“The tree of life is being politely buried”

Platonist said, "what is now being proposed is several different trees of life?" I believe that this is all that can definitely be concluded at the moment. At present I think the term common ancestry is more appropriate than common descent. But this is me personally. Maybe as I read more of the Darwinian literature, I will learn more and change my mind. That is the best place to find the information. Right now SINEs, LINES, pseudo-genes, ERVs and other homologies indicate some commonalities and if one assumes a gene pool of a population that is much larger than what exist today for any species, genera, family, order or class, micro evolution would explain a lot of what we see in the world. But no naturalistic process can explain where all the variation came from. Allen MacNeill shows up periodically and has told us at least 47 times about his 47 engines of variation but as you can see I asked him above for data on what each produced and as of yet have not had an answer. This speculation about an original gene pool is all conjecture but fits the data as far as I know. The origin of these large gene pools is what is truly a mystery. The creation of variation is the issue not natural selection or common elements in various species. It will always be the main issue. jerry

So rather than a universal common ancestor and a tree of life, what is now being proposed is several different trees of life? That mammals and reptiles, birds and dinosaurs have no connection to one another? Platonist

Allen, We have seen your list before and use it constantly as a reference. But is it the source for the original gene pool? How much research is there that these sources which you list really had an effect of the genomes and produced the variety that we see. No one doubts that each has happened. One of the things about human nature is to crow when you are proven correct and I see no crowing about the changes that have been made to separated populations through your laundry list of variation change processes. If such a list exist then we can eat some crow. Another thing that is becoming evident is that many of the so called species are really just variants or slight modifications of each other and represent restrictions on a previously larger gene pool. As populations drift off for whatever reason and face new environments and loose the diversity that existed in their previous population they thus exhibit less variation. How much new variation is being introduced into these separate populations to compensate this lost variation? If you want to get ID's attention such research would do it. Does it exist? Or is is just conjecture? If it does exist, give us the significant results in laymen's terms so all can appreciate it. jerry

Allen, How reasonable do you think it is that there have been multiple origins of fundamentally different life forms? tribune7

In #26 jerry asks: "Where did all the variety in a population originate from?" Here's a list: http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html Allen_MacNeill

Allen, Your reading comprehension skills are lacking and you are starting to sound like the American press. Can you read what I said and not someone else's interpretation of it. Now I admit I am not the best writer and there are others here who are much more precise than I am but I believe the average person should get what I said and not put there own personal spin on it. Which is why I said for you to come here more often to be able to represent ID more accurately and not put your own bias on it. I am not a Deist but a traditional Christian. I believe that life on this earth was created by an intelligent being 3.5-3.8 billion years ago and unlike some ID people who believe in front loading, believe that the evidence points to one or more interventions since that time. Multi-celled animals would be one. Do you give your student the Mike Sherman article to read and to speculate on how the Cambrian Explosion occurred and how a preceding organism must of had all those genes that were not being used but which were necessary for the variety of multi-celled organisms that then unfolded? What process led to that. Any way to clear up your misunderstanding. I am referring to micro evolution alone and that the genome might have been designed to allow small variations to occur and this with the help of the natural selection process (yes, I insist it is a process but it is not an issue but just semantics) allow small variations to arise that adapt to changing environments. But the limits on these changes are such that no novel complex capabilities occur naturally. I say the last because the empirical evidence supports this and neither you, Will Provine, or any other evolutionary biologist has ever been able to demonstrate otherwise. The logic is it can not happen in the time observed. Even if the universe was infinitely old as thought by many till recent and still assumed by some, the sequence of events for life are time bound and the time is not enough for all the parent gene pools to have arisen naturally. So that is my position and except for the possible design of the genome to allow change, is the general position of ID. So most of what you teach in your evolutionary biology course is accepted by ID and it is only when you go off the reservation and allow speculation to become dogma that we disagree. ID are the ones on firm scientific grounds and evolutionary biology for part of its paradigm is ascribing to magic for explanations. jerry

