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Microbe evolution virtually finished 2.5by ago

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With all the major evolution done so early, microbe evolution has been retired for a very long time. No wonder we can’t evolve new pathways in the lab!

From ScienceDaily

New research shows that for microbes, large-scale evolution was completed 2.5 billion years ago.

“For microbes, it appears that almost all of their major evolution took place before we have any record of them, way back in the dark mists of prehistory,” said Roger Buick, a University of Washington paleontologist and astrobiologist.

All living organisms need nitrogen, a basic component of amino acids and proteins. But for atmospheric nitrogen to be usable, it must be “fixed,” or converted to a biologically useful form. Some microbes turn atmospheric nitrogen into ammonia, a form in which the nitrogen can be easily absorbed by other organisms.

About 2.5 billion years ago some microbes evolved that could add oxygen to ammonia to produce nitrate. These microbes are on the last, or terminal, branches of the bacteria and archaea domains of the so-called tree of life, and they are the only microbes capable of carrying out the step of adding oxygen to ammonia. This indicates that large-scale evolution of bacteria and archaea was complete about 2.5 billion years ago, Buick said. “Countless bacteria and archaea species have evolved since then, but the major branches have held,”

“All microbes are amazing chemists compared to us.” Buick said.

Comments
Neither Penny’s hypothesis about the origin of eukaryotes nor the evidence upon which it is based (which is very thin and ambiguous) are widely accepted by most evolutionary biologists.
That is because it poses too many problems for them. Mainly that eukaryotes contain too much complex specified information to have arisen first from non-living matter. Also the paper is just a couple of years old. In comparison the SET has been around more than 10x as long. Yet it too is built on evidence that is very thin and ambiguous.
Compare this to the answer that ID provides: vision is the way it is because that’s how the “intelligent designer” intended it to be.
Please provide the reference or admit you are just erecting another strawman.Joseph
March 5, 2009
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bfast, I never said anything about a timeline changing. Actually I am making us more informed than Allen. The 600 million + is for multi-cellular life. That is where the action is and what Darwin was concerned about. At 600 million years ago the best there might have been is a few worms crawling around leaving trace fossils and then presto a relatively short time later there was the Cambrian Explosion and before that all those irreducibly complex systems had to arise to give rise to eyes, nervous systems, digestive systems, immunity systems etc. Hox genes, pax genes, sox genes, __x genes, etc. (These people must have read Dr. Seuss's Fox in Sox.) What the Darwinist fall back on is all the changes in the environment driving the endless variety of novelties but they still have to deal with the information requirements that had to arise out of nowhere. How did they just poof into existence.jerry
March 5, 2009
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Hello Allen, WIth respect to your note about micorbes: Thiomargarita namibiensis is a giant at nearly 1 mm and quite visible to the human eye. Most of its volume, however, is in the form of stored nitrate, not living tissue. Still, a genuine macrobe. MichaelMichael Tuite
March 5, 2009
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Allen, You must be aware that it was those pesky little worms that only left trace fossils that may have ended the ice planet. One scenario is that they produced methane which is a greenhouse gas and this caused the exponential rise in global warming we see in the various markers for temperature. Similar to what we see with our fondness for Big Macs may be costing us by the increase in cow methane in the atmosphere. And I guess as James Burke used to say there was a trigger effect or connections. These make nice stories and in all these stories there is some truth. But as I said the war will be won on information generation and not climatic changes. Did you also know that the earth was probably situated in the galactic arm at the time of the Cambrian. I am surprised this is not brought forward as an opportunity for massive mutation rates from our neighbors. We are here to help but it is information that is the key.jerry
March 5, 2009
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Jerry:
to 300 million years from 6,000 years and then to 4.5 billion years and now it is back to 600+ million years under your ice scenario. Is that difficult to understand?
Jerry, please don't make us IDers look too illinformed. Allen_MacNeill has presented no new timescale. If you read the discussion on this board for the last few years you will see that the cambrian explosion, where multicellular life blossomed into all of its glory has always been about 600 million years ago (actually more like 550, but that's hair splitting.) Again, the timeline has not changed for many years. First life -- about 3.5 billion years ago. Multicellular life (there is some question of when the first multicellular came into being) about 600 million years ago. Allen_MacNeill's level of twiddling with the timescale -- zero.bFast
March 5, 2009
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I believe I know what the Darwinian response would be to this... The Evolutionist's (non-ID supporter) working principle is -- Once you find something that works really well you stick with it. So their reasoning would be --- We can tell that bacteria have evolved by evidence of common descent. And we can tell that bacteria DO evolve by studying them in the lab. Just presenting this to everyone for their consideration. Responses welcome.SeekAndFind
