Scientific American: Horizontal gene transfer more common than thought

_{Denyse O'Leary

July 2, 2014

horizontal gene transfer, News}

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And therefore, Darwinism less common, though good luck getting many to draw that out. Here:

There are a few examples of gene swapping between eukaryotes — the domain of life that includes fungi, plants and animals — and even from bacteria to eukaryotes (see ‘Bacterial gene helps coffee beetle get its fix’). But such events, known as horizontal gene transfer, were thought to be rare.

But Daniel Muller, a microbial ecologist at the University of Lyons in France, and his colleagues have cast doubt on that assumption after studying bacteria in the soil around the roots of plants. They found that the bacterial gene acdS, used to promote the growth of plant roots, was also present in several types of fungus. Their work is published today in Proceedings of the Royal Society B.

Muller and his colleagues scanned the genomes of 149 eukaryotes, and found acdS-like genes in 65 of them — 61 in fungi and 4 in parasitic microorganisms called oomycetes, including Phytophthora infestans, the microbe responsible for the Irish potato famine. After analysing the organisms’ genetic family trees, the researchers determined that the most likely explanation was that three different kinds of bacterium had donated the gene to the fungi and oomycetes in a total of 15 different horizontal-gene-transfer events.

Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do. If HGT proves a factor in evolution, it carves a piece out of Darwin’s territory.

See also Horizontal gene transfer from moss to ferns

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Comments

Acartia_bogart, you have displayed an understanding of basic biology. You seem to know about DNA and phenotypes. That's great. But your response does not address the question. Is it correct to assert that the role of variation in evolution is to supply, not just material, but "raw" material? This question arose because it is a form of the original question, which is whether it is correct to say that evolution by HGT is within the realm of Darwinian evolution. I agree that the real issue is not where the variation comes from. This is where people like Ford Doolittle have confused the issues. HGT represents a form of lateral inheritance, and its importance in evolution makes the tree of life more like a net. Darwinians like Ernst Mayr didn't predict this. But neither did anyone else. Biologists didn't predict lateral inheritance, just like we didn't predict hydrothermal vent communities living on hydrogen sulfide, and we didn't predict reverse transcription, and we didn't predict prions or chemiosmotic coupling or non-canonical genetic codes. All of these things were surprises that contradicted simplifying assumptions made previously. So what? We could still have Darwinian evolution if abundant random variation were inserted into organisms from the outside. Furthermore, this variation could include macromutations like the transfer of an entire gene, or the sudden origin of a new gene by duplication. Darwinism doesn't deny that macromutations happen. However, Darwinism *does* deny that macromutations are the basis of evolutionary change. This is the part of Darwinism that is contradicted by HGT. HGT is a challenge to Darwinism, not because the hereditary substances come from outside the organisms, but because, in evolutionary events of HGT, the variations actually incorporated in evolution are macromutations, not "slight" or "infinitesimal" as Darwin demanded in his theory. Their use in evolution violates the doctrine of _natura non facit saltum_. To describe such variations as "raw material" is to abuse the words "raw material". To say that a fully formed, specific sequence is the "raw material" out of which "natural selection" builds a gene, is to abuse the words "raw material". So far your comments have failed to address this issue. The argument that HGT can be included in Darwinism on the grounds that "Darwin couldn't have known this" would be laughable if it weren't so sadly common. If Darwinism is a cult, rather than a theory, then defending the founder of the cult personally is the proper response to a challenge to Darwinism. But this kind of argument has no place in science. Good scientific theories are *supposed* to be predictive. They are supposed to fit facts that haven't been seen yet. They are also supposed to *right*. If they are wrong we reject them, not claim that the original proposer of the theory couldn't possibly have known that the theory was wrong.arlin_{July 8, 2014
