He is starting with responses to the reviews by

Jerry Coyne (professor of evolutionary biology at the University of Chicago);

Sean Carroll (professor of developmental biology, University of Wisconsin); and

Michael Ruse (professor of philosophy at Florida State University).

After several other expected major reviews are published in the coming month, he plans to post a comprehensive response.

The blog also includes an early post that provides an interview style series of "Question & Answer With Michael J. Behe".

JAM: I'm talking about the nested hierarchy based on really, really basic identities and differences, such as whether your blastopore ends up as your mouth or your anus.

Holy Deuterostome!

But a very pertinent point.

eric: Let's assume there is no problem with anything regarding evolution since the origin of the phyla.

I assume you mean the Cambrian Explosion. So we now accept that the Theory of Evolution reasonably explains the history of life over the past half a billion years. Um, except that many phyla are known to have predecessors in the Precambrian, and some phyla didn't evolve until well after that time.

eric: When we look at the fossil record regarding the greatest challenge, we observe that the connections between the phyla are imaginary points and lines added despite the absence of actual fossil findings to support those assumed connections.

There is considerable evidence of the evolution of many phyla. But I'm not sure we would expect to find many fossils for some of the transitions.

More basically, you don't understand how a nested hierarchy is constructed. No matter how many fossils or genomes we collect, they will always just represent points on the phylogenetic tree. But by comparing a wide variety of traits, we can show that they fit one-and-only-one nested hierarchy. And this nested hierarchy applies to everything from genomes to fossils across time.

eric: If we remove the imaginary connections, the actual data does not describe a tree. Instead, it describes a series of parallel lines that is more like a forest than a tree, e.g. like this.

That assertion is not supported by the data. At least back to the origin of the Domains, the phylogenetic tree is reasonably well-supported, and before that, horizontal evolution"”certainly not parallel lines, perhaps even a tangle.

eric: There are at least two possibilities.

I can think of at least a third. That you are not aware of the actual data, and you have already decided what is in the Gap.

eric: IOW, why should option #2 be excluded as a valid scientific hypothesis, especially since we are now beginning to be capable of planting life on other planets ourselves.

You have already admitted that evolutionary processes explain the diversity of life over the last half a billion years, with powerful evolutionary forces leading to everything from fish evolving into birds and primitive plants evolving into roses. There is substantial evidence in phylogeny that the various phyla originated from a small number of domains, and considerable evidence of somewhat different evolutionary mechanisms to explain the origin of the domains.

Sure, maybe someone planted a monolith a billion years ago. But there is no particular reason to posit different mechanisms when the ones we know about seem sufficient to the job, and the Gap is somewhat expected considering the distance of time and the state of our empirical methods. In any case, nothing known today indicates anything other than natural evolutionary processes.

eric: Rokas and Carroll refered to a study that "omitted 35% of single genes from their data matrix because those genes produced phylogenies at odds with the conventional wisdom".

Rokas and Carroll support the Theory of Common Descent: They just think it is going to be hard to discern the exact order of divergence from the available evidence.

Wolf et al. excluded some of the data because they considered them obvious artifacts from automatically produced alignments, compositional bias of the sequences, or misidentification of orthologs. As we are on the leading edge of the technology, there are going to be anomalies.

eric: Regarding the latter, it is cherry picking to display the cases and the intermediate stages where embryos are most similar, and to disregard the earlier stages and/or other cases where they are more dissimilar.

Scientists are not ignoring the data. I suspect the reason you know about embryos (and the developmental hourglass) is because of evolutionary biologists.

eric: Evidence of common descent within any phylum is irrelevant because that is not being questioned here.

So mice and men and birds and toads share a common ancestor and they diverged through evolutionary processes over millions of years.

eric: Why shouldn't option #2 be permitted and recognized as a valid scientific hypothesis?

Go for it. Frame your idea as a valid hypothesis. Make the observations. Let us know what you find.

Eric:To JAM, Most of your response seems to be assuming that I was arguing against evolution or common descent since the time of the origin of the original body plans/frameworks.

I made no such assumption. Nice try, though!

If you look at some of my other connected posts, you will find that I am exploring the implications of accepting the nested hierarchy…

If you're looking at those implications, you can't ignore the sequence evidence and you can't pretend that we're only looking at similarities.

… and following it back to the various original body plans/frameworks (i.e. to the origin of the phyla).

Consequently, I was not exclusively considering fossil evidence.