March 5, 2009
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Allen, Before you make a big deal of it. I know Lord Kelvin published a range and I used 300 million to be on the generous end of the range for evolution. It is meaningless now since he was wrong.jerry
March 5, 2009
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Allen, Apparently, you have no imagination. It must be selection. Yes it would be easier to see what I meant if instead of "earth" the word "time" or "period for the development of life on earth" was substituted but I took a literary license and used the concept of the earth being shortened again after it was lengthened to 300 million years from 6,000 years and then to 4.5 billion years and now it is back to 600+ million years under your ice scenario. Is that difficult to understand?jerry
March 5, 2009
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In #27 jerry wrote:
"Now the earth for evolution is shortened again and is there enough time for all this miraculous change to take place." [sic]
Sorry, this phrase doesn't make sense. What did you mean to write?Allen_MacNeill
March 5, 2009
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The question of why we have the senses that we do is a very interesting one. As just one example, consider the sense of sight. As a type G-0 yellow-white dwarf star, the sun gives off a relatively narrow range of electromagnetic radiation, including (from longest wavelength to shortest) radio waves, infrared radiation, "visible (red, orange, yellow, green, blue, and purple) light", and ultraviolet light. Almost all of these wavelengths of electromagnetic radiation can penetrate the Earth's atmosphere (although the shorter wavelengths of ultraviolet light are somewhat attenuated by absorption by ozone/O3 in the upper atmosphere). So, which wavelengths of electromagnetic radiation can we perceive? The answer depends on who you define as "we". Vertebrates have visual pigments in the cone cells of the retina that can absorb only three of these wavelengths: red (absorbed by the rhodopsin protein erythrolabe, which absorbs sunlight in the range of 564–580 nanometers), green (absorbed by the rhodopsin protein chlorolabe, which absorbs sunlight in the range of 534–545 nanometers), and blue (absorbed by the rhodopsin protein cyanolabe, which absorbs sunlight in the range of 420–440 nanometers). So, we vertebrates can only directly perceive red, green, and blue light (that's why color computer monitors generate only red, green, and blue pixels). However, most insects (including honey bees) have different visual pigments, and so see very different colors than we do. They do not have a visual pigment that corresponds to vertebrate erythrolabe, and so cannot perceive the color we call "red". However, they have a visual pigment vertebrates do not have, which can absorb light in the near ultraviolet range. Hence, insects can see colors (including ultraviolet) that we cannot see, and so the world appears very different to them. So far, no organism on Earth has been discovered that can perceive the radio waves given off by the sun. This is probably because to do so would require absorptive structures several meters in length (the wavelength of most radio waves). So, one answer to Domoman's question is that, taken as a whole, living organisms can perceive (or at least absorb) a range of light from the far infrared to the near ultraviolet, but lack receptors for most of the electromagnetic spectrum (such as radio waves, gamma radiation, etc). In other words, the range of electromagnetic radiation that can be perceived by living organisms matches quite closely the range of electromagnetic radiation given off by the sun and transmitted through the Earth's atmosphere (with the exception of radio waves, which are too long to by absorbed by any known biological molecule). That this is the case is exactly what one would expect to have evolved by natural selection, which can only work with what is available. Furthermore, it illustrates one of the basic ideas of evolutionary descent with modification: that the solutions to evolutionary problems vary from group to group as the result of historical contingency. Vertebrates see red, green, and blue, while insects see green, blue, and ultraviolet because two of our visual pigments (chlorolabe and cyanolabe) evolved before the divergence of insects and vertebrates from our common ancestor, while the third visual pigment evolved independently in the two groups, resulting in two different sets of perceived colors. Compare this to the answer that ID provides: vision is the way it is because that's how the "intelligent designer" intended it to be. Which of these answers to Domoman's query involves detailed empirical scientific investigation, and which simply relies on unsupported assertions?Allen_MacNeill
March 5, 2009
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Allen, You and the other evolutionary biologists may be backing yourself into an undesirable corner. The claim since Darwin has been we need time, deep time for evolution to work. Lord Kelvin squashed Darwin with his calculations that the earth might be at best 300 million years old but then the discovery of radio activity showed that the earth was billions of years old. And all was well in the Darwin camp. Now the earth for evolution is shortened again and is there enough time for all this miraculous change to take place. After all even the punctuated equilibrium people say it takes tens of millions of years for one protein to form through mutations. The whole argument will be won on the likelihood of novel proteins forming in a specified time. