“truth” “reality” “fact” “cause” “nature” “chance” “natural laws” “explanation” etc.—are all terms loaded with epistemological baggage, and are far from obvious in their meaning;

(2) scientists themselves are human and, aside from the established reality of some of the cruder forms of dishonesty—plagiarism, plotting on e-mail how one might undermine certain journals which publish material one doesn’t like, writing e-mails to other scientists telling them not to trust so-and-so’s editorial decisions because he is Christian, etc.—their beliefs as human beings (about the non-existence of God, for example) unconsciously shape their judgements of what is probable, reasonable, strong evidence, weak evidence, etc.;

(3) the definition of “science” itself is culture-related; the word meant different things in the ancient world, the medieval world, the Renaissance world, the 17th century, etc.  Right now, design inferences are defined (explicitly by the NCSE and Judge Jones, and implicitly by the vast majority of working scientists) as outside of science.  This was not the case 350 years ago and may not be the case 50 years from now.)

You are right about the term “Darwinism.”  In the late 19th-century it had a biological reference to evolution understood as heavily dependent upon natural selection.  I still use the term today in the biological sense—a theory of evolution based on the ideas of Darwin (though sometimes, for convenience, I include neo-Darwinism as well, since the two are closely related, with neo-Darwinism supplying the Mendelian genetics and the idea of random mutation).  I don’t use “Darwinism” in the sense of “social Darwinism” or “an atheistic theory of origins” etc.  I try to use words with more historical accuracy than do some of my co-religionists.  So my objection to Darwinism and neo-Darwinism is not that they are ungodly, carnal, wicked philosophies of life, but that they explain the evolutionary process very poorly.

Lou Jost - #78546

April 15th 2013

Eddie, I know that science is a human activity andobservation is theory-laden (I took every available Phil. of Science class as an undergrad, which admittedly was not a huge number….). But Darwin and Wallace’s theory of evolution was not influenced by their theological views (indeed, it went against their recieved views), except when Wallace “chickened out” on including humans. (As you know, Darwin chickened out too, initially, but that was more of a political move.)

Eddie - #78550

April 15th 2013


If you took a philosophy of science course, you were unusual among science undergraduates.  History and/or philosophy of science is/are almost never required of undergrad science majors in in mainstream universities, and even at universities which have impressive programs in history/philosophy of science, very few of the science students avail themselves of the opportunity to take such courses as electives.  (I can just hear the biology prof’s advice to a student entering the junior year:  “If you want to be better prepared for grad school and a research career, don’t waste your time with subjective, non-scientific stuff like history and philosophy of science; take some more math or biochemistry or genetics.  You aren’t more likely to win a scholarship because you know something about Darwin and his times, but you are more likely to do so if your mathematical ability to handle genetics is better than that of your peers.”)

But then, you were originally a physics student, and in my experience the physics/astronomy students were more often interested in the broader questions about the nature and methods and grounds of science than the biology/biochemistry students, who seemed to be predominantly concerned with getting into medical school, or with detailed studies of small technical questions relevant to a career in medical research or the like.  

You do not understand what I mean about the theological basis of Darwin’s thinking.  I do not mean Darwin’s conscious religious opinions about creation prior to the Beagle voyage, etc.  I’m talking about the theological “climate of opinion” in the 19th century, which was rapidly changing, and Darwin’s theory was compatible with the avant-garde side, not the reactionary side.  To understand this climate of opinion, you need to know something about Enlightenment thought and 19th-century thought, and how it spread from philosophical and theological quarters into all other areas of thought, including the natural sciences—the borders between areas not being as rigid then as they later became.

The idea of a God who preferred to work through secondary causes rather than through miraculous interventions was becoming extremely popular among the more educated churchmen and theologians, and the idea of progressive change from the simpler to the more complex over time was also very much in vogue.  Darwin could not have avoided coming into contact with such ideas, given the educated class he belonged to, and in any case his remarks about God and religion, scattered through his work, indicate familiarity with the ideas of the time.  As I said, for the general background, read Lovejoy.  For a detailed study of Darwin’s explicit or tacit religious assumptions, read Hunter (though as I said I don’t agree with everything Hunter says).  For a  fresh appraisal of Wallace, read the works of Flannery.