Yet that's all you go on about below. Let's look at the sequence evidence surrounding the origin of the phyla and see if there are troubling discontinuities.

If we accept the pattern of the nested hierarchy, keeping in mind the "process of diminishing morphological plasticity as evolution proceeds from higher to lower taxa" discussed by researcher Kazuo Kawano, that presents the problem of how the original frameworks/body plans were established.

Not if we look at the sequence evidence. Does Kawano do that, or is he a dinosaur?

When we look at the fossil record regarding the greatest challenge,…

And why are you trying to claim that you aren't limiting yourself to fossils?

… we observe that the connections between the phyla are imaginary points and lines added despite the absence of actual fossil findings to support those assumed connections. Examples here and here.

That's the fossil evidence! What do we get from the sequence evidence?

If we remove the imaginary connections, the actual data does not describe a tree.

But the sequence evidence does describe a tree. Why aren't you looking at all the evidence?

There are at least two possibilities.

1. The absence of those intermediate connecting fossils…

Fossils again! I'm beginning to think that you are afraid to look at any other evidence.

2. We find no fossils connecting those lines because there were no such intermediates on Earth to leave any such fossils.

What do we find when we look at sequences? Your whole game is fossils, Eric!

NOTE:
The question I am posing is not "Does this prove "¦?"
It's not even "Are you convinced / persuaded that "¦?"
I am specifically asking this:
I am asking on what basis the possibility of intelligent agency is excluded as a permissible scientific hypothesis.

Because it's not consistent with the data. That's why Behe had to misrepresent the data, perfectly deliberately, to derive a low probability.

You accused Meyer of cherry picking, yet there is certainly cherry picking going on with both the molecular studies of descent and with similarities of embryos.

Is it the norm, Eric? And is this the best defense of Meyer you've got? A tu quoque fallacy?

Regarding the former, to give one indication, Rokas and Caroll refered to a study that "omitted 35% of single genes from their data matrix because those genes produced phylogenies at odds with the conventional wisdom".

If you're going to use the plural "studies," you're gonna have to come up with more than one case. Why not just admit that you don't want to look at the evidence? I'm not talking about individual studies–I'm talking about analysis of the evidence itself that you can do yourself on the Web.

Some despair that adding additional data will never yield a consistent phylogeny.

I don't know anyone who does. Virtually all the additional data make the phylogenies more, not less, consistent.

But the beauty of this is that you can engage with the sequence evidence all by yourself.

Regarding the latter, it is cherry picking to display the cases and the intermediate stages where embryos are most similar, and to disregard the earlier stages and/or other cases where they are more dissimilar.

Straw man, Eric. I'm not talking about mere similarity. I'm talking about the nested hierarchy based on really, really basic identities and differences, such as whether your blastopore ends up as your mouth or your anus. Do you realize that you are very predictable, and every predictable response you give only betrays your unfamiliarity with actual evidence?

According to expectations based on evolutionary theory, the earliest stages are supposed to be the most similar. But they are not.

No, according to embryology and basic biophysics, there are plenty of ways to deform a basic ball of cells that don't disrupt gastrulation. Try studying some real embryology instead of parroting creationist arguments.

Nevertheless, for the sake of the question at hand, I am requesting that we pretend and assume that there are no problems at all with any of these issues. They are irrelevant to the question I am asking.

They are highly relevant.

Evidence of common descent within any phylum is irrelevant because that is not being questioned here. It is being assumed. [And BTW, Meyer's paper was focused on the origin of information needed for the origin of the higher taxonomic categories, so there is no mystery why issues about subsequent evolution would be irrelevant to his paper.]

I'm not talking about subsequent evolution. I'm talking about the easily-examined evidence that makes fossil gaps irrelevant in understanding the origins of phyla.

Evidence of similarities between phyla is also irrelevant since both options #1 and #2 above allow for such similarities.

Eric, it's a standard creationist dodge to pretend that nested hierarchies represent nothing more than similarities.

Did you notice that you changed the question?
I didn't ask "Would you consider the fossil evidence persuasive?"

I know. But obviously, you are unwilling or afraid to look at all the other relevant evidence.

I essentially asked, "What if option #2 is correct? What would that imply?" It is a very different kind of question "” one designed to explore implications.

It's a silly question. The scientific question is, "What would that predict?" The answer is that it would make clear predictions about the nested hierarchy breaking down when we look at the sequence evidence.

Again, no quotes or studies are needed–you can look for yourself.

Given all the similarities you allude to,…

I'm not alluding to mere similarities. I'm alluding to nested hierarchies.

