PZ Myers. 2005 Dec 30. A signature of a radiation in metazoan evolution. <http://pharyngula.org/index/weblog/radiation_signature/>. Accessed 2008 Dec 04.
Posted on M00o93H7pQ09L8X1t49cHY01Z5j4TT91fGfr on Friday, December 30, 2005
A signature of a radiation in metazoan evolution
How real is the Cambrian explosion? In a sense, it wasn't an explosion at all in any commonly understood meaning of the term—it was a relatively rapid apparent diversification of animal phyla over the course of at least tens of millions of years, at a rate that is compatible with unexceptional rates of evolution. Even at the most 'explosive' rate that can be inferred from the observations, this is not an event that challenges evolutionary theory, nor should it give comfort to creationists of any stripe.
However, there are controversies here. 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. Some of the molecular data supports an early divergence, and there are known pre-Cambrian trace fossils and fossils—the phosphatized embryos of the Doushantuo formation, about 600 million years old, are a good example.
There are also other ambiguities to be resolved. The relationships of many animal phyla are confusing, and who branched from whom remains to be resolved. In the diagram below, the dashed lines in the tree are the problem: do they branch exactly as shown? How deep in time do those branches go?
The fossil record and evolution of 9 of the 35 currently recognized metazoan phyla suggest that most animal phyla diverged/arose at the beginning of the Cambrian (C) period. The thick lines represent the known ranges of fossils from their first appearance in the fossil record. Thin lines represent the inferred metazoan phylogeny based on fossil data. Dashed lines represent an amalgam of three conservative estimates of the inferred metazoan phylogeny.
Rokas, Krüger, and Carroll have taken an ambitious molecular approach to answer those questions. What they have done is examine 50 genes in each of 17 different species spanning 9 phyla, making a special effort to collect new data from phyla underrepresented in previous work: Porifera, Cnidaria, Platyhelminthes, Mollusca, Annelida, and Priapulida. The goal was to obtain sufficient data to resolve those branches in the animal family tree.
Their results are the kind that are most challenging to present: they were abstract and negative. Despite all their data, an alignment of 12,060 amino acids in proteins from all those phyla, the relationships of many of the taxa remain murky. The diagram below summarizes the tree they found. The numbers at the branches are the results of maximum likelihood/maximum parsimony analyses (big numbers are better, reflecting greater certainty in the validity of the branch point), while branches without numbers were not resolvable statistically.
The lack of resolution in phylogenetic relationships among major metazoan phyla. Values above internodes correspond to support values from ML and MP analyses, respectively. Only internodes with significant support in at least one of the two analyses (ML and MP) or internodes present in majority-rule consensus trees of both analyses are drawn. Analyses were also performed by Bayesian inference. Although certain analyses provided strong support for particular clades, analyses of different subsets of taxa produced significantly different and conflicting results.
Hmmm. All that work, and the branching is still blurry. The investigators evaluated a number of possible problems to see if they were the source of the difficulty. For instance, long branch attraction is a common problem, so they reanalyzed the data, excluding some of the long branched taxa to see if it sharpened up the results. It didn't help.
They speculated that there could be a few "rogue" taxa, whose position in the tree was problematic, so they threw the least stable groups out of the analysis to see if that helped. It didn't.
They didn't think that missing data from some taxa would affect the results, but they reanalyzed, excluding the two phyla with the most incomplete data sets. They were right, it didn't improve their analyses. They tried multiple other approaches to figure out why exactly they couldn't discriminate many of the branch points.
Maybe it's simply a shortcoming of their methods: they don't have the capability to resolve events that occurred several hundred million years ago. To address that, they used their same techniques on a completely different kingdom, the fungi, in which we don't know of any major threshold event comparable to the Cambrian explosion. Those results are diagrammed below; metazoa are in the top half of the tree, while fungal taxa are in the bottom half. The key point is that in most cases, it worked! They could see the relationships of the various fungal taxa with a high degree of statistical significance.
The contrast in phylogenetic resolution between the clades of Metazoa and Fungi. Values above internodes are as in Fig. 1. Eleven out of 13 internodes in the fungal clade are significantly supported by both optimality criteria (ML and MP), whereas only 4 out of 14 internodes in the metazoan clade are significant. Analyses were also performed by Bayesian inference.