JayM said, "Just to be clear, Jerry, are you proposing an ID variant here? It seems that you’re saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention." No, No, No. All I am saying is that the design of the cell and the organism itself allows for variation to occur and that this makes good design. Once the cell is available and once a multi cell gene pool is available by means unknown but probably due to an intelligent input, a lot of the variants of life play out through naturalistic processes. This is entirely consistent with Behe's Edge of Evolution. "If I understand you correctly, that’s an interesting alternative to traditional ID theory. How would we scientifically demonstrate that intelligence was involved in the those “processes and structures”? Is there a CSI equivalent?" This is my speculation but is entirely consistent with ID and may prove nonsense in the long run. But I wanted to tweak Allen MacNeill who lost his reading comprehension skills when he read my answer. Allen operates under a template that we are dumb here and has to show it with his patronizing answers. I will answer Allen next. I think the evidence points to micro evolution as a major force in providing variety in the world. Look around you and you will see an amazing variety that varies by environment. Most of this can can be explained by micro evolution without producing much new FCSI in the animal world. Apparently the plant world is more likely to combine genomes but I know little of it. The animal world looks like it is more a result of devolution or a narrowing of the original gene pool over time to various sub-populations and these are what we see as the variety. Just plain old micro evolution working to create variety as a population adapts to a different environment. Sort of a vanilla type of evolution but evolution it is. And these types of examples are what the Darwinist exult in to show their theories work. Whoopie Doo. ID accepts all of this and it is trivial but the Darwinists do not realize by using these examples they are undermining their theory which is really the creation of new FCSI. Or in other words where did the original gene pool come from? Where did all the variety in a population originate from? This I do not believe arose through naturalistic means. Now my speculative addition is that the genome itself was designed to allow these minor changes to take place. The error correction eliminates most of the changes and if it didn't then there would be a lot less successful reproduction. But it lets a small amount of variation to get through and this random process allows for some beneficial mutations to take place but never enough that a wholesale amount of FCSI takes place. So I again say this is purely speculative and I have no clue how you would research this but is the genome itself designed to allow this process to proceed. But I will repeat this is pure speculation but even with saying this 10 times or even 20 times people will say I hold this or that ID holds this as gospel. You know the process. jerry

jerry #23 and JayM #24:

"...you’re saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention."

It certainly seemed that way to me, too. If so, jerry, you have essentially adopted exactly the same position taken by Darwin at the conclusion of the Origin of Species. If the universe itself (i.e. purely "natural" processes, such as those described by Darwin) can produce life and living organisms, then the entire purview of ID is limited to the creation of the universe and the natural laws by which it operates. This is, of course, a purview that most evolutionary biologists (myself included) have never aspired to (nor even addressed), and which I believe is completely beyond the scope of any conceivable science. How would one go about empirically validating or falsifying the idea that whatever it was that created the universe did so in such a way as to make possible the origin and evolution of life without the subsequent intervention of an "intelligent designer", a position you seem to be advocating? I have already blogged on the similarity between this position and deism here: http://evolutionlist.blogspot.com/2006/04/is-intelligent-design-distinguishable.html So, jerry, exactly how does your position differ from deism, if indeed it does? Allen_MacNeill

jerry @23

No Allen, the designer is the intelligence that came up with the processes and structures of both the cell and organism and thus enables the population of an organism to adapt to many of the various environments it encounters.

Just to be clear, Jerry, are you proposing an ID variant here? It seems that you're saying that the universe is designed to produce life but that the mechanisms by which that life arises require no intelligent intervention. If I understand you correctly, that's an interesting alternative to traditional ID theory. How would we scientifically demonstrate that intelligence was involved in the those "processes and structures"? Is there a CSI equivalent? JJ JayM

"That “designer” is the environment in which those organisms have evolved." No Allen, the designer is the intelligence that came up with the processes and structures of both the cell and organism and thus enables the population of an organism to adapt to many of the various environments it encounters. In other words, natural selection whether you want to call it an outcome or I want to call it a process (three sub-processes make one long process), is great design by an intelligence. Sometimes the population cannot adapt and then the party's over. jerry

I apologize if I somehow gave the impression that I think that natural selection is a "random process". Nothing could be further from the truth. Natural selection is neither "random" nor is it a "process". Natural selection has three prerequisites: 1) variation 2) heredity 3) reproduction Given these three prerequisites, the outcome is: 4) non-random unequal survival and reproduction, which evolutionary biologists usually refer to as "natural selection". That is, natural selection is an outcome, not a process. The three prerequisites are processes. Several of the processes by which variation is produced include a random component (there is a list of many of these processes at http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html). However, not all of them are random, nor is the outcome (i.e. natural selection) at all random. Indeed, the environment "controls or channels" the outcome of the processes listed, producing the phenotypic characteristics of living organisms (not all of which are adaptations). In other words, it is quite literally the case that there is indeed a "designer" of the myriad characteristics of living organisms. That "designer" is the environment in which those organisms have evolved. Allen_MacNeill

