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The Sound of Taxonomy Exploding

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“The phylogeny of the animals is currently incompletely resolved and has undergone major reorganisations over the past few years, mainly as a result of analyses of rRNA gene sequences”…
Kaboom!

Large-scale sequencing and the new animal phylogeny

Although comparisons of gene sequences have revolutionised our understanding of the animal phylogenetic tree, it has become clear that, to avoid errors in tree reconstruction, a large number of genes from many species must be considered: too few genes and stochastic errors predominate, too few taxa and systematic errors appear. We argue here that, to gather many sequences from many taxa, the best use of resources is to sequence a small number of expressed sequence tags (1000–5000 per species) from as many taxa as possible. This approach counters both sources of error, gives the best hope of a well-resolved phylogeny of the animals and will act as a central resource for a carefully targeted genome sequencing programme.

12/23/06 Update: Here’s another article that describes the problem in even more stark terms:

Bushes in the Tree of Life

Quotes of note (my emphasis and brackets):

Here we discuss how and why certain critical parts of the TOL [Tree of Life] may be difficult to resolve, regardless of the quantity of conventional data available. We do not mean this essay to be a comprehensive review of molecular systematics. Rather, we have focused on the emerging evidence from genome-scale studies on several branches of the TOL that sharply contrasts with viewpoints—such as that in the opening quotation [a quote by Dawkins that implies we’ll get the TOL correct eventually]—which imply that the assembly of all branches of the TOL will simply be a matter of data collection. We view this difficulty in obtaining full resolution of particular clades—when given substantial data—as both biologically informative and a pressing methodological challenge. The recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics. Now, as the field is transformed from a data-limited to an analysis-limited discipline, it is an opportune time to do so.”

Three observations generally hold true across metazoan datasets that indicate the pervasive influence of homoplasy at these evolutionary depths. First, a large fraction of single genes produce phylogenies of poor quality. For example, Wolf and colleagues [9] omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom (Figure 2D). Second, in all studies, a large fraction of characters—genes, PICs or RGCs—disagree with the optimal phylogeny, indicating the existence of serious conflict in the DNA record. For example, the majority of PICs conflict with the optimal topology in the Dopazo and Dopazo study [10]. Third, the conflict among these and other studies in metazoan phylogenetics [11,12] is occurring at very “high” taxonomic levels—above or at the phylum level.

For instance, theory [34] and simulation analyses [8] predict that a small fraction of substitutions will be homoplastic by chance (about 2–5%, depending upon model assumptions and evolutionary distances). However, analysis of the elephant/sirenian/hyrax dataset and the coelacanth/lungfish/ tetrapod dataset indicates that the actual level of homoplasy is ~10% of amino acid substitutions in the first case (178 homoplastic/1,743 total substitutions) and ~15% in the second case (588 homoplastic/3,800 total substitutions), several times greater than expected [8,34]. Similar high levels of homoplasy exist in datasets from other bushy clades [35] (unpublished data) and hold irrespective of analytical methodology [8].

Although it may be heresy to say so, it could be argued that knowing that strikingly different groups form a clade and that the time spans between the branching of these groups must have been very short, makes the knowledge of the branching order among groups potentially a secondary concern.”

Comments
Thank you for the primer on the history of biological classification systems. I am reasonably familiar with this topic, but hopefully the information will be useful to others who may be following this thread. Today is a little busy in the real world, but I look forward to continuing our illuminating discussion soon, and trust in your patience in the mean time. If you have a little time today, I would still be interested in your response to my comment #54, regarding hypotheses in ID explanations.Anthemis
December 29, 2006
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Anthemis, Okay I take the blame for not communicating well, I am trying to use two different definitions at once. Let me give you some background on nested hierarchies. Nest hierarchies were invented by Carolus Linnaeus who understood biological organisms to be designed. He wrote in the preface to a late edition of Systema Naturae:
Creationis telluris est gloria Dei ex opere Naturae per Hominem solum -- The Earth's creation is the glory of God, as seen from the works of Nature by Man alone. The study of nature would reveal the Divine Order of God's creation, and it was the naturalist's task to construct a "natural classification" that would reveal this Order in the universe.