Hunter argues that Darwin’s thought was theological through and through; I think that is an exaggeration, for the reasons that you give; but Hunter’s exaggeration is preferable to the standard story in popular science works and journalism, in which Darwin’s dispassionate observational science caused him to overcome his theological prejudices.  (Cue for violins:  come in with passionate music suggesting heroism.)  A close reading of the Origin, combined with a similar close reading of his Autobiography and letters, indicates that theological questions (about God, chance, design, laws of nature, the problem of animal suffering, etc.) were never far from his mind, and influenced how he approached the question of evolution.

melanogaster - #78581

April 16th 2013

“I can just hear the biology prof’s advice to a student entering the junior year: “If you want to be better prepared for grad school and a research career, don’t waste your time with subjective, non-scientific stuff like history and philosophy of science; take some more math or biochemistry or genetics.”

You have a remarkable ability to replace evidence with fantasy, Eddie. I can’t imagine any of my peers saying that. As for those to whom I am not a peer, can you hear Nobel Laureate J. Michael Bishop advising someone that way?

What do you think Mike Bishop majored in as an undergrad?

Eddie - #78590

April 16th 2013


I was speaking of professors.  Are you saying you are a professor somewhere?  Funny, last time you indicated your identity here, you said you were a researcher at a private institute.  Have you changed jobs since then?  Do tell us where you work now.

I have no idea who Mike Bishop is, and therefore I will not characterize his motivations or his likely advice for undergrads.  However, most biology professors are not Nobel Laureates.  I was describing the typical case.  But in fact I can imagine a good number of Nobel Laureates giving a student exactly the speech that I gave.  You don’t win a Nobel Prize in a scientific discipline for having a wide knowledge of the history and philosophy of your discipline.  You win it for uncovering new mechanisms in nature.  And I’m not saying it should be otherwise.  I’m simply describing the bloody-minded attitude toward scientific education that most Ph.D.s in the sciences have.  It’s about acquiring specialist expertise, so that one can do well in the world of grant applications, tenure-seeking, etc.

melanogaster - #78613

April 16th 2013

“I was describing the typical case.”

No, you were fabricating, just as you did with your 9M years claim. You don’t have a sufficient sample size to come up with a typical case.

“But in fact I can imagine a good number of Nobel Laureates giving a student exactly the speech that I gave.”

That’s odd, because of the several that I know, I can’t imagine a single one of them doing so. There is only one that I can imagine doing so, but I didn’t know him—it’s based on hearsay from those who worked with him.

Thanks for admitting that you are falsely portraying your imagination as fact, though.

“You don’t win a Nobel Prize in a scientific discipline for having a wide knowledge of the history and philosophy of your discipline. You win it for uncovering new mechanisms in nature.”

And the way you uncover new mechanisms in nature is typically through going in with a wide knowledge of everything, including history and philosophy of your discipline.

“And I’m not saying it should be otherwise. I’m simply describing the bloody-minded attitude toward scientific education that most Ph.D.s in the sciences have.”

I’m simply saying that your claim has no basis in my experience, and your response shows it to be a fabrication.

“It’s about acquiring specialist expertise, so that one can do well in the world of grant applications, tenure-seeking, etc.”

You’ve got it all wrong, as usual, but that fits with your abject fear of evidence.

Eddie - #78631

April 17th 2013


I don’t believe you know a single Nobel Laureate.  And there is only one way that you can prove that you do.

I don’t care if my claim has any basis in your experience.  It has a basis in my experience.  And I have more university experience than you do.  You work in a research lab outside of a university context (unless you were lying to the former management here when you identified yourself).  

Eddie - #78541

April 15th 2013


Your comparison with celestial mechanics is not on the mark.  The causes of the motions of planets are relatively simple, and good approximations of their past motions are possible (despite the mathematical complications of many bodies interacting at once), and this allows for fairly precise retrodiction (assuming the non-intervention of foreign bodies into the solar system).  By contrast, evolutionary mechanisms are much more poorly understood than the mechanisms of celestial mechanics; they are more complicated, and evolutionary theory is in ferment at the moment, with the recent discussions over evo-devo (Carroll etc.), convergence (Conway Morris), self-organization (Newman, etc.), genetic self-engineering (Shapiro), etc.  We do not have an account of evolutionary causality as straightforward as Newton’s Laws (or Newton’s Laws modified by Einstein etc.), and our retrodictions are much less reliable because of that.