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Arlin, based on your reductionist description of raw material, only the four nucleotides (or the atoms composing them) would be considered raw material. This may be true if all you are doing is defining the raw material for DNA. But that is not what we are talking about. We are talking about the raw material that is acted on by natural selection. Natural selection does not act on DNA directly, or the genes coded within it. It acts on the variation within the phenotypic expression of the DNA within a population. So, in short, it doesn't matter where that variation comes from. If it comes from mutations causing a change in a protein, natural selection can act on it. If it comes from the inclusion of a fully functional gene through HGT that is expressed in the phenotype, natural selection can act on it. Even if it comes from the inclusion of new genes in a population due to interbreeding between two related species (or population), natural selection can act on it. All of these processes, and probably more, are sources of raw material for natural selection.Acartia_bogart_{July 7, 2014
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Acartia_bogart, the words "raw materials" cannot be stretched to mean anything. Try googling images for "raw materials". What do you see? Iron ore, bauxite, sand, wood pulp, etc. These are all raw (not processed), used in bulk, and transformed in the process of manufacturing. Paper does not look like wood pulp. Nails do not look like iron ore. Computer chips do not look like sand. Now, let's pretend this is an SAT test and you are faced with one of those "analogy" questions. True or false: raw materials are to finished products as variation is to evolution. When Dobzhansky said that variation was like the raw material entering a factory, he meant it. When the architects of neo-Darwinism said that mutation provided "raw materials", they meant to say that the role of variation in evolution is like the role of sand in making a sand-castle (or a computer chip). They believed that the shape of the individual grains of sand didn't matter, because the sand was used in bulk and transformed. For an educated person or a scientist from the previous century, the concept of a "material cause" was familiar. Aristotle said that a thing can have many causes at the same time. He used the analogy of a house. The bricks and beams are the material from which the house is made. They are material causes. A craftsman assembles the bricks and beams into a house. The craftsman is often called the "efficient cause". Usually when scientists are invoking "forces", they are referring to efficient causes. But there is also a plan or design from which the house is built. That is the "formal cause" that explains why the house has the shape that it does. And ultimately we could say it is the intention of the designer (the real estate developer) that caused the house to be built. That is the "final" or "ultimate" cause. Darwinians refer to selection as an efficient cause, a formal cause, and even as a final cause. They refer to variation only as a material cause. However, a laterally transferred gene is not a raw material. It is not raw, but already evolved. It is not used in bulk (we don't use 1000 laterally transferred genes to make one new gene). It is not transformed by the process of manufacturing (only tweaked). One cannot say fairly that a laterally transferred gene merely provides substance, without providing form. It provides form as well. The shape of the final gene is very much determined, very specifically determined, by the shape of the laterally transferred gene. In fact, that is precisely how laterally transferred genes are identified, because we can tell where they come from! When you say that variation is "raw material", you mean something completely different than what these words are intended to convey. Your argument does not justify the use of "raw materials". You say, literally, that because mutations "result in an increase in variation", they are "raw materials". That is not the definition of a raw material. A raw material is raw, it is used in bulk, it is transformed unrecognizably, and provides substance only, not form. So, the correct answer to the SAT question, is "FALSE". This is not just a problem with old textbooks. Contemporary research papers-- even in evo-devo-- also invoke "raw materials." This is because evolutionary biology is in a state of confusion. Reformers have been saying for years that we need to rethink the role of variation in evolution. It hasn't really happened.arlin_{July 7, 2014
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Arlin:
But once again, you are equating “Darwinian evolution” with any process that involves differential reproduction, and this is a mistake.
I must respectfully disagree. Darwin's original theory was developed with very little knowledge about what mutations were. The mutations that were known at the time were those that resulted in gross, and almost always deleterious, morphological deviations from the norm. That is the context under which he said that the lucky mutation wasn't his idea. What Darwin also wasn't aware of is the process by which certain traits/features could become fixed in a population without them having any known adaptive advantage (i.e., drift). Given this context, it is fair to say that Darwinian evolution really is dominated by differential reproduction.
For instance, every textbook of evolution says that the role of variation in evolution is that it provides “raw materials” for selection. But a laterally transferred gene is not a raw material. It is a fully formed specific sequence, not a pile of atoms. Therefore, the evolutionary theory presented in textbooks is not consistent with HGT.