Allen MacNeill said "But neutral or slightly deleterious genetic changes (such as those produced by the vast majority of HGTs) are exactly the opposite of what one would expect to see as the work of an “intelligent designer”. " I think your conclusion is a non sequitur and indicates that you do not understand ID. Your assumption that the intelligent designer doesn't tailor his HGT's to produce adaptive changes is just your assumption and is not based on any logic I know of. The intelligent designer may indeed use random processes knowing that an overall set of boundary and initial conditions will channel these so called random processes to a desired end. That is why natural selection and everything else the latest synthesis dreams of is consistent with ID. What is not consistent with ID are the erroneous conclusions most holders of the latest synthesis have about the power of naturalistic processes to produce novel complex new capacities. Such conclusions have never been demonstrated and for which someone such as Will Provine says he has faith they are true but for which he has no evidence. But it is interesting that you refer to Darwinian evolution as a random process like the works of the intelligent designer you erroneously assumed to operate in a random manner in order to tweak us. I thought the mantra was that Darwinian processes were anything but random. But then you also say that the HGT's can have a beneficial effect so maybe that intelligent designer who was playing cards was using random processes to improve the survivability of the species after all. What is it that you do believe? Not much of anything you said is anything ID would disagree with except your presumption that random processes may not somehow be controlled or channeled. Allen, you really should check in here more often so you understand what ID is all about and won't pass on false assumptions about ID to others. You are a fount of information and for that we are eternally grateful. Just don't wrongfully malign us by misrepresenting us to others. jerry

MacNeill Finds a sparkly new toy and states: Unlike the vast majority of HGTs, these beneficial HGTs rapidly proliferate in the populations in which they arise, in exactly the way Darwin proposed in 1859. Guess we can all forget about the scores of failed predictions of Darwin and blindly follow the God of chance now (note you have not even demonstrated a fitness level increase above parent level in native parent environment, thus falsifying the principle of Genetic Entropy, with this example of variation, nor WILL YOU EVER with any other variation you have listed!!!!, but hey I guess I'm just being picky in actually requiring evolution to stand up to scientific rigor, LOL): You might want to work on these major failed predictions (of Biblical proportion I might add LOL) before you go blowing your own horn: Darwin’s Predictions Cornelius G. Hunter http://www.darwinspredictions.com/ bornagain77

Horizontal gene transfer (especially as the result of viral transduction) has been known to occur for almost half a century. In my undergraduate genetics course (which I took in the spring of 1972) we did a lab in which we used lambda bacteriophage to transfer genetic material from one bacterial colony to another. Ergo none of the mechanisms of HGT described in the article in New Scientist are all that new. Indeed, I have listed at least six mechanisms of HGT in my blog on the "engines of variation" located at: http://evolutionlist.blogspot.com/2007/10/rm-ns-creationist-and-id-strawman.html In that list, they are numbers 28, 29, 33, 36, 40, and 41. Most of these HGT mechanisms have been known for decades and are among the best understood mechanisms of increasing both genetic and phenotypic variation. What is relatively new is the application of the information gained about HGT to phylogenetic reconstruction. As has been pointed out by several commentators, HGT is the rule among bacteria, and apparently occurs fairly frequently among eukaryotes as well. Evolutionary biologists, and especially phylogeneticists and systematists have been using HGT data for phylogenetic reconstruction for over a decade, even among eukaryotes. So, once again this is not new. But, does the increasing recognition of HGT and its use in phylogenetic reconstruction mean that the current theory of evolution is invalid, or that ID can explain these phenomena better? On the contrary, the more we learn about HGT the more it seems to be even more random and undirected than vertical gene transfer (i.e. genetic recombination and heredity via reproduction). To be specific, the overwhelming majority of identified HGTs are of non-coding DNA sequences that have no detectable effect on the phenotypes of the organisms in which it has occurred. That is, almost all of the DNA sequences that have been unambiguously shown to be the result of HGT are sequences that do not code for proteins nor participate in the regulation of coding sequences. Rather, they are sequences that have "gone along for the ride", especially as the result of RNA retroviral HGT. Such sequences are so common that they are routinely used to construct and modify genetic phylogenies, as well as to determine genetic homologies. The vast majority of HGTs are essentially neutral genetic mutations, as first described by Kimura in his neutral theory of molecular evolution. As such, they produce an immense amount of genetic variation without producing a corresponding amount of phenotypic variation. Furthermore, when such phenotypic variation does occur, it is more often deleterious than beneficial (usually mildly deleterious, as pointed out by Tomiko Ohta in her "nearly neutral theory" of molecular evolution). Only very rarely are such HGTs beneficial, and then only in relatively restricted ecological and evolutionary settings. But neutral or slightly deleterious genetic changes (such as those produced by the vast majority of HGTs) are exactly the opposite of what one would expect to see as the work of an "intelligent designer". Such an entity would (as several of the commentators in this thread have suggested) tailor HGTs to produce adaptive (i.e. beneficial) changes in the phenotypes of the recipients of its HGTs. Either that, or the "intelligent designer" doesn't "tailor" its HGTs at all, but rather produces them randomly, rather like a dealer in a card game. But in that case, the actions of a soi dissant "intelligent designer" would be indistinguishable from Darwinian evolution, and including any reference to its actions (and/or inferring its existence) would be unnecessary (and would therefore violate Occam's razor). One last point: although the vast majority of HGTs produce either no phenotypic effect or slightly deleterious phenotypic effects, a relatively small number produce phenotypic effects that are correlated with increased survival and/or reproductive success. Unlike the vast majority of HGTs, these beneficial HGTs rapidly proliferate in the populations in which they arise, in exactly the way Darwin proposed in 1859. That is, they are preserved and passed on (while deleterious HGTs are eliminated), and thereby become more common over time among the populations in which they occur. Allen_MacNeill