I don’t say that past inferences about evolution are entirely unreliable, but the degree of confidence they are assigned should reflect both the vastly greater complexity of biological phenomena and the fact that the field of evolutionary mechanisms is in ferment at the moment and that it may be a couple of decades before the dust clears

And to be fair, in some of the technical articles I have seen, this modesty and caution is evident, and I praise the biologists involved for their restraint.  Such modesty and restraint is rarely evident in the culture-war books, blogs, talks, etc. of Dawkins, Coyne, Myers, Scott, Miller, Collins, Rosenhouse, Shallit, Matzke, Moran, and many TEs.  Nor is it evident in the showboating of certain scientists and their journalistic friends when some new fossil (“Ardi” or the like) is trumpeted as the decisive breakthrough.  One is far more likely to see comparisons of the certainty of evolutionary biology with the certainty of the theory of gravitation, the atomic composition of matter, or the germ theory of disease, than the admission that there is far more about evolutionary mechanisms that we don’t know than that we know.

It’s this boastful, arrogant, imperialistic attitude that I’ve been objecting to, not modest proposals for partial evolutionary mechanisms.  And while your tone is more modest than that of the people I’ve been complaining about, I’ve heard very little protest from you when the people on your side grandstand in the way that I’m talking about.  You seem to be far more exercised about over-claims on the design side than about over-claims on your own side.  How much time do you spend on Panda’s Thumb, TalkOrigins, Skeptical Zone, etc., chastising the people there for their excessive certainty and lack of scientific nuance?

For example, when you see (as I have seen on Darwinian sites) claims that evolutionary trees derived from fossil evidence and those derived from genomic evidence always match, and there has never been a case where the two appear to be in conflict, do you give that a pass, or do you demand a little more objectivity?  Would you call such claims “crap” on the grounds that they are dishonest about (or unaware of) contrary empirical evidence?  And this goes back to the human side of science that I talk about in my other reply, below.  Like myself and everyone else, your judgments are influenced by your existing convictions, and you do not always respond exactly in proportion to the epistemological offense in all circumstances.

Regarding my alleged double standard regarding design inferences, please understand, as I’ve told you before, that I’m not a typical ID proponent.  I take much more seriously than many ID proponents the definition of ID as a theory of design detection.  This means that I am much less interested in ID as an alternative historical explanation.  I see ID as a primarily ahistorical theory of causation.  I see its job as to identify design (as opposed to law or chance) as a real cause of something, wherever design is a real cause of something.  I do not see its job as to give an account of the means or mechanism by which design is implemented.

That is, I see design theory as an information science, not as a historical science—and here I differ from many rank and file ID fans, and also from some of the leaders, such as Stephen Meyer.

If I may put it as crudely as possible:  suppose that at some future date ID theorists could prove that the first living cell could not have arisen via chance and natural laws alone, but required design as well as those other factors.  If that could be established, then reductionist, materialist scientific accounts of origins would be wrong—even if ID proponents could not say a word about the time and place and methods of “design insertion.”

An analogy:  we have discovered ancient artifacts whose purpose we do not know, whose date and place of origin are uncertain, and whose makers are unknown to us.  But we can tell that they are designed objects which did not arise through combinations of chance and natural law alone.  Our design inference is not invalidated by a fact that we cannot give a historical account of the production of the device.  Similarly, it is logically possible that we could infer that the first living cells were designed, while being unable to give an account of their designer or the details of their emergence.  That is all that I ask of ID theory.  If ID theory can do that, then Dawkins, Coyne, etc. are wrong.  And such a demonstration, if it could be given, would be no trivial achievement.

Lou Jost - #78547

April 15th 2013

Yes, I mostly agree with this. It is logically possible to find evidence of design, as I have said many times here. I (along with Larry Moran and I think Jerry Coyne) that it is not unscientific to look for evidence of design. I just think that no such evidence has been presented yet. 

On that topic, I have one minor and one  major technical criticism of Kirk Durston’s work. Writing it up will have to wait though, as I have too much other work right now. See you later, Lou

beaglelady - #78548

April 15th 2013

Please name some of these ancient artifacts.  Do we know they were made by humans?  How can we tell? Did the manufacturers create them with their hands? 

When scientists find ancient artifacts, they love to attempt to reproduce them, using only the technology and resources known to exist at the time.  So they have a good idea of how flint was knapped, beads were created, etc. 