Which brings us back to the question I'm asking:
Why shouldn't option #2 be permitted and recognized as a valid scientific hypothesis?

Because it's not consistent with all the data. We can use sequence data to go back to the first common ancestor of all the eukaryotic phyla, for example. We can use structural data, too. Have you ever looked at any?

One reasonable place to consider for the front-loading of design is at the origin of the phyla, i.e. the basic body plans/frameworks. From there, descent (meaning literally a process that is predominantly downhill) could proceed according to the nested hierarchy.

The first question is: Is this a legitimate reason to exclude consideration of this possibility (as was done regarding Meyer's paper)?

Zachriel: Still arguing Gaps. …

Are you wanting to claim that science should not study discontinuities? Or that discontinuities that are from long ago should be ignored? Or that science should be obligated to deny that an apparent discontinuity could be an actual discontinuity?

If you have contributions concerning the question I'm actually asking, please share them.

Zachriel: … We don't expect every organism to fossilize, especially those without hard body parts.

That excuse is not holding up as an adequate explanation, as Meyer points out. Nevertheless, that is not the question at hand.

Zachriel: However, despite what you claim, the nested hierarchy is strongly supported by the evidence (as it applies to most taxa). …

Why do you suppose that I am arguing against the nested hierarchy?

Zachriel: I just want to be clear. You do reject common descent, or you wouldn't object to 'evolutionists drawing their common descent diagrams' (which are normally done through statistical analysis by computer of a large number of traits, by the way).

That is an incorrect understanding of what I am saying. I'm taking as an assumption all descent since the origin of the phyla according to the nested hierarchy exactly as described by the evolutionist researcher Kazuo Kawano.

For your other questions, see also my preceding response to JAM.

If you look at some of my other connected posts, you will find that I am exploring the implications of accepting the nested hierarchy and following it back to the various original body plans/frameworks (i.e. to the origin of the phyla).

Consequently, I was not exclusively considering fossil evidence. I wasn't even questioning fossil gap issues since the origin of the phyla. Let's assume there is no problem with anything regarding evolution since the origin of the phyla.

If we accept the pattern of the nested hierarchy, keeping in mind the "process of diminishing morphological plasticity as evolution proceeds from higher to lower taxa" discussed by researcher Kazuo Kawano, that presents the problem of how the original frameworks/body plans were established.

"To understand how these frameworks [basic types] were established is the greatest challenge to evolutionary biology" (p. 51).

When we look at the fossil record regarding the greatest challenge, we observe that the connections between the phyla are imaginary points and lines added despite the absence of actual fossil findings to support those assumed connections. Examples here and here.

If we remove the imaginary connections, the actual data does not describe a tree. Instead, it describes a series of parallel lines that is more like a forest than a tree, e.g. like this.

There are at least two possibilities.

1. The absence of those intermediate connecting fossils at the origin of the phyla is an illusion. Those intermediates were present, but not fossilized or not yet found.

2. We find no fossils connecting those lines because there were no such intermediates on Earth to leave any such fossils. (Whether they share some common descent origin somewhere else is not even excluded. The question is strictly about their history on Earth. What is the best explanation of their presence here?)

NOTE:
The question I am posing is not "Does this prove …?"
It's not even "Are you convinced / persuaded that …?"
I am specifically asking this:

I am asking on what basis the possibility of intelligent agency is excluded as a permissible scientific hypothesis.

IOW, why should option #2 be excluded as a valid scientific hypothesis, especially since we are now beginning to be capable of planting life on other planets ourselves.

If you have some thoughts on that question, I hope you'll share them.

For the record and since you asked, here are some answers to other questions you raised.

eric: The obvious distinguishing prediction is that we should find a genuine discontinuity in the fossil record at the introduction of the basic frameworks / body plans for life.

JAM: The more important distinguishing prediction is that we should find genuine discontinuities in evidence other than fossils. Do we find that in, say, the sequence evidence? The embryological evidence?
…
JAM: Great! Let's discuss the sequence evidence in that context. Does Meyer cite any discontinuities in the sequence evidence?

You accused Meyer of cherry picking, yet there is certainly cherry picking going on with both the molecular studies of descent and with similarities of embryos.

Regarding the former, to give one indication, Rokas and Caroll refered to a study that "omitted 35% of single genes from their data matrix because those genes produced phylogenies at odds with the conventional wisdom". Some despair that adding additional data will never yield a consistent phylogeny.