Sal Gal #16, Huh? I thought I made it quite clear my comments were directed toward HGT and that hybrid evolution was a distinct but related category. I know there were some individuals who thought early on that HGT applied to higher creatures on a large scale, which would then invalidate the traditional TOL, but that notion did not gain steam until the last couple years AFAIK. So I don't understand the point you are trying to make with me. On a side note, HGT is being inferred primarily because the uneven distribution of information which implies that the information should not have been inherited vertically if unguided processes are presumed to be the cause. But this data is compatible with multiple ID-compatible hypotheses, from intelligent evolution to explicit front-loading to punctuated design to others. It's only with Darwinism that the number of hypotheses is narrowed significantly by these early findings. For ID, hypotheses would be narrowed and rejected based upon further understanding of the overall biological system, and whether or not certain predicted mechanisms exist. Patrick

Hybrid evolution is nothing more than gene flow and is part of micro evolution or whatever the latest evolutionary synthesis is called and in reality is counter "devolution" but not really evolution because the hybrids are from an original larger gene pool and have just been separated. Thus, their combination is not really progress but just back to the future. The new gene pool after the gene flow is still smaller than the original. The last is a slight over statement since there is the possibility for some small mutational increase to either or both of the mating gene pools. Hybridization is completely in sync with ID and Behe's edge of evolution. Interesting topic, but nothing to refute ID. Actually it reinforces ID. So Mike Arnold is conducting ID research and he doesn't even know it. Go Mike!!!!! A question is Sal Gal Semiotic 007? jerry

Patrick,

But just in the last couple years there’s been many indications that the TOL also fails for higher creatures, as mentioned in my comment #1.

No, O'Leary brought up hybrid evolution some time back, and a commenter pointed out that the NSF has been funding investigation of it since 1990. The Darwinian establishment seems rather tolerant of dissenters with data. ;)