Under Linneaus' system not every feature had to fit because it was an "artificial classification." You just needed to get things in a general groups. In this use of the term, there is no problem putting designed things into nested hierarchies. When nested hierarchies are used in the Darwinian sense, features need to line up much more stringently. If the theory is correct, you should be able to describe the exact branching of the tree. But in fact you can't, you can't get any closer than an approximation, which is no better than the system Linneaus divised under the assumption of design. The bacteria/eukaryote/archae is perfect example. It is easy to place organisms into one of the three groups, but good luck trying to find the tree from whence they came.Jehu
December 28, 2006
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Re comment 56: I apologize if I misunderstood you. You posted this statement on Christmas afternoon: "If you tried to arrange things designed by humans into phylogenies you would become frustrated by the mosiac pattern that the unique and shared features form" and this is the one I agree with. Your position now is that "putting cars into makes, models, and years would probably create a nested hierarchy consistent with the highest percentage of parsimony informative characteristics", and this I do disagree with. My wager would be that this exercise would not be able to find any significant phylogenetic structure in the data, and that the resulting cladogram would be very close to an unresolved polytomy (i.e. a comb-like diagram with no two "species" more closely related to each other than to the rest). However, what you or I would wager is not really evidence. I think this would be a genuinely interesting and instructive exercise to try, and the results should be quite publishable. I hope that someone reading this will be inspired to try it.Anthemis
December 28, 2006
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Anthemis,
In reply to Jehu, comment #45: with all due respect, I do not actually make your point, nor do I agree with it, as suggested by the subtle clue in my next sentence “This is very, very, very, very far from being the case with living organisms.” Living organisms overwhelmingly do fit into a nested hierarchy in the way that human-designed artefacts, as we both agree, do not.
Actually we do not agree. You in fact made my point originally. Let's look at what you actually said.
On the contrary, it is not usually possible to arrange human-designed artifacts into an unambiguous nested hierarchy. Try it with cars – should you make the first level split according to engine size, country of origin, manufacturer, fuel source, transmission type, body style, passenger capacity, etc., etc.? Choosing any of these as the primary split will give you a different nested hierarchy, and there is obviously no particular reason to claim that one of these is the “right” or the “natural” one.
To begin with, this is a problem with biological organisms as well. For example, according to the Rokas article, in the elephant/sirenian/hirax clade 64% of parsimony informative mitochondrial features support and alternative tree. In the chordate/arthopod/nematode clade, in a study of over 1000 parsimony informative characters, 57% supported an alternative tree. And as we have already seen, in the bacteria/eukaryote/archae clade there is not tree to speak of. Now with cars, I would wager that putting cars into makes, models, and years would probably create a nested hierarchy consistent with the highest percentage of parsimony informative characteristics. Many features will obviously contradict but hey - that is how it is with biology as well.Jehu
December 28, 2006
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Anthemis, Thanks for finding a copy of the Scientific American article. I was aware the diagram was from that article but I couldn't find it on online. Note that from this article, Doolitte does not believe the evidence supports common descent from a single common ancestor. As the caption states,
This “tree” also lacks a single cell at the root; the three major domains of life probably arose from a population of primitive cells that differed in their genes.
The article notes that the diagram is actually "misleadingly simple."
Though complicated, even this revised picture would actually be misleadingly simple , a sort of shorthand cartoon, because the fusing of branches usually would not represent the joining of whole genomes, only the transfers of single or multiple genes. The full picture would have to display simultaneously the super-imposed genealogical patterns of thousands of different families of genes (the rRNA genes form just one such family).
