Meyer has never read Your Inner Fish or Endless Forms Most Beautiful: The New Science of Evo Devo. If Meyer had, then he wouldn’t have even been able to write this chapter. Well… he probably would have given what he’s done to mangle science so far.
The second section of Chapter 13 is called “The Roles of Genes and Proteins in Animal Devlopment”. That’s a massive topic. It’s a huge topic. The book I linked to, Endless Forms Most Beautiful” is an entire book on a subject that Meyer discusses in six paragraphs.
His beginning line in this section is
As much as any other subdiscipline of biology, developmental biology has raised disquieting questions for neo-Darwinism.
I need to make a brief aside here. Please bear with me.
When I use the word “evolution” or “evolutionary theory”, I am referring to the most current version of the theory. How it stands as I write the article. I don’t use a lot of the terms to describe the different versions of evolution that have appeared in the last 150 years.
As each new major discovery in biology has taken place, evolution has been modified (sometimes a little, sometimes not at all) to fit with the new data, the new discoveries.
Darwinism, (how I hate that term) is what Darwin thought, his theory as described in his book. Natural selection and common descent. Indeed, even at the time, Darwin didn’t know anything about genetics.
Then we go into what is often referred to as Neo-Darwinism. That is, the “new Darwinism”. New is a relative term as this phrase was first coined in 1895. It has been used in a variety of ways over the last 120 odd years. As formalized, it was used by a group of biologists until the 1930s to mean that “natural selection was all there was”.
Next is the Modern Synthesis. It was developed in the late 30s and early 40s and used both (the recently developed) population genetics to show that Mendelian genetics was consistent with natural selection and gradual evolution. Some of the greatest biologists of any time were involved with this development (Huxley, Fisher, Haldane, Wright, Mayr, and Dobzhansky).
Of course, then in the early 70s we get punctuated equilibria, which isn’t really a new theory of evolution, but an extension that shows that gradual evolution is neither required nor (perhaps) sufficient.
Now, of course, we’re getting deep into molecular biology in a very real way. Even 20 years ago it took millions of dollars and teams of scientists to determine the total genome of a single organism. Now, the same project might take a few tens of thousands of dollars and a few scientists. Technology for this work has improved to the point where there are desktop models of genetic code readers.
We’ve also worked on evolution from a completely different angle, that of developmental biology. The science of EvoDevo (Evolutionary Developmental Biology). It was referenced in the famous Kitzmiller trial. Dr. Kevin Padian (in 2005) (NOTE: The “A” is a link to this text in the full trial transcript.)
A. I’m a fossil like everybody else. No, genes and molecules get a lot of press, and deservedly so. The research on them has been amazing over the past half century. The new discovery has just come at an incredible rate. They’re just revealing all sorts of new things about the world we never could have imagined. We could have hoped we could have known, but we wouldn’t have known how.
But, oddly enough, the most recent great advances in biology are coming with the integration of this new molecular evidence with what we already know from comparative anatomy, from fossils, and from geology.
An example I could give you is like the hottest area in biology today is called evo-devo or evolutionary developmental biology. Evo-devo is not a rock group. And the thing about it is that the whole premise of evo-devo is that we are now understanding a lot more about the genes that actually code for the development of organisms. That is, we know the genes that make you line up in a front-to-back axis and make your limbs sprout and make you have wings instead of hoofs or whatever it happens to be.
These are under the command of a relatively well-organized system of genes that are universal among a great many organisms. And you can even transplant parts of these into other organisms, and they’ll work properly, which is really amazing.
And why paleontology and evolutionary biology is relevant to this is because, for one thing, in the fossil record we see a lot of forms that are not present in any kind of shape today. Configurations of hands and wings and skulls that we can see by examination of the genetic structure and functions of development actually are produced in certain ways and they mimic what we see in the past.
So, oddly enough, paleontology, evolutionary biology are coming back front and center to be integrated in this very hot new area. (my emphasis)
That all being said, some scientists use Neo-Darwinism to mean “the current state of evolutionary theory”. I don’t. I think it’s a historical term and when referencing the current state, one should just say “evolutionary theory”, but that’s me.
There are scientists who do this and those that don’t. The difference is that they explain the context in which they use the terms.
In my experience, creationists like Meyer use these terms as pejoratively as possible. But let’s explore, for a moment, how Meyer might have used the term.
The first option is that Meyer means Neo-Darwinism as a historical term. He is a historian of science after all. In which case, he is perfectly correct. The modern knowledge of development and embryology was barely into its infancy at the time the word “Neo-Darwinism” was being used.
In this case, Meyer is perfectly correct. But what does this discussion have to do with modern evolutionary theory. How is embryology a problem for a science that has embraced evolution and developmental biology for over a decade now?
In this case, Meyer is speaking of a historical footnote. It’s the rough equivalent to asking why the Wright brothers didn’t include flares for confusing heat seeking missiles on the Wright Flyer.
