#55750: Arun — 12/30  at  01:46 PM
What argument prevents the Creationist from claiming that the Cambrian explosion is one instance of when design occurred, and that the lack of resolution is because the phyla that emerge from the Cambrian truly did not have a common ancestor?

#55751: — 12/30  at  01:46 PM
Of course the Cambrian was an explosion -- an explosion of fossils. The little critters got going and started making index fossils so us geo-types could correlate strata from widely-separated locations. That really doesn't say much about the first occurance of the phyla,just when they started making fossilizable bits.

There doesn't seem to be any way of generally educating people about deep time, and that helps creationists immensely. But even earth science students -- who presumably want to understand geologic time -- have trouble getting their minds around this stuff at first.

#55753: — 12/30  at  02:02 PM
Hmmm I am missing two major groups there... morevoer, what if morphology DOES provide a robust resolution for some aspects of the tree? Would that then have any bearing on how fast the "explosion" was?
Unresolved phylogenies do not seem an airtight argument to infer suddeness of change. And what about the other molecular estimates of older, precambrian splitting of major phyla? What about the precambrian mollusc kimberella, the excavated galleries? What about the fair possibility that each branch started earlier as smaller, softer and less fossilizable forms?

#55754: Alex — 12/30  at  02:04 PM
Arun-

The observation that this radiation is nested within the larger tree of life should do the trick. That is to say, all of these phyla taken as a whole have antecedents. Having said that, Creationists seem to claim an awful lot of rather questionable things and I have complete faith they will continue to do so.

#55757: — 12/30  at  02:37 PM
I'd agree that the "explosion" of fossilizable body parts probably was a real explosion--this, and possibly the development of eyes, mobility, etc., are the kinds of developments that might well generate a classic predator-prey arm's race: either a given lineage is fortunate enough to get with the program quickly or it's gone. Which may in turn furnish a partial explanation for the "muddiness" of the divergence points. An enormous number of lineages may have gone extinct in a relatively short time, so that we're looking at a visible "explosion" of the fossilizable survivors embedded in a larger (and largely "invisible") mass extinction of the non-fossilizable non-survivors.

I think the question addressed here though is whether the underlying lineage divergences occurred at roughly the same time, or over a longer "deeper" time, or over a short but different time, or what?

This study may suggest that the divergences occurred in a relatively short time, and long enough ago, that the presice sequence of the divergences that led to the existing phyla simply cannot (yet) be cleanly discriminated.

Whether this divergence event and the dawn of fossilizable forms occurred at roughly the same time does not yet appear to be answered, though it is apparently suggested that--like the appearance of fossilizable forms--the divergence event also occurred in a comparably-compressed timeframe.

Does the Carroll et al. study attempt to assign any sort of absolute time to these murky events, PZ, or is it entirely aimed at attempting to discern the divergences themselves in an achronic manner?

#55758: Stephen Erickson — 12/30  at  02:40 PM
It doesn't surprise me that sequence data were unable to resolve such distantly related taxa.

A nifty alternative approach is to use the arrangement (not sequences) of mitochondrial genes in metazoans. From the abstract of Larget et al (2005):

"Genome arrangements are a potentially powerful source of information to infer evolutionary relationships among distantly related taxa. Mitochondrial genome arrangements may be especially informative about metazoan evolutionary relationships because (1) nearly all animals have the same set of definitively homologous mitochondrial genes, (2) mitochondrial genome rearrangement events are rare relative to changes in sequences, and (3) the number of possible mitochondrial genome arrangements is huge, making convergent evolution of genome arrangements appear highly unlikely."

http://mbe.oxfordjournals.org/cgi/content/abstract/22/3/486

The computational difficulties in applying this approach are more difficult than I had originally appreciated when first reading this paper. But they were still able to get some interesting results.