Again, I must disagree. Natural selection acts on the expression of the genes, not the DNA itself. If a functional gene is transferred from another species, and it is adaptive, natural selection may act to result in it becoming ubiquitous amongst the population. Conversely, if it is deleterious, it may be eliminated by natural selection. So, whether it is a spot mutation that slightly alters a protein, or the transfer of a fully functional gene that codes for a completely new protein (at least for that population), they both result in an increase in variation in that population and, therefore, are raw material that can be acted on by natural selection. But your inference about text books being out of date is a valid one, especially in high schools. All text books, by there nature, can only deal with existing information. And given the length of time it takes to write a text book, the information in them is often many years old by the time it is published. This is made worse by the fact that schools are always dealing with budget issues and they often will use the same text book for many years, even if new versions have been published. Unfortunately, given the speed with which science progresses, I can't see any solution to this.Acartia_bogart_{July 7, 2014
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Sorry if I mischaracterized your position. But once again, you are equating "Darwinian evolution" with any process that involves differential reproduction, and this is a mistake. I realize that this mistake is very common, but that doesn't make it any more defensible. When someone like Allen Orr is giving a keynote address and presenting a mathematical model based on a process in which a mutation appears and is then accepted or rejected, and he calls this "Darwinian adaptation", this is also a mistake. Darwin said that the lucky mutations theory of adaptation was "not mine", and he said this because he did not believe evolution worked in that way. Your statement that "HGT is not inconsistent with modern evolutionary theory because HGT has been known to be common . . . " is also based on a categorical error. The fact that a phenomenon is known by evolutionists does not mean that this phenomenon is consistent with theoretical statements made by the same evolutionists. For instance, every textbook of evolution says that the role of variation in evolution is that it provides "raw materials" for selection. But a laterally transferred gene is not a raw material. It is a fully formed specific sequence, not a pile of atoms. Therefore, the evolutionary theory presented in textbooks is not consistent with HGT. Evolutionary biologists need to work out these inconsistencies. I am confident that they can do so, but one of the first steps is get past the stage of unthinking denial and wooly thinking that allows words to shift in meaning in whatever way seems to defend the past statements of authorities.arlin_{July 7, 2014
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Sorry if I mischaracterized your position. But once again, you are equating "Darwinian evolution" with any process that involves differential reproduction, and this is a mistake. I realize that this mistake is very common, but that doesn't make it any more defensible. When someone like Allen Orr is giving a keynote address and presenting a mathematical model based on a process in which a mutation appears and is then accepted or rejected, and he calls this "Darwinian adaptation", this is also a mistake. Darwin said that the lucky mutations theory of adaptation was "not mine", and he said this because he did not believe evolution worked in that way. Your statement that "HGT is not inconsistent with modern evolutionary theory because HGT has been known to be common . . . " is also based on a confusion. The fact that a phenomenon is known by evolutionists does not mean that this phenomenon is consistent with theoretical statements made by teh same evolutionists. For instance, every textbook of evolution says that the role of variation in evolution is that it provides "raw materials" for selection. But a laterally transferred gene is not a raw material. It is a fully formed specific sequence, not a pile of atoms. Therefore, the evolutionary theory presented in textbooks is not consistent with HGT. Evolutionary biologists need to work out these inconsistencies. I am confident that they can do so, but one of the first steps is get past the stage of unthinking denial.arlin_{July 7, 2014
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Arlin, I have never claimed to be a Darwinian. In fact if you read my comments on other posts you will note that I have taken exception to the creationist approach of calling all evolutionary biologists Darwinists. As such, my comment here was only referring to HGT and Darwinian evolution (i.e., natural selection). And as such, HGT is totally consistent with Darwinian evolution because he did not know what the source of variation was. In fact, he had not ruled out the inheritance of acquired characteristics. And HGT is not inconsistent with modern evolutionary theory because HGT has been known to be common amongst bacteria for many decades now and the theory has been modified to account for it. We now know that it also occurs in multi-celled organisms, but its affects are minuscule as compared to those seen in bacteria. The HGTs that have been seen in "higher" organisms would still be considered "gradual" variations when the entire phenotype is looked at. Unless you are aware of any HGTs resulting in new senses, changed modes of mobility, larger or smaller brains, etc. And once established in an organism's genome, the HGT can be acted upon by natural selection. So, again, how does this cause a problem for either Darwinian evolution or modern evolutionary theory?Acartia_bogart_{July 7, 2014