Mike Arnold, a full professor in the Department of Genetics at the University of Georgia, is a great example of how a young researcher can challenge mainstream evolutionary theory and succeed, both scientifically and professionally. He includes “web of life” in the list of research interests on his vita. Prof. Arnold literally wrote the book on Natural Hybridization and Evolution (1997), but points to an article that appeared in Evolution three years prior to his birth, “Hybridization as an Evolutionary Stimulus” (1954). He began his investigation of the topic in 1988, as a postdoctoral researcher. When he was hired as an untenured assistant professor at UGA in 1989, he immediately submitted proposals for further research to the National Science Foundation, and won grants in 1990 and 1991. He gave his first invited talk, “Hybrid Zones and the Evolutionary Process,” to the 1990 International Congress of Systematic and Evolutionary Biology. He has made many invited presentations since. You are quite right in indicating that the scientific establishment long resisted the notion that natural hybridization contributes significantly to evolution, but quite wrong in suggesting that present consideration of the possibility is a panicked attempt at patch-up. In the 1950’s, the influential Ernst Mayr argued, as Darwin had, that hybrids had little impact on evolution. When “funny looking” specimens came along, there were several things one might guess they were, other than hybrids. But as methods of genetic analysis improved, evidence accumulated that hybridization might play a greater role in evolution than widely supposed. As best this non-biologist can tell, the current interest in hybridization is data-driven. And Prof. Arnold is a point in case that hard data, obtained through hard work, will gain for a divergent view on evolution not only interested audiences, but substantial research funding. His data “have derived from analyses of population genetics, phylogenetics, reproductive biology, pollinator behavior, eco-physiology, molecular evolution and, most recently, linkage/QTL mapping of fitness traits.” You remark that “these [butterfly metamorphosis] researchers contemplate replacing Darwin’s ‘tree of life’ - the governing paradigm - with a network.” It appears you’ve missed out on some old science news, and have misinterpreted the abstract. Surely if you’d read the full paper you’d have learned that the authors were saying that an idea that began to gain serious consideration two decades ago, and that now has good empirical support, might be useful in explaining metamorphosis. This is a very interesting example of a) the existence of inertia in mainstream beliefs, b) the possibility of gaining attention and funding for divergent notions that are backed by some hard data, and c) institutional support of a young scientist challenging mainstream beliefs. I have to comment, as I have before, that ID advocates do not seek anything as modest as shift of a scientific paradigm, but a radical change in the very meaning of science. To admit non-material (or non-natural, as IDists used to say) causes to scientific explanations would have huge ramifications for all of science, and it is not surprising that funding agencies and academic institutions regard individuals who propose such a thing quite differently than they do divergent thinkers like Mike Arnold.

Sal Gal

Here is a short video of my impression of Rosenhouse explaining that there "nothing to see here" http://www.youtube.com/watch?v=rSjK2Oqrgic Jehu

As for Rosenhouse comments: 1. Magazines regularly use hype to generate sales. The title might have been the product of the editorial staff, not the writer. If Creationists--or any other organization or group--were to misrepresent the scientific information then that would indeed be a problem. But first they have to actually do that...criticizing a group for potential future actions not taken seems pretty low. 2.

In reality, though, the article has only the yawn-worthy old-news that horizontal gene transfer among single-celled organisms means that the metaphor of a tree of life must be modified.

That's not the case. Years ago it was believed that HGT only caused a web for single-celled organisms but the tree of life held firm for higher creatures. But just in the last couple years there's been many indications that the TOL also fails for higher creatures, as mentioned in my comment #1. Never mind if there exists large-scale mechanisms for epigenetic cell heredity exist (aka Lamarckianism revived). Yes, that's still vertical evolution but what if among these epigenetic factors there exists pro-active mechanisms for sampling external information and then passing it on? I've personally said for years than any smart designer would build in the capability to adapt to environments that may change radically, either through latent unexpressed information or by other means such as the above. Patrick

I Like Hunter's conclusion: Conclusions In the century and a half since Charles Darwin proposed his theory of evolution, science has discovered a plethora of contradictory information. Many predictions of the theory have been falsified, including foundational expectations. The theory has consistently failed and as a consequence it has grown far more complex than anything Darwin ever envisioned. Evolution is not a good scientific theory and in this sense it is comparable to geocentrism. Both theories grew ever more complicated in response to the evidences of the natural world, adding epicycle upon epicycle. In stark contrast to these evidential problems, evolutionists believe that their theory is a fact. Evolution is a fact, they say, just as gravity is fact. This remarkable claim is an indicator that there is more to evolution than merely a scientific theory. In light of the scientific evidence, the claim that evolution is a fact may seem to be absurd. But it is not. The fact of evolution is a necessary consequence of the metaphysical assumptions evolutionists make. Metaphysical assumptions are assumptions that do not derive from science. They are made independent of science. These metaphysical assumptions that evolutionists make would be difficult to defend as necessarily true outside of evolutionary circles, but within evolution their truth is not controversial. All of this means that the scientific problems with evolution are relegated to questions of how evolution occurred. The science cannot bear on questions of whether or not evolution occurred. bornagain77

Oops, accidently hit the post button. Let's try again. Interestingly, some Darwinists are complaining about the article itself. On his Evolution Blog, Jason Rosenhouse (also a contributor at Panda's Thumb)bemoansThe Trouble with Science Journalism. Disgusted he writes:

...when science journalists hype some small advance as a fundamental change in our view of the world, it is usually scientists themselves who pay the price for the irresponsible reporting. [We] could have asked for no better illustration of [this] point than the cover of the current issue of New Scientist magazine. The cover sports a big green tree with the words “Darwin Was Wrong.” I hope they sell a lot of magazines with that load of tripe, since they certainly were not thinking about the generations of school kids and church-goers who will now be treated to that cover in every creationist power point presentation between now and the Rapture. How many people do you think will actually read the article to discover what it was, precisely, that Darwin got wrong? If the article, by Graham Lawton, had some real news to report that would justify such a headline, then that would be one thing. In reality, though, the article has only the yawn-worthy old-news that horizontal gene transfer among single-celled organisms means that the metaphor of a tree of life must be modified. Scientific American published a far more informative version of the same article back in February of 2000.

This is perfect example of what Cornelius G. Hunter was talking about on this new website which I wrote about here yesterday. DonaldM

Interestingly, some Darwinists are complaining about the article itself. On his Evolution Blog, Jason Rosenhouse (also a contributor at Panda's Thumb) DonaldM

So life is a like a web and not like a tree? A few years ago I read an article on a young earth creationist site that said essentially the same thing. Only they called it a mosiac instead of a tree. Apparently the young earthers came to this conclusion through dissecting organisms rather than genetic sequencing. Jehu

And thus should end the argument that nested hierarchy is evidence for universal common descent for at least two reasons: 1- Webs to not lead to nested hierarchies 2- Nested hierarchies demand a direction- for example the lower levels have all the characteristics of the higher levels PLUS characteristics defining their set and level. Evolution does not have a direction. Traits and characteristics can be lost or gained all depending on what is provided and what works. So if "twin nested hierarchies" were evidence for UCD, does this count as evidence against it? Joseph

Patrick raises legitimate concerns about just how HGT is identified. Putting these to the one side, if we accept HGT, it seems to me that the only way in which HGT begins to make sense is if you first postulate an "organizational program", present in the genetic code, which is fully capable of utilizing whatever is "tranferred" horizontally. Within the context of a genome that is composed of but 3% genes, and with highly conserved regions existing in non-genic areas of the genome, I think such an assumption of organizational program (OPs) is a sensible one. This could easily mean that what we call basic "body-plans" are, in fact, OPs that have the ability to incorporate HGT genetic sequences. A consequence of such a OP-HGTsequence relationship is a degree of 'independence' between the two. This independence, if it exists, however, puts pressure on the RM + NS scenario of since this independence 'buffers' the OP from NS, thus making it harder to explain the development of the OP in the first place. That is, if the OP can shuffle DNA sequences in and out, then NS is selecting the genetic sequences being shuffled, and not the OP system itself. If the answer to this riddle is simply that the OP was "selected" for while using a "constant" pool of genes, then one has to ask how the 'independence' developed; and, especially, where did the information come from? Nothing but complicated answers arise from such speculations. From an ID perspective, such a interdependent relationship can easily be explained by design; i.e., the "designer" foresaw interchangeability. Thus, drawing on Occham's Razor, ID is the much simpler explanation, and thus offers greater explanatory power regarding what modern-day genomics is daily informing us. PaV

I see that Patrick (#1) has quoted, slightly abbreviated, the two paragraphs I quoted here: https://uncommondesc.wpengine.com/intelligent-design/darwins-big-mistake-gradualism/#comment-302659 My subsequent comments may be a partial answer to bFast's question as to how this impacts ID:

This is particularly fascinating when one considers that most of the genetic manipulation done by humans (a subset of ID) is in fact guided horizontal gene transfer. That bit about “The most likely agents of this genetic shuffling are viruses” is, barring studies on the probability of viruses accounting for such massive HGT in a reasonable timeframe, simply whistling past the graveyard. HGT by an intelligent agent would be expected to be much more efficient than unguided HGT, as we have seen during the last 20 years. It remains to be seen how efficient natural viral or other unguided HGT is, but it is a reasonable bet that it is orders of magnitude too small to reasonably account for the facts as known. This would make excellent research material for someone wishing to do ID-related research. It always amuses me when an opponent of ID asks why the Intelligent Designer (they always mean God in this context) didn’t re-use successful components. The evidence seems to be more and more that He (or he, she, they, etc.) did. The opponents’ rhetoric is coming around to bite them.

