Denisovans and the species problem

Could someone please explain to me what "the Denisovans seem to have made about a 5% contribution to the genome of living Melanesians" means. I know I am doing something stupid, but I don't know what. We're 98 percent the same genome as Chimps, but Melanesians got 5 percent from Denisovans. Is that 5 percent of the 2 percent that makes us different from Chimps? It is obvious to me that the 98 percent and the 5 percent can't be a percentage of the same thing, but I'd like to understand what I am missing here. Thanks in advance.
Ron

Answers in Genesis Wrote: (Indeed, given the original definition of species as referring to organisms that could interbreed successfully, treating them as separate species doesn’t make sense. However, that definition is no longer observed.)

Of course the reason for the "species problem" is that descent with modification is true. That is where species come from. That is why they are not nice neat packages the way that creationists want them to be. This is completely consistent with evolutionary theory.

It might be more appropriate to define species by genetic discontinuity, since genetic divergence is an inevitable consequence of reproductive isolation. This approach would also allow for the determination of levels of introgressive hybridization, which seems to be the case here.

Apparently, there was some interbreeding in the past of some Denisovans and some modern humans. Apparently some of these genes, which can be distinguished from the lineage they introgressed into due to the degree of genetic divergence, can still be found in some modern populations. That is where the 5% figure comes from. It doesn't have anything to do with the divergence of humans from chimps, since they last shared a common ancestor before the split of modern humans and Denisovans.

It is obvious to me that the 98 percent and the 5 percent can’t be a percentage of the same thing, but I’d like to understand what I am missing here. Thanks in advance. Ron

Ron Bear said: Could someone please explain to me what "the Denisovans seem to have made about a 5% contribution to the genome of living Melanesians" means. I know I am doing something stupid, but I don't know what. We're 98 percent the same genome as Chimps, but Melanesians got 5 percent from Denisovans. Is that 5 percent of the 2 percent that makes us different from Chimps? It is obvious to me that the 98 percent and the 5 percent can't be a percentage of the same thing, but I'd like to understand what I am missing here. Thanks in advance. Ron

We teach the various definitions of a species in our 100-level Bio course. I always thought that the viable-offspring definition was the consensus view since its the least arbitrary but then Neanderthals wouldnt be a separate species.
I suspect that any other 2 organisms separated by the equivalent time/genetic distance/morphology would be considered the same species and its just our human bias that splits them into another species

Thanks for explaining. So Denisovans contributed roughly .05 percent of the entire genome of Melanesians. That makes it so that the math squares up on my original question. Also it makes sense to me that if someone is trying to determine how I am related to you or how either of us is related to a Denisovan, it wouldn't make sense to look at the entire genomes. It makes sense to look at the differences between the genomes.
Thanks,
Ron

RodWl said: I always thought that the viable-offspring definition was the consensus view since its the least arbitrary but then Neanderthals wouldnt be a separate species.

I suspect that any other 2 organisms separated by the equivalent time/genetic distance/morphology would be considered the same species and its just our human bias that splits them into another species

I've talked with my local open air creationist preacher about the new finding about Denisovan (we have weekly coffee then screaming matches). After we got through all the BS about dating methods and sequencing his argument position was that of Magic Man done it.
To quote: "If the fossils seem old it's because god made them seem that way. If the DNA seems like it was sequenced it's because god made it seem that way, not because it actually is that way".
That's right. God, the great deceiver.

Your open air creationist is indulging in what has been called the "deceptive God blasphemy".

There is a good bit of species criteria discussion on the "Why Evolution is True" blog, centered on how many elephant species. I've studied interspecies hybridization some, and have just been reading a manuscript about why two sister species hybridize here, but not there, and what it all means. I suspect the large majority of sexually reproducing biparental animal species are well isolated genetically out in nature. Instances of interspecies hybridization are, I think, relatively rare and therefore interesting as a situation which tests the theory of species being genetically isolated.

Cautiously, and commendably IMO, the scientists declined to classify the Denisovans taxonomically, given that we know almost nothing about their anatomy.

This is basic Creation Science! There were giants in the earth in those days; and also after that, when the sons of God came in to the daughters of men, and they bore children to them, the same became mighty men which were of old, men of renown.

Twelve thousand years old. But I actually asked this guy, "OK, dinosaur fossils-- how does that fit into your scheme of life? What's the deal?" He goes: --"God put those here to test our faith."
--"I think God put you here to test my faith, dude. I think I've figured this out."
Does that-- That's what this guy said. Does that bother anyone here? The idea that God might be @#$%ing with our heads? Anyone have trouble sleeping restfully with that thought in their head? God's running around burying fossils: "Ho ho! We'll see who believes in me now, ha ha! I'm a prankster God. I am killing me, ho ho ho!"
You know? You die, you go to St. Peter:
"Did you believe in dinosaurs?"
"Well, yeah. There were fossils everywhere. (trapdoor opens)
Aaaaarhhh!"
"You #$@@$#in' idiot! Flying lizards? You're a moron. God was %$#%#in' with you!"
"It seemed so plausible, aaaaaahh!"
"Enjoy the lake of fire, @#$@er!"

You don't see the "test our faith" trope very often these days, probably because of the obvious theological problems. Then again, the story of Abraham and Isaac would seem to argue in favor of such a god. Not to mention that in the Eden story, the snake was telling the truth and god was lying about the tree.

JF: Human genes differ from each other by about 0.1%

http://www.sciencedaily.com/releases/2007/09/070904072204.htm. (from 2007) While the SNP events outnumbered the non-SNP variants, the latter class involved a larger portion (74%) of the variable component of Dr. Venter's genome. This data suggests that human-to-human variation is much greater than the 0.1% difference found in earlier genome sequencing projects. The new estimate based on this data is that genomes between individuals have at least 0.5% total genetic variation (or are 99.5% similar) The researchers suggest that much more research needs to be done on these non-SNP variants to better understand their role in individual genomics.

genome.gov: Genetic Variation Program Overview Most of any one person's DNA, about 99.5 percent, is exactly the same as any unrelated person's DNA. Differences in the sequence of DNA among individuals are called genetic variation.

Raven, not that I doubt you, but can you give a citation for that estimate, and does it use the same index of similarity as the human-chimp figure of 1.3%, based on site differences in aligned sequences?

Raven, not that I doubt you, but can you give a citation for that estimate, and does it use the same index of similarity as the human-chimp figure of 1.3%, based on site differences in aligned sequences?

I'm not a practicing Biologist, so I can safely say that I don't think species exist. Within a genera (or possibly a larger group, thanks John), it's just a continum.

Humans like to be able to put things into neat boxes, but clines just don't allow organisms to fit into neat little boxes. They have to be really big boxes, and then what's the point of putting them into boxes.

Jim Thomerson said: Your open air creationist is indulging in what has been called the "deceptive God blasphemy". There is a good bit of species criteria discussion on the "Why Evolution is True" blog, centered on how many elephant species. I've studied interspecies hybridization some, and have just been reading a manuscript about why two sister species hybridize here, but not there, and what it all means. I suspect the large majority of sexually reproducing biparental animal species are well isolated genetically out in nature. Instances of interspecies hybridization are, I think, relatively rare and therefore interesting as a situation which tests the theory of species being genetically isolated.

Excuse me for the shameless self-promotion. But I think the evidence that modern humans population derrive genes from Neanderthal and Denisnovans is a really good way to edge into the species problem.

As others have said, the difficulty we find in drawing a bright white line between species is actually a prediction of descent with modification and something of a problem for creationists who want to separate our species from the rest of creation.

david winter said: As others have said, the difficulty we find in drawing a bright white line between species is actually a prediction of descent with modification and something of a problem for creationists who want to separate our species from the rest of creation.

OgreMK5, I'm a retired fish alpha taxonomist. I spent my career identifying fish species and considering their relationships at the generic and family levels. This includes describing new species and genera, and producing keys for species identification. My experience does not support your idea that species ordinarily form continua.

Mike Elzinga said: I guess ID/creationists just have to accept the fact that bread dough can’t turn into bread and cake batter can’t turn into a cake.

I am not a biologist so I can give you no insight into what a species is. But why do you want to introduce a term for a quality that you cannot define? Compare it with the concept of aether, we did away with this, once we understood what was actually happening, without any pain.

We have known what was actually happening in biology for even longer. Darwin drew his 'I think' tree and we have never looked back.

If we could zoom in on the tree so as to see individual creatures, we would find that each twig consisted of myriads of little lives which intersect and branch while remaining part of the twig. Sometimes the twig will bifurcate and the two parts go their separate ways. Highly magnified, it may not be possible to tell exactly where the separation occurred or where it became irrevocable (where no lives are able to cross from one to another or, if they do, fail to produce fertile offspring).

Knowing what we do, is it sensible to try to cut some slice out of a branch of the tree and say that this is a particular 'species'?

mrg said:

Mike Elzinga said: I guess ID/creationists just have to accept the fact that bread dough can’t turn into bread and cake batter can’t turn into a cake.

Oh, but those are the product of an Intelligent Baker.

Alan Barnard said: Knowing what we do, is it sensible to try to cut some slice out of a branch of the tree and say that this is a particular 'species'?

Mike Elzinga said:

mrg said:

Mike Elzinga said: I guess ID/creationists just have to accept the fact that bread dough can’t turn into bread and cake batter can’t turn into a cake.

Oh, but those are the product of an Intelligent Baker.

Not when I do it. :-)

mrg said:

Mike Elzinga said:

mrg said:

Mike Elzinga said: I guess ID/creationists just have to accept the fact that bread dough can’t turn into bread and cake batter can’t turn into a cake.

Oh, but those are the product of an Intelligent Baker.

Not when I do it. :-)

I can sympathize. When we get to a certain age, it's difficult to make things rise any more.

Mike Elzinga said: Ah; Viagara instead of yeast in the bread dough! I hadn’t thought of that.

Jim Thomerson said: OgreMK5, I'm a retired fish alpha taxonomist. I spent my career identifying fish species and considering their relationships at the generic and family levels. This includes describing new species and genera, and producing keys for species identification. My experience does not support your idea that species ordinarily form continua.

mrg said:

Mike Elzinga said: Ah; Viagara instead of yeast in the bread dough! I hadn’t thought of that.

I was thinking of several rejoinders to that, but they tend to accelerate the descent of the conversation rapidly.

http://books.google.com/books?id=sltlCl1XgJwC&printsec=frontcover&dq=Belize+Thomerson&source=bl&ots=3KDj5NqlCN&sig=r6gcD3Eg6WWZuxUTMQNqylaF0Fk&hl=en&ei=ZBc6TeqEJcO78gakufiPCg&sa=X&oi=book_result&ct=result&resnum=1&ved=0CBMQ6AEwAA#v=onepage&q&f=false

We identified 15 species of cichlids from Belize. We identified Petenia splendia, and left the other 14 species in Cichlasoma, knowing that revisions of the new world cichlids were underway, and probably most or all of them are no longer in Cichlasoma. C. maculacauda occurs in southern Belize, and the very similar C. synspilum in northern Belize. I suspect additional collections in central Belize might uncover a cline, but we did not have specimens to support anything more than vague suspicions.

Mike Elzinga said: Yeah; to say nothing of the irony of having it all ending up on the Bathroom Wall.

OgreMkV said: I'm not a practicing Biologist, so I can safely say that I don't think species exist. Within a genera (or possibly a larger group, thanks John), it's just a continum. Humans like to be able to put things into neat boxes, but clines just don't allow organisms to fit into neat little boxes. They have to be really big boxes, and then what's the point of putting them into boxes.

Alan Barnard said: Knowing what we do, is it sensible to try to cut some slice out of a branch of the tree and say that this is a particular 'species'?

John Harshman said: No, genera aren't continua. Diversity is clumped, and there are few smooth clines between populations. (There are some.)

Firstly, why, if species have descended from other species by insensibly fine gradations, do we not everywhere see innumerable transitional forms? Why is not all nature in confusion instead of the species being, as we see them, well defined?

As luck would have it had introduced the species problem and such to my biology class in early December starting with a collection of human skull images that have been typed by race. I ask the students to naively classify what they see into species groups. After they come up with their ideas and debate a bit I reveal my chicanery, and then present them with a randomized image of the hominid skulls from the Smithsonian. It forces them to confront the phenotypic similarity in a rather visceral way. Fast forward a few weeks and they had read and discussed the Chris Stringer lecture from the Talk Origins archive, and discussed the relative humanity of Neanderthals right before winter break. I was then able to discuss after break the serious implications for the Neanderthal and Denisovan DNA sequencing. I felt that those sequences were much better at reinforcing the application of the species problem to humans, rather than as an introduction, which was suggested above.

raven said: AFAIK, the human human and human chimpanzee differences use the same type of sequence analysis.

20th century biologist me has been thinking about the Phylogenetic Species Concept. Is this a reasonable statement of the concept? A species originates at a speciation event and exists through time until it becomes extinct. This adds a time, historical, dimension to the the species which we don't see when we look at species, as we do, in a little slice of time. So what we see, in the moment, is a Biological Concept Species or whatever. I have the feeling I am missing something here.

Identifying the exact point at which a species branches off from another is a bit like identifying the precise boundary between a tree branch and the tree trunk (or its parent branch).

Henry

I am not sure this helps, but I heard this once on Canadian TV and it sticks with me because it helped drive it home. I also wonder what you guys here think of this:

Lets imagine we are standing face to face with a modern chimpanzee. We hold that hand of our mother and her other hand is holding the hand of her mother. So on it goes down the generations. Opposite us the chimp is doing the same. With an average separation of 1 meter (just over a yard for you non metric types) a line would stretch from Windsor (Canadian side of the boarder from Detroit) down the line until at around Toronto something interesting would happen. The Chimp line and your line would be holding the opposite hands of the same mother.

If you stretch these two lines out to one continuous line, there is no point at which you can say everyone on this side is Human and everyone on that side is Chimp without breaking up a mother and child. It is only easy to identify one or the other because all the ancestors are already dead. The concept of species works really well in those situations.

But for some species such as ring species not all the intermediates are dead. Some of them have dead intermediates but the species themselves are still closely related enough that they could interbreed, even if poorly. There are all sorts of variations in between.

I hope that makes it clear or at the vary least is a new way to look at it. I understood this stuff before I heard this but it changed the way I saw species anyways.

I hope it wasn't boringly basic for many of you either :)

Jim Thomerson said: 20th century biologist me has been thinking about the Phylogenetic Species Concept. Is this a reasonable statement of the concept? A species originates at a speciation event and exists through time until it becomes extinct.