#55759: — 12/30  at  02:40 PM
I'd agree that the "explosion" of fossilizable body parts probably was a real explosion--this, and possibly the development of eyes, mobility, etc., are the kinds of developments that might well generate a classic predator-prey arm's race: either a given lineage is fortunate enough to get with the program quickly or it's gone. Which may in turn furnish a partial explanation for the "muddiness" of the divergence points. An enormous number of lineages may have gone extinct in a relatively short time, so that we're looking at a visible "explosion" of the fossilizable survivors embedded in a larger (and largely "invisible") mass extinction of the non-fossilizable non-survivors.

Despite my musings above, however, I don't think this study directly addresses whether the underlying lineage divergences occurred at roughly the same time, or over a longer "deeper" time, or over a short but different time, or what, than the fossilization event.

This study apparently does suggest that the divergences occurred in a relatively short time, and long enough ago, that the presice sequence of the divergences that led to the existing phyla simply cannot (yet) be cleanly discriminated.

Whether this divergence event and the dawn of fossilizable forms occurred at roughly the same time does not yet appear to be answered, though it is apparently suggested that--like the appearance of fossilizable forms--the divergence event also occurred in a comparably-compressed timeframe.

Does the Carroll et al. study attempt to assign any sort of absolute time to these murky events, PZ, or is it entirely aimed at attempting to discern the divergences themselves in an achronic manner?

#55761: charlie wagner — 12/30  at  02:45 PM
This is old news. I wrote in Sept. 2000:

"The real issue is that for a very long period of time there were only unicellular organisms, bacteria, algae, etc. and then at one point in time, somewhere around 600 m.y.a., a great leap foward occurred and multicellular animals made their appearance all at once, and in a very short period of time. All of the invertebrate body plans were "found" if
you will, in a period of time that was "the blink of an eye" in evolutionary and geological time. After that time, no new body plans were ever found again. One must wonder why this was so.
You can fiddle with the dates and the boundaries, but you can't ignore the larger picture of sudden, widespread appearance of a multitude of different groups of invertebrates. I don't think that this is a scenario that favors the mechanism of mutation and natural selection, which calls for the gradual accumulations of beneficial mutations over long periods of time. And why so many different kinds of animals? And how did they come to be distributed world-wide? These are the questions that keep me awake at night."

and this:

"I agree that all living organisms are related and probably had a common origin. My question addresses the adequacy of copying errors and selection to create the complex and varied body plans that we see appear in the lower Cambrian.
You agree that no one knows the cause of the Cambrian explosion, but why are you so repelled by the possibility that new genetic material may have been introduced from outer space? This is a common reaction that I encounter wherever I go to talk about this subject.
Har-har-har-de-har-har!!! Genes from Space...Right!!!

It seems to me like a plausible alternative to the problem posed by the evidence.
And by the way, I've never believed, and still do not believe that major adaptations of new processes, structures etc. can ever be driven by environmemtal changes. When I first heard the theory about human-chimp divergence being brought on by the ancestral populations being separated by geological changes, I damn near laughed my ass off.
And the oceans...there's a poser. Conditions on the sea floor are fairly uniform from one place to another, yet evolutionists would have us believe that the thousands of different species that live there evolved as a result of differences in their environment.
The evidence for space genes is there, we just have to uncover it. It may take time. We gave darwinism 140 years to find the transitional fossils, and yet, they're still missing, just like they were in 1859.
Maybe you could give us panspermists a few more years, ok?"

and this:

"Darwin himself was more than slightly concerned about the ramifications of the Cambrian explosion. In his book he writes:
"Consequently, if the theory be true, it is indisputable that before the lowest Cambrian stratum was deposited, long periods elapsed, as long as, or probably far longer than, the whole interval from the Cambrian age to the present day; and that during these vast periods the world swarmed with living creatures." (Ch 10, pg 313)
Now Darwin, following the only path available to him at the time, explained this problem as an artifact of preservation. Walcott, in his analysis of the Burgess fauna, took the
same position, that the ancestry of the Cambrian fauna was concealed in sediments that were now buried below the oceans. Now, in the year 2000,
it is clear to us that these rock layers are not missing. In addition, paleontology has revealed to us the rocks of the pre-cambrian (vendian) are not totally devoid of fossils. While there is some evidence for a long period of pre-cambrian evolution, the appearance of diverse,
shelly fossils is sudden, wide-spread, and remains an enigma. It is clearly not an artifact of inadequate preservation.
Now, turning to the time periods involved. I think that it's safe to say that this still remains a controversial issue. I will certainly grant you 20 million years from the Vendian to the first appearance of small, shelly fauna. But the Cambrian explosion is not just a story of hard skeletons, as seen in the Chengjiang and Burgess fauna. Large numbers of soft-bodied groups are represented in a well preserved state, and in widely diversified form. This rapid diversification in the lower Cambrian established all of the major body plans that are present in modern fauna. It is also safe to say that there is still much discussion
and disagreement among the experts themselves as to the relationships of some of the groups, as well as how rapidly the metazoan radiation occurred and what triggered it. In short, both the Chengjiang and the Burgess have presented scientists with as many questions as it answers.
Now if you look at the very oldest of the fossils, they are found in rocks of about 650-700 million years ago, although some doubtful examples have been found in older rocks. But it nowhere approaches Darwin's hope that during these pre-cambrian times "the world swarmed with living creatures". Where there metazoans in the pre-cambrian? Of
course there were. But the "explosion" that is referred to, is not the appearance of metazoans, but the burst of innovation, and the rapid diversification of not only metazoans, but algae and protists as well.
Many explanations have been offered for this momentous event, including changes in the physical environment, critical levels of oxygen in the atmosphere and changes in the chemistry of the oceans. But any plausible hypothesis has to also account for the expansion of soft-bodied groups as well as skeletons. Other explanations are organism
centered, rather than environment centered. Examples include larger size, which may have triggered an increase in complexity or the development of life strategies, such as predation. However, in spite of all the hypotheses, no one emerges as a clear and satisfactory explanation and the emergence of metazoans remains a central enigma in
biology today.
I myself find most of the suggested explanations less than satisfying. Was there enough time for a darwinian mechanism to do the job? We just don't know. We do know, however, that it appears that nearly a billion years passed with no movement towards multicellularity, and then at one point in time, a very rapid expansion and diversification of multi-cellular organisms occurred. It also appears
that while some simple metazoans did exist in older rocks, the burst of innovation and diversification was indeed rapid and widespread, and occurred in a rather short period of time. Now we can argue till kingdom come about what happened but the fact remains that we weren't there and we have damned little evidence to go on.
Therefore I suggest that we follow this path. Continue to collect data, and hopefully in the near future an explanation will emerge that is clear and convincing. But I
think that it's unscientific, given the present uncertainty, to rule out the extra-terrestrial immigration of genetic material from outer space.
You don't eliminate a hypothesis just because you don't like it, or even because there's no present evidence for it. You rule it out if and when it is clearly demonstrated to be false."

Sean (and his associates), while I admire his work, is clearly behind the curve on this.

Read the whole thread HERE:
http://tinyurl.com/7mcz8

#55762: — 12/30  at  02:46 PM
Sorry for the partially-overlapping "double" post. Bleh!

#55766: PZ Myers — 12/30  at  03:32 PM
They don't try to estimate a time, I'm afraid.

Charlie, Carroll and company have something you don't: data.

#55769: Kristine Harley — 12/30  at  04:00 PM
Could the so-called cambrian "explosion" have something to do with the environmental conditions at that time being more condusive, for whatever reason, than were previous eras to fossilization of organisms, and not necessarily an indication of relatively rapid diversification of these organisms? In other words, since the fossil record could represent only a tip of the iceberg in terms of indicating the true numbers of species that have existed, I'm wondering if more creatures were actually fossilized during this time than the previous (due to the environment or, as chilean suggests, there being a plethora of "softer and less fossilizable forms" earlier).