Massive HGT is just what we would expect with an intelligent designer. Paul Giem

Paul, If I recall correctly, you are a philosopher. Perhaps you can explain to me the meaning of "probability of abiogenesis." I'm sure you don't have subjective (Bayesian) probability in mind. Are you thinking in terms of objective (frequentist) probability? If the universe is all that has been, is, or ever will be, then there is no logical basis for talking in terms of the relative frequency of universes in which abiogenesis occurs. That is, the universe is not the result of some process that stands outside the universe. How can one speak rigorously of an objective probability of abiogenesis? Sal Gal

bfast wrote: "I fail to see how the article would draw an ID conclusion." You're right -- ID doesn't emerge as the leading competitor directly from these puzzles, which is why Bapteste, Doolittle, et al., vigorously reject ID. Naturalistic evolution with multiple starting points, a mangrove-like geometry, etc., is still naturalistic evolution. To infer ID requires more (some of which Patrick alludes to), which I haven't discussed. Paul Nelson

I fail to see how the articles sited seriously challenge the naturalistic RV+NS paradigm.

It does not, it just changes and narrows the focus. The direct challenge would be if the mechanisms surrounding HGT are found to be limited in capability in biological reality. At that point you'd find some Darwinists backpedaling and claiming that a TOL "must" be the reality. The last ditch fallout shelter would be the claim that the "resolution on our analysis of past events is not perfect" or something to that effect. Patrick

I am still a bit baffled. I fail to see how the articles sited seriously challenge the naturalistic RV+NS paradyme. I fail to see how the article would draw an ID conclusion. As far as the tree of life goes, it would appear that each gene has its own tree of life. If HGT is as ubiquitous as the article suggests, then viewing genes as belonging to an organism isn't ideal, rather, viewing genes as living on islands is more correct, where HGT is "island hopping". Again, it shows unexpected features in biology, but this data does not directly challenge naturalism. It does not directly challenge RV+NS. I would agree with Mark Frank that this is the best example of scientists viewing the Origin as being in error. However, changing the focus from an organism to a gene isn't a huge modification of The Orgin. bFast

I guess this answers Dave's question: Do Darwinists acknowledge flaws in Origin of Species? Mark Frank

Last year we had some Darwinists on UD grating against statements like this:

"The tree of life is being politely buried, we all know that," he says. "What's less accepted is that our whole fundamental view of biology needs to change." and While vertical descent is no longer the only game in town, it is still the best way of explaining how multicellular organisms are related to one another - a tree of 51 per cent, maybe.

Maybe? I've been watching this play out over the years and one thing I've noticed is that the overwhelming creative powers of unguided HGT are inferred from comparing sequence data:

...it is becoming increasingly apparent that HGT plays an unexpectedly big role in animals too. As ever more multicellular genomes are sequenced, ever more incongruous bits of DNA are turning up. Last year, for example, a team at the University of Texas at Arlington found a peculiar chunk of DNA in the genomes of eight animals - the mouse, rat, bushbaby, little brown bat, tenrec, opossum, anole lizard and African clawed frog - but not in 25 others, including humans, elephants, chickens and fish. This patchy distribution suggests that the sequence must have entered each genome independently by horizontal transfer. Other cases of HGT in multicellular organisms are coming in thick and fast. HGT has been documented in insects, fish and plants, and a few years ago a piece of snake DNA was found in cows. The most likely agents of this genetic shuffling are viruses, which constantly cut and paste DNA from one genome into another, often across great taxonomic distances. In fact, by some reckonings, 40 to 50 per cent of the human genome consists of DNA imported horizontally by viruses, some of which has taken on vital biological functions.

40 to 50 percent? Holy moly batman! Well, then unguided HGT which results in beneficial constructive mutations must occur fairly often. But every time I attempt to find information on the OBSERVED capabilities of unguided HGT in higher creatures I've found little to nothing. What about observed limitations of unguided processes? HGT just begs the question of where the original genes came from. If standard vertical evolution didn’t make us what we are, but we resulted from reassembly of genes by HGT shuffles, then where did the original genes come from? We still have no clue of a mechanism for evolution of new genes, to say nothing of the control mechanism for the genes, without which all the genes in the world will be just so much junk. Now if the intelligent evolution hypothesis is true, or partially true, we should be looking for guided inter-species mechanisms for information networking and modification. Obviously they exist to a certain point as seen with plant hybrids, but we're looking for the capabilities of a second category. Patrick