Unless you have drunk the cool-aid, you have to realize that there is no evidence of common descent in the eukaryote/bacteria/archaea clade. You have to come up with so many hypothesis and theories to explain how the mosiac of features arose by common descent that your claim that common descent is powerful because of its "observations explained per hypothesis" completely fails.Jehu
December 28, 2006
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Jehu, re comment 52: it would help to clarify the basis of our disagreement if you could indicate which component(s) of my assertion you believe are not true. (A) a statement like "the designer chose to provide the Asian tiger mosquito with wings" is a hypothesis. (B) a statement like "the designer chose to provide the monarch butterfly with wings" is a different hypothesis to the one mentioned in (A) (C ) these types of hypotheses are required by ID theory (D) the choices made by the designer to provide different species with wings were made independently of each other (E) there are exactly 761,600 species of living and extinct winged animals (of course there are not, but if you have a more accurate estimate of this number you are welcome to substitute it).Anthemis
December 28, 2006
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Jehu, re comment 51: I could not agree more that many things are more complex in real life than in high school textbooks: evolutionary biology is certainly one of them. I don't have any particular preconception as to how tidy, simple, or elegant the real evolutionary relationships of living organisms and their ancestors will turn out to be - the important thing is to reconstruct them in a way that best accounts for the evidence with the smallest possible number of ad-hoc hypotheses. Regarding the eukaryote/bacteria/archaea clade, those interested can find your diagram in context (always a helpful thing to do) in a 2000 Scientific American article posted at http://shiva.msu.montana.edu/courses/mb437_537_2004_fall/docs/uprooting.pdf. The caption indicates that it is intended as a schematic or symbolic representation of the hypothesis that there was "rampant lateral gene transfer" between the various unicellular lineages that later gave rise to existing prokaryotes and eukaryotes. This is an article in a popular scientific magazine that proposes an idea of how the TOL will look when its roots are better known. To find out which of these links are currently supported by hard evidence, it is necessary to get into the primary research literature.Anthemis
December 28, 2006
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The design explanation requires about 761,600 hypotheses, one for each of the independent choices that the designer made to put wings on each species that has them (about 1,100 species of bats, 10,000 species of birds, maybe 750,000 species of insects, and a few hundred pterosaurs).
That is simply not true.Jehu
December 28, 2006
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Anthemis, Just becuase the theory of common descent can wave its hand and claim a simple explanation for common feature doesn't mean the evidence actually fits the pattern of common descent. And although your theory sounds quite simple in a High School text book, in real life, after you are done with the special pleading horizontal gene transfer, homoplasy, and convergence your theory isn't nearly so tidy and in fact still cannot determine where the branches of the tree of life actually connect. Have you even bothered to see what the “tree of life” looks like for the eukaryote/bacteria/archea clade? I posted the link. http://bp0.blogger.com/_DZH2cmCoois/RXnVrGuxoeI/AAAAAAAAAFs/UNaC28PV_Xw/s1600-h/Doolittle_Web_of_Life.jpg This is an elegant theory?Jehu
December 28, 2006
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DaveScot: I realize that the articles did not mention ID, but some of the commenters here - perhaps not yourself - appear to think that they support the ID position. For instance PaV says "Suffice it to say that IDists would never have gone on this wild-goose chase", bFast says "The map that is being presented looks more like the life is the product of an active genetic engineer", and Jehu says "You end up with branches that don’t really connect. So again, the pattern in nature reflects the pattern of design." However, it is interesting to know that at least some ID proponents accept common descent. I still think that ID requires far more ad-hoc hypotheses than common descent does. Incidentally, I don't think genotype versus phenotype is really the issue here. Both morphological and molecular data can be used in cladistic analysis and the approach is essentially similar for both types of data. For the reasons already discussed, it is possible for there to be apparent inconsistencies within either of these types of study, as well as between them. Many studies combine morphological with molecular data, the "total evidence" approach.Anthemis
December 28, 2006
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Anthemis The design explanation requires about 761,600 hypotheses, one for each of the independent choices that the designer made to put wings on each species that has them This is incorrect. ID has no argument with descent with modification. But that's beside the point since the article made no mention of ID at all. It merely underscores the fact that genotype is often at odds with phenotype and has caused a major reorganization of the tree of life in recent years. Please stay on topic.DaveScot
December 28, 2006