What's the problem?
AIG is right on.
They are simply from migration from Babel.
I would add that this all once again demands presumptions about genetics.
The Asian type would be a adaptation that happened after leaving the rest of mankind. so it follows the earliest remains would show likeness to other peoples that remained rather pure upon settlement. I mean New Guinea folk have been there from the beginning, and without much later people joining them, and so their genetics would be least changed from the original. The Asian in between simply from adaptation needs or interbreeding changed more in genetics.
These remains are simply early Asians before genetic variety. They are not directly related to New Guineas but the same original people expanding everywhere.
Creationism can always give a better answer because its based on better foundations.

Robert Byers said:[SNIP]

Henry J said: Identifying the exact point at which a species branches off from another is a bit like identifying the precise boundary between a tree branch and the tree trunk (or its parent branch). Henry

Robert Byers said: What's the problem? AIG is right on. They are simply from migration from Babel. I would add that this all once again demands presumptions about genetics. The Asian type would be a adaptation that happened after leaving the rest of mankind. so it follows the earliest remains would show likeness to other peoples that remained rather pure upon settlement. [etc., etc., etc.]

Henry J said: Still, genetic divergence seems to be the best way to decide these issues. It allows for the determination of reproductive isolation, time of divergence and even introgressive hybridization. It might still be somewhat arbitrary, but at least it is a real measure of something important.

DS said: Exactly. The distinction will always be a somewhat arbitrary point along a continuum. But it's even worse than that, because sometimes parts can swap after the branch point, maybe even long after the branch point.

The concept of species is useful but also problematic, not least of all because a clear cut definition is elusive http://en.wikipedia.org/wiki/Species_problem.

I'll put aside the difficulty of applying the concept to prokaryotes (which are a massive part of the biosphere). Even in diploid/polyploid eukaryotes capable of meiosis, the concept is tricky.

At the current time, it is the human practice to subdivide the biosphere very finely into species.

This is tricky for a number of reasons.

First of all, many species have remarkably different free-living morphology at various times during development. Biologists aren't likely to be fooled by that any more but it was a problem historically.

Second of all, we define species very finely, and on the basis of behavior and morphology. We then run into the problem that some species, as we define them, interbreed with other species.

The biasing factor is that the implied definition of species is "any biological population that is sufficiently unique in some aspect of interest to humans to give it a separate name".

Also - as I noted back in the Neanderthal threads, any interbreeding between humans and other "hominid species" has strong implications. A low percentage of "Neanderthal genes" could mean limited interbreeding between populations of equal size - or it could mean complete assimilation of a much smaller Neanderthal population into a much larger H. sapiens population. Or it could mean something in between.

I know the idea that a population with a single unique characteristic is seen as a species as the "Autapomorphic Species Concept". I don't think it is the same as the "Phylogenetic Species Concept", but maybe it is.

When I first studied what is now known as Gnatolebias zonatus and G. hoignei, the question was whether they were ecophenotypes of a variable species; the former in savanna pools and the latter in forest pools. At that time they had not been taken together. I found a consistent difference of in one of the fin ray counts, which made me think they were two species (Autapomorphy, I suppose). I did hybridization experiments and they wouldn't even try under conditions where both would spawn on a daily basis. So I described G. hoignei as new. Later we found their chromosomes were so different that production a a viable hybrid was unlikely, and their breeding behavior in nature was quite different. We also found them coexisting in an area cleared for agriculture, for at least several years, with no sign of interbreeding. DNA analysis has them as sister species.

stevaroni said:

DS said: Exactly. The distinction will always be a somewhat arbitrary point along a continuum. But it's even worse than that, because sometimes parts can swap after the branch point, maybe even long after the branch point.

Branches can also be forced to grow back together by the application of outside forces

Leszek said: Lets imagine we are standing face to face with a modern chimpanzee. We hold that hand of our mother and her other hand is holding the hand of her mother. So on it goes down the generations. Opposite us the chimp is doing the same. With an average separation of 1 meter (just over a yard for you non metric types) a line would stretch from Windsor (Canadian side of the boarder from Detroit) down the line until at around Toronto something interesting would happen. The Chimp line and your line would be holding the opposite hands of the same mother. If you stretch these two lines out to one continuous line, there is no point at which you can say everyone on this side is Human and everyone on that side is Chimp without breaking up a mother and child. It is only easy to identify one or the other because all the ancestors are already dead. The concept of species works really well in those situations.

It’s an old question in biology: what is a species? Many answers have been given over the years – I counted 26 in play, and recently a new one, the “polyphasic” concept (basically a consilience of many lines of evidence) has been introduced in bacterial and other microbial contexts, and which may apply to macrobial species too.

RBH said: Or as the man said, I can't say exactly when day ends and night begins, but I sure as hell can tell the difference between them. :)

"Though no man can draw a stroke between the confines of night and day, yet light and darkness are upon the whole tolerably distinguishable." -- Edmund Burke

Here is a scenario for you. A population of the species which is the last common ancestor of humans and chimps undergoes some sort of event which separates it into two allopatic populations. After a while, due to genetic drift, differential selection pressures, whatever, a speciation event has occurred. Now there are two species, one the first common ancestor of humans, and the other, the first common ancestor of chimps. The last common ancestor of humans and chimps is now extinct. That's my story and I'm stickin' to it.

A snippet of conversation

Guy who is annoyed by creationism, "How did all the animals fit on the ark?"

Student at Liberty Baptist, seriously: They didn't have to take each variety, not a pair of polar bears, brown bears, grizzly pairs, black bears. Just one pair of bears was enough."

I regret to say I don't know what the explanation for how all the different kinds of bears reappeared.

Neanderthal & Denisovan contributions to some humans' genomes are ~5% despite a long breeding interval after they became extinct. Assuming the interbreeding occurred in stable mating pairs, this suggests that Neanderthals & Denisovans could talk. Or that modern humans could not, at the time of interbreeding.

I suggest that human societies would disfavor matings with beings that can't talk. Tribal support is evolutionary significant, and talking is distinctly useful as well.

veritas36 said: I regret to say I don't know what the explanation for how all the different kinds of bears reappeared.

Are the iron and oxygen in FeO, Fe₃O₄, and Fe₂O₃ “different species” of iron and oxygen?

The crystalline structures of bulk quantities of these compounds are different. Are these different species?

Does that mean that the crystals have different gene pools?

What happens when one form evolves into another given the appropriate environment? Is that natural selection producing different species?

How about the many forms of even a single atom carbon? There is graphite, diamond, fullerenes, graphene, etc.. Between the carbon and its many collective forms, which are the “genes” and which are the “species?”

What about the icicles hanging from eaves? As the days go by, they come and go and branch. Where is the common ancestor of two different icicles? Where in a bifurcation do two icicles become different icicles?

Start with any huge collections of atoms and molecules all doing their thing in whatever environment is current. If some of these collections start going off in a different direction than others, how is that any different from the issues involved in speciation?

The only thing we can say they are different when there are enough accumulated differences to allow us to distinguish within a given resolution.

Tiny differences in patterns can be perceived by rapidly switching back and forth between them; otherwise they are indistinguishable.

This entire discussion over speciation is only a problem because of the historical tradition of classifying and cataloguing things that were clearly different (at least in appearance). As technology gets better, so does the resolution; but below that resolution, we can’t distinguish.

John Harshman said:

Jim Thomerson said: 20th century biologist me has been thinking about the Phylogenetic Species Concept.

No, that's not the phylogenetic species concept. I'm not sure it has a name. Perhaps the lineage species concept? way to think about it.

mrg said:

veritas36 said: I regret to say I don't know what the explanation for how all the different kinds of bears reappeared.

That's where "created kinds" comes into play. All the Ark had to do was carry one pair of each "kind". On recovery, they went through a phase of hyperevolution (yes, creobots will embrace evolution, if only for as long as it takes them to get out of a tight spot). I regret to say that I DO know the explanation. Fortunately, I can generally keep suchlike segregated on the exterior side of my baloney filter.

Mike Elzinga said: I wonder how many different species of religion they would say there were.

veritas36 quoted: Student at Liberty Baptist, seriously: "They didn't have to take each variety (on Noah's Ark), not a pair of polar bears, brown bears, grizzly pairs, black bears. Just one pair of bears was enough."

Jim Thomerson said: Here is a scenario for you. A population of the species which is the last common ancestor of humans and chimps undergoes some sort of event which separates it into two allopatic populations. After a while, due to genetic drift, differential selection pressures, whatever, a speciation event has occurred. Now there are two species, one the first common ancestor of humans, and the other, the first common ancestor of chimps. The last common ancestor of humans and chimps is now extinct. That's my story and I'm stickin' to it.

Mike Elzinga said: Are the iron and oxygen in FeO, Fe₃O₄, and Fe₂O₃ “different species” of iron and oxygen?

But why do you want to introduce a term for a quality that you cannot define?

Les Lane said:

But why do you want to introduce a term for a quality that you cannot define?

The term "species" is an historical relic of the time when species were defined by morphology and believed to be separate and distinct.

John Harshman said:

Mike Elzinga said: Are the iron and oxygen in FeO, Fe₃O₄, and Fe₂O₃ “different species” of iron and oxygen?

Well, the irons are. That is in fact what chemists call them. But it may not surprise you to learn that the same word can have different meanings in different contexts. I'm not sure of the relevance of bringing non-organisms into it. But "species" does have a real meaning in biology. I don't see a reason to dispense with it

Most species known today are defined on morphology and are thought to be separate and distinct. It's a grand tradition.

Jim Thomerson said: Most species known today are defined on morphology and are thought to be separate and distinct. It's a grand tradition.

Exactly. If you can’t define species, that’s a problem for creationism, not evolution.

Ron Bear said: Could someone please explain to me what "the Denisovans seem to have made about a 5% contribution to the genome of living Melanesians" means. I know I am doing something stupid, but I don't know what. We're 98 percent the same genome as Chimps, but Melanesians got 5 percent from Denisovans. Is that 5 percent of the 2 percent that makes us different from Chimps? It is obvious to me that the 98 percent and the 5 percent can't be a percentage of the same thing, but I'd like to understand what I am missing here. Thanks in advance. Ron

Jeremiah Tattersall said: I've talked with my local open air creationist preacher about the new finding about Denisovan (we have weekly coffee then screaming matches). After we got through all the BS about dating methods and sequencing his argument position was that of Magic Man done it. To quote: "If the fossils seem old it's because god made them seem that way. If the DNA seems like it was sequenced it's because god made it seem that way, not because it actually is that way". That's right. God, the great deceiver.

Hygaboo Andersen said:

Ron Bear said: Could someone please explain to me what "the Denisovans seem to have made about a 5% contribution to the genome of living Melanesians" means. I know I am doing something stupid, but I don't know what. We're 98 percent the same genome as Chimps, but Melanesians got 5 percent from Denisovans. ... [and so on, adequately answered by me earlier]

What I think the evolutionists mean by this is that modern Melanesians are descendant from a combination of Denisovans and monkey while other people are descendant from only monkeys.

Robert Byers said: What's the problem? AIG is right on. They are simply from migration from Babel. I would add that this all once again demands presumptions about genetics. The Asian type would be a adaptation that happened after leaving the rest of mankind. so it follows the earliest remains would show likeness to other peoples that remained rather pure upon settlement. I mean New Guinea folk have been there from the beginning, and without much later people joining them, and so their genetics would be least changed from the original. The Asian in between simply from adaptation needs or interbreeding changed more in genetics. These remains are simply early Asians before genetic variety. They are not directly related to New Guineas but the same original people expanding everywhere. Creationism can always give a better answer because its based on better foundations.

Les Lane said:

But why do you want to introduce a term for a quality that you cannot define?

The term "species" is an historical relic of the time when species were defined by morphology and believed to be separate and distinct.

Exactly. If you can’t define species, that’s a problem for creationism, not evolution.

— DS

Hygaboo Andersen said: What I think the evolutionists mean by this is that modern Melanesians are descendant from a combination of Denisovans and monkey while other people are descendant from only monkeys.

DS said: Apparently, there was some interbreeding in the past of some Denisovans and some modern humans. Apparently some of these genes, which can be distinguished from the lineage they introgressed into due to the degree of genetic divergence, can still be found in some modern populations. That is where the 5% figure comes from. It doesn't have anything to do with the divergence of humans from chimps, since they last shared a common ancestor before the split of modern humans and Denisovans.

In a nutshell, "they're all just humans".

Looking at COPEIA, 2010 #4, I find descriptions of one new frog, and 12 new fish species. All are based on morphological differences from known species, and two also include comparison of allozyme patterns. There is an article on use of gill pore papillae morphology for identifying lamprey species, and a report of the first known natural hybridization event between largemouth and smallmouth black basses. All very interesting!

It isn't just the 8 people on the ark that you have to worry about. We will eventually have whole genome sequences (from multiple individuals) of the Denisovans and Neandertals. They will have to try to reconcile how three such distinct populations could arise from one man and one woman made from the rib of the man. There isn't much genetic diversity among these two individuals especially since they were considered to be pinnacle of creation.

There are pretty much only two options. Either a huge amount of genetic variation was packed into these two individuals and segregated out, or an equally huge amount of genetic variation is due to mutation after the fall. There could be a combination of the two, but even the amount of each that had to occur in the combination is mind boggling if you only have a couple thousand years to generate it.

The first one doesn't stand up to scrutiny because we will have whole genome sequences and there will be very little chance that enough recombination events occurred within the possible four haplotypes that existed in the first two individuals to generate the distinct lineages.

The second fails because there is too little time for the mutations to accumulate. It isn't just absurdly high mutation rates that are required, but it is likely that the Denisovan and Neandertal genomes will show evidence of as high amounts of purifying selection as is found in modern human genomes. For a coding sequence, by chance, the number of replacement substitutions (mutations that change the amino acid sequence of the encoded protein)should outnumber silent substitutions by around 2:1, but we find that the number of silent mutations outnumber the replacement substitutions by 2:1 or more. This means that a whole lot of replacement substitutions have been removed by selection. These replacements had a large enough negative effect on the population that they were selected out of the gene pool. As certain creationist have pointed out there is a cost to selection. Real science has several orders of magnitude more time for this selection to have occurred than just a couple thousand years.

There is one possible out. The Nephlim of the Bible were supposed to be the sons of the gods that had bred with humans. Since we have no god DNA to compare we can't say how different the various gods were in the DNA that they transmitted to the human stock. 5 backcrosses to any single god lineage would produce genomes over 95% of that god lineage. So you could create distinct populations in this way. We would then have to figure out if the 5% of our DNA (for those or us that are of relatively recent non African origin) came from hanky panky with a god like Baal or his Neandertal offspring before we migrated out of the middle east, and took over the rest of the world after the flood. Apollo or Thor could have left their mark on the New Guineans during a tropical vacation.

Maybe the Neandertals or the Denisovans were the true purely human descendants of Adam and Eve. It should be a hoot to watch the YECers try to use the sequence data to try and sort that one out.