#55772: — 12/30  at  04:42 PM
Well, I'm interested in the evolution of the invertebrates, and I can tell you that the Chaetognatha are a most relevant phylum that were not included in this study, despite the fact that new morphological and molecular analysis coincide in that they are the basalmost protostomes. That was an advance in knowledge right there towards the very base of the metazoan tree. So I don't care how famous Carroll is, if you ignore advances and leave out a phylum with a crucial phylogenetic position, you just cannot realibly blame lack of phylogentic resolution on the suddeness of the cambrian explosion; its easy to get unresolved phylogenies if you weed out groups to ignore advances in phylogeny, right? Looks like they WANT lack of resolution, to be evidence for the explosion, not like they "just tripped on it" doing their best resolve the phylogeny.
I know we live in a DNA-loving world, but morphological evidence can lots of times be consistent with, and predict, the molecular results. An, extensive, consistent morphological analysis is very respectable to me,; yet it was not even considered to try to resolve the metazoan tree. Again, not using this information suggest to me that the intent and conclusion of this paper appear to be something very far from a sincere attempt to resolve the phylogeny. I dont' like it at all.
BTW, I hope that the presence of crackpot commentaries about pangenesis is not any noise relevant enough to drown discussion on my criticism of this work.

#55773: charlie wagner — 12/30  at  05:08 PM
Paul wrote:

"Charlie, Carroll and company have something you don't: data."

Agreed.

And their data supports the views I have been expressing for many years. The cambrian explosion was real, not an artifact and the paleo data is stronger than the molecular data. You wrote:
"One camp holds that the rapid divergence of the metazoan phyla in the Cambrian is real: the different phyla all arose sometime around the boundary, 543 million years ago, and then evolved into the various forms we see now. This interpretation is supported by the fossil record, in which the first recognizable representatives of the phyla are found from roughly the same period.
Another interpretation is that the Cambrian explosion is only apparent: that the divergence occurred well before 543 million years ago, and that there was a long period of undetectable evolution. The major groups of animals separated 600 or perhaps even as much as 700 million years ago, flourished as small wormlike forms that would have fossilized poorly, and what the Cambrian represents is an emergence of larger forms with hard body parts that fossilized well."
The former view is strongly supported by observational data from the fossil record. The latter view is easily debunked (as I stated 5 years ago) by the fact that large assemblages of soft bodied fossils have been discovered in the Burgess and Chengjiang and none show the evidences for these presumed but undiscovered forms.

Credit where credit is due, Paul.

#55774: — 12/30  at  05:11 PM
Well, I think we can be fairly sure that the bilaterian "body plan" was around for a fair amount of time before the "main" Cambrian explosion, based on little verniwhatchahoosis.

And the gene-clock dates--not to mention the fozzilized embryos, tracks, etc.--are also fairly strong evidence that small and simple multicellular animals were, again, on the scene for some fair amount of time before the "explosion"

So, ignoring the "jump" from single-celled to multicelled, which we have no present reason to believe occurred in any kind of "explosion" (though it may well have been a unitary event), we appear to be dealing with at least two semi-"explosive" radiations--the one leading to the diversification of the most-successful phyla, and the one which left us with the Cambrian record of fossilizable creatures.

Maybe these took place at roughly the same time, maybe they didn't. I rather doubt it, frankly, despite my (not particularly original) "arm's race" hypothesis given above).

Once you've got animals "big" and mobile enough to begin directing their own detailed motion on and through the seafloor--rather than just anchoring in place or drifting in the medium--it seems not unreasonable to speculate that a whole wealth of new niches would have opened up.

And, again, once you get the first development of some of the things we actually see in the Cambrian itself--defensive and offensivehard parts, segmented body plans, limbs, eyes, etc.--a whole new arm's race would ensue.

As to Charlie's one-and-only-one radiation of body plans, sigh, as has been explained here and elsewhere many times, this is nothing but hindsight and terminology. A more accurate way of looking back is to "watch" the splitting points coming back together. Whether we call sufficiently long-split lineages different species, different phyla, different kingdoms, is terminology, not some artifact immutably impressed upon the critters themselves.