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In reply to Jehu, comment #45: with all due respect, I do not actually make your point, nor do I agree with it, as suggested by the subtle clue in my next sentence "This is very, very, very, very far from being the case with living organisms." Living organisms overwhelmingly do fit into a nested hierarchy in the way that human-designed artefacts, as we both agree, do not.Anthemis
December 27, 2006
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Replying to DaveScot's comment#43: I'm not sure if you are referring to the Rokas and Carroll article or to Philippe and Telford. However, I have in fact read both of these articles, as well as many others. (No-one can read them all, when they come out at a rate of 7,000 or 8,000 per year.) Nowhere do they assert that the ongoing effort to reconstruct the tree of life using phylogenetic methods has been futile or unproductive. Nowhere do they assert that characters are distributed across the animal and plant kingdoms in the sort of random, matrix-filling way that would make it impossible to do cladistic reconstruction. Indeed, they point to the impressive progress that has been made in assembling large parts of the tree, such as recognizing the clade Afrotheria among the mammals, to pick one example out of thousands that they could have chosen. The general outlines of the flowering plant tree, for instance, are largely complete (look up the work of the Angiosperm Phylogeny Group). Because these are both review-type articles, they focus on challenging areas where new types of data and analysis may be needed to resolve questions that have not yet been settled. The type of problems that these papers address are generally to do with the order in which these large, already-assembled portions of the tree should be in turn connected at their bases, reflecting evolutionary events that took place in the very distant past. The Philippe article suggests a new type of data that could be used to clarify some of the points that have not been settled by the methods used to date. This is what scientists do all the time, but it takes time. I personally feel that a more fertile approach than theirs might be the use of so-called rare genomic changes such as large deletions, insertions or transpositions in the genome. These are analogous to whole-word insertions or deletions, and therefore have a much higher information content than the single-letter level nucleotide changes used in most phylogenetic reconstructions to date. (Rokas, A., and W.H. Holland. 2000. Rare genomic changes as a tool for phylogenetics. Trends in Ecology & Evolution 15: 454-459.) I am also well aware of convergent evolution, as are the authors of these articles. Wings are indeed the classic example. The evolutionary explanation is that true wings originated four times, in insects, birds, bats, and the extinct pterosaurs. (Of course, a detailed examination of wings from these four groups shows that, while alike in function, they are radically different in their underlying structure.) Thus, the evolutionary explanation requires 4 hypotheses. The design explanation requires about 761,600 hypotheses, one for each of the independent choices that the designer made to put wings on each species that has them (about 1,100 species of bats, 10,000 species of birds, maybe 750,000 species of insects, and a few hundred pterosaurs). Actually even this is an underestimate, as it leaves out many undescribed or extinct species, as well as all the design choices that were made not to put wings on countless thousands of other species that could have used them. Thus at a conservative estimate the evolutionary explanation is 190,400 times more powerful than the design one, in terms of observations explained per hypothesis. Biologists do not throw convergent evolution around at will as a get-out-of-jail-free card. The algorithms that are used to reconstruct phylogeny are explicitly based on the principle of maximum parsimony, which means, precisely, finding the smallest possible number of instances of convergent evolution that you have to hypothesize to explain the observed data. If you look in any of the dozens of papers published every week on phylogenetic reconstruction you will see examples of "maximally parsimonious trees".Anthemis
December 27, 2006
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It looks like humans have twice as many regulatory genes in common with sharks than fish, even though sharks supposedly diverged from the human lineage 530 million years ago .
Cartilaginous fishes represent the living group of jawed vertebrates that diverged from the common ancestor of human and teleost fish lineages about 530 million years ago. We generated ~1.4x genome sequence coverage for a cartilaginous fish, the elephant shark (Callorhinchus milii), and compared this genome with the human genome to identify conserved noncoding elements (CNEs). The elephant shark sequence revealed twice as many CNEs as were identified by whole-genome comparisons between teleost fishes and human.
Ancient Noncoding Elements Conserved in the Human Genome http://www.sciencemag.org/cgi/content/abstract/314/5807/1892 What would be really cool is if they did a knock-out study of those NCE's, like with the mouse, and found no significant difference.Jehu
December 27, 2006
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Sorry, that last post was botched. Anthemis,
On the contrary, it is not usually possible to arrange human-designed artifacts into an unambiguous nested hierarchy. Try it with cars – should you make the first level split according to engine size, country of origin, manufacturer, fuel source, transmission type, body style, passenger capacity, etc., etc.? Choosing any of these as the primary split will give you a different nested hierarchy, and there is obviously no particular reason to claim that one of these is the “right” or the “natural” one.