Eddie - #78552

April 15th 2013


Have you not heard of the Antikythera mechanism?  It puzzled scientists and historians for 100 years.  Its purpose was unknown.  Look it up.  There are pictures of it on the web.  Do you really think that “this thing came together due to natural laws plus chance, not design” was a plausible explanation for it, even before its purpose was uncovered?  Are you saying that scientists/historians had no right to conclude “this thing was designed” until they could give a full historical account of how it was built, and when, and where, and by whom?  If not, then we’re not disagreeing.  If so, then I think you’re wrong.

Similarly, it is possible, in principle, to show that the first living cell required design, even if one cannot date the event, or describe the mode of production, or identify the designer or manufacturer.  The question “whether X is designed” can sometimes be answered without being able to answer a whole host of other questions.

Lou appears to agree with this as a general statement.  Do you?  If not, why not?

beaglelady - #78555

April 15th 2013

Do you really think that “this thing came together due to natural laws plus chance, not design” was a plausible explanation for it, even before its purpose was uncovered?

No, of course not.  I never gave the remotest suggestion that ancient artifacts came together by chance.  But didn’t we always know that humans made it, not God, especially since it was found in a shipwreck? Also, we had no idea who or what was making Devil’s Corkscrews until a fossil critter was found in one. But nobody every concluded that God had made it. 

The question “whether X is designed” can sometimes be answered without being able to answer a whole host of other questions.

I agree wholeheartedly! But in science one answer leads to further research. No scientist would be happy with “don’t ask, don’t tell” when it comes to questions of the designer’s identity, abilitites, motives, etc.  And everyone knows who you-know-who is, anyway.



melanogaster - #78583

April 16th 2013

“Similarly, it is possible, in principle, to show that the first living cell required design, even if one cannot date the event, or describe the mode of production, or identify the designer or manufacturer.”

Why would you draw the line for life at the cell? And what about the reality of the development and physiology of living things suggests design or manufacture? You’ve already unwittingly offered up an empirical test of YOUR design hypothesis with your crazy claims about how mammals are “put together.” Why not test it against the extant evidence for whales specifically, and vertebrates in general? We’ve got a lot of developmental biology on hind limbs, flippers, and blowholes to examine. Oh, and don’t forget those sequences—even you can test hypotheses against the actual sequence data.

Do you not see the hilarity of you arguing that degrees and departments are of the utmost importance, while I’m pointing out that any moderately intelligent layperson with sufficient motivation can DIY—if you’re really interested in approaching the truth?

beaglelady - #78587

April 16th 2013

 The question “whether X is designed” can sometimes be answered without being able to answer a whole host of other questions.

Another thought: Why stop there?  Finding designed objects leads scientists to ask a “whole host of other questions.” They want to know how our ancestors knapped flint, for example.

Eddie - #78592

April 16th 2013


I have no objection if you wish to push any question further.  For example, if I were able to prove that the first cell was designed, you would be very welcome to speculate upon who the designer was.  And I would be very willing to listen to your speculations.  But it is not necessary to know who the designer was, to know that it was designed.  And the issue between ID people and “chemical origin of life” people is whether or not life was designed.  That’s the first order of business on the table.  Let’s deal with the most pressing question first.

beaglelady - #78593

April 16th 2013

Why can’t we deal with the identity of the designer? Isn’t that part of science? 

Eddie - #78605

April 16th 2013


I don’t think you understood me.  I never said “can’t”; I invited you to offer any speculation about the identity of the designer that you like.

It would, however, be pointless for you to speculate on the identity of the designer of the first cell, if you think the first cell wasn’t designed at all, but just happened because of the right combinations of unguided sloshings and unguided bondings in a primordial soup.  

I’m open to any “scientific” method you can propose for identifying the designer.  I can’t think of any such method, but if you can, by all means share it.  

beaglelady - #78615

April 16th 2013

Why aren’t ID folks interested in  identifying the designer, her motives, etc. ?

Eddie - #78630

April 17th 2013


Do these endless variations on the same question—a question already answered—indicate a genuine lack of understanding on your part of what I am saying, or are you just being childishly combative again?

If it’s the latter, grow up.

If it’s the former, you’ve been told a thousand times, on BioLogos and elsewhere, that ID proponents do not think that the identity of the designer, in the case of biological phenomena, can  be determined by science.  What is it about this that you find difficult to understand?