One possibility is that, unlike fungal history, the speciation events that produced the metazoan phyla were so tightly compressed that they can't be resolved at this distant remove—in other words, that the Cambrian explosion represented a real burst of macroevolutionary branchiness that occurred in a narrow window of time. They tested this hypothesis with a simulation of another known rapid adaptive radiation, the emergence of the mammalian orders. The mammals diverged 107 million years ago over a span of 42 million years, so the window of time is comparable to that of the Cambrian explosion, only much more recent. They then simulated an additional 500 million years of molecular evolution to produce a data set that could be analyzed, and found again that the passage of that much time would obscure the relationships between the orders.
What they propose, then, is that the lack of resolution is data, and represents a positive signature of an adaptive radiation. They come down on the side of the reality of the Cambrian explosion—it is comparable to other situations in which a lineage rapidly diversifies as it exploits a novel or otherwise empty environment.
An accompanying Perspectives article by Jermiin et al. raises some objections to the analyses that were out of my depth, but in particular mentions that some of the assumptions of homogeneity in rate and site of change in genes are unrealistic, and calls for further detailed study of how genes change over time—they are less pessimistic about the resolvability of the branches, and think there is room for improvement in the study. They suggest that it's a step in the right direction of reconciling paleontological and molecular data, and hint that there are 26 more phyla that haven't yet had a similarly rigorous examination yet…there is much work to be done!
Jermiin LS, Poladian L, Charleston MA (2005) Is the "Big Bang" in animal evolution real? Science 310:1910-1911.
Rokas A, Krüger D, Carroll SB (2005) Animal evolution and the molecular signature of radiations compressed in time. Science 310:1933-1938.
Posted by PZ Myers on 12/30 at 02:19 PM
Science • EvoDevo • 0 Trackbacks • Other weblogs • Permalink
Science • EvoDevo • 0 Trackbacks • Other weblogs • Permalink
- 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?
-
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.#: Posted by on 12/30 at 01:46 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?#: Posted by on 12/30 at 02:02 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. -
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?#: Posted by on 12/30 at 02:37 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.#: Posted by Stephen Erickson on 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?#: Posted by on 12/30 at 02:40 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#: Posted by charlie wagner on 12/30 at 02:45 PM -
Sorry for the partially-overlapping "double" post. Bleh!
#: Posted by on 12/30 at 02:46 PM
-
They don't try to estimate a time, I'm afraid.
Charlie, Carroll and company have something you don't: data. -
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).
#: Posted by Kristine Harley on 12/30 at 04:00 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.#: Posted by on 12/30 at 04:42 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.#: Posted by charlie wagner on 12/30 at 05:08 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.#: Posted by on 12/30 at 05:11 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. -
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.... -
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.#: Posted by on 12/30 at 08:06 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.#: Posted by charlie wagner on 12/30 at 09:05 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.#: Posted by on 12/30 at 09:38 PM -
Heh. He said "priapulid".
#: Posted by on 12/30 at 10:36 PM
- Charlie Wagner was abducted by aliens, but they soon learned not to comply when he asked them to "pull his finger."
-
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. -
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#: Posted by on 12/31 at 02:34 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.#: Posted by on 12/31 at 03:28 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.
#: Posted by on 12/31 at 03:31 AM
-
Any of the professionals here familiar with the discussion of the explosion by Nick Lane in 'Oxygen'?
If so, what do you think of it?#: Posted by on 12/31 at 04:49 AM -
i think it's clear that this is only a preliminary result. more phyla, more groups per phyla and more genes will give better resolution.
#: Posted by on 12/31 at 06:08 AM
-
Bob O'H
Re: estimating divergence dates with molecular data. I'm using a coalescent approach to estimate divergence between two closely-related species, and getting a date of divegence between these species in the late Pleistocene (~400,000 ybp). Unfortunately, the confidence intervals around this date are approximately 100,000 generations. My data are 6 unlinked loci, about 1 kb each, in ~20 individuals from each species. While Rojas et al. have a larger data set (and a really impressive one at that) that is about 10X the size of my data, they are trying to estimate divergence times that are more than 1000 times those that I'm trying to estimate. I would imagine that the statistical confidence would decrease dramatically on any estimates of dates, which Given all the years that have past since the 'explosion', it would be extremely difficult to date divergence and reject the null model that all divergences occurred (roughly) simultaneously, because using any dating method the CIs would be broadly overlapping for most or all of the nodes in question.#: Posted by Bryan Carstens on 12/31 at 07:29 AM -
(Hm, second page isn't showing up here for some reason.)