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Acartia_bogart, the mistake you are making is that you are letting "Darwinian evolution" include anything that involves differential reproduction. This was not Darwin's position. "Gradualism" can mean many things, but one of the things it meant for Darwin was that the variations used in evolution are "infinitesimal" or "slight" (his words), and that they blend together, so that change is always smooth. He was led to this position because he believed that organisms are so exquisitely adapted that they can't have evolved by any process that involved abrupt changes, only by a process that involved continuous shifts. Most scientists in Darwin's time disagreed with this position. Most scientists today disagree with this position. In the theory that Darwin called "natural selection", the struggle for life shapes organisms in response to conditions by shifting a blending mass of infinitesimal variation. When challenged with the idea that his theory was not a theory of evolution, but only a theory addressing the differential survival of whatever "new births" happen to occur, Darwin literally said that this might be a very good theory but it is "not mine". When challenged famously by Fleeming Jenkin with the idea that evolution could not occur by blending, but was more likely by discrete inheritance of sports, Darwin chose deliberately to stake his theory on blending. What makes the Darwinian position unique is that, once you have assumed abundant random infinitesimal variation, then variation merely becomes a "raw material" and external selection is the only true cause at work-- the real explanation for everything. But if this Darwinian position is not correct, then one must look at the internal causes of variation to truly understand creativity and directionality in evolution. Darwinians traditionally dismiss such "internalist" thinking as a form of antiscientific mysticism. The application of Darwin's infinitesimalism to DNA and proteins is obvious. Any sequence can change into any other sequence 1 residue at a time. That is the smallest unit of change, thus it is the Darwinian position. This position has been falsified a million times over in molecular evolution. We know that non-gradual changes such as gene duplications and lateral gene transfers are important in evolution. So, Acartia_bogart, your position is actually not Darwinism. You are a DiNO, a Darwinian-in-Name-Only. You actually do not believe what Darwin believed, and what was accepted by most of his 20th century followers such as Fisher.arlin_{July 7, 2014
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This is irrelevant to the claim News made, but, FWIW: We already know that HGT is not so common that it "severely undercuts" out confidence in phylogeny in general. In some specific cases (like the root of the tree of life)HGT is common enough that the species tree will probably nevery be reconstructed (thought the gene trees can be). In other groups, like plants and animals HGT is so rare it's not a major problem. You account for differences between gene trees and species trees (including some which are direct prediction of simple pop. gen. models) but including many gene tress in your analysis.wd400_{July 7, 2014
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wd400: Isn't it true that if HGT is more common than thought, then one of the repercussions will be that our confidence in phylogenetic trees is severely undercut? How in the world do you know if you're dealing with a "gene tree" or a "species tree"? How do you trace such things?PaV_{July 6, 2014
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A mutation can be vertically inherited. A horizontally acquired piece of DNA can be vertically inherited. So how is this a problem for Darwinian evolution? As far as I can see, it simply broadens the source of variation for natural selection to act on. Since one of IDs arguments with evolution is that the mutation rates in a population aren't sufficient to explain the rates of change, the presence of HGT only weakens this argument because you must now include the mutation rates in groups that are not part of the population. It's basic math and probability.Acartia_bogart_{July 6, 2014
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So, once again, when it comes to HGT, this manner of sharing information has absolutely no means of explaining the ‘origin’ of the information encoded in the section of sequence that is being transferred.
So, tell News this.wd400_{July 6, 2014
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wd400: ID as we know it wouldn't, in my opinion, even exist as it does today without our having entered the "information age." (you know, what Al Gore invented) Because of computers and computer code---the digital age---we understand that "machine" languages, like human languages, encode "information." When we look at the "genetic code," we see 'coded' language. And it is only natural to understand the genetic code as containing information. Just as consonants and vowels provide the sounds by which we communicate language, sounds which are then translated into written form, so it is with the biological code, except in this case it is not 'sounds' but 'nucleotides.' Now language, quite obviously, cannot exist without there being some kind of delimitation of 'sound' itself. We know that intelligent agents know how to delimit these sounds, and that the whole gambit of human languages 'delimit' the spectrum of sounds to form individual languages. When it comes to the genetic code, that which is 'delimited' is, as already state, the sequence of nucleotides. The question then is: what is responsible for this delimitation? The neo-Darwinian answer is: chance. This is not acceptable. Sir Fred Hoyle, an atheist (are you paying attention "Evolve"?) did a simple calculation with cytochrome C and concluded that its having coming