I understood this the very first time I read an ID author who addressed the question of the identity of the designer.  I understood it with perfect clarity.  That was in about 2005.  You’ve been reading about ID for at least that long, and you still haven’t understood it?

beaglelady - #78634

April 17th 2013

So “don’t ask, don’t tell”  if you know it’s you-know-who.


Eddie - #78637

April 17th 2013


Grow up.  Baiting and sneering aren’t arguments.

Was the first living cell designed?

Answer yes or no.

Then explain how you arrived at your answer.

If you answered yes, can you tell who the designer was by the methods of science?

Answer yes or no.

Then explain how you arrived at your answer.

beaglelady - #78648

April 17th 2013

No, I really don’t believe so.  I have know way of knowing for sure, of course.  


btw, did you like your article on the origins of the whale body plan?

Eddie - #78655

April 17th 2013


So if the first living cell was not designed, then how can God be said to be responsible for it?  Or don’t you believe that he was?

But, supposing that he was somehow responsible for it (even though it was undesigned!) what did he do to ensure that this undesigned first cell would come into existence?  Or did he roll the dice and let chance decide whether or not it would come into existence?  (After all, you love Polkinghorne, and according to you, P. says that God deliberately chooses not to know the future, so such a belief on your part would be possible.)

I’m having trouble finding any coherence at all in your view of theistic evolution.  It appears to me that you keep your evolution and your God in two separate compartments, and that you have invested no effort in trying to work out the relationship between the two.


beaglelady - #78678

April 18th 2013

Without God’s creation there could be no cells.  What do you think happened?  Did God drop one cell into a pond? If so, what happened next?

Did you like that article on the origins of the whale body plan? I thought you’d be interested, since you’ve been calling for such information.


Eddie - #78690

April 18th 2013

On whales, see my 78689 below.

I’ll pick up the origin of cells in a new post.

melanogaster - #78582

April 16th 2013

“For example, when you see (as I have seen on Darwinian sites) claims that evolutionary trees derived from fossil evidence and those derived from genomic evidence always match, and there has never been a case where the two appear to be in conflict, do you give that a pass, or do you demand a little more objectivity?”

I have never seen anything of the sort. If you are going to credibly claim that such claims exist, a link or two (since you used the plural) would be appropriate.

Eddie - #78591

April 16th 2013

I did not say that such claims were made in peer-reviewed literature.  I have seen them made many times on blog sites by people who affect to knowledge of these matters.  I have not kept a record of who said these things when.  If the people making these claims were well-known people, such as Ken Miller or Coyne etc., you can be sure that I would have links for you.  But I have better things to do than catalogue the bluffs of scores of mouthy commenters.  If you do not believe me when I say I have seen such claims, I really don’t care.

Certainly I have never seen you jump in to contradict such claims.  Nor have I seen any of your Darwinian allies that post on the various web sites do so.  False claims made by ID proponents, or creationists, you and your friends will jump on immediately; false claims made by people on your own side—not so much.  I wonder why.

melanogaster - #78580

April 16th 2013

“This is not true; he [Darwin] came to his theory through his field work…Wallace came to his theory via exactly the same route as Darwin, from extensive firsthand experience of species distribution patterns around the globe, combined with the trigger of Malthus’ essay.”

It’s clear that at some level, Eddie understands this all too well. Otherwise, why would he go to such great lengths to avoid the evidence? If Eddie really thought he was right, why wouldn’t he abandon his present academic career to work with one of his heroes in the ID movement, and get that vaunted (only among evolution denialists, it seems) second PhD?

melanogaster - #78578

April 16th 2013

“I’ve asked for no more detail in the case of whale evolution than the physicists can give me for the birth and development of a typical star.”

You haven’t even acknowledged one of the most important details when it was provided to you on a platter:


Any neutral observer would conclude that you are engaging in a rhetorical stunt.

“What I get is the vague generality: “It happened by random mutation, drift, and natural selection.”

That’s an patently false claim:


beaglelady - #78602

April 16th 2013

The article is titled “Developmental basis for hind-limb loss in dolphins and origin of the cetacean bodyplan”


That is exactly the kind of article that Eddie has been asking for! 

melanogaster - #78614

April 16th 2013

So the only rational conclusion is that Eddie is extremely insincere when he asks for evidence.

It seems that evidence is the last thing he’s seeking.

Eddie - #78689

April 18th 2013

No, beaglelady, it’s not.