Mike Elzinga said: I was merely pointing out that condensed matter systems, no matter what their level of complexity, can and do branch.

Ron Okimoto said: It should be a hoot to watch the YECers try to use the sequence data to try and sort that one out.

Scott F. said:

Mike Elzinga said: I was merely pointing out that condensed matter systems, no matter what their level of complexity, can and do branch.

Perhaps a concrete example of what you are describing might help. For example, looking just at a single carbon atom and its bonds, you can't tell what assemblage it belongs to. Step out one level of complexity, and you see it is part of a hexagonal ring of carbon atoms. But you still can't tell what assemblage it belongs to. Step out another level, and you see that this carbon ring is part of a sheet of interconnected carbon rings. Only at the next level out can you tell if this pattern is part of graphite or of a nano-tube.

If a person is brought up to hear and read the word of God then it is only natural that they would believe that the creation was by God. John ch 1 vs 1-3 In the beginning was the word, and the word was with God ……..then in vs 4 In him was life and the life was the light of man. It is the beginning of an explanation of the creation, Genesis ch 1 vs 1 In the beginning God created the heavens and the Earth. Genesis ch 2 vs 1-3 ……God rested from all his work which he had done in creation, then in vs 4 These are the generations of the heavens and the Earth. It doesn't go into the chemistry that is there for adventure to analyze. Jesus couldn't comment on evolution as Darwin wasn't around at that time. Jesus never implied that he was anything but the son of man through out the history of the Earth, Philippians ch 2 v 6-7….being born in the likeness of men. In Genesis ch 1 vs 26-27 Then God said let us make man in our image in our likeness.... Then Genesis ch 3 vs 22 ......the man has become like one of us.
Jesus left us with a new covenant John ch 13 vs 34 and that was to love one another, that is one of the things that not only humans can do. What direction does evolution offer or Darwin, only that the animal kingdom naturally selects, but to what end, I feel there is more to life than that. John ch 15 vs 5. There is a purpose for the branch and that is that it goes in the right direction.

M.W. said: What direction does evolution offer or Darwin, only that the animal kingdom naturally selects, but to what end, I feel there is more to life than that. John ch 15 vs 5. There is a purpose for the branch and that is that it goes in the right direction.

It conflates the probability that a particular winner has won with the probability that someone has won.

I'd just like to go OT for a moment and thank the commenters for always giving me interesting diversions. I never thought that a post about the genetic differences between different species of humans would have me reading about ducks on Wikipedia for an hour.

Paul Burnett said:

Ron Okimoto said: It should be a hoot to watch the YECers try to use the sequence data to try and sort that one out.

As if there are any YECs who could "try to use the sequence data" - 99.99+ percent of YECs don't have a clue what the term means: Genome sequencing isn't mentioned in Genesis, so it can't exist in their universe.

Flint said: And is even more suspect because the "winners" of this particular lottery got to postdict the rules that made them the winners.

M.W. said: It [the Bible] doesn't go into the chemistry that is there for adventure to analyze. Jesus couldn't comment on evolution as Darwin wasn't around at that time. Jesus never implied that he was anything but the son of man through out the history of the Earth,...

M.W. said: What direction does evolution offer or Darwin, only that the animal kingdom naturally selects, but to what end, I feel there is more to life than that.

Hmm. Species form continua if you're looking back in time but are usually discrete when taking a slice at any moment in time, just as tree branches all connect if you trace them back to the trunk but are discrete if you apply a hedge trimmer. Sometimes we see a case where branching is ongoing.

And our usual quote from Burke: "Though no man can draw a stroke between the confines of day and night, yet light and darkness are upon the whole tolerably distinguishable."

Maybe "Though no man can draw a stroke between the confines of dog and wolf, yet sharks and labradors are upon the whole tolerably distinguishable."

david winter said:

John Harshman said:

Jim Thomerson said: 20th century biologist me has been thinking about the Phylogenetic Species Concept.

No, that's not the phylogenetic species concept. I'm not sure it has a name. Perhaps the lineage species concept? way to think about it.

Either the "general lineage species concept" or the "evolutionary species concept". Part of the problem of dealing with these terms,as you pointed out, is that we want 'species' to mean the same thing when we look at modern species as we look at fossil species. It's possible that "lineage species" could go through multiple distinct morphlogical forms over time and get given different names by paleontologists over the course of its evolution

veritas36 said: I suggest that human societies would disfavor matings with beings that can't talk. Tribal support is evolutionary significant, and talking is distinctly useful as well.

M.W. said: What direction does evolution offer or Darwin, only that the animal kingdom naturally selects, but to what end, I feel there is more to life than that.

M.W. said: If a person is brought up to hear and read the word of God then it is only natural that they would believe that the creation was by God. John ch 1 vs 1-3 In the beginning was the word, and the word was with God ……..then in vs 4 In him was life and the life was the light of man. It is the beginning of an explanation of the creation, Genesis ch 1 vs 1 In the beginning God created the heavens and the Earth. Genesis ch 2 vs 1-3 ……God rested from all his work which he had done in creation, then in vs 4 These are the generations of the heavens and the Earth. It doesn't go into the chemistry that is there for adventure to analyze. Jesus couldn't comment on evolution as Darwin wasn't around at that time. Jesus never implied that he was anything but the son of man through out the history of the Earth, Philippians ch 2 v 6-7….being born in the likeness of men. In Genesis ch 1 vs 26-27 Then God said let us make man in our image in our likeness.... Then Genesis ch 3 vs 22 ......the man has become like one of us. Jesus left us with a new covenant John ch 13 vs 34 and that was to love one another, that is one of the things that not only humans can do. What direction does evolution offer or Darwin, only that the animal kingdom naturally selects, but to what end, I feel there is more to life than that. John ch 15 vs 5. There is a purpose for the branch and that is that it goes in the right direction.

Scott F said:

M.W. said: It [the Bible] doesn't go into the chemistry that is there for adventure to analyze. Jesus couldn't comment on evolution as Darwin wasn't around at that time. Jesus never implied that he was anything but the son of man through out the history of the Earth,...

Yes, but the chemistry was still there, as was evolution. Chemistry didn't magically start with Tapputi, and evolution didn't magically start with Darwin. When God created the world, he created both chemistry and evolution at the same time. If Jesus had any divine omniscience, he would have known about both.

(Indeed, given the original definition of species as referring to organisms that could interbreed successfully, treating them as separate species doesn’t make sense. However, that definition is no longer observed.)

John Kwok said: Actually the correct term would be the "chronospecies concept"

I would concur with your observation david if most lineages did indeed show "phyletic gradualism", but, on the contrary, there seems to be widespread data in support of rapidly brief divergence at the onset and long-term morphological stasis, which is what one would expect from "punctuated equilibrium".

I should mention that my BS and MS were in geology and I did a study of Cretaceous marine micro fossils for my MS thesis.

I did a little reading up on the Phylogenetic Species Concept. It is seen in different lights by different folks (Isn't that amazing?) But the theme of monophyly and uniqueness (autapomprphy) seem widespread. I don't have any problem with that.

My favorite species concept is the "Sophisticated Biological Species Concept" which is biological species as I understand it applied a particular case in the real world. However, the most widely used species concept is the morphospecies concept. The large majority of modern day animals were described as morphospecies. I described Rivulus corpulentis based on a jar of preserved fish on the shelf at the California Academy of Sciences. Clearly a morphospecies, but I am confident that should it be examined in nature, it will be found to be a biological species.

So I regard morphospecies as a stand in for biological species. And, generally, when we are able to study the situation further, do hybrid experiments, look at syntopic relatives, etc. the morphospecies turns into the biological species it represents.

I don't see a difference in kind between modern and fossil morphospecies, just a difference in how easy it is to decide if they are actually biological species.

Scott F said:

M.W. said: It [the Bible] doesn't go into the chemistry that is there for adventure to analyze. Jesus couldn't comment on evolution as Darwin wasn't around at that time. Jesus never implied that he was anything but the son of man through out the history of the Earth,...

Yes, but the chemistry was still there, as was evolution. Chemistry didn't magically start with Tapputi, and evolution didn't magically start with Darwin. When God created the world, he created both chemistry and evolution at the same time. If Jesus had any divine omniscience, he would have known about both.

John Harshman said:

John Kwok said: Actually the correct term would be the "chronospecies concept"

No, a chronospecies is an arbitrary division of a lineage. The concept being discussed was an entire branch of the tree, from speciation to extinction (and counting new speciation as extinction of the ancestor). That's quite different.

I would concur with your observation david if most lineages did indeed show "phyletic gradualism", but, on the contrary, there seems to be widespread data in support of rapidly brief divergence at the onset and long-term morphological stasis, which is what one would expect from "punctuated equilibrium".

The problem with PE is that it assumes biological species and morphospecies are the same, for which there is no evidence. All the paleontological data can show, at most, is that morphological evolution is characterized by episodes of rapid and slow change. But it can't show that the rapid episodes are coincident with speciation in the BSC sense, i.e. branching events. Or, to put it in Gouldian terms, we can't distinguish between punctuated phylogenesis and punctuated anagenesis.

John Kwok said: Sorry John, as a former paleobiologist, I respectfully beg to differ. Starting with Niles Eldredge's work on phacopid trilobites, we do see instances of branching events in the metazoan fossil record that would substantiate "speciation" events yielding to long-term morphological stasis of a given species (which I will concede that if one were to operate strictly on a biological species concept, there is no way to distinguish into a morphospecies any instances of sympatric speciation). For "punctuated anagenesis" to occur, the best examples are within the protistan fossil record, especially amongst the radiolarians and foraminifera.

And I felt that life should be fair, and was deeply troubled when I found out it isn’t - back when I was about eight.

harold said: The fact that we can perceive that a process of selection is often part of the evolution of life on earth is not a reason to think that we, or any other living beings, should find life "pointless", meaningless", etc.

Death: Humans need fantasy to *be* human. To be the place where the falling angel meets the rising ape. Susan: With tooth fairies? Hogfathers? [The Diskworld analog of Santa Claus] Death: Yes. As practice, you have to start out learning to believe the little lies. Susan: So we can believe the big ones? Death: Yes. Justice, mercy, duty. That sort of thing. Susan: They're not the same at all. Death: You think so? Then take the universe and grind it down to the finest powder, and sieve it through the finest sieve, and then show me one atom of justice, one molecule of mercy. And yet, you try to act as if there is some ideal order in the world. As if there is some, some rightness in the universe, by which it may be judged. Susan: But people have got to believe that, or what's the point? Death: You need to believe in things that aren't true. How else can they become?

John Harshman said:

John Kwok said: Sorry John, as a former paleobiologist, I respectfully beg to differ. Starting with Niles Eldredge's work on phacopid trilobites, we do see instances of branching events in the metazoan fossil record that would substantiate "speciation" events yielding to long-term morphological stasis of a given species (which I will concede that if one were to operate strictly on a biological species concept, there is no way to distinguish into a morphospecies any instances of sympatric speciation). For "punctuated anagenesis" to occur, the best examples are within the protistan fossil record, especially amongst the radiolarians and foraminifera.

Sorry, John. As a current systematist, I also respectfully beg to differ. We have no way of knowing if those were branching events. If we find two disparate morhpologies in the same locality, we can often suppose that they are separate species (with caveats for sexual and other dimorphism, ecotypes, preservational artifacts), but the appearance of two such morphotypes can often be explained by migration. Or, if geographic sampling is good, as with the Eldredge Phacops instance, we can't tell if there were already two morphologically similar species before one of them experienced punctuated anagenesis. And cryptic/sibling species are very common, and would be even more common if we had only the limited information for extant species that can be gleaned from fossils. I'm certainly not the first to point this out.

Most of my taxonomic/systematic work has been on Rivulid killifishes. I don't know of any fossil forms. Something to be said for that.

John, I did allude to your concerns to an extant in my prior post. The phenomenom of long-term morphological stasis, at least amongst metazoans, is now fairly well established in the fossil record. We can quibble as to whether these are in fact clusters of sympatric species, etc. but the patterns are real and can not be easily dismissible as you contend.

John Harshman said:

John, I did allude to your concerns to an extant in my prior post. The phenomenom of long-term morphological stasis, at least amongst metazoans, is now fairly well established in the fossil record. We can quibble as to whether these are in fact clusters of sympatric species, etc. but the patterns are real and can not be easily dismissible as you contend.

Stasis only means that morphological change is punctuated. (As an aside, I don't think stasis is as well documented as you think, but never mind that part.) At the moment I'm not questioning the pattern of stasis and punctuation. I'm questioning whether punctuation is coincident with speciation. You haven't addressed my point at all so far. By the way, sympatric speciation isn't necessary here. All that's required is that the species be in sympatry when one of them experiences morphological punctuation.

John Kwok said: When I speak of punctuated equilibrium, I am not referring at all to phyletic gradualism/punctuated anagenesis (I am actually skeptical of the latter term, since I am aware of substantial instances of PG within the protistan fossil record.). I am referring to some kind of rapid morphological divergence from an ancestral to a descendant population that would indicate speciation as defined on the basis of morphology.

It isn't tautological to theorise that there are episodes of rapid morphological change; whether or not there are such episodes (it looks like there are) is an empirical question.

MW, since you like the Gospel according to John, how about John 6:46-56? Do you take that literally?

The Pope does, and Benedict XVI, John Paul II, and Pius XII have all said there are no problems with the biological theory of evolution, specifically with regard to the evolution of the human body.

fusilier
James 2:24

Do I take John 6 vs 46-56 literally, the thing about that is if Jesus said it then he meant it, you have to take into consideration why Jesus came and if that was the persuasion of some at that time he would do everything to save a lost soul, but for that way of salvation it is now 2011 years long gone. I take note of what Paul said in 1 Corinthians ch 8 vs 13. At the last supper Jesus used bread and wine for us to remember him by, but first for a person to search their conscience as to their own partaking of the ceremony. If you are hinting that it was through the partaking of that procedure that we became the same human species as he was, then if we eat lamb for example the process would be the same, but I don't think there is any evidence of that, but he was special, he was a healer, so you never know it could be the case, similar to if you were to make a vaccine from some one who had recovered from an illness. Medical processes have developed greatly over the millenniums.

The phenomenom of long-term morphological stasis, at least amongst metazoans, is now fairly well established in the fossil record.

SAwells said: It isn't tautological to theorise that there are episodes of rapid morphological change; whether or not there are such episodes (it looks like there are) is an empirical question.

CMI has posted their article on the Denisovans today:
http://creation.com/denisovan

Pretty much what you'd expect: (paraphrasing in one sentence) "The Denisovans are what we expect from the dispersal after the Flood, proving the Truth of the Bible, but an embarrassment for evilutionists who can't explain them."

mrg -

Interestingly, I am familiar with the television version of Terry Pratchett's Hogfather. http://en.wikipedia.org/wiki/Terry_Pratchett's_Hogfather

I happened to come across it accidentally on television. It must have been shown in the US.