Regarding the latter, it is cherry picking to display the cases and the intermediate stages where embryos are most similar, and to disregard the earlier stages and/or other cases where they are more dissimilar. According to expectations based on evolutionary theory, the earliest stages are supposed to be the most similar. But they are not.

Nevertheless, for the sake of the question at hand, I am requesting that we pretend and assume that there are no problems at all with any of these issues. They are irrelevant to the question I am asking.

Evidence of common descent within any phylum is irrelevant because that is not being questioned here. It is being assumed. [And BTW, Meyer's paper was focused on the origin of information needed for the origin of the higher taxonomic categories, so there is no mystery why issues about subsequent evolution would be irrelevant to his paper.]

Evidence of similarities between phyla is also irrelevant since both options #1 and #2 above allow for such similarities.

eric: What if the absence of fossils connecting the phyla is because there were no connections between the phyla by undirected common descent on Earth? What would that imply?

JAM: It wouldn't imply anything. I'd look at the other evidence, because all the common descent predictions apply to all the evidence, not just fossils.

Did you notice that you changed the question? I didn't ask "Would you consider the fossil evidence persuasive?" I essentially asked, "What if option #2 is correct? What would that imply?" It is a very different kind of question — one designed to explore implications.

I don't think many people would think that option #2 "wouldn't imply anything". Of course it would imply something. Independent phyla aren't just going to pop into existence, accidentally having the same or similar genetic codes and other similarities.

Given all the similarities you allude to, I expect that most people would accept that the lack of historical connection here on Earth would imply either common / mutual descent elsewhere (with transport to here) or else common design.

Which brings us back to the question I'm asking:
Why shouldn't option #2 be permitted and recognized as a valid scientific hypothesis?

What would happen if we believed that the fossil evidence is telling us the truth, instead of supposing that it is misleading or illusory?

But why would we only look at fossil evidence?

What if the absence of fossils connecting the phyla is because there were no connections between the phyla by undirected common descent on Earth? What would that imply?

It wouldn't imply anything. I'd look at the other evidence, because all the common descent predictions apply to all the evidence, not just fossils.

Are you not aware that there's plenty of other evidence? Zachriel laid it out very clearly:
A clear nested hierarchy is seen in nearly all biological taxa, independently supported by morphology, genomics, embryonics, fossil succession, individual structures, microbiology, biogeography. Even the exceptions, such as endogenous retroviruses, are instructive. It conceivably didn't have to be this way. But that's the way it is.

Why do you keep trying to pretend that the fossil evidence is all there is?

Yet others tell a different story, i.e. that the journal won't publish such articles again because it was not science. Many articles are found by some to be less than persuasive without being called "not science".

IMO, Meyer behaved unethically because he had already published what was in his review in a book. For most journals, authors sign a document affirming that none of the content of their manuscript has been published elsewhere.

So he manages to both be at fault for being unoriginal in quoting the results of many other scientists and also at fault for not being scientific.

He also manages to be unoriginal in having previously published most of the contents of the paper.

Why? Because he infers intelligent agency from the scientific data?

No, because he cherry-picks from the data of others without publishing any new data himself. Can you cite another article from any another field that promotes an idea counter to consensus that contains neither new data nor predictions?

3. Meyer's paper cites a variety of sources of scientific evidence debunking failed attempts to dismiss the Cambrian explosion as mere illusion.

Have you looked at the evidence he cited, and have you looked at evidence that he didn't cite?

The obvious distinguishing prediction is that we should find a genuine discontinuity in the fossil record at the introduction of the basic frameworks / body plans for life.

The more important distinguishing prediction is that we should find genuine discontinuities in evidence other than fossils. Do we find that in, say, the sequence evidence? The embryological evidence?

The chain of intermediates will not be found because they were never there. Additional evidence shows and will show that the counter explanations for the discontinuity do not hold up (cf. Meyer's paper).

Great! Let's discuss the sequence evidence in that context. Does Meyer cite any discontinuities in the sequence evidence?

eric: The obvious distinguishing prediction is that we should find a genuine discontinuity in the fossil record at the introduction of the basic frameworks / body plans for life. The chain of intermediates will not be found because they were never there.

Please take a close look at your claim. It'a a prediction that we will never find something to fill a Gap. You do realize this is a negative declaration. Maybe it just didn't leave evidence that our methods are capable of discerning. Maybe we haven't looked in the right place.

In any case, there is considerable evidence of the Precambrian evolution of a number of phyla.