into existence by "chance" was completely unlikely and illogical. The alternative to this is "intelligence," since we know that intelligent beings have brought into existence so many known and living languages. So, for the vast majority of IDists, the only concern we have with neo-Darwinian=Darwinian mechanisms is this: can it help provide an explanation for the kind of delimitation that marks the genetic code. So, once again, when it comes to HGT, this manner of sharing information has absolutely no means of explaining the 'origin' of the information encoded in the section of sequence that is being transferred. Do you see what we're getting at here? We're defending no one. You have, on the other hand, a proclivity of nit-picking every post here at UD. It's your not so subtle way of saying: "You don't know what you're talking about." You seem to take some sort of morose delectation in this habit. I, on the other hand, find it annoying. However, it is always good to have someone around to keep us honest. We need to be challenged---yet, hopefully, also understood.PaV_{July 6, 2014
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Evolve, instead of accusing Theists of bad motives, you are welcome to present evidence that information can be generated by unguided material processes and settle the issue once and for all! Three subsets of sequence complexity and their relevance to biopolymeric information - Abel, Trevors Excerpt: Three qualitative kinds of sequence complexity exist: random (RSC), ordered (OSC), and functional (FSC).,,, Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC. FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, Testable hypotheses about FSC What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses: Null hypothesis #1 Stochastic ensembles of physical units cannot program algorithmic/cybernetic function. Null hypothesis #2 Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function. Null hypothesis #3 Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function. Null hypothesis #4 Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time. We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified. http://www.tbiomed.com/content/2/1/29bornagain77_{July 6, 2014
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wd400, Creationists will jump on to anything that breaks the pattern of vertical descent because it provides them a chance to invoke their magician-in-the-sky. So you'll see them making a lot of noise about HGT, orphan genes and similar phenomena. Creationists, If HGT happens with one or a few genes, then there are a lot of other genes that are acquired by normal vertical descent. So family trees and inter-species relationships can still be constructed and deciphered using those vertically transmitted genes. Phenomena such as HGT, de novo gene synthesis leading to the formation of orphan genes etc are fully expected in a natural setting. They don't support the presence of your imaginary designer. Now get over it.Evolve_{July 6, 2014
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OK, I'll try and catch the typos if y'all try and catch the meaning of what I say. Once more, from the top. News thinks that HGT and "Darwinism" are competing explanations on some level "If HGT happened, Darwinism didn't; if HGT explains some event Darwinism's domain is reduced). As both PaV and JDD say (while apparently defending News?) this is not the case. To take from JDD, HGT and doesn't answer questions about the origin of "information" 'in the slightest'. It would be silly to say "that which inheritance explains Darwinism doesn't", why isn't just as silly to say the same for HGT?wd400_{July 5, 2014
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wd400:
Just for the sake of absolute clearness. HGT describes the path by which a given gene ended up in a genome. It’s doesn’t preclude that the so-called “information” in the gene arose by natural selection, or that the gene’s being fixed in a population is the result of natural selection (the gene, once inside a genome being just another variant to potentially be selected for or against).
As a favor to us, (I already cleaned it up a bit) when you're in a hurry, can you check your spelling and grammar errors. Sometimes it's a bit much. And it looks like you're hurried. But, . . . Having said this,................ You don't seem to realize that what you suggest is an "assumption" made by Darwinists, yet to be proven. IOW, where did the information come from? The usual "Get-Out-Of-Jail" card for this question is to simply say: "Oh, but that's an OOL question." This, of course, is equivalent to saying: "Well, the question of how "dogs" came about is unknown; but, what we do know is that these 'breeds' are the result of artificial selection." This, to me, frames quite well where both sides stand. We want to know where the 'dogs' came from. For 'breeds,' we have evidence; for the "origin of dogs," we do not.PaV_{July 5, 2014
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(1) HGT event transfers existing DNA from one organism to another (2) The recipient of the DNA may have a new function from this act of HGT (3) HGT is only concerned with the transfer of pre-existing DNA (4) As a result, in this context new functionality received by this recipient organism is not occurring through mechanisms of gradual change through random mutation of an organism's existing DNA to produce, through selection, new function. (5) Therefore, HGT does not explain addition of new information, but rather borrowed information (6) Therefore, this does not fit under Darwinian evolution in the strictest sense as it is not explaining how that functional information arose from non-functionality. It merely explains a transfer. Now this does not mean it is not a mechanism that evolution can use, but we are still left with the problem of how the information rose in the