Despite my massively above average knowledge of classic British fantasy by US/Canadian, and probably even by UK standards, I had not heard of the books. I had no idea what I was watching but it was quite entertaining.

harold said: I happened to come across it accidentally on television. It must have been shown in the US.

John Harshman said:

John Kwok said: When I speak of punctuated equilibrium, I am not referring at all to phyletic gradualism/punctuated anagenesis (I am actually skeptical of the latter term, since I am aware of substantial instances of PG within the protistan fossil record.). I am referring to some kind of rapid morphological divergence from an ancestral to a descendant population that would indicate speciation as defined on the basis of morphology.

Ah, so in fact PE is correct by definition, if we use your definition. PE is a theory that most morphological change happens during speciation events. If we define "speciation event" as "episode of morphological change", then PE reduces to a claim that there are episodes of rapid morphological change. That's hardly what Eldredge and Gould had in mind, but it has the advantage of being tautological, and therefore always true. Why you would be skeptical about punctuated anagenesis while embracing punctuated equilibria is beyond me, since under your definition they're the same thing.

harold said: John Kwok -

The phenomenom of long-term morphological stasis, at least amongst metazoans, is now fairly well established in the fossil record.

Part of the problem is that morphological stasis is at least partly a subjective perception. We don't have good units for measuring it. We probably could make fairly objective methods of measuring genetic change over time within given lineages or subsets of local biospheres, using sampling, with the caveat that the selection of what and who to measure would be a subject of deserved controversy. In my view, the "battle" between PE and "gradualism" is a battle between exaggeratedly extreme straw man versions of each. It's highly reasonable to think that metazoans sometimes radiate rapidly into new niches, and also highly reasonable to think that in some stable environments, highly adapted populations are morphologically stable over long periods of time.

John Kwok said:

harold said: John Kwok -

The phenomenom of long-term morphological stasis, at least amongst metazoans, is now fairly well established in the fossil record.

Part of the problem is that morphological stasis is at least partly a subjective perception. We don't have good units for measuring it. We probably could make fairly objective methods of measuring genetic change over time within given lineages or subsets of local biospheres, using sampling, with the caveat that the selection of what and who to measure would be a subject of deserved controversy. In my view, the "battle" between PE and "gradualism" is a battle between exaggeratedly extreme straw man versions of each. It's highly reasonable to think that metazoans sometimes radiate rapidly into new niches, and also highly reasonable to think that in some stable environments, highly adapted populations are morphologically stable over long periods of time.

Neither Eldredge or Gould (or any of their supporters in paleobiology BTW) would claim that you don't see any morphological change within a lineage. Rather, what they have contended is that the net statistical change is zero - hence morphological stasis - and thata any observed variation is really ecophenotypic variation, not the punctuated anagenesis that John Harshman has suggested.

I've heard quite a lot about Gould's work, but i would really like to read it for myself.

Anybody have a link or perhaps a know a good book i could check out?

Jimmy said: Anybody have a link or perhaps a know a good book i could check out?

John Kwok said: Sorry John, think you need to read again Eldredge and Gould's work. In the very first paper on Punctuated Equilibrium (though the term itself wasn't coined until 1972 by Steve Gould), Eldredge, in a paper published in either 1970 or 1971 proposed that what he saw in his trilobites was some form of allopatric speciation. This is what I think both he and Gould had in mind when they wrote their classic 1972 paper in which they compared and contrasted punctuated equilibrium with phyletic gradualism.

Where I am remiss in my earlier comment is that I forgot to mention the analogy from allopatric speciation

As for "punctuated anagenesis" there is an extensive body of literature that supports it for Protista (and, if I'm not mistaken, Diatoms too), but more in the sense of true phyletic gradualism over time.

how you tell whether a given morphological change was accompanied simultaneously by speciation. I contend that you can’t.

John Harshman said:

John Kwok said: Sorry John, think you need to read again Eldredge and Gould's work. In the very first paper on Punctuated Equilibrium (though the term itself wasn't coined until 1972 by Steve Gould), Eldredge, in a paper published in either 1970 or 1971 proposed that what he saw in his trilobites was some form of allopatric speciation. This is what I think both he and Gould had in mind when they wrote their classic 1972 paper in which they compared and contrasted punctuated equilibrium with phyletic gradualism.

Of course they were. They were in fact proposing a paleontolgoical interpretation of Mayr's peripatric speciation. So? How is that relevant?

Where I am remiss in my earlier comment is that I forgot to mention the analogy from allopatric speciation

It isn't an analogy. It *is* allopatric speciation. But none of this is relevant to our argument. You can't recognize speciation in the fossil record.

As for "punctuated anagenesis" there is an extensive body of literature that supports it for Protista (and, if I'm not mistaken, Diatoms too), but more in the sense of true phyletic gradualism over time.

Punctuated anagenesis isn't phyletic gradualism. It's punctuated. That's why the word "punctuated" is in the name. The question is how you tell PA from PE, i.e. how you tell whether a given morphological change was accompanied simultaneously by speciation. I contend that you can't. You can occasionally tell that what looked rather like a single population has become two morphologically divergent populations. But that could also be a PA event in one (or both) of two formerly sibling species. How can you distinguish sort of event (PE) from the other (prior speciation followed at some indeterminate interval by PA)? There is of course a good model for the latter: character displacement.

Flint said:

how you tell whether a given morphological change was accompanied simultaneously by speciation. I contend that you can’t.

OK, I'm confused. I've seen many different approaches to categorizing speciation, which are not mutually antagonistic, but which are instead useful for different purposes. And one of those purposes has to do with morphological change. Generally, at least as I understand it, morphological diversion in practice requires breeding isolation for some period of time between populations. Or are we saying here that a single breeding population might undergo significant morphological change without speciation, breaking the statis? And this strikes me as problematical - if we have a continuously interbreeding population which undergoes some morphological changes over time, is there EVER a point where we'd say the population "deserves to be called" a new species? I'm starting to wonder whether we have more terms than we have conditions to describe with them.

Neither Eldredge or Gould (or any of their supporters in paleobiology BTW) would claim that you don’t see any morphological change within a lineage. Rather, what they have contended is that the net statistical change is zero - hence morphological stasis - and thata any observed variation is really ecophenotypic variation

John Kwok said: John, you are persisting in believing that there are branching events that are more anagenesis than in actual splitting of lineages (which could be viewed as speciation if there is continuous sedimentation going on). </blockquote. I persist in believing nothing of the sort. I'm claiming nothing more than that the branching events and the morphological divergence are not the same thing, or at least we have no way of telling if morphological divergence is coincident with branching. We can't directly observe splitting of lineages in the fossil record. We can only observe divergence of morphology. That might be happening during or at any time after a branching event, and we have no real way of knowing.

If you have finely recorded microstratigraphic sections and see one morphological lineage diverging into two, then that's speciation.

If you want to define speciation as morphological divergence, yes. But if you are talking about biological species, which is indeed what PE is an attempt to describe, then no. "One morphological lineage" could easily conceal multiple biological species. And if one of them experiences a change, all that does is make the prior separation visible to paleontologists.

If would be punctuated anagenesis if and only if there was one lineage persisting in the stratigraphic section in question and that there were enough net zero statistical change in its morphology that would rule out that lineage tracking ecophenotypic variation.

The second part was quite confused. Punctuated anagenesis would require other than net zero change in morphology. But your conclusion of anagenesis in this case is reasonable. We might suspect PE only if we see two morphotypes where we had previously seen only one. If we see one replaced by another, PE is ruled out. (Of course, the problem of geographic sampling makes even this conclusion ambiguous -- absent adequate sampling, we could be seeing only migration and extinction, with no necessary evolution at all.) And even if we see two morphotypes, we can't say that we have seen branching, since we may have seen only the morphological divergence of prior sibling species.

I've not done any of this kind of work myself, but colleagues have shown me work which involved establishing landmarks on an organism, or structure, and seeing how the landmarks positions change in relation to each other with growth, or across a group of species, or whatever. So I have the impression there are accepted methods to quantify morphology.

John Harshman said:

John Kwok said: John, you are persisting in believing that there are branching events that are more anagenesis than in actual splitting of lineages (which could be viewed as speciation if there is continuous sedimentation going on). </blockquote. I persist in believing nothing of the sort. I'm claiming nothing more than that the branching events and the morphological divergence are not the same thing, or at least we have no way of telling if morphological divergence is coincident with branching. We can't directly observe splitting of lineages in the fossil record. We can only observe divergence of morphology. That might be happening during or at any time after a branching event, and we have no real way of knowing.

If you have finely recorded microstratigraphic sections and see one morphological lineage diverging into two, then that's speciation.

If you want to define speciation as morphological divergence, yes. But if you are talking about biological species, which is indeed what PE is an attempt to describe, then no. "One morphological lineage" could easily conceal multiple biological species. And if one of them experiences a change, all that does is make the prior separation visible to paleontologists.

If would be punctuated anagenesis if and only if there was one lineage persisting in the stratigraphic section in question and that there were enough net zero statistical change in its morphology that would rule out that lineage tracking ecophenotypic variation.

The second part was quite confused. Punctuated anagenesis would require other than net zero change in morphology. But your conclusion of anagenesis in this case is reasonable. We might suspect PE only if we see two morphotypes where we had previously seen only one. If we see one replaced by another, PE is ruled out. (Of course, the problem of geographic sampling makes even this conclusion ambiguous -- absent adequate sampling, we could be seeing only migration and extinction, with no necessary evolution at all.) And even if we see two morphotypes, we can't say that we have seen branching, since we may have seen only the morphological divergence of prior sibling species.

Jim Thomerson said: I've not done any of this kind of work myself, but colleagues have shown me work which involved establishing landmarks on an organism, or structure, and seeing how the landmarks positions change in relation to each other with growth, or across a group of species, or whatever. So I have the impression there are accepted methods to quantify morphology.

harold said: John Kwok said -

Neither Eldredge or Gould (or any of their supporters in paleobiology BTW) would claim that you don’t see any morphological change within a lineage. Rather, what they have contended is that the net statistical change is zero - hence morphological stasis - and thata any observed variation is really ecophenotypic variation

I have no reason to disagree with this part of John Kwok's statement. My point is that while it is all very good to talk about amount of morphologic variation, except in cases where there is a simple size change in a defined anatomic element of a lineage, we lack a strong, consistent methodology of objectively quantify morphologic variation. I stand by that point. Stephen Jay Gould is one of my all time favorite writers. I have enjoyed many of his works on a variety of topics. As I noted above, it is my view that it is obvious that, to the human eye, lineages may seem to be "stable" or to "change rapidly" depending on the circumstances, what aspect we have chosen to look for changes in, and how we define "rapidly" and "slowly".

harold said: As I noted above, it is my view that it is obvious that, to the human eye, lineages may seem to be "stable" or to "change rapidly" depending on the circumstances, what aspect we have chosen to look for changes in, and how we define "rapidly" and "slowly".

John Kwok said: John we are arguing past each other.

Didn't you read where I said a paleobiological speciation event? I know full well that Punctuated Equilibrium doesn't account for a complex of sympatic species that may exist due to some kind of niche partitioning or benavior (e. g. one species is diurnal and the other nocturnal). Nor would it account for ring species. Again, what I find most intriguing about this is that there is indeed long-term morphological stasis within a morphospecies that continues from shortly after the "birth" of the species until it goes extinct.

John Harshman said:

John Kwok said: John we are arguing past each other.

I would put it differently. I would say that you don't understand what I'm saying.

Didn't you read where I said a paleobiological speciation event? I know full well that Punctuated Equilibrium doesn't account for a complex of sympatic species that may exist due to some kind of niche partitioning or benavior (e. g. one species is diurnal and the other nocturnal). Nor would it account for ring species. Again, what I find most intriguing about this is that there is indeed long-term morphological stasis within a morphospecies that continues from shortly after the "birth" of the species until it goes extinct.

But if PE refers only to morphospecies, not biological species, it's nearly tautological. Yes, morphospecies experience stasis. If they didn't, they'd be divided up into multiple morphospecies. Stripped of a connection to biological species, PE is reduced to a statement that rates of evolution vary through the history of a lineage. Interesting, but much less interesting than the original claims of PE.

John Kwok said: I strongly disagree. I have referred to paleobiological speciation events, which are true lineage splitting events, (not some persisting lineage in which there is rapid morphological change via some form of punctuated anagenesis or phyletic gradualism), in which one descendant population emerges from an ancestral, much larger, population (as woudl be the case if the descendant population in question is a peripheral isolate of the former, while both continue to persist in the fossil record.).

I also agree with you that puncutuated equilibrium does not account for closely related species that are morphologically the same but differ due to some kind of habitat differentiation (e. g. are nocturnal and diurnal for example) or ring species. In fact that is why I have emphasized the term morphospecies.

The best examples of punctuated anagenesis or phyletic gradualism can be seen in the marine Protista or Diatom fossil record. In stark contrast, at least for marine metazoans, we see paleobiological speciation events followed by long-term morphological stasis.

John Harshman said:

John Kwok said: I strongly disagree. I have referred to paleobiological speciation events, which are true lineage splitting events, (not some persisting lineage in which there is rapid morphological change via some form of punctuated anagenesis or phyletic gradualism), in which one descendant population emerges from an ancestral, much larger, population (as woudl be the case if the descendant population in question is a peripheral isolate of the former, while both continue to persist in the fossil record.).

How do you know that you're looking at a splitting event, not the subsequent divergence of two species that actually split a while ago?

I also agree with you that puncutuated equilibrium does not account for closely related species that are morphologically the same but differ due to some kind of habitat differentiation (e. g. are nocturnal and diurnal for example) or ring species. In fact that is why I have emphasized the term morphospecies.

Why couldn't punctuated equilibrium apply to sibling species? What I'm saying is that you just can't tell if a morphological change in the fossil record is or is not happening at the same time as a split of lineages. This is a simple claim, but you keep bringing up tangential arguments that have no bearing on that claim. By the way, sibling species may not differ in habitat. If they're sympatric, they must partition resources in some way, but it could be as simple as feeding in different parts of the same tree. And of course there are plenty of allopatric sibling species too.

The best examples of punctuated anagenesis or phyletic gradualism can be seen in the marine Protista or Diatom fossil record. In stark contrast, at least for marine metazoans, we see paleobiological speciation events followed by long-term morphological stasis.