I have sometimes wondered about where fungi fit in the evolutionary history of life. Do I understand from the charts here that they originate around the time of the C. explosion, like the phyla of animals in question? And are they "contained within" Animalia or not? (I guess this would explain the motility of slime molds
)
#: Posted by Keith Douglas on 12/31 at 09:50 AM -
Hi Alex
But this is one thing that bothers me, it REALLY does not matter how much they worked and how hard, this is no reason to reach conclusions that just cannot be inferred from the data. This is not about rewarding work per se, no matter how impressive or high-tech it is.
If they got their hands on some priapulid tissue, well congratulations, but the taxon sampling remains lousy, despite the fact that so many different genes were done. It is my impression from previous work done by people REALLY trying to solve the phylogeny, that fewer, better chosen genes over a decent taxon sampling will render far more consistent results.
I understand that for the purpose of the argument, the specific sequence of branching is irrelevant (not so if we were reconstructing steps in morphological evolution); however their argument that this is a "natural politomy" DOES require there be not much "sequence of splits" whatsoever, but that we have politomies, right? Therefore phylogeny is doubtlessly being used to inferr "quick evolution". At the very moment we acknowledge that we'd do well to separate the question of cladistics from the question of whether or not the Cambrian "explosion" was really an adaptive radiation or merely a taphonomic artifact, we recognize that the basic argument of the paper is misleading.
If their aurgument relies most heavily on mere simulations on the computer screen, with an entirely different clade, fungi, as the "control", well that's a stretch far beyond my good will, thanks. I expect this work will do better with the crowd of general evolution enthusiasts, all too willing to gape at the 'state of the art' work, than with the people really concerned with the early evolution of the metazoa. Specially because resolution of metazoan phylogeny has progressed, and will continue to do so.#: Posted by on 12/31 at 02:10 PM -
Alex
But this is one thing that bothers me, it REALLY does not matter how much they worked and how hard, this is no reason to reach conclusions that just cannot be inferred from the data. This is not about rewarding work per se, no matter how impressive or high-tech it is.
If they got their hands on some priapulid tissue, well congratulations, but the taxon sampling remains lousy, despite the fact that so many different genes were done. It is my impression from previous work done by people REALLY trying to solve the phylogeny, that fewer, better chosen genes over a decent taxon sampling will render far more consistent results.
I understand that for the purpose of the argument, the specific sequence of branching is irrelevant (not so if we were reconstructing steps in morphological evolution); however their argument that this is a "natural politomy" DOES require there be not much "sequence of splits" whatsoever, but that we have politomies, right? Therefore phylogeny is doubtlessly being used to inferr "quick evolution". At the very moment we acknowledge that we'd do well to separate the question of cladistics from the question of whether or not the Cambrian "explosion" was really an adaptive radiation or merely a taphonomic artifact, we recognize that the basic argument of the paper is misleading.
If their aurgument relies most heavily on mere simulations on the computer screen, with an entirely different clade, fungi, as the "control", well that's a stretch far beyond my good will, thanks. I expect this work will do better with the crowd of general evolution enthusiasts, all too willing to gape at the 'state of the art' work, than with the people really concerned with the early evolution of the metazoa. Specially because resolution of metazoan phylogeny has progressed, and will continue to do so.#: Posted by on 12/31 at 02:11 PM -
Alex
But this is one thing that bothers me, it REALLY does not matter how much they worked and how hard, this is no reason to reach conclusions that just cannot be inferred from the data. This is not about rewarding work per se, no matter how impressive or high-tech it is.
If they got their hands on some priapulid tissue, well congratulations, but the taxon sampling remains lousy, despite the fact that so many different genes were done. It is my impression from previous work done by people REALLY trying to solve the phylogeny, that fewer, better chosen genes over a decent taxon sampling will render far more consistent results.