#55776: Alex — 12/30  at  05:50 PM
Chilean-

I think we'd do well to separate the question of specific cladistic relationships from the question of whether or not the Cambrian "explosion" was really an adaptive radiation or merely a taphonomic artifact. Morphological data are likely more useful for the former than for the latter. Since molecular data are more straightforward to use in quantitative models, we can do nifty things like simulate adaptive radiations and test real-world data against the simulation results. For this purpose, the actual branching order itself may only be of secondary interest.

Of course you are right that an increased taxon sampling would improve this study. But, one should not underestimate the high effort involved in gathering 50 single-copy genes for even a single taxon. This is not something that can be slapped together easily.

#55777: PZ Myers — 12/30  at  06:05 PM
Yeah, one thing I did not emphasize enough was that this was not a study where they just delved into the genomics databases and fished out a bunch of readily available sequences. The authors had to specifically seek out and sequence the genes from a number of those taxa.

Man, I remember the days when cloning and sequencing one gene from a model system was worth a Ph.D....

#55782: — 12/30  at  08:06 PM
That was some awesome statistical analysis, cudos to the authors. They even continued to verify the low resolution/bad data problem which is suspected when throwing out data sets doesn't change results.

charlie,

The main stream hypothesis can not be verified nor ruled out due to lack of data. As you can see from PZ's account, there are still _a lot_ of gene data and phyla to go through.

The hypothesis you suggest is unnecessary and so extremely unlikely a priori that it is deemed crackpot, as you well know. And don't you think this very paper shred it to pieces? It shows that fungi isn't similarly affected by "extra-terrestrial immigration of genetic material" which it should be according to you.

I am sure many biologists are happy that you have brought to their attention the impossibility of panspermia to explain cambrian diversification.

#55783: charlie wagner — 12/30  at  09:05 PM
Torbjorn wrote:

"I am sure many biologists are happy that you have brought to their attention the impossibility of panspermia to explain cambrian diversification."


I'm not so sure that it's a good idea to try and deny the reality of what happened in the Cambrian. the point is valid and you would be well advised to concede it.

"Spectacular Fossils Record Early Riot of Creation"
by John Noble Wilford
New York Times April 23, 1991

"New fossil discoveries in China hailed as among the most spectacular in this century, show the dramatic transformation of life from primeval single-celled organisms to the complex multicellular precursors of modern fauna was more sudden, swift and widespread than scientists had thought.
From cream-colored sediments of what was a sea floor 570 million years ago, paleontologists have extracted specimens of 70 species of trilobites, worms, sponges and various ancestors of crustaceans, spiders and insects. They are not only the oldest such fossils ever found but, more remarkably, their soft body parts as well as skeletal and shell remains are unusually well preserved.
The fossils give scientists their first glimpse of the strange creatures that populated the seas in the early stage of what is known as the cambrian explosion. The cambrian gelogical period, from 570 million to 500 million years ago saw the appearance of increasingly complex marine animals in a riot of shapes and anatomical designs anticipating much of life as it is today"
<snip>
"Dr Jan Bergstrom, a paleontologist at the Swedish Museum of Natural History...said they suggested that the cambrian transition was 'a revolution, perhaps more than evolution'.
Most of the Chinese fossils, Dr. Bergstrom said, resemble species identified in the Burgess Shale..."

[Bergstrom expands on this in his own paper in "Research and Development" (Winter 1991) by pointing out that the Chengjiang fossils are not much different from the Burgess fossils despite their 40 million year difference in time. This is enigmatic, considering the fact that evolution should have been proceeding rapidly during this time, as it
apparently had in the preceeding time period.]
<snip>

"The similarities (with the Burgess fossils) are the basis for the conclusion that the diversification and proliferation of new life forms must have occurred rapidly at the onset on the cambrian period.
"Evolution of these creatures must have been a sudden and widespread phenomenon" Dr. Bergstrom and his colleagues wrote..."
<snip>
"As the full import of the discovery is recognized, scientists are describing the fossils as 'genesis material' and one of the most exciting finds...since the Burgess."
"Dr. Andrew Knoll, a Harvard University expert on early life said:
'We knew from the Burgess that there was a tremendous diversity of life in the Cambrian. Most of everything that was going to happen, all the ways of making invertebrate animals, had already happened by the mid-cambrian. Now it seems that new life forms were invented within the first few million years of the cambrian."
<<snip>
"Dr. Bergstrom said it was quite possible that..."you could have the formation of an entirely new type of animal within thousands of years."