You keep equating punctuated anagenesis with phyletic gradualism. Please stop. And do you consider that a paleobiological speciation event is something quite distinct from a modern speciation event? If so, what makes it different? If you're giving up all claims that a morphological species is also a biological species, you are also giving up claims to PE's main thesis, as well as claims to be able to detect actual splitting events in the fossil record. At most you can determine that a splitting event happened some time prior to observed differentiation. Shall I mention that I also doubt that small, peripherally isolated populations are generally very important in evolution? Mayr's model of speciation isn't a very useful model.

John Harshman said:

John Kwok said: I strongly disagree. I have referred to paleobiological speciation events, which are true lineage splitting events, (not some persisting lineage in which there is rapid morphological change via some form of punctuated anagenesis or phyletic gradualism), in which one descendant population emerges from an ancestral, much larger, population (as woudl be the case if the descendant population in question is a peripheral isolate of the former, while both continue to persist in the fossil record.).

How do you know that you're looking at a splitting event, not the subsequent divergence of two species that actually split a while ago?

I also agree with you that puncutuated equilibrium does not account for closely related species that are morphologically the same but differ due to some kind of habitat differentiation (e. g. are nocturnal and diurnal for example) or ring species. In fact that is why I have emphasized the term morphospecies.

Why couldn't punctuated equilibrium apply to sibling species? What I'm saying is that you just can't tell if a morphological change in the fossil record is or is not happening at the same time as a split of lineages. This is a simple claim, but you keep bringing up tangential arguments that have no bearing on that claim. By the way, sibling species may not differ in habitat. If they're sympatric, they must partition resources in some way, but it could be as simple as feeding in different parts of the same tree. And of course there are plenty of allopatric sibling species too.

The best examples of punctuated anagenesis or phyletic gradualism can be seen in the marine Protista or Diatom fossil record. In stark contrast, at least for marine metazoans, we see paleobiological speciation events followed by long-term morphological stasis.

You keep equating punctuated anagenesis with phyletic gradualism. Please stop. And do you consider that a paleobiological speciation event is something quite distinct from a modern speciation event? If so, what makes it different? If you're giving up all claims that a morphological species is also a biological species, you are also giving up claims to PE's main thesis, as well as claims to be able to detect actual splitting events in the fossil record. At most you can determine that a splitting event happened some time prior to observed differentiation. Shall I mention that I also doubt that small, peripherally isolated populations are generally very important in evolution? Mayr's model of speciation isn't a very useful model.

John Kwok said: 1) Again if we are seeing a lineage splitting event

yes, I agree with Eldredge and Gould that such speciation events do indicate the emergence of species as discrete entities that are born and eventually do die.

2) If there are two sibling species emerging from an ancestral species (which persists in the fossil record), then you can’t tell them apart if their morphology is the same, which is what you would expect from sympatric speciation. If there are substantial differences between the two, then of course it is possible to have them evolve via punctuated equilibrium.

3) There are different models of allopatric speciation, and one we haven’t discussed at length is what one would call vicariant speciation in which you would see a splitting of a large ancestral population into two smaller descendant ones due to the creation of some kind of barrier.

4) If you have a Protistan or Diatom lineage that is noted by brief, rapid instances of morphological change followed by long-term stasis), then it is fair to refer to it as punctuated anagenesis, especially if it repeats itself. If, howver, such change is more gradual, then it should be referred to as phyletic gradualism. In neither instance do you see any genuine lineage splitting, but instead, morphological change within the same lineage, so it would be fair to group the two togetner as evolutionary patterns distinct from punctuated equilibrium.

John Harshman said:

John Kwok said: 1) Again if we are seeing a lineage splitting event

Let's stop right there. What do you mean "lineage splitting event"? What you actually see, at most, is a unimodal distribution of some characteristics gradually (or rapidly, if you prefer) becoming a bimodal distribution. You interpret that as a splitting event. I'm asking how you can say that, when divergence of two species that were already separate, but had previously been similar morphologically, would show exactly the same pattern.

yes, I agree with Eldredge and Gould that such speciation events do indicate the emergence of species as discrete entities that are born and eventually do die.

I know you do. I'm asking how you can make that assumption.

2) If there are two sibling species emerging from an ancestral species (which persists in the fossil record), then you can’t tell them apart if their morphology is the same, which is what you would expect from sympatric speciation. If there are substantial differences between the two, then of course it is possible to have them evolve via punctuated equilibrium.

That's totally opaque as well as irrelevant to our disagreement. I'm not talking about sympatric speciation. Nor, in fact, are sibling species what we would expect, particularly, from sympatric speciation, at least to any greater degree than we would expect from allopatric speciation.

3) There are different models of allopatric speciation, and one we haven’t discussed at length is what one would call vicariant speciation in which you would see a splitting of a large ancestral population into two smaller descendant ones due to the creation of some kind of barrier.

Please stop trying to educate me about things every evolutionary biologist should know already. Assume I know that stuff until I present evidence to the contrary. Again, this is irrelevant too.

4) If you have a Protistan or Diatom lineage that is noted by brief, rapid instances of morphological change followed by long-term stasis), then it is fair to refer to it as punctuated anagenesis, especially if it repeats itself. If, howver, such change is more gradual, then it should be referred to as phyletic gradualism. In neither instance do you see any genuine lineage splitting, but instead, morphological change within the same lineage, so it would be fair to group the two togetner as evolutionary patterns distinct from punctuated equilibrium.

How do you know? How can you distinguish punctuated equilibrium (involving speciation) from punctuated anagenesis (not involving speciation)? Again, this requires the assumption that you can identify single species in the fossil record, and distinguish one species from two sibling species.

John Kwok said: I think you need to learn something about biostratigraphy, sedimentology as well as invertebrate paleobiology, John and I have neither the time nor patience to educate you here. Thank you for your condescension. Are you even reading anything I write? I can see no sign of it, if so. Please. I took paleontology from Dave Raup, Dave Jablonski, and Jim Hopson.

1) Again if you have a stratigraphic sequence that demonstrates a continuous record of sedimentation and see in that, the rapid emergence of one population splitting off from another, then it is a speciation event (though I've used the caveat paleobiological speciation event for the reasons I have stated twice already.)

Yes, you have repeated many claims without seeming to notice my objections, much less respond to them. How do you know there is "one population splitting off from another" rather than "one population becoming recognizably distinct from another"?

2)You've been the one picking on me about sibling species so I felt compelled to explain what exactly I am referring to.

Yes, and you responded with irrelevant comments about sympatric speciation. You have never responded to my actual point.

3) I wrote that more for the benefit of others reading these comments who are unfamiliar with modes of speciation, and also to remind you that punctuated equilibrium may not be primarily a product of peripatric speciation.

I need no reminding. (Though if peripatric speciation isn't the usual mode, the original rationale for PE disappears.)

4) Look again at my first comment posted here. If you see only rapid evolutionary transformation within a single lineage followed by long-term stasis, then that's clearly an instance of punctuated anagenesis.

Yes, and I'm asking how you can tell the difference between 1) transformation in a single lineage, when there are sibling species present, one of which doesn't transform, and 2) splitting of lineages, of which one transforms and the other doesn't.

5) Again what I find most intriguing about punctuated equilibrium is that it has formally recognized the persistence of long-term morphological stasis within marine metazoans (at least). That and the realization that species are discrete entities through time, who have "births" and "deaths".

Stasis may be interesting, but it isn't the central claim of PE, which is about speciation. But yes, stasis is interesting. Species as temporally discrete entities is probably hallucination brought on by identification of speciation with punctuation.

John Harshman said:

John Kwok said: I think you need to learn something about biostratigraphy, sedimentology as well as invertebrate paleobiology, John and I have neither the time nor patience to educate you here. Thank you for your condescension. Are you even reading anything I write? I can see no sign of it, if so. Please. I took paleontology from Dave Raup, Dave Jablonski, and Jim Hopson.

1) Again if you have a stratigraphic sequence that demonstrates a continuous record of sedimentation and see in that, the rapid emergence of one population splitting off from another, then it is a speciation event (though I've used the caveat paleobiological speciation event for the reasons I have stated twice already.)

Yes, you have repeated many claims without seeming to notice my objections, much less respond to them. How do you know there is "one population splitting off from another" rather than "one population becoming recognizably distinct from another"?

2)You've been the one picking on me about sibling species so I felt compelled to explain what exactly I am referring to.

Yes, and you responded with irrelevant comments about sympatric speciation. You have never responded to my actual point.

3) I wrote that more for the benefit of others reading these comments who are unfamiliar with modes of speciation, and also to remind you that punctuated equilibrium may not be primarily a product of peripatric speciation.

I need no reminding. (Though if peripatric speciation isn't the usual mode, the original rationale for PE disappears.)

4) Look again at my first comment posted here. If you see only rapid evolutionary transformation within a single lineage followed by long-term stasis, then that's clearly an instance of punctuated anagenesis.

Yes, and I'm asking how you can tell the difference between 1) transformation in a single lineage, when there are sibling species present, one of which doesn't transform, and 2) splitting of lineages, of which one transforms and the other doesn't.

5) Again what I find most intriguing about punctuated equilibrium is that it has formally recognized the persistence of long-term morphological stasis within marine metazoans (at least). That and the realization that species are discrete entities through time, who have "births" and "deaths".

Stasis may be interesting, but it isn't the central claim of PE, which is about speciation. But yes, stasis is interesting. Species as temporally discrete entities is probably hallucination brought on by identification of speciation with punctuation.

John Harshman said:

John Kwok said: I think you need to learn something about biostratigraphy, sedimentology as well as invertebrate paleobiology, John and I have neither the time nor patience to educate you here. Thank you for your condescension. Are you even reading anything I write? I can see no sign of it, if so. Please. I took paleontology from Dave Raup, Dave Jablonski, and Jim Hopson.

1) Again if you have a stratigraphic sequence that demonstrates a continuous record of sedimentation and see in that, the rapid emergence of one population splitting off from another, then it is a speciation event (though I've used the caveat paleobiological speciation event for the reasons I have stated twice already.)

Yes, you have repeated many claims without seeming to notice my objections, much less respond to them. How do you know there is "one population splitting off from another" rather than "one population becoming recognizably distinct from another"?

2)You've been the one picking on me about sibling species so I felt compelled to explain what exactly I am referring to.

Yes, and you responded with irrelevant comments about sympatric speciation. You have never responded to my actual point.

3) I wrote that more for the benefit of others reading these comments who are unfamiliar with modes of speciation, and also to remind you that punctuated equilibrium may not be primarily a product of peripatric speciation.

I need no reminding. (Though if peripatric speciation isn't the usual mode, the original rationale for PE disappears.)

4) Look again at my first comment posted here. If you see only rapid evolutionary transformation within a single lineage followed by long-term stasis, then that's clearly an instance of punctuated anagenesis.

Yes, and I'm asking how you can tell the difference between 1) transformation in a single lineage, when there are sibling species present, one of which doesn't transform, and 2) splitting of lineages, of which one transforms and the other doesn't.

5) Again what I find most intriguing about punctuated equilibrium is that it has formally recognized the persistence of long-term morphological stasis within marine metazoans (at least). That and the realization that species are discrete entities through time, who have "births" and "deaths".

Stasis may be interesting, but it isn't the central claim of PE, which is about speciation. But yes, stasis is interesting. Species as temporally discrete entities is probably hallucination brought on by identification of speciation with punctuation.

John Kwok said: I think you have been all too condescending yourself, John. By your own admission you haven't taken courses in stratigraphy and sedimentology. Again if you have a continuous record of sedimentation within a stratigraphic sequence and see a lineage splitting event in which a new lineage emerges from another, then I'd call that a speciation event. As for your very last comment, may I have your permission to share it with Niles Eldrege? Am sure he'd find it most fascinating.

John Harshman said:

John Kwok said: I think you have been all too condescending yourself, John. By your own admission you haven't taken courses in stratigraphy and sedimentology. Again if you have a continuous record of sedimentation within a stratigraphic sequence and see a lineage splitting event in which a new lineage emerges from another, then I'd call that a speciation event. As for your very last comment, may I have your permission to share it with Niles Eldrege? Am sure he'd find it most fascinating.

Actually, I never said I hadn't. And in fact I have. Look, this could be an interesting discussion if you would bother just once to address my argument directly. How do you distinguish 1) one lineage splitting from another from 2) one member of sibling species pair undergoing anagenesis? And by posting to a public forum, I have shared my comment with anyone who cares to notice it. Now, if you were going to respond rationally to this argument, as I see it you have one option only. You can claim that sibling (or perhaps "cryptic" would be less confusing for you) species are rare. Obviously, the more common they are the more likely you are to miss the true speciation event, and the rarer they are the fewer you miss. Now you have instead chosen two approaches: 1) simply assert that you know best by virtue of your superior brain and 2) simply repeat your initial claim over and over without engaging my argument. Try something else.

One of the central claims of Punctuated equilibrium is the persistence of morphological stasis over the course of geological time, which I am sure both David Raup and David Jablonski reminded you of.

1) Have yet to read of "sibling species" in the Protista and Diatoms and frankly I doubt that they exist.

2) You're trying to play "gotcha" and I'm not interested. In the situation to described, the species that transforms is the descendant of the ancestral species (which doest not transform, but instead, remains in its prior state of morphological stasis.

John Harshman said:

One of the central claims of Punctuated equilibrium is the persistence of morphological stasis over the course of geological time, which I am sure both David Raup and David Jablonski reminded you of.

Yes, the claim of general stasis is the part of PE that I think can be salvaged, because it can in principal be tested. I can't say I think its prevalance has been very well tested, but it could be.

1) Have yet to read of "sibling species" in the Protista and Diatoms and frankly I doubt that they exist.

Has anyone been looking for them? You probably have to sequence a large sample and look for divergent clades. It wouldn't be easy.

2) You're trying to play "gotcha" and I'm not interested. In the situation to described, the species that transforms is the descendant of the ancestral species (which doest not transform, but instead, remains in its prior state of morphological stasis.

It's an interesting philosophical question to ponder what the "ancestral species" would be. But the point to make is that the ancestral species wasn't there at the time. It was some time in the past, and you didn't notice the true speciation event because it didn't involve significant morphological change. You still have yet to engage my fundamental question. I'm not trying to play gotcha here; I'm trying to have an argument (the full half hour, not just the 5 minutes). But you won't even notice the question.

John Kwok said: I strongly beg to differ, the paleobiological literature does show now numerous examples of morphological stasis. As for "sibling species" in the Protista and Diatoms, you are talking about two groups well studied by both micropaleontologists and biological oceanographers. Am certain that if they did exist, we would have known about them.

John Harshman said:

John Kwok said: I strongly beg to differ, the paleobiological literature does show now numerous examples of morphological stasis. As for "sibling species" in the Protista and Diatoms, you are talking about two groups well studied by both micropaleontologists and biological oceanographers. Am certain that if they did exist, we would have known about them.