I understand that for the purpose of the argument, the specific sequence of branching is irrelevant (not so if we were reconstructing steps in morphological evolution); however their argument that this is a "natural politomy" DOES require there be not much "sequence of splits" whatsoever, but that we have politomies, right? Therefore phylogeny is doubtlessly being used to inferr "quick evolution". At the very moment we acknowledge that we'd do well to separate the question of cladistics from the question of whether or not the Cambrian "explosion" was really an adaptive radiation or merely a taphonomic artifact, we recognize that the basic argument of the paper is misleading.
If their argument relies most heavily on mere simulations on the computer screen, with an entirely different clade, fungi, as the "control", well that is a stretch far beyond my good will, thanks. I expect this work will do better with the crowd of general evolution enthusiasts, all too willing to gape at the 'state of the art' work, than with the people really concerned with the early evolution of the metazoa. Specially because resolution of metazoan phylogeny HAS progressed, and will continue to do so.#: Posted by on 12/31 at 03:18 PM -
It is evident to all, I think, that the problem of the 'Cambrian Explosion' cannot be solved from within the boxes of either Darwinism or creationism. The molecular approach - an attempt to solve the problem from the Darwinian side - merely sidesteps the palaeontological issue by substituting a different sort of evidence, still on the assumption that all organisms do have a common ancestor (an assumption which the problem itself is not permitted to challenge). There is, nonetheless, a third way of interpreting the evidence that combines some of the better insights of the other two and avoids the worst! I have every hope that in due time this will be the interpretation that free-thinkers interested in such issues will recognise as Darwinism's principal rival.
http://www.earthhistory.co.uk#: Posted by Steven Robinson on 01/01 at 07:39 AM -
Don't even bother with Robinson's sight. A cursory examination leads one to a conclusion that is obvious from his post. He is clueless.
BTW - many of the graphics used on the sight appear to be outright copyright violations.#: Posted by on 01/01 at 08:13 AM -
Hi Alex
It does not matter how much they worked, but whether their interpretation of the data is correct. The taxon sampling remains unsatisfactory. My impression from work done by others is that fewer, better chosen genes over a better taxon sampling will render more consistent results.
This paper is an argument that there is a NATURAL POLITOMY towards the base of the metazoa. I agree we'd certainly 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. The paper does exactly this mistake, because tree structure is being used to infer time lapses of events. This is not a straight-forward conclusion and as such it fails to convince me. Other factors may still explain the lack of resolution for the battery of 60 genes.
Their argument relies most heavily on simulations on the computer screen using fungi (older, unicellular, not as fossilizable) as a "control". That is a stretch that not everyone will welcome.
I think people involved in the subject may not be too impressed by this work.#: Posted by on 01/01 at 05:20 PM -
Keith,
The experts here should be able to give the correct answer, but meanwhile I managed to dig up some unverified texts, since I got interested too.
First, in http://www.world-of-fungi.org/Mostly_Mycology/Jon_Dixon/fungi_origin.htm there is a timeline from RNA work (due to lack of fossils): "Due to the effect of the variable rates of evolution between the major kingdoms (Animal, plant and fungi), it is still not determined the exact sequence of divergence of the kingdoms. However, estimates of times of key events can still be formulated. Once again, all from evidence inferred from molecular sequence data, it appears that eukaryotes and bacteria shared their last common ancestor around 2000 millions of years ago. Plants, animals and fungi then began to diverge from one another in the region of 1000 millions of years ago. The important event to note here is that plants diverged first, thus fungi and animals shared a common ancestor more recently than either did with plants. The divergence of animals from fungi has been estimated at 965 millions of years ago."
So the animal/fungi split is well before the cambrian event under discussion. (Something I simply assumed from the context of the paper discussed in my argument with charlie.)
And from wikipedia one sees: "Originally classified as plants, fungi are not true plants because they are heterotrophs (they do not fix their own carbon through photosynthesis but use the carbon fixed by other organisms.) Fungi are more closely related to animals, than to plants but unlike animals they absorb their food rather than ingest it and their cells have cell walls surrounding them. For these reasons, these organisms are now placed in their own kingdom, Fungi.