First of all, the article in question is 4 pages long.  The sort of explanation I am looking for, as I made clear to Lou, would be more like 400 pages long.

Second, let’s look at the article’s self-description:

“Interpreting our results in the context of both the cetacean fossil record and the known functions of Shh suggests that reduction of Shh expression may have occurred ≈41 million years ago and led to the loss of distal limb elements. The total loss of Shh expression may account for the further loss of hind-limb elements that occurred near the origin of the modern suborders of cetaceans ≈34 million years ago. Integration of paleontological and developmental data suggests that hind-limb size was reduced by gradually operating microevolutionary changes. Long after locomotor function was totally lost, modulation of developmental control genes eliminated most of the hind-limb skeleton. Hence, macroevolutionary changes in gene expression did not drive the initial reduction in hind-limb size.”

Let’s look at the choice of words:  

“may have” occurred 41 million years ago.

“may have” led to the loss of distal limb elements.

Doesn’t sound like a firm establishment of an efficient-cause chain to me.  (Though I applaud the intellectual honesty of the authors for not-overclaiming, the way most of the commenters here do, and the way Coyne, etc., and Miller, etc. do.)

“hind-limb size was reduced by gradually operating microevolutionary changes”

Which no one in the ID camp denies is possible.

“modulation of developmental control genes eliminated most of the hind-limb skeleton”

Which “developmental control genes”?  Do the authors have any idea?  Or are they just faking it?  How about specifying the genes in question?  If I said, “a car part” controls the flow of fuel into the ignition chamber, wouldn’t you want to know which part?

“macroevolutionary changes in gene expression did not drive the initial reduction in hind-limb size”

Which does not rule out the possibility that “macroevolutionary changes” were responsible for other aspects of whale evolution, beyond the “initial reduction in hind-limb size.”  But of course, the distinction between “macroevolutionary” and “microevolutionary” changes is not explained, so it’s hard to tell what content those words have for these particular authors.  For example, do they think that “macroevolutionary” changes are merely “microevolutionary” changes carried on for a longer time, or are a different and more fundamental kind of change?  The wording here would suggest the latter, but I can’t tell for sure.

This is why I’ve stopped looking up the articles that people here cite as “proof” of the capability of macroevolutionary mechanisms.  Whenever I look them up, they are almost always simply lists of similarities between fossils or lists of similarites between genomes, sprinkled with speculations about possible genomic changes, loaded with words such as “may have” “could have” “might have” etc.  They never say things such as:  “In Lab X, Professor Y determined that by knocking out Genes A and B, you can make a hippo grow a flipper instead of a foot, so we argue that Genes A and B were, roughly Q million years ago, lost from this particular line of artiodactyls.”  It’s never that precise.  Never anything like the precise attributions of causality you get in physics, chemistry, and engineering.  That’s what I meant by saying the evolutionary theory is the sketchiest of sciences.  

Sorry, beaglelady, you will have to do better than that.  Give me a map of the artiodactyl genome, and tell me what I have to change in that genome to get a cetacean.  Circle the genes involved, and tell me how each one would be modified, deleted, etc.  Tell which new genes would have to be added.  Tell me which non-coding DNA would be involved as well (you know, all the “junk DNA” which we now know—no thanks to neo-Darwinism—is no longer junk), and how it would have to change.  Show me that developmental biologists would agree that each of these proposed genomic changes is feasible from a developmental point of view.  And show me with reference to the environment at the time that such changes would confer a selective advantage.  

I want a series of pictures, like shots of Lon Chaney turning into the Wolf Man.  Only I want a genomic commentary, with specific genes mentioned, and a developmental commentary, and an ecological commentary, to accompany each picture.  If you can’t find any articles or books that do that, don’t bother citing any more to me; I don’t intend to look at them.

And if you and Fruitfly think I am demanding too much evidence, tough; those are my conditions for believing that neo-Darwinian changes could turn an artiodactyl into a whale.  If you want to persuade me, that’s what you’ve got to do.  And if you don’t care what I believe, that’s fine with me. 

beaglelady - #78695

April 18th 2013

You should understand why it’s a hypothetical pathway.  Scientists aren’t about to give up and declare that God ripped their legs off and threw them into the ocean. Especially since some of them retain vestigial hind limbs. And in fetuses the hind limb buds do begin to form.God is apparently trying very hard to convince us that evolution happened. 