Some day it might be nice to discuss your favorite examples of stasis, but that isn't the main issue we were discussing. And are you really using micropaleontologists as your argument against sibling species? The point about sibling species is that paleontologists can't detect them. Now oceanographers might be better. Do you know of any projects in which oceanographers have sequenced large numbers of supposedly identical individuals? I'd have to say that just amplifying the DNA from a single individual would be a challenge.

John Harshman said: Some day it might be nice to discuss your favorite examples of stasis, but that isn't the main issue we were discussing. And are you really using micropaleontologists as your argument against sibling species? The point about sibling species is that paleontologists can't detect them. Now oceanographers might be better. Do you know of any projects in which oceanographers have sequenced large numbers of supposedly identical individuals? I'd have to say that just amplifying the DNA from a single individual would be a challenge.

Could you be more specific? On Brett's web site, and judging only from titles, I find only this:

Brett, C.E., Ivany, L., Baugh, H.L., and Wall, P, 2008, Coordinated stasis revisited: Taxonomic and ecologic stability in the Devonian of New York: Paleobiology.

Well, it's a start.

And now, since we apparently agree that cryptic species exist, even in diatoms and forams, would you agree that they present an operational problem for detecting splitting events, that is for distinguishing PE from PA?

John Harshman said: Could you be more specific? On Brett's web site, and judging only from titles, I find only this: Brett, C.E., Ivany, L., Baugh, H.L., and Wall, P, 2008, Coordinated stasis revisited: Taxonomic and ecologic stability in the Devonian of New York: Paleobiology. Well, it's a start. And now, since we apparently agree that cryptic species exist, even in diatoms and forams, would you agree that they present an operational problem for detecting splitting events, that is for distinguishing PE from PA?

John Kwok said:

John Harshman said: Could you be more specific? On Brett's web site, and judging only from titles, I find only this: Brett, C.E., Ivany, L., Baugh, H.L., and Wall, P, 2008, Coordinated stasis revisited: Taxonomic and ecologic stability in the Devonian of New York: Paleobiology. Well, it's a start. And now, since we apparently agree that cryptic species exist, even in diatoms and forams, would you agree that they present an operational problem for detecting splitting events, that is for distinguishing PE from PA?

No, I think we are still in disagreement, especially when I noted that we can see splitting events of morphospecies, with a descendant species emerging from an ancestral one (which is true only for punctuated equilibrium, NOT punctuated anagenesis). I think the problem you cite with regards to cryptic species isn't nearly as serious as you contend. If that was really an important issue, then I highly doubt that such prominent biologists as Douglas Futuyma and Massimo Pigliucci would recognize the importance of morphological stasis.

John Kwok said: No, I think we are still in disagreement, especially when I noted that we can see splitting events of morphospecies, with a descendant species emerging from an ancestral one (which is true only for punctuated equilibrium, NOT punctuated anagenesis). I think the problem you cite with regards to cryptic species isn't nearly as serious as you contend. If that was really an important issue, then I highly doubt that such prominent biologists as Douglas Futuyma and Massimo Pigliucci would recognize the importance of morphological stasis.

John Harshman said:

John Kwok said: No, I think we are still in disagreement, especially when I noted that we can see splitting events of morphospecies, with a descendant species emerging from an ancestral one (which is true only for punctuated equilibrium, NOT punctuated anagenesis). I think the problem you cite with regards to cryptic species isn't nearly as serious as you contend. If that was really an important issue, then I highly doubt that such prominent biologists as Douglas Futuyma and Massimo Pigliucci would recognize the importance of morphological stasis.

So basically your argument here amounts to an appeal to authority. Can't be anything to it, because Futuyma and Pigliucci haven't complained. In fact that's wrong. Stasis is the phenomenon they're talking about. That's different from what you're claiming, which is that stasis is broken only during speciation. It's the association of punctuation with speciation that we're arguing about here. Nothing to do with the reality of stasis. I'll say it again. The fossil record is capable of documenting stasis. It is not capable of documenting whether punctuation is associated (chiefly, or wholly) with speciation, because the fossil record isn't good at letting us recognize speciation. And the reason for this is the existence of cryptic species. You claim to see a descendant species emerging from an ancestral one. I claim that you must first rule out the alternative, that there are two species already present, not easily distinguished by fossils and so presenting the same appearance as a single species, one of which undergoes punctuated anagenesis while the other one doesn't. Note that in this case there is still stasis, and there is still punctuation. The fossil record is capable of identifying both of these. What I claim it can't do is determine that the punctuation is coincident with speciation. I am not playing any semantic word games. But your statement "under Punctuated Equilibrium, both the descendant and ancestral species would have populations that persist, demonstrating morphological stasis" is nonsensical. Under PE, the ancestral species would persist and would show stasis, while the descendant species would undergo a punctuation event during speciation, showing non-stasis. While that's a correct description of PE, it does nothing to advance the claim that PE can be distinguished from PA in the presence of sibling species. Again, if we start with two indistinguishable species and one of them undergoes PA, there is no way to tell that apart from PE. In that case, what looks to you like the ancestral species is, initially, two species. What looks like the speciation event is PA in one of the species. And what looks like the ancestor/descendant pair, finally, is really just the same two species you began with; your ancestor is the species that didn't change, and your descendant is the species that did. But no speciation has happened in this scenario. So: how do you tell your scenario from mine? I claim that you can't. You can only, at best, argue that such cryptic species pairs are rare. Would you like to do that?

John Harshman said:

John Kwok said: No, I think we are still in disagreement, especially when I noted that we can see splitting events of morphospecies, with a descendant species emerging from an ancestral one (which is true only for punctuated equilibrium, NOT punctuated anagenesis). I think the problem you cite with regards to cryptic species isn't nearly as serious as you contend. If that was really an important issue, then I highly doubt that such prominent biologists as Douglas Futuyma and Massimo Pigliucci would recognize the importance of morphological stasis.

So basically your argument here amounts to an appeal to authority. Can't be anything to it, because Futuyma and Pigliucci haven't complained. In fact that's wrong. Stasis is the phenomenon they're talking about. That's different from what you're claiming, which is that stasis is broken only during speciation. It's the association of punctuation with speciation that we're arguing about here. Nothing to do with the reality of stasis. I'll say it again. The fossil record is capable of documenting stasis. It is not capable of documenting whether punctuation is associated (chiefly, or wholly) with speciation, because the fossil record isn't good at letting us recognize speciation. And the reason for this is the existence of cryptic species. You claim to see a descendant species emerging from an ancestral one. I claim that you must first rule out the alternative, that there are two species already present, not easily distinguished by fossils and so presenting the same appearance as a single species, one of which undergoes punctuated anagenesis while the other one doesn't. Note that in this case there is still stasis, and there is still punctuation. The fossil record is capable of identifying both of these. What I claim it can't do is determine that the punctuation is coincident with speciation. I am not playing any semantic word games. But your statement "under Punctuated Equilibrium, both the descendant and ancestral species would have populations that persist, demonstrating morphological stasis" is nonsensical. Under PE, the ancestral species would persist and would show stasis, while the descendant species would undergo a punctuation event during speciation, showing non-stasis. While that's a correct description of PE, it does nothing to advance the claim that PE can be distinguished from PA in the presence of sibling species. Again, if we start with two indistinguishable species and one of them undergoes PA, there is no way to tell that apart from PE. In that case, what looks to you like the ancestral species is, initially, two species. What looks like the speciation event is PA in one of the species. And what looks like the ancestor/descendant pair, finally, is really just the same two species you began with; your ancestor is the species that didn't change, and your descendant is the species that did. But no speciation has happened in this scenario. So: how do you tell your scenario from mine? I claim that you can't. You can only, at best, argue that such cryptic species pairs are rare. Would you like to do that?

John Kwok said: I don't think you really understand Punctuated Equilibrium at all, because BOTH the ancestor and descendant species would exhibit morphological stasis (In the case of the descendant that would be after its morphological divergence from the ancestral species.). I said when the populations persist, that they would show morphological stasis, NOT during the actual lineage-splitting event, which again, under conditions of continuous sedimentation does represent a speciation event.

As for making an "argument from authority", I think you ought to plead guilty too, since you thought it necessary to tell me that you studied paleontology with David Raup, David Jablonski and James Hopson. Do you think I really care?

I think this discussion has outlived its usefulness and I bid you a good day.

This is my last comment (I hope on this thread), but anyone who reads my discussion with John Harshman should understand that he has failed to understand my references to biostratigraphy, stratigraphy and sedimentology. Had he demonstated some understanding, I strongly doubt that we'd be at such an impasse. As for his insistance on cryptic species, his an argument based partly on incredulity, since most metazoan taxa are not comprised of closely related cryptic sibling species. As I have alluded to a recent comment, the existence of cryptic species in Protists and Diatoms is relatively rare (with Diatoms being the rarest).

John Kwok said: This is my last comment (I hope on this thread),

but anyone who reads my discussion with John Harshman should understand that he has failed to understand my references to biostratigraphy, stratigraphy and sedimentology.

Had he demonstated some understanding, I strongly doubt that we'd be at such an impasse. As for his insistance on cryptic species, his an argument based partly on incredulity, since most metazoan taxa are not comprised of closely related cryptic sibling species. As I have alluded to a recent comment, the existence of cryptic species in Protists and Diatoms is relatively rare (with Diatoms being the rarest).

Sorry John, but for someone who claimed to know Geraat Vermeij well enough to tell if he always gave his lectures from his memory (and also to express your disdain for him simply because he's not enthusiastic about cladistics - I happen to think he's mistaken here myself - but I won't "crucify" him for his indifference toward cladistics, which, I suspect, is what you would prefer to do to Vermeij if it was entirely up to you.), you are once again ignoring the important points with respect to biostratigraphy, stratigraphy and sedimentology that I have been trying to make here, and since you insist on refusing to acknowledging them, then you have no business in not respecting my contention that, under conditions where continuous sedimentation has been preseved in the geological column, then it is possible to identify real speciation events in the fossil record and distinguish them from either instances of the first appearance of immigrant taxa or some form of ecophenotypic variation.

I didn't have a Brett reference handy, but instead, only referred you in more general terms, to the work he has been doing with his students and Niles Eldredge. Maybe after you read that, I might be interested in resuming our discussion, but not until then.

John Harshman said: Finally, an attempt at the real question. Fitting that it should be after you've already declared victory and gone home. In my experience, cryptic species tend to appear when you start looking for them seriously, using the right sort of data. You could of course be right with regard to any particular taxon, but as far as I can see the simpler the apparent morphology, the more a problem cryptic species might be. But thanks for finally responding to the question. That helps. And thanks for the reference you almost provided, to Brett.

I've examined a lot fish skeletons. There are sister species which have identical skeletons, species which show considerable skeletal variation, and any number of uninformative bones. With fragmented skeletons, it might be very difficult to correctly recognize species. There is a reason paleontologists count genera or families when talking about comparative diversities.

John Kwok said: Sorry John,

but for someone who claimed to know Geraat Vermeij well enough to tell if he always gave his lectures from his memory (and also to express your disdain for him simply because he's not enthusiastic about cladistics - I happen to think he's mistaken here myself - but I won't "crucify" him for his indifference toward cladistics, which, I suspect, is what you would prefer to do to Vermeij if it was entirely up to you.),

you are once again ignoring the important points with respect to biostratigraphy, stratigraphy and sedimentology that I have been trying to make here, and since you insist on refusing to acknowledging them, then you have no business in not respecting my contention that, under conditions where continuous sedimentation has been preseved in the geological column, then it is possible to identify real speciation events in the fossil record and distinguish them from either instances of the first appearance of immigrant taxa or some form of ecophenotypic variation.

I didn't have a Brett reference handy, but instead, only referred you in more general terms, to the work he has been doing with his students and Niles Eldredge. Maybe after you read that, I might be interested in resuming our discussion, but not until then.

John Kwok said: Again, you've made a mountain out of a molehill with regards to cryptic species. I don't think it is as serious an issue as you might contend.

John,

Carl Brett, Niles Eldredge, and Brett's students (I believe one of Eldredge's too) have published a number of papers on their work, but I don't have the references handy. You'll have to dig it for yourself (Not trying to be obtuse but I'm actually off to hear Massimo Pigliucci speak in short while and then, after that, have other business to do in Manhattan.).

When you've demonstrated some familiarity with stratigraphy and sedimentology, then I'll converse with you more on this.

John Harshman said:

John Kwok said: Again, you've made a mountain out of a molehill with regards to cryptic species. I don't think it is as serious an issue as you might contend.

Excellent. You have finally begun an attempt to address my claims. So, how would we know if it's a serious issue? Probably by using modern taxa as a guide. In birds, it's often very hard to tell closely related species apart, even with complete skeletons, which you seldom get in fossils. I once worked in a lab next to a nemertine systematist, who, every time he looked at a new beach, found as many as a dozen new, cryptic species, that he couldn't distinguish at all morphologically. It would be nice to find a review of cryptic species across taxa, but I don't know of any. But based on my personal experience, I consider it a major problem, especially for fossils, for which we have limited data to discriminate species.

John Harshman said: But based on my personal experience, I consider it a major problem, especially for fossils, for which we have limited data to discriminate species.

John Kwok said:Carl Brett, Niles Eldredge, and Brett's students (I believe one of Eldredge's too) have published a number of papers on their work, but I don't have the references handy.

John Kwok said: Would you care to explain that to generations of systematic paleobiologists, John? Your comment is utterly without merit and is absurd. Am sure David Raup, David Jablonski and James Hopson would be in agreement with me (I'm merely mentioning them since you were so kind to inform me that you had studied paleontology with them.).

John K:

While I'm here, I would like to clarify one issue and explain another.

First, let's get clear on what we're arguing about. Would you agree that if cryptic species are common, that would make it difficult to distinguish punctuated speciation from punctuated anagenesis using the fossil record?

Second, let me drop another couple of names. I first encountered the cryptic species problem (which I believe I've mentioned I am not making up) in a class on speciation team-taught by Jerry Coyne and Paul Sereno. I wish I could remember whose paper it was; there was a nice figure that explained it simply. But the case is also stated nicely in the book Genetics, Paleontology, and Macroevolution by Jeffrey S. Levinton, which I recommend quite aside from his treatment of this particular point.

John Harshman said:

John Kwok said: Would you care to explain that to generations of systematic paleobiologists, John? Your comment is utterly without merit and is absurd. Am sure David Raup, David Jablonski and James Hopson would be in agreement with me (I'm merely mentioning them since you were so kind to inform me that you had studied paleontology with them.).

So your whole argument here is just name-dropping, while reading minds. Hey, and they're my names you're dropping. I'm hardly the first person to bring up this problem. It's surprising you haven't run into it before. And that isn't an answer.