The other choice is that Meyer is speaking of modern evolutionary biology. In which case he is dead wrong. Developmental biology is not a problem for evolution and it never has been. Again, evodevo has been around for a decade and there’s never been any “profound difficulty cutting to the very core of the neo-Darwinian view of life.”
In Endless Forms Most Beautiful, Dr. Carroll uses pages 307-328 to talk about the references, papers, resources, and further reading. Part 1 of that books is called “The Making of Animals”. Part 2 is called “Fossils, Genes, and the Making of Animal Diversity”.
Let me just quote from the preface of that book
The key to understanding form is development, the process through which a single-celled egg gives rise to a complex, multi-billion-celled animal. This amazing spectacle stood as one of the great unsolved mysteries of biology for nearly two centuries. And development is intimately connected to evolution because it is through changes in embryos that changes in form arise. Over the past two decades (note: this book was published in 2005), a new revolution has unfolded in biology. Advances in developmental biology and evolutionary developmental biology (dubbed “Evo Devo”) have revealed a great deal about the invisible genes and some simple rules that shape animal form and evolution. Much of what we have learned has been so stunning and unexpected that it has profoundly reshaped our picture of how evolution works. Not a single biologist, for example, ever anticipated that the same genes that control the making of an insect’s body and organs also control the making of our bodies.
That simple paragraph simply shows that Meyer doesn’t have a clue what he’s talking about… or he (as I have come to believe) is deliberately misrepresenting science. Endless Forms Most Beautiful was written nearly a decade before Darwin’s Doubt. Meyer’s questions and concerns have been addressed by scientists for years. But he still trots them out as if no one knows.
And to drive the point home, the fact that people still believe what Meyer says is true just underscores the need for better science education in the US (and everywhere).
Again, we see that Meyer isn’t saying anything of value. At least he said in just a few paragraphs.
I’d like to comment on one more thing here. Here’s is Meyer comment after describing a host of technical things that may or may not be accurate.
Transcriptional regulators and factors are themselves controlled by complex circuits and signals transmitted by other genes and proteins, the overall complexity and precision of which is breathtaking.
Yes, these things are stunning complex. They are massively complex. They make the world economy look like the accounting system my 7-year-old uses to determine if he has enough money for his next LEGO set. Here’s an example chart.
Meyer thinks that this is so insanely complex that only an intelligence could have created it. That’s the entire discussion here.
Meyer, in spite of what he claims, is using this entire book to talk about a “God of the Gaps” argument. It’s so complex that only God could do this.
That’s it. That’s his whole argument.
I have asked multiple people on a variety of forums (including this very blog) to post a page number where Meyer described the evidence for Intelligent Design. Not the evidence against evolution, but the evidence for Intelligent Design. So far, not a single person has been able to list a single page in this book that describes the evidence for ID.
My detractors (and there are many, Hi Casey!) will complain that I don’t actually offer up a refutation of Meyer’s claims here. Of course, claims made without evidence can be dismissed in the same way.
But, I do provide the evidence. Endless Forms Most Beautiful, the New Science of Evo Devo. It’s a pretty complex text, which is why I guess Meyer hasn’t read it. If you choose to get it and read (and please do), be aware that it can be technical. By Dr. Carroll is a good writer and will lead you through the evidence, with explanations of the experiments and data that support his statements. And you go through the pages in the back of the book that contain more information.
Let me give an example of why the creationists bother me for this. They don’t provide their data, but if I fail to debunk every single statement of Meyer’s, they win. I have, in my files, a copy of the final report on the World Trade Center Collapse. It’s 248 pages. And the primary purpose of the file is to provide evidence that supports something that everyone witnessed. Two planes impacted the WTC and brought the two main buildings crashing to the ground.
Yet, there are still people who believe that this is all a cover up. That the government caused it, allowed it, or blew up the buildings directly and all kinds of other BS. No matter what evidence you provide to these people, they will not accept it.
I’m not doing this to provide the evidence that creationists demand. It is trivial for them to look it up themselves. There are thousands, if not millions, of papers on every subject they could come up with. They might have to spend a few years learning new sciences (as I have had to) and reading dozens of peer-reviewed articles a week. Many are available on the internet for free. Both Science and Nature often run subscription specials that grant access to their entire archive of PDFed papers.
But they don’t do it. They aren’t interested in learning about the reality of the world, they are evangelizing. They are trying to convince us that science, which has provided every tool and device that they use every day, is wrong about everything. And their chosen holy book is right.
I’m not doing this for them. I’, doing this for all the people who have to put up with their crap every day. Science teachers dealing with school boards. Parents dealing with science teachers. And anyone else who needs a reference to why Stephen Meyer is a liar and a charlatan.
Stay tuned, more to come. Maybe Meyer will reference a paper or make a claim that is current.
 I’ll also note that creationists (including the amateur ones) are experts at purposefully using terms ambiguously in order to promote their ideas.
 Darwin’s Doubt pg 259