first place, which is the main cause and driving force behind what ID asks, hence the criticism of HGT being given so much weight as a mechanism to explain some of evolution (and failing to address the bigger question). For example, if you had 2 different computers and they were running many different programs, and you wanted to know who wrote the code for each program on the individual computers. If you found identical programs on each, and knew that one computer was older than the other, you would not answer the question "who wrote this program" by saying "it was transferred over from computer A to computer B." That is how it got onto that computer, but not who programmed it or how it was programmed. As the context of this forum and what we are asking and additionally, what Darwinism seeks to ask (how did functionality arise), it seems fair to say that HGT does not answer that in the slightest. I do not hence understand why there is such "confusion" over this one statement. I.e. if a new function in an organism came from borrowed information from another organism then you cannot attribute that specific event to Darwinian mechanisms. You may argue that the original gene in the donating organisms did arise through Darwinian mechanisms but aside from that being an assumption, it is irrelevent when talking about the context of how that organism gained this new function if HGT was involved. It was HGT, not Darwinian evolution.Dr JDD_{July 5, 2014
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wd400, I've read Mung's comments and they are not mistaken. I've read your comments and you are not only mistaken but intellectually dishonest! Moreover, only one person on this thread is getting paid to believe in Darwinism, and it is not Mung! Lynn Margulis Criticizes Neo-Darwinism in Discover Magazine (Updated) - Casey Luskin April 12, 2011 Excerpt: Population geneticist Richard Lewontin gave a talk here at UMass Amherst about six years ago, and he mathemetized all of it--changes in the population, random mutation, sexual selection, cost and benefit. At the end of his talk he said, "You know, we've tried to test these ideas in the field and the lab, and there are really no measurements that match the quantities I've told you about." This just appalled me. So I said, "Richard Lewontin, you are a great lecturer to have the courage to say it's gotten you nowhere. But then why do you continue to do this work?" And he looked around and said, "It's the only thing I know how to do, and if I don't do it I won't get grant money." - Lynn Margulis - biologist http://www.evolutionnews.org/2011/04/lynn_margulis_criticizes_neo-d045691.htmlbornagain77_{July 5, 2014
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Mung,I read your comment. Twice now. You are mistaken.wd400_{July 4, 2014
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Acartia_bogart:
Hence my argument that ID takes credit for all things that are good and lays all things that are bad on evolution. If ID is correct then the designer must also be responsible for heritable diseases like Huntingtons, haemophilia, Marfans, Tay Sachs, colour blindness, sickle cell, etc.
This is just moronic. ID admits that arguments such as yours can be bad and yet still be the result of intelligent design. Of course, since by your own admission your posts cannot reliably be distinguished from nonsensical ramblings, I should certainly not assume that anything I write will be understood by you. But you're not the only one who reads these posts.Mung_{July 4, 2014
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wd400:
It’s it really this difficult for IDists to admit one of their fellow-travellers is confused?
No. In fact, Salvador Cardoza, who at least claims to be an ID'ist, regularly deletes my posts from his threads. But given that you never responded to my post, it's not at all clear to me that you aren't the one who is confused. Since you seem to have missed it:
Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do
That’s true by definition. What’s your problem?Mung_{July 4, 2014
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Acartia_bogart, you claimed that vertebrates in the early Cambrian would falsify evolution, when shown vertebrates were in the early Cambrian, you suddenly said you made an error. How convenient! That is moving the goal posts whether you admit it or not. How about becoming even more honest and admit nothing will ever falsify Darwinism in your mind because of your philosophical (atheistic) bias? :) Now that would REALLY be an honest admittance of an error! ,,,You are shown evidence that bacteria have been the basically the same, both morphologically and molecularly for as far back as we can measure (hundreds of millions of years), and you do not consider that a problem for Darwinism. If you worked for me I would fire you on the spot for stating such an insane statement! Neo-Darwinism, the modern synthesis, (which wd400 defends tooth and nail) is dependent on the central dogma being true. Thus finding "The genome is an ‘organ of the cell’, not its dictator” is a direct contradiction to the primary tenet of the modern synthesis. Since you readily admit this view is false, do you now want to ditch wd400 and his defense of the modern synthesis, and leave him on his own, and now join James Shapiro in the 'natural genetic engineering' camp? Or perhaps Kaufman in the self organization camp? How life changes itself: the Read-Write (RW) genome. - 2013 Excerpt: Research dating back to the 1930s has shown that genetic change is the result of cell-mediated processes, not simply accidents or damage to the DNA. This cell-active view of genome change applies to all scales of DNA sequence variation, from point mutations to large-scale genome rearrangements and whole genome duplications (WGDs). This conceptual change to active cell inscriptions controlling RW genome functions has profound implications for all areas of the life sciences. http://www.ncbi.nlm.nih.gov/pubmed/23876611 Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf Also of interest from the preceding paper, on page 22, is a simplified list of the ‘epigentic’ information flow in the cell that directly contradicts what was expected from the central dogma (Genetic Reductionism/modern synthesis model) of neo-Darwinism. etc.. etc..bornagain77_{July 4, 2014