[Or, of course, they certainly could have arrived suddenly on earth from
elsewhere...]

These observations certainly appear to me to be incompatible with a darwinian scenario of variation and selection, based on the slow accumulation of beneficial mutations over a long period of time. In fact, it sort of nails the coffin shut on gradualism, which is the
foundation of darwinian theory. Clearly, the fossil record falsifies the darwinian paradigm.
These discoveries were made 15 years ago. It's old news. It's settled, as far as I'm concerned. The only reason it's still an issue is because so many scientists simply refuse to let go of the darwinian weltanschauung and continually invent new "explanations" and create new obfuscations. Let it go, for god's sake.

#55784: — 12/30  at  09:38 PM
charlie,

On all accounts you are a onetrack mind; if the mainstream theory has not yet proven a certain gap, suggest a most unlikely or already falsified alternative, preferably with "extraterrestrial immigration" or "infinite age of universe" thrown in.

Now it seems you can not even stay on your track. First you say (#55761): "Was there enough time for a darwinian mechanism to do the job? We just don't know." And now you say (#55783): "Clearly, the fossil record falsifies the darwinian paradigm."

What is clear is that you have not yet an digested that the paper under discussion show that your postulated "extra-terrestrial immigration of genetic material" has not affected fungi similarly as invertebrates. This clearly falsifies your hypothesis so it must be ruled out according to your own words (#55761). Let it go, for humanity's sake.

#55786: — 12/30  at  10:36 PM
Heh. He said "priapulid".

#55787: bill — 12/30  at  10:47 PM
Charlie Wagner was abducted by aliens, but they soon learned not to comply when he asked them to "pull his finger."

#55788: Neil — 12/30  at  11:58 PM

Man, I remember the days when cloning and sequencing one gene from a model system was worth a Ph.D....

Not even so long ago - that's more or less what I did for my Ph.D. about 10 years ago. Now I work in a group analysing data from 9 microbial genomes.

Genomics has really revolutionised studies of microbial phylogeny and evolution. I'm sure the same will happen for eukaryotes in the near future, when whole genome sequencing becomes routine enough that many more genomes will become available.

#55789: — 12/31  at  02:34 AM
PZ: thanks for another illuminating commentary. I'm enjoying keeping up with the wider evolutionary literature, without having to go through the papers myself.

A couple of coments:
1. The Jermiin et al. commentary trots out a few standard problems, but without showing how they would affect things. Personally, I'm not too worried about them: they may have an effect, they may not. But they are problems that need to be worked on. Heavy duty stats will be required...

2. The coalescence people have been working on methods to estimate variation in rates of coalescence (from which they can infer different demographic parameters). Something similar could be done with this data: estimate how the rate of divergence changes over time, and see if there's a bump somewhere near the Burgess shales.

Now they've got the data, it deserves to be tortured until it reveals the location of the explosives used.

Bob

#55790: — 12/31  at  03:28 AM
Very facinating discussion, which I'm not really able to appreciate the finer nuances of.

Even the debunking of Charlie adds something, which even makes it worth the time it take to scroll by his posts. Charlie, if you want people to take the time to read your posts, you should add some breaks and empty lines in the text. I don't mind reading your stuff, even though it quite often is nonsense, scientifically pseaking. But I won't waste too much effort on it.

#55791: — 12/31  at  03:31 AM
The resolution problem reminds me a little of optical resolution etc. When sources (or peaks or frequencies) are close together, you need to be close enough (or using a fine enough scale) to be able to resolve them. Too far away, or with too much noise added, and they seem like a single entity, or disappear into the background altogether. Whereas other sources further apart or nearer are easy to resolve as separate objects.