The Fungi are a monophyletic group, meaning all varieties of fungi come from a common ancestor. Mycologists (scientists who study fungi) believe they are monophyletic because they have chitin in their cell walls and are absorbtive heterotrophs, along with other shared characteristics."#: Posted by on 01/01 at 05:51 PM -
Hi guys,
I would like to add one comment:
the middle Hox genes (Hox4-8) are thought to be key genes in the elaboration of the bilaterian body plan, as anterior and posterior Hox genes were already present in Cnidaria.
These 4 genes duplicated form one common ancestor. Interestingly, the temporal succession of their duplication, that you could in principle infer from a phylogenetic tree using the middle Hox genes of one species with the other Hox genes as outgroups is very poorly resolved. And this holds true using the large number of Hox genes that have been cloned and analysed from all major phyla.
So independently from the dataset in Rokas et al., the middle Hox genes, that are likely to have played a major role in the evolution of the bilateral-symmetric body plan, also appear to have evolved in a very short time, without having accumulated enough mutations to resolve the sequence of their duplication.#: Posted by on 01/02 at 08:01 AM -
Well it REALLY does not matter how much they worked, but whether their interpretation of the data is correct. If they got their hands on some priapulid tissue, that’s great, but the taxon sampling remains unsatisfactory. My impression from work done by others is that fewer, better chosen genes over a better taxon sampling will render far more consistent results.
This paper is an argument that there is a NATURAL POLITOMY towards the base of the metazoa. I agree we'd certainly 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. I believe the paper does exactly this mistake. Tree structure IS being used to infer time lapses of events. This is not a straight-forward conclusion and as such it fails to convince me. Other factors may still explain the lack of phylogenetic resolution.#: Posted by on 01/02 at 11:51 AM -
The immediate and scurrilous reaction of ‘Vandalhooch’ is not of course an example of best practice.
My point is worth repeating: It is evident to all (excepting one person, granted) that the problem of the 'Cambrian Explosion' cannot be solved from within the boxes of Darwinism or creationism. This blog has had contributions from both points of view, and they’re not going to lead to any solution. So far as those on the Darwinian side are concerned, moreover, this is because the problem itself is not permitted to challenge the assumption that causes the problem.
I drew attention to my website because of its developing a third, intermediate way through this dilemma. The paper by Rokas et al. illustrates the situation well. Their analysis suggests that fungi have a common ancestor but that the other taxa (phyla) do not. Why not run with this straightforward implication and see where it leads? You will, after all, have the fossil record with you all the way! At the moment the rules seem to be: if an analysis supports our belief in a common ancestry for all life, we’ll accept it; if it doesn’t, we’ll think of reasons why not – a game where ‘heads I win, tails you lose’. Is such a logically closed system really the environment in which science should be practised in this post-Copernican age? Is that really free thought?#: Posted by Steven Robinson on 01/02 at 01:10 PM -
"The immediate and scurrilous reaction of ‘Vandalhooch’ is not of course an example of best practice."
Well, he seems to be correct. You are introducing a lot of unnecessary adhocs. It would point to lack of clues about how science is done, since it tries to avoid these things.
"It is evident to all (excepting one person, granted) that the problem of the 'Cambrian Explosion' cannot be solved from within the boxes of Darwinism or creationism."
That seems to be another hint of lack of clues - it's called 'evolution', not the creationist tag 'Darwinism'. Further you seem to make an unwarranted conclusion - it seems to me biologists and/or most people discussing here expects evolution to eventually make a description, or at least that no other hypotheses will do better.
"Is that really free thought?" It's parsimony, commonly used in science and it's theories.#: Posted by on 01/03 at 04:08 AM -
Hi -
I am Dirk, co-author of the study discussed here. I was largely responsible for the bench work and data preparation, and I am a mycologist by training. To be honest, I would have loved to also look at the fungi more, since of course the fungi with other taxon sampling will show lack of resolution in my opinion. The main thing of this paper is though that given fungi and animals are approximately of the same age (and it would not matter if they are older), why do they differ in resolution. And that the lack of resolution might be a signature of a rapid burst in deep time. There was enough time passed to allow for this lack of resolution to be perceived now. If the animals are older than that, still you would have such lack of resolution.#: Posted by on 01/06 at 10:51 AM