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Ba77: "Acartia_bogart, nice of you8 to move the goal posts when shown vertebrates are in the early Cambrian. " It is nice to see that when someone admits an error, you ascribe it to something else. I envy the fact that you are infallible. You must be proud (and insufferable). "I’m certainly not ‘picking nits’ to say that modern bacteria have not varied from ancient bacteria." Reading comprehension was never your strong suit, was it? I said that I was the one who was picking nits. "You claim that variation of modern bacteria proves that bacteria have far more plasticity than what we witness for ancient bacteria, yet:" When did I say this? I simply said that the lack of genetic variation in populations would falsify evolution. None of your references suggested that genetic variation within any population, modern or ancient, was not present. "The modern synthesis is falsified mainly because it is now shown that,,, “The genome is an ‘organ of the cell’, not its dictator” - Denis Nobel – President of the International Union of Physiological Sciences" It is "NOW" shown? Where have you been for the last 40+ years? It has been well understood for at least half a century that the expression of many genes, and the impact on the whole organism, is greatly affected by environment, both internal and external. I was taught evolutionary theory in the 70s and this is what was taught to me. I remember specifically being told that the genome is not a blueprint, as you imply evolutionary theory states. Hell, anyone who has identical twins, as I do, knows this first hand.Acartia_bogart_{July 4, 2014
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a_b, if you want a glimpse of the future debate, read Atheist philosopher Thomas Nagel’s new book, “Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False". Natural Design vs "Unnatural" Design is the future debate. Materialist view is simple talking. Won't be taken seriously sorry. Spoiler alert, Mind & Cosmos is a difficult read IMO. It's no "Darwin's Doubt". Stephen Meyers book is a page turner:)ppolish_{July 4, 2014
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Acartia_bogart, nice of you8 to move the goal posts when shown vertebrates are in the early Cambrian. Typical Darwinian response and further proof that Darwinism is unfalsifiable. I could list many more instances where Darwinian predictions have been proven false. But what is the use, you will just ignore them and cling to your atheistic belief because that is what you want to believe no matter what the evidence says to the contrary. I'm certainly not 'picking nits' to say that modern bacteria have not varied from ancient bacteria.
The Paradox of the "Ancient" (250 Million Year Old) Bacterium Which Contains "Modern" Protein-Coding Genes: “Almost without exception, bacteria isolated from ancient material have proven to closely resemble modern bacteria at both morphological and molecular levels.” Heather Maughan*, C. William Birky Jr., Wayne L. Nicholson, William D. Rosenzweig§ and Russell H. Vreeland ; http://mbe.oxfordjournals.org/cgi/content/full/19/9/1637 “Raul J. Cano and Monica K. Borucki discovered the bacteria preserved within the abdomens of insects encased in pieces of amber. In the last 4 years, they have revived more than 1,000 types of bacteria and microorganisms — some dating back as far as 135 million years ago, during the age of the dinosaurs.,,, In October 2000, another research group used many of the techniques developed by Cano’s lab to revive 250-million-year-old bacteria from spores trapped in salt crystals. With this additional evidence, it now seems that the “impossible” is true.” http://www.physicsforums.com/showthread.php?t=281961 Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber Dr. Cano and his former graduate student Dr. Monica K. Borucki said that they had found slight but significant differences between the DNA of the ancient, 25-40 million year old amber-sealed Bacillus sphaericus and that of its modern counterpart, (thus ruling out that it is a modern contaminant, yet at the same time confounding materialists, since the change is not nearly as great as evolution's 'genetic drift' theory requires.) http://www.sciencemag.org/cgi/content/abstract/268/5213/1060 Static evolution: is pond scum the same now as billions of years ago? Excerpt: But what intrigues (paleo-biologist) J. William Schopf most is lack of change. Schopf was struck 30 years ago by the apparent similarities between some 1-billion-year-old fossils of blue-green bacteria and their modern microbial counterparts. "They surprisingly looked exactly like modern species," Schopf recalls. Now, after comparing data from throughout the world, Schopf and others have concluded that modern pond scum differs little from the ancient blue-greens. "This similarity in morphology is widespread among fossils of [varying] times," says Schopf. As evidence, he cites the 3,000 such fossils found; http://www.thefreelibrary.com/Static+evolution%3A+is+pond+scum+the+same+now+as+billions+of+years+ago%3F-a014909330 Geobiologist Noffke Reports Signs of Life that Are 3.48 Billion Years Old - 11/11/13 Excerpt: the mats woven of tiny microbes we see today covering tidal flats were also present as life was beginning on Earth. The mats, which are colonies of cyanobacteria, can cause unusual textures and formations in the sand beneath them. Noffke has identified 17 main groups of such textures caused by present-day microbial mats, and has found corresponding structures in geological formations dating back through the ages. http://www.odu.edu/about/odu-publications/insideodu/2013/11/11/topstory1 Scientists find signs of life in Australia dating back 3.48 billion years - Thu November 14, 2013 Excerpt: “We conclude that the MISS in the Dresser Formation record a complex microbial ecosystem, hitherto unknown, and represent one of the most ancient signs of life on Earth.”... “this MISS displays the same associations that are known from modern as well as fossil” finds. The MISS also shows microbes that act like “modern cyanobacteria,” http://www.cnn.com/2013/11/13/world/asia/australia-ancient-life/