John Harshman said: John K: While I'm here, I would like to clarify one issue and explain another. First, let's get clear on what we're arguing about. Would you agree that if cryptic species are common, that would make it difficult to distinguish punctuated speciation from punctuated anagenesis using the fossil record? Second, let me drop another couple of names. I first encountered the cryptic species problem (which I believe I've mentioned I am not making up) in a class on speciation team-taught by Jerry Coyne and Paul Sereno. I wish I could remember whose paper it was; there was a nice figure that explained it simply. But the case is also stated nicely in the book Genetics, Paleontology, and Macroevolution by Jeffrey S. Levinton, which I recommend quite aside from his treatment of this particular point.

John Harshman said:

John Kwok said:Carl Brett, Niles Eldredge, and Brett's students (I believe one of Eldredge's too) have published a number of papers on their work, but I don't have the references handy.

Brett's online CV only mentions one of them, unless the titles aren't very suggestive. I'm a bit stuck.

John Harshman said:

John Kwok said:Carl Brett, Niles Eldredge, and Brett's students (I believe one of Eldredge's too) have published a number of papers on their work, but I don't have the references handy.

Brett's online CV only mentions one of them, unless the titles aren't very suggestive. I'm a bit stuck.

John Kwok said: I might also add that I have other, more immediate, priorities than compiling a Carl Brett bibliography on your behalf, of which the most pressing one is finishing a revised draft of an unpublished novel that I expect to start shopping to potential literary agents sometime next month. As far as I am concerned, this discussion is now over. Hope yours is a good day, John.

Deklane said:

John Kwok said: I might also add that I have other, more immediate, priorities than compiling a Carl Brett bibliography on your behalf, of which the most pressing one is finishing a revised draft of an unpublished novel that I expect to start shopping to potential literary agents sometime next month. As far as I am concerned, this discussion is now over. Hope yours is a good day, John.

There's a novel here all right. I envision it told from the standpoint of a normal mortal caught in the crossfire between two mighty wizards flinging arcane magical spells at each other along with elegant insults that may sound like professions of deep respect but have hidden zingers. The observer doesn't know what the fight is about or why the wizards are mad at each other, he doesn't understand the spells or even the insults, but the fireworks are certainly impressive to watch.

John Kwok said:

Deklane said:

John Kwok said: I might also add that I have other, more immediate, priorities than compiling a Carl Brett bibliography on your behalf, of which the most pressing one is finishing a revised draft of an unpublished novel that I expect to start shopping to potential literary agents sometime next month. As far as I am concerned, this discussion is now over. Hope yours is a good day, John.

There's a novel here all right. I envision it told from the standpoint of a normal mortal caught in the crossfire between two mighty wizards flinging arcane magical spells at each other along with elegant insults that may sound like professions of deep respect but have hidden zingers. The observer doesn't know what the fight is about or why the wizards are mad at each other, he doesn't understand the spells or even the insults, but the fireworks are certainly impressive to watch.

No, mine is a near future alternative history post-cyberpunk novel set in the USA and Europe. If I wanted to write what you've described, then I would have written it.

Deklane said:

John Kwok said:

Deklane said:

John Kwok said: I might also add that I have other, more immediate, priorities than compiling a Carl Brett bibliography on your behalf, of which the most pressing one is finishing a revised draft of an unpublished novel that I expect to start shopping to potential literary agents sometime next month. As far as I am concerned, this discussion is now over. Hope yours is a good day, John.

There's a novel here all right. I envision it told from the standpoint of a normal mortal caught in the crossfire between two mighty wizards flinging arcane magical spells at each other along with elegant insults that may sound like professions of deep respect but have hidden zingers. The observer doesn't know what the fight is about or why the wizards are mad at each other, he doesn't understand the spells or even the insults, but the fireworks are certainly impressive to watch.

No, mine is a near future alternative history post-cyberpunk novel set in the USA and Europe. If I wanted to write what you've described, then I would have written it.

Er... you did write it. Just now.

When will I learn to be quiet and let the grown-ups talk? I was just expressing in humorous terms my reaction to the exchange of views you and John Harshman just had. Way over my head but fascinating to watch. You two might as well be mighty wizards engaging in combat over matters I know nothing about (Clarke's line about advanced science seeming like magic appropriate here). But when it counts you're on the same side, and I'll leave it at that.

John Kwok said: Species have been well defined by generations of paleobiologists John, especially those working in micropaleontology and invertebrate paleobiology. I suggest you start looking at the history of paleontology instead of telling me who taught you paleontology at the University of Chicago. Your point is utterly without merit, unless you are discussing vertebrate paleobiology.

I strongly disagree since I have been careful to refer to morphospecies, from the very beginning, in case you haven’t noticed. As for Levinton’s work - I have ample respect for it - but I think here he’s mistaken.

As far as I am concerned, this discussion is now over. Hope yours is a good day, John.

John Harshman said:

John Kwok said: Species have been well defined by generations of paleobiologists John, especially those working in micropaleontology and invertebrate paleobiology. I suggest you start looking at the history of paleontology instead of telling me who taught you paleontology at the University of Chicago. Your point is utterly without merit, unless you are discussing vertebrate paleobiology.

Oddly enough, you also say:

I strongly disagree since I have been careful to refer to morphospecies, from the very beginning, in case you haven’t noticed. As for Levinton’s work - I have ample respect for it - but I think here he’s mistaken.

So when I say it, I'm ignorant, but when Levinton says it, you have great respect. Interesting. Now if you really meant to refer only to morphospecies, we would have no argument. But in that case you couldn't also be talking about lineage splitting, since lineage splitting refers to biological species. A single morphospecies can include several biological species, which is my point, and a new morphospecies can arise without any splitting event, which is also my point.

As far as I am concerned, this discussion is now over. Hope yours is a good day, John.

By my count, this is the third time the discussion has been over. We'll see if third time is the charm.

John Kwok said: Levinton is in the distinct minority and he has made much of the same arguments since the mid 1970s. Again, you need to follow this: I reject his criticisms of Punctuated Equilibrium, especially when there major evolutionary biologists, including several of his Stony Brook colleagues, who accept tis reality (though they do not go as far as Eldredge and Gould and Pigliucci might in suggesting that we are in need of an "Extended Modern Synthesis". Again I am sorry, but this discussion really has to end. I have a very bad cold which need to shake off and must return to my writing.

John I said that morphospecies from the very outset could hide species complexes of cryptic species, sympatrically-derived species and ring species. All you have done is recycle arguments that Levinton and a handful of others, such as the late Thomas J. M. Schopf (a former colleague of Raup's at Chicago), were saying from the early 70s to early 80s. Sorry I have no interest in playing that game, and moreover, if you are so interested in quote mining me, then you have ample time to dig up work by Brett, Eldredge and their students, including one of Carl's former students, an Evangelical Protestant Christian, Keith Miller, who was actively involved in the Kansas Board of Education debates in the prior decade.

John Kwok said: Levinton is in the distinct minority and he has made much of the same arguments since the mid 1970s. Again, you need to follow this: I reject his criticisms of Punctuated Equilibrium, especially when there major evolutionary biologists, including several of his Stony Brook colleagues, who accept tis reality (though they do not go as far as Eldredge and Gould and Pigliucci might in suggesting that we are in need of an "Extended Modern Synthesis".

Again I am sorry, but this discussion really has to end. I have a very bad cold which need to shake off and must return to my writing.

John Kwok said: John I said that morphospecies from the very outset could hide species complexes of cryptic species, sympatrically-derived species and ring species. All you have done is recycle arguments that Levinton and a handful of others, such as the late Thomas J. M. Schopf (a former colleague of Raup's at Chicago), were saying from the early 70s to early 80s. Sorry I have no interest in playing that game, and moreover, if you are so interested in quote mining me, then you have ample time to dig up work by Brett, Eldredge and their students, including one of Carl's former students, an Evangelical Protestant Christian, Keith Miller, who was actively involved in the Kansas Board of Education debates in the prior decade.

Nope it is not an argument based on authority, John. Really advise you learn something about stratigraphy and sedimentology. As for Schopf, he edited and published the 1972 Eldredge and Gould punctuated equilibrium paper for a symposium volume published by W. H. Freeman, and still regarded Gould as a friend when he died unexpectedly from a heart attack in the early 1980s. As for Levinton, his wife has worked closely with Eldredge in the past (So purely for personal reasons I have no interest in attacking him.).

John Harshman said:

John Kwok said: John I said that morphospecies from the very outset could hide species complexes of cryptic species, sympatrically-derived species and ring species. All you have done is recycle arguments that Levinton and a handful of others, such as the late Thomas J. M. Schopf (a former colleague of Raup's at Chicago), were saying from the early 70s to early 80s. Sorry I have no interest in playing that game, and moreover, if you are so interested in quote mining me, then you have ample time to dig up work by Brett, Eldredge and their students, including one of Carl's former students, an Evangelical Protestant Christian, Keith Miller, who was actively involved in the Kansas Board of Education debates in the prior decade.

You display a distinct stripe of paranoia. Nobody is quote-mining you. I've tried to engage your argument honestly, as I see it. But I don't see you doing much. Nor have you answered my claims other than to reject them out of hand, and drop names of people who may agree with you, without attempting to explain why my argument is wrong. Feel free not to reply.

John Kwok said: Nope it is not an argument based on authority, John. Really advise you learn something about stratigraphy and sedimentology.

As for Schopf, he edited and published the 1972 Eldredge and Gould punctuated equilibrium paper for a symposium volume published by W. H. Freeman, and still regarded Gould as a friend when he died unexpectedly from a heart attack in the early 1980s. As for Levinton, his wife has worked closely with Eldredge in the past (So purely for personal reasons I have no interest in attacking him.).

Sorry John, I have sought to answer your questions again and again, but you seem disinterested in paying heed to what I have said. As for quote-mining, you have done that - or have at least come close - by cutting and pasting comments I had written.

John Kwok said:

John Harshman said:

John Kwok said: John I said that morphospecies from the very outset could hide species complexes of cryptic species, sympatrically-derived species and ring species. All you have done is recycle arguments that Levinton and a handful of others, such as the late Thomas J. M. Schopf (a former colleague of Raup's at Chicago), were saying from the early 70s to early 80s. Sorry I have no interest in playing that game, and moreover, if you are so interested in quote mining me, then you have ample time to dig up work by Brett, Eldredge and their students, including one of Carl's former students, an Evangelical Protestant Christian, Keith Miller, who was actively involved in the Kansas Board of Education debates in the prior decade.

You display a distinct stripe of paranoia. Nobody is quote-mining you. I've tried to engage your argument honestly, as I see it. But I don't see you doing much. Nor have you answered my claims other than to reject them out of hand, and drop names of people who may agree with you, without attempting to explain why my argument is wrong. Feel free not to reply.

Sorry John, I have sought to answer your questions again and again, but you seem disinterested in paying heed to what I have said. As for quote-mining, you have done that - or have at least come close - by cutting and pasting comments I had written.

Kwok, at the moment you are coming across as someone so unwilling to admit error that you are willing to simply obfuscate until the other person gives up in disgust. If you have a specific rebuttal, make it. I don't believe that you can, actually.

Malchus said: Kwok, at the moment you are coming across as someone so unwilling to admit error that you are willing to simply obfuscate until the other person gives up in disgust. If you have a specific rebuttal, make it. I don't believe that you can, actually.

Kwok, neither of us had engaged in any ad hominems at all - your ignorance of that particular fallacy is interesting.

And I might add that your counter-point does not actually address Harshman's argument. Apparently you are unable to do so.

Malchus said: And I might add that your counter-point does not actually address Harshman's argument. Apparently you are unable to do so.

John Kwok said: I have told John Harshman that there are stratigraphic sections which document continuous sedimentation, and it is in those locations where one could see lineage-splitting events that could be seen as examples of speciation (Assuming that you also sample broadly enough to ensure that you are not picking up the first appearance of some immigrant taxon.). He doesn't have a background in stratigraphy and sedimentology and doesn't like my answer.

I also said that since I view these as morphospecies, that it is possible that we are missing out on cases of cryptic species or of subsequently sympatric speciation.

However, I disagree with him that the problem is as serious as he contends.

Neither you nor John Harshman have a background in stratigraphy and sedimentology and therefore, you aren't qualified to criticize me, or even resort to ad hominem attacks.

As far as I am concerned this discussion is now over.

John Harshman said:

John Kwok said: I have told John Harshman that there are stratigraphic sections which document continuous sedimentation, and it is in those locations where one could see lineage-splitting events that could be seen as examples of speciation (Assuming that you also sample broadly enough to ensure that you are not picking up the first appearance of some immigrant taxon.). He doesn't have a background in stratigraphy and sedimentology and doesn't like my answer.

But I do have a background in stratigraphy and sedimentology. At least I took a course in it. The reason I don't like your answer is that it isn't an answer. You would have to explain how to distinguish splitting from anagenesis in one of two or more cryptic species.

I also said that since I view these as morphospecies, that it is possible that we are missing out on cases of cryptic species or of subsequently sympatric speciation.

But if they're morphospecies, they have no necessary connection to splitting events. If there are cryptic species, a new morphospecies, even with a perfect depositional record, could be the result of something other than a splitting event.

However, I disagree with him that the problem is as serious as he contends.

I'm not even sure you understand what the problem is. At least you've been dancing around it for quite a while without a straight answer. Now we could have a real discussion about the crux of it all, i.e. how common cryptic species are. That is in fact the only relevant matter to discuss, but you don't seem to realize that.

Neither you nor John Harshman have a background in stratigraphy and sedimentology and therefore, you aren't qualified to criticize me, or even resort to ad hominem attacks.

Stratigraphy and sedimentology aren't relevant to the central question, even if I didn't know anything about them. And I do anyway. Still, you could try to educate us. What about stratigraphy, etc., renders the cryptic species problem nonexistent?

As far as I am concerned this discussion is now over.

...for the fifth time, by my count, though I may have missed one or two.

John Kwok said: I'm not interested in posting more "spilled ink" over this.

Have a good day John. C'est fini.

John Harshman said:

John Kwok said: I'm not interested in posting more "spilled ink" over this.

No, we haven't been repeating a debate, since the original didn't involve, on one side, simple accusations of "you don't know stratigraphy".

Have a good day John. C'est fini.

6th time.

John Kwok said: You have not addressed any of my arguments with regards to stratigraphy and sedimentology, so I have to wonder whether you have a background.

Anyway, if you read your history of science, you will see that similar - if not identical - arguments have been made for years.

Where we might agree is realizing that Punctuated Equilbrium itself does not pose a direct challenge to the Modern Synthesis Theory of Evolution, though there are some who believe it does.

John Harshman said:

John Kwok said: You have not addressed any of my arguments with regards to stratigraphy and sedimentology, so I have to wonder whether you have a background.