You actually make my point. Designed things fit into nested hierarchies as well or as bad as natural things. In order to create a phylogenetic tree, things like horizontal gene transfer, convergent evolution, and homoplasy to make it work and even then specific branches cannot be resolved because genetic parsimony informative characters contradict. For example, let’s look at what the “tree of life” looks like for the eukaryote/bacteria/archea clade. http://bp0.blogger.com/_DZH2cmCoois/RXnVrGuxoeI/AAAAAAAAAFs/UNaC28PV_Xw/s1600-h/Doolittle_Web_of_Life.jpgJehu
December 26, 2006
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Anthemis,
On the contrary, it is not usually possible to arrange human-designed artifacts into an unambiguous nested hierarchy. Try it with cars – should you make the first level split according to engine size, country of origin, manufacturer, fuel source, transmission type, body style, passenger capacity, etc., etc.? Choosing any of these as the primary split will give you a different nested hierarchy, and there is obviously no particular reason to claim that one of these is the “right” or the “natural” one. You actually make my point. Designed things fit into nested hierarchies as well or as bad as natural things. In order to create a phylogenetic tree, things like horizontal gene transfer, convergent evolution, and homoplasy to make it work and even then specific branches cannot be resolved because genetic parsimony informative characters contradict. For example, let's look at what the "tree of life" looks like for the eukaryote/bacteria/archea clade. http://bp0.blogger.com/_DZH2cmCoois/RXnVrGuxoeI/AAAAAAAAAFs/UNaC28PV_Xw/s1600-h/Doolittle_Web_of_Life.jpg
Jehu
December 26, 2006
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anthemis it is not usually possible to arrange human-designed artifacts into an unambiguous nested hierarchy If you'd read the article you'd discover we are finding a lot of ambiguities in the tree of life now as we do it by genotype instead of phenotype. In regard to taxonomy by phenotype you're failing to mention all the many instances of so-called convergent evolution. ToE has all these convenient cop-outs to explain the exceptions to the rules like the rule of nested hierarchies. Wings, for instance, are inherited so that all winged creatures fit into a nested hierarchy, except when they don't then it's convergent evolution so you can have bugs, bats, and birds all in separate groups yet all sharing a common design feature.DaveScot
December 26, 2006
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On the contrary, it is not usually possible to arrange human-designed artifacts into an unambiguous nested hierarchy. Try it with cars – should you make the first level split according to engine size, country of origin, manufacturer, fuel source, transmission type, body style, passenger capacity, etc., etc.? Choosing any of these as the primary split will give you a different nested hierarchy, and there is obviously no particular reason to claim that one of these is the "right" or the "natural" one. Any attempt to use this to develop a phylogeny of cars would be futile, because cars have not evolved by a process of common descent with modification from a single ancestral car. They have been individually designed by engineers who could pick and choose design elements from the whole range of possibilities and combine them in arbitrary ways. You want diesel, you want front-wheel drive, you want it to be a convertible, you want manual transmission …? Yep, we can do that for you. Just about the whole matrix of possible combinations has been tried or could be tried. This is very, very, very, very far from being the case with living organisms. Any given species is put together using a tiny fraction of the possible design solutions available over the whole space of living organisms, and they are combined in a very limited and stereotyped number of ways. This is what makes it possible to do cladistic analysis. Take the springtails. This is a group of small arthropods, most of whom can jump vigorously. They do this using an organ called the furcula on the underside of the abdomen, which is flipped sharply away from the body to propel the animal off the substrate. Jumping is clearly a useful thing to be able to do to escape your enemies or attack your prey, and lots of other animal groups have specialized in it: fleas, flea beetles, salticid spiders, grasshoppers, frogs, gerbils, kangaroos, etc. There are about 8,000 known species of springtails. A few of these have no furcula, but are still clearly and recognizably springtails in every other way. So let's suppose there are 7,500 springtail species with furculas. I don't know how many other animal species are specialized jumpers, but it is clearly a lot. Let's say there are 20,000 of them. EVERY springtail that jumps has a furcula. NO OTHER JUMPING ANIMAL SPECIES ON THE FACE OF THE EARTH has a furcula. The common-descent explanation of these observations requires one uncontroversial fact (that only animals with furculas will have offspring with furculas), and one hypothesis: that all living springtail species are descended from an ancestral springtail species that had a furcula. The design explanation requires 27,500 hypotheses, and it requires them to fall into a very specific pattern. It requires that when each of the 7,500 springtail species was designed, and the time came to implement the jumping function, the designer reached into the tool box and said "OK, let's give this one a furcula." When designing each of the 20,000 other jumping animals, he reached in and said "I think we'll skip the furcula this time – let's try something else. Maybe we'll give it expanded muscles in the hind femur." So in terms of observations explained per hypothesis, the evolutionary explanation in this case has 27,500 times the explanatory power of the design explanation. Note, too, that the common-descent explanation is entirely falsifiable, and therefore testable. This one would be falsified by a single observation of a beetle or a spider with an unambiguous springtail-type furcula. You can choose whichever you like, but general in science we choose single, simple, powerful, testable, explanations over multiple, ad-hoc, weak, untestable ones. There is nothing whatsoever unique or special about this example. The same account could be given for just about any typical character of any taxon. This is why the evolutionary hierarchy of common descent is now almost universally recognized as the fundamental organizing principal of biological taxonomy. Oh, and to forestall one possible complaint, I hear someone say "Your argument is circular because you are using the presence of a furcula to decide whether an animal is a springtail or not". Sorry, not so. Springtails have plenty of other defining characters by which they can be recognized, and a springtail with the furcula chopped off is still very recognizably a springtail.Anthemis