You claim that variation of modern bacteria proves that bacteria have far more plasticity than what we witness for ancient bacteria, yet:
Scant search for the Maker Excerpt: But where is the experimental evidence? None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of 20 to 30 minutes, and populations achieved after 18 hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another, in spite of the fact that populations have been exposed to potent chemical and physical mutagens and that, uniquely, bacteria possess extrachromosomal, transmissible plasmids. Since there is no evidence for species changes between the simplest forms of unicellular life, it is not surprising that there is no evidence for evolution from prokaryotic to eukaryotic cells, let alone throughout the whole array of higher multicellular organisms. - Alan H. Linton - emeritus professor of bacteriology, University of Bristol. http://www.timeshighereducation.co.uk/story.asp?storycode=159282
The modern synthesis is falsified mainly because it is now shown that,,,
“The genome is an ‘organ of the cell’, not its dictator” - Denis Nobel – President of the International Union of Physiological Sciences
,,, thus directly contradicting the reductive materialistic premise that the modern synthesis is built upon. You have no evidence that 'random' mutations can generate information. In fact all the evidence we have (Behe) tells us that random mutations degrade information! Natural selection, to the extent that it does anything, preserves and reduces information. Natural selection is a eliminative force, not a generative force! HGT is very sophisticated information sharing. Information sharing to cope with adaptation to differing environments (and perhaps a few other functions). It is an insult to intelligence to insist they are just randomly swapping information. There is no evidence that HGT can solve the insurmountable information problem for Darwinists. For Darwinists to co-opt HGT without addressing the primary question of 'how does the information originate?' is disingenuous to put it mildly. supplemental note: The 'simplest' life on earth, which can't even be seen with the naked eye is far more complex than Darwin could have dared imagine:
To Model the Simplest Microbe in the World, You Need 128 Computers - July 2012 Excerpt: (the parasitic) Mycoplasma genitalium has one of the smallest genomes of any free-living organism in the world, clocking in at a mere 525 genes. That's a fraction of the size of even another bacterium like E. coli, which has 4,288 genes.,,, The bioengineers, led by Stanford's Markus Covert, succeeded in modeling the bacterium, and published their work last week in the journal Cell. What's fascinating is how much horsepower they needed to partially simulate this simple organism. It took a cluster of 128 computers running for 9 to 10 hours to actually generate the data on the 25 categories of molecules that are involved in the cell's lifecycle processes.,,, ,,the depth and breadth of cellular complexity has turned out to be nearly unbelievable, and difficult to manage, even given Moore's Law. The M. genitalium model required 28 subsystems to be individually modeled and integrated, and many critics of the work have been complaining on Twitter that's only a fraction of what will eventually be required to consider the simulation realistic.,,, http://www.theatlantic.com/technology/archive/2012/07/to-model-the-simplest-microbe-in-the-world-you-need-128-computers/260198/
Music and verse:
Mandissa - Overcomer http://myktis.com/songs/overcomer/ Isaiah 6:3 And they were calling to one another: "Holy, holy, holy is the LORD Almighty; the whole earth is full of his glory."
bornagain77_{July 4, 2014
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"When the debate becomes Naturally Guided Design versus Supernaturally Guided Design, the Science will make more sense. Make better sense. What? Naturally guided design? What the f--- is that? If it's natural, it's not designed.Acartia_bogart_{July 4, 2014
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Just for the sake of absolute clearness. HGT describes the path by which I given gene ended up in a genome. It's doesn't preclude that the so-called "information" in the gene arose by natural selection, or that the gene's being fixed in a population is the result of natural selection (the gene, once itside a genome being just another variant to poentially be selected for or against).wd400_{July 4, 2014
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I have no idea what this has to do with the idea that Anything HGT does, Darwinian evolution (natural selection acting on random mutation) did not do... It's it really this difficult for IDists to admit one of their fellow-travellers is confused?wd400_{July 4, 2014
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When the debate becomes Naturally Guided Design versus Supernaturally Guided Design, the Science will make more sense. Make better sense. The "Appearance of Design" gang are holding back the good Science. The truer Science.ppolish_{July 4, 2014
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