You are correct that I have not addressed any of your stratigraphic arguments. In fact I have failed even to recognize that you were making any such arguments. Perhaps you could repeat them here, briefly, so I could try to at least notice them.

Anyway, if you read your history of science, you will see that similar - if not identical - arguments have been made for years.

Not sure which arguments you mean here, or what history of science you mean. Is there indeed a history of PE somewhere?

Where we might agree is realizing that Punctuated Equilbrium itself does not pose a direct challenge to the Modern Synthesis Theory of Evolution, though there are some who believe it does.

That depends on what you think the content of PE is. I think the original formulation does constitute a challenge to the Modern Synthesis, in that it requires a mechanism that prevents adaptive evolution except under special conditions (speciation in small, peripheral populations). Since we know of no such mechanism, acceptance of PE would suggest that the synthesis is be least very incomplete. Now, if you reduce PE to the idea that there is widespread stasis, that doesn't necessarily conflict at all.

John Kwok said: I have said more than once that if you have a stratigraphic section that shows continuous sedimentation and you sample broadly enough to rule out the arrival of immigrant taxa, then the lineage-splitting event is probably at the very least, a morphospecies speciation event.

As for how you are reading Punctuated Equilibrium, even as far back as the early to mid 1970s, none other than Ernst Mayr regarded it as a simple extrapolation of allopatric speciation as applied to the fossil record (which, I might add, is what Eldredge himself was hinting at in his very first paper on it - approximately a year before the Eldredge and Gould 1972 paper which formally introduced Punctuated Equilibrium).

Both points I have made more than once and you have either ignored them or dismissed them. Really have no more time to discuss this further.

Sorry John, I strongly disagree with all of your points. You seem to think that cryptic species are far more common, when, having studied with David Jablonski, you should have garnered some insight with regards to the role of larval dispersal in affecting the survival of species, especially during mass extinctions (If we have widely distributed organisms that rely upon larval dispersal, then it wouldn't be possible to have sufficient reproductive isolation occurring that would result in cryptic species.). If cryptic species were really a problem, then I doubt that prominent neontologists like Douglas Futuyma and Massimo Pigliucci, would recognized the reality of evolutionary stasis.

The most interesting aspects of Punctuated Equilibrium are its recognition of evolutionary stasis and that species are real entities that have births and deaths. Not once have you addressed these.

Anyway this discussion has gone on far enough. I am still trying to fight off a bad cold and must return to my writing.

John Kwok said: Sorry John, I strongly disagree with all of your points.

You seem to think that cryptic species are far more common, when, having studied with David Jablonski, you should have garnered some insight with regards to the role of larval dispersal in affecting the survival of species, especially during mass extinctions (If we have widely distributed organisms that rely upon larval dispersal, then it wouldn't be possible to have sufficient reproductive isolation occurring that would result in cryptic species.).

If cryptic species were really a problem, then I doubt that prominent neontologists like Douglas Futuyma and Massimo Pigliucci, would recognized the reality of evolutionary stasis.

The most interesting aspects of Punctuated Equilibrium are its recognition of evolutionary stasis and that species are real entities that have births and deaths. Not once have you addressed these.

Anyway this discussion has gone on far enough. I am still trying to fight off a bad cold and must return to my writing.

John Harshman said:

John Kwok said: I have said more than once that if you have a stratigraphic section that shows continuous sedimentation and you sample broadly enough to rule out the arrival of immigrant taxa, then the lineage-splitting event is probably at the very least, a morphospecies speciation event.

Yes, you have said this more than once. And every time I have pointed out that this isn't true. You can't equate a morphospecies speciation event (which is nothing more than a difference between earlier and later populations) with a lineage-splitting event unless you make the assumption that no cryptic species are present. Continuous sedimentation is irrelevant. The very best record, even preservation of every individual in the populations, will not distinguish morphological change with lineage splitting from morphological change without splitting in one of a set of cryptic species.

As for how you are reading Punctuated Equilibrium, even as far back as the early to mid 1970s, none other than Ernst Mayr regarded it as a simple extrapolation of allopatric speciation as applied to the fossil record (which, I might add, is what Eldredge himself was hinting at in his very first paper on it - approximately a year before the Eldredge and Gould 1972 paper which formally introduced Punctuated Equilibrium).

Not just allopatric speciation: Mayr's particular model of allopatric speciation, or peripatric speciation. Mayr's model requires that most of the time, in large populations, the existence of "coadapted gene complexes" prevents response to selection. Only in small, isolated populations, in which drift can overcome selection, can a "genetic revolution" allow rapid change. This is the original mechanism of stasis and rapid change assumed by PE. We can now be pretty sure that Mayr's ideas were just wrong. PE is thus left with a choice: find a new mechanism by which stasis can be broken only during speciation (which is the challenge to the modern synthesis), or abandon claims to be a theory about speciation and just talk about stasis (my second option).

Both points I have made more than once and you have either ignored them or dismissed them. Really have no more time to discuss this further.

7th time. Yes, you make your points over and over, and over and over I explain why they're wrong, and you never respond except to repeat your original claim.

John Kwok said:

Malchus said: And I might add that your counter-point does not actually address Harshman's argument. Apparently you are unable to do so.

It does Malchus but you are simply too dense to realize it. I suggest you delve into the literature and learn something about stratigraphy and sedimentology. As for not addressing Harshman's points, that's baloney. I have, but he doesn't like my answers.

1) No, if you have very patchy environments which foster reproductive isolation, you would still see speciation occurring. During times of normal, background extinction, those taxa that have broader larval dispersal, would be those least resistant to extinction (and the ones most likely to exhibit long-term evolutionary stasis). i would also suspect that given their broader geographic ranges, it would be hard to separate out cryptic species if they exist within.

2) Instead of arguing with me over the prevalence of evolutionary stasis, at least amongst marine metazoans, dig it up in the literature. That literature does exist. Again I'm not your online library resource.

Malchus said: No, actually you haven't. It's becoming fairly clear that you simply don't understand the problem. You might try learning something about evolutionary biology, John, before jumping to an incorrect position on a point like this. I realize that biology isn't your field - computer programming, I believe is your area - but really. Evolutionary biology isn't that complicated.

John Kwok said:

Malchus said: And I might add that your counter-point does not actually address Harshman's argument. Apparently you are unable to do so.

It does Malchus but you are simply too dense to realize it. I suggest you delve into the literature and learn something about stratigraphy and sedimentology. As for not addressing Harshman's points, that's baloney. I have, but he doesn't like my answers.

John Kwok said: 1) No, if you have very patchy environments which foster reproductive isolation, you would still see speciation occurring. During times of normal, background extinction, those taxa that have broader larval dispersal, would be those least resistant to extinction (and the ones most likely to exhibit long-term evolutionary stasis). i would also suspect that given their broader geographic ranges, it would be hard to separate out cryptic species if they exist within. 2) Instead of arguing with me over the prevalence of evolutionary stasis, at least amongst marine metazoans, dig it up in the literature. That literature does exist. Again I'm not your online library resource.

And you Malchus seem incapable of doing anything but hurtling insults at me. Have yet to read one substantial contribution you have tried to make with regards to either sedimentology geology or evolutionary biology in reply to my comments in this thread.

The existence of morphological stasis in the fossil record is something that invertebrate paleontologists in the 19th Century recognized. However, it wasn't until the advent of the Modern Synthesis that we had a younger generation of inverebrate paleobiologists like Eldredge, Gould, Stanley and others, who opted to gain insights from the Modern Synthesis into explaining patterns such as morphological stasis that they were seeing in the fossil record (Though in this case, paleobiology came late to the "game" so to speak, and it was only due to the "Young Turks" like those I have cited.).

As for myself, I was never really interested in determining which mode of speciation was responsible for punctuated equilibrium. Instead, what I found of interest was the long-term persistence of morphologically identical taxa over time, especially the long-term survival of taxa existing in the same, or similar, enviroments, which have been the subject of extensive research by some University of Chicago paleobiologists and their former students.

John Kwok said: 1) No, if you have very patchy environments which foster reproductive isolation, you would still see speciation occurring. During times of normal, background extinction, those taxa that have broader larval dispersal, would be those least resistant to extinction (and the ones most likely to exhibit long-term evolutionary stasis). i would also suspect that given their broader geographic ranges, it would be hard to separate out cryptic species if they exist within.

2) Instead of arguing with me over the prevalence of evolutionary stasis, at least amongst marine metazoans, dig it up in the literature. That literature does exist. Again I'm not your online library resource.

And John, I'm not disputing that there are cryptic species have been present in the history of life prior to the Recent. But all we have for the last five hundred forty-three odd million years is a fossil record based on hard-part shelly invertebrates, and I have to use that data, nothing else, to support the prevalence of morphological stasis at least amongst Marine metazoa.

If you want a relatively recent example of some kind of long-term stasis, may I suggest looking at the work published by Derek Briggs and his team (I don't think he's the lead author BTW) that was published last spring in Nature on the discovery of a Burgess Shale-like fauna in Early Ordovician strata from North Africa. It's evidence like that I base my conclusions, not what Eldredge, Gould, Futuyma or Pigliucci have said.

1) I do in the sense that those taxa that are geographically more broadly distributed - as a result of their laval dispersal strategies - would be the ones most likely to exhibit prolonged morphological stasis.

2) I think we can recognize splitting events in marine Metazoans. Where we can't recognize them obviously is in terrestrial environments since these aren't nearly as well-preserved as nearshore marine ones.

3) No, I believe they are not the same species, but instead, belong to the same clades as the Burgess Shale ones. If you want relevant examples, I suggest you look at Brett et al.'s work for starters. And now you seem to accept morphological stasis as a reality, when for the longest time you were questioning its existence.

John Kwok said: 1) I do in the sense that those taxa that are geographically more broadly distributed - as a result of their laval dispersal strategies - would be the ones most likely to exhibit prolonged morphological stasis.

John Kwok said: 1) I do in the sense that those taxa that are geographically more broadly distributed - as a result of their laval dispersal strategies - would be the ones most likely to exhibit prolonged morphological stasis.

2) I think we can recognize splitting events in marine Metazoans. Where we can't recognize them obviously is in terrestrial environments since these aren't nearly as well-preserved as nearshore marine ones.

3) No, I believe they are not the same species, but instead, belong to the same clades as the Burgess Shale ones. If you want relevant examples, I suggest you look at Brett et al.'s work for starters. And now you seem to accept morphological stasis as a reality, when for the longest time you were questioning its existence.

John Harshman said: Or, if your cold and your novel are too pressing, just stop responding.

John Kwok said: And you Malchus seem incapable of doing anything but hurtling insults at me. Have yet to read one substantial contribution you have tried to make with regards to either sedimentology geology or evolutionary biology in reply to my comments in this thread. The existence of morphological stasis in the fossil record is something that invertebrate paleontologists in the 19th Century recognized. However, it wasn't until the advent of the Modern Synthesis that we had a younger generation of inverebrate paleobiologists like Eldredge, Gould, Stanley and others, who opted to gain insights from the Modern Synthesis into explaining patterns such as morphological stasis that they were seeing in the fossil record (Though in this case, paleobiology came late to the "game" so to speak, and it was only due to the "Young Turks" like those I have cited.). As for myself, I was never really interested in determining which mode of speciation was responsible for punctuated equilibrium. Instead, what I found of interest was the long-term persistence of morphologically identical taxa over time, especially the long-term survival of taxa existing in the same, or similar, enviroments, which have been the subject of extensive research by some University of Chicago paleobiologists and their former students.

John Kwok said:

Malchus said: No, actually you haven't. It's becoming fairly clear that you simply don't understand the problem. You might try learning something about evolutionary biology, John, before jumping to an incorrect position on a point like this. I realize that biology isn't your field - computer programming, I believe is your area - but really. Evolutionary biology isn't that complicated.

John Kwok said:

Malchus said: And I might add that your counter-point does not actually address Harshman's argument. Apparently you are unable to do so.

It does Malchus but you are simply too dense to realize it. I suggest you delve into the literature and learn something about stratigraphy and sedimentology. As for not addressing Harshman's points, that's baloney. I have, but he doesn't like my answers.

You're absolutely right, evolutionary biology isn't complicated at all. What is complicated however, are the perspectives of a neontologist (Harshman) who has worked only with vertebrates and a former invertebrate paleobiologist (yours truly).

Malchus said: Kwok, you were never an invertebrate paleobiologist. As I recall, you took a few courses in the field. Exaggerating your accomplishments wins you no points here.

John Kwok said:

Malchus said: No, actually you haven't. It's becoming fairly clear that you simply don't understand the problem. You might try learning something about evolutionary biology, John, before jumping to an incorrect position on a point like this. I realize that biology isn't your field - computer programming, I believe is your area - but really. Evolutionary biology isn't that complicated.

John Kwok said:

Malchus said: And I might add that your counter-point does not actually address Harshman's argument. Apparently you are unable to do so.

It does Malchus but you are simply too dense to realize it. I suggest you delve into the literature and learn something about stratigraphy and sedimentology. As for not addressing Harshman's points, that's baloney. I have, but he doesn't like my answers.

You're absolutely right, evolutionary biology isn't complicated at all. What is complicated however, are the perspectives of a neontologist (Harshman) who has worked only with vertebrates and a former invertebrate paleobiologist (yours truly).

I propose Ben's Law:

"Given enough time, every conversation which includes John Kwok will eventually become about John Kwok."

ben said:[SNIP}

mrg said:

ben said:[SNIP}

"Eventually"?

LOL!

John Kwok said:

Malchus said: Kwok, you were never an invertebrate paleobiologist. As I recall, you took a few courses in the field. Exaggerating your accomplishments wins you no points here.

John Kwok said:

Malchus said: No, actually you haven't. It's becoming fairly clear that you simply don't understand the problem. You might try learning something about evolutionary biology, John, before jumping to an incorrect position on a point like this. I realize that biology isn't your field - computer programming, I believe is your area - but really. Evolutionary biology isn't that complicated.

John Kwok said:

Malchus said: And I might add that your counter-point does not actually address Harshman's argument. Apparently you are unable to do so.

It does Malchus but you are simply too dense to realize it. I suggest you delve into the literature and learn something about stratigraphy and sedimentology. As for not addressing Harshman's points, that's baloney. I have, but he doesn't like my answers.

You're absolutely right, evolutionary biology isn't complicated at all. What is complicated however, are the perspectives of a neontologist (Harshman) who has worked only with vertebrates and a former invertebrate paleobiologist (yours truly).

I have a master's degree in which my specialty was invertebrate paleobiology and I reviewed several manuscripts that were published in several notable scientific journals. That's more than I can say about you. You'll have to excuse me, but I'm trying to shake off a very, very bad cold.

Malchus/John Kwok said: [A lot of pointless griping about trivial differences.]