December 26, 2006
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We know the pattern of design because we have things designed by humans all around us. Computers, cars, appliances, wirelss phones. They have designed elements and specific parts in common don't they? If you wanted to you could arrange them into nested hierarchies couldn't you? Yes, very easily. All of these statments are also true about biological organisms found in nature. The pattern of nature fits the pattern of design. The patterns also match if you attempt phylogenies. If you tried to arrange things designed by humans into phylogenies you would become frustrated by the mosiac pattern that the unique and shared features form. (just for the sake of argument because obviously such things don't reproduce) Instead of a phylogenic tree you would get no further then a bush, where the branches don't really connect. And this is exactly what happens with biological oranisms found in nature. You end up with branches that don't really connect. So again, the pattern in nature reflects the pattern of design.Jehu
December 25, 2006
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Yeah, "poof an accident happened" is so much better.DaveScot
December 25, 2006
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I'm saying that using coalescent theory (which is a straightforward and well accepted theory that traces a set of sampled alleles back through time probabilistically generation by generation to a common ancestor and can also be used to simulate data under a specified topology), demographic histories can be found that explain a vast range of observed data. The trick for a given sample of genes, is to find the history that most likely would have generated the observed data. In some cases using standard systematic/phylogenetic methods that don't take these population processes into account will result in the wrong topology. It is somewhat analogous to long branch attraction with parsimony, where distant lineages will attract each other in tree reconstruction because of multiple hit mutations (homoplasy). Evolution is complicated, and there is no way we can solve all problems with one method, but at least we are working on it. We do not search for explanations ad hoc. we use existing theory to best explain the observations. And we recognize when a problem is unsolvable with the available data. Then we go out and get more data. I am not trying to 'predict ' what is going to happen in the future in the sense that you mean. But by trying to reconstruct the past we might find evolutionary patterns that will help us predict what will happen to given species under changing climate or habitat fragmentation, for example, or id areas where we might expect more new species to arise, etc... i'd like to see how ID is more predictive ... i guess "poof it was designed" is a pretty good ad hoc argument. but how does this PREDICT anything hmmm?thecoalescent
December 25, 2006
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coalescent So you're saying that no matter what NDE can explain it. We here already knew evolution can explain everything. It can't predict future evolution at all but it can explain every finding ad hoc. That's sure some powerful theory, huh?DaveScot
December 25, 2006
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"With the human/chimp/gorilla clade it is not 5% that support alternative phylogenic relationships , it is 21% of parsimony informative characters. Is that expected from a model of common descent?" Indeed this is also possible. Theory predicts some situations where, under the right conditions, >50% of the genome will actually support the WRONG topology. In these situations it is not a problem with common descent or with molecular phylogenetics, but simply an artifact of population demographic history. In other words, there may be problems that are difficult or unsolvable using nucleotide composition data alone, but this does not mean that speciation in a common descent framework did not occur.thecoalescent
December 24, 2006
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With all those explosions nowadays, it sounds as if evolutionists are almost finished digging their own grave. With so much evidence against NDE being dug out by the evolutionists themselves all the time there hardly is much need for ID research. I have always been intrigued by this passage by Behe in DBB: “The result of these cumulative efforts to investigate the cell – to investigate life at the molecular level – is a loud, clear, piercing cry of “design” The result is so unambiguous and so significant that it must be ranked as one of the greatest achievements in the history of science. The discovery rivals those of Newton and Einstein, Lavoisier and Schrödinger, Pasteur and Darwin. The observation of the intelligent design of life is as momentous as the observation that the earth goes around the sun or that disease is caused by bacteria or that radiation is emitted in quanta. The magnitude of the victory, gained at such great cost through sustained effort over the course of decades, would be expected to send champagne corks flying in labs around the world. This triumph of science should evoke cries of “Eureka!” from ten thousand throats, should occasion much hand-slapping and high-fiving, and perhaps even be an excuse to take a day off.” Now, ten years later it seems that the time for science to wake up is just around the corner.Dizzy
December 24, 2006
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The fact that 5% of genes support alternative phylogenetic relationships is certainly not unexpected in a common descent framework.