Eddie - #78707

April 18th 2013


I’ve never said that evolution didn’t happen.  I’ve said that the mechanism championed by yourself and Fruitfly isn’t adequate to explain it.  I’ve said that it seems much more likely that design is involved at some level.  (Which does not rule out the involvement of several mechanisms, including mutations and selection, which help to realize the design.)

I suspect that you have badly confused “arguments for common descent” with “arguments for neo-Darwinism”; this causes you to react with knee-jerk fury against arguments against neo-Darwinism, as if they are automatically arguments against common descent.  But you should know the two things are distinct, from reading Behe’s books—oh, I forgot, you haven’t read Behe’s books.  You know they are wrong without having read them.  As you know that the scientists interviewed by Mazur are wrong without having read the interviews.  

In any case, the article you cited doesn’t come anywhere near explaining what I asked for.  Nor would I have expected it to.  Every article that has been cited to me in the past has been equally a bust, as far as what I’m looking for.  

You and Fruitfly can save your effort and not cite me any such articles in the future.  Nothing less than a longish book, arranged stepwise in the manner I indicated to Lou, would be adequate to convince me.  So either provide me with the name of such a book, or give up trying to convince me.

See the next page of comments for the discussion of the origin of life.

beaglelady - #78749

April 19th 2013

You don’t like the phrase “may have.”  Yet you have called for hypothetical pathways and have bashed scientists whom you perceive to be over-confident about what actually happened. 

Eddie - #78762

April 19th 2013


I approve of “may have” as a corrective to overconfidence.  My point is twofold:

That is not the tone of Fruitfly and others who have posted here; they very rarely use subjunctive verbs, and nearly always use indicative ones.

These articles you and others keep pointing out  each deal with very tiny pieces of the puzzle.  I’ve asked for a big-picture presentation that incorporates hundreds of these tiny pieces in one place—a book of several hundred pages, with diagrams of hypothetical genomes and corresponding anatomical stages, showing a pathway by which all these hypothetical little steps might lead coherently from one creature to another that is very different.  And neither your nor anyone else can point me to any such integrative account, for the whale, or the flagellum, or any organism, system, organ, etc.  

And I don’t fault you for even that, as long as you stop pretending these things are as certain as you think they are.  What is intellectually offensive about the Darwinists here is not their hypothesis, but their certainty. 


Seenoevo - #78545

April 15th 2013

To Lou Jest:

“Your [Eddie’s] demand for step-by-step proof for a distant-past evolutionary scenario is not reasonable, and it is telling that you never demand anything similar from design advocates.”

Maybe this is because evolutionists have always insisted evolution works slowly, in a step-by-step fashion, while design advocates (including creationists) are far less beholden, if at all, to centuries and steps. It’s only reasonable then that one should question an evolutionist on details of what is central to his theory.


“Yet we have exact laws of physics that are tested in the lab… which is more reasonable, to assume our known laws apply until proven otherwise, or to think the laws do not apply …”

How long did these laws take to evolve? How many steps were needed?

These, likewise, are not questions one need ask of an I.D. advocate or of a creationist. However, they might reasonably be asked of an evolutionist.

What’s your answer?

Seenoevo - #78596

April 16th 2013


You wrote to Eddie: “You haven’t even acknowledged one of the most important details when it was provided to you on a platter: pnas.org/content/103/22/8414”

And you provided that link a second time: pnas.org/content/103/22/8414

I looked at that link, which provides an abstract which reads in part

“Among mammals, modern cetaceans (whales, dolphins, and porpoises) are unusual in the absence of hind limbs. However, cetacean embryos do initiate hind-limb bud development. In dolphins, the bud arrests and degenerates around the fifth gestational week.”

This sounds like embryonic recapitulation. I hope my hearing is off, because I thought embryonic recapitulation was long ago discredited, sometime after Haeckel’s fraud was exposed.


Other extracts from the abstract (with my EMPHASES):

“Interpreting our results in the context of both the cetacean fossil record and the known functions of Shh SUGGESTS that reduction of Shh expression may have occurred ≈41 million years ago…

“The total loss of Shh expression MAY account for the further loss of hind-limb elements …

“Integration of paleontological and developmental data SUGGESTS that hind-limb size was reduced by …”


MAY I SUGGEST that if this is supposed to be “one of the most important details” supporting billy goat-to-wally whale evolution, you got trouble in River City.

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