With the human/chimp/gorilla clade it is not 5% that support alternative phylogenic relationships , it is 21% of parsimony informative characters. Is that expected from a model of common descent?Jehu
December 23, 2006
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Please be as specific as possible in explaining how you derive your predictions about this from your hypothesis.
I derive my predictions because it is the pattern I observe in designed things.Jehu
December 23, 2006
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I would be interested to know what you, or other posters here, predict about what the ancestry map would look like if life were “the product of an active genetic engineer”. Please be as specific as possible in explaining how you derive your predictions about this from your hypothesi
Just off the top of my head, you would except the following: 1. Numerous features of common design similar to those in similar organisms but slightly fine tuned for the specific organism. 2. Some unique features not found in similars orginisms. 3. Some features not found in similar organisms but found in unsimilar organisms 3. Features will follow more of a mosiac pattern than a tree pattern. 4. Numerous features that confer a slight benefit but not a "selective advantage."Jehu
December 23, 2006
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I'm not sure that the situation is as desperate as you seem to believe, bFast. It makes sense to me that it would be harder to reconstruct either very recent divergences such as the gorilla/chimp/human one (because there has not been enough time for sequences to diverge much) or very ancient ones such as those between the major animal phyla (because there has been so much time that divergence has overwritten most of the original resemblances). But over vast tracts of the middle ground between very ancient and very recent divergences, there has been massive progress piecing together the relationships. Molecular methods don't have any trouble establishing, say, that gorilla, chimps, and humans, as a clade, are more closely related to each other than they are to lemurs or hedgehogs. Or take a look at this paper that recovers large amounts of well-supported tree-like structure in the largest flowering plant family: http://www.mnh.si.edu/biodiversity/bdg/FunkEtAl2005Supertree.pdf As an added bonus in this one, there is lots of biogeographic structure that is consistent with the phylogeny, just as you would expect if different branches of the tree had diversified in different parts of the world. It may not all yet be "nice and clean" - real life isn't usually. But there are certainly large amounts of hierarchical structure there that looks awfully like a genealogy, whether it's oak-tree like or bush-like, and more of it is coming into focus every day. (This year's total of papers for "molecular phylogeny" on Google Scholar is up to 8,310 today). I would be interested to know what you, or other posters here, predict about what the ancestry map would look like if life were "the product of an active genetic engineer". Please be as specific as possible in explaining how you derive your predictions about this from your hypothesis.Anthemis
December 23, 2006
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The fact that 5% of genes support alternative phylogenetic relationships is certainly not unexpected in a common descent framework. Depending on historical parameters such as ancestral population sizes and divergence times, as well as levels of hybridization and introgression during the initial period of divergence, coalescent theory predicts that a substantial proportion of the genome can reveal incongruent phylogenies. For example, if the size of a common ancestral population (or of the two diverging populations) is fairly large, genetic drift will act much more slowly, and lineages will remain in the diverging populations that reflect the ancestral state rather than the actual population history. The same effect can appear if internodes are short. In other words, genes can show discordant patterns if branches are short and fat. The problem with traditional systematics is that it often ignores population genetics, and the process of speciation is inherently an population genetics problem. There has been a ton of work on this issue but for a good early review see Maddison 1997 (syst biol).thecoalescent
December 23, 2006
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Anthemis, when 5% of the genes studied say that the gorilla is a closer cousin to us than the chimp is, that does not fit the NDE theory. The issue is not the shape of the oak/aspen/peach, its the fact that genetic studies are not supporting a nice clean common ancestry map. The map that is being presented looks more like the life is the product of an active genetic engineer.bFast
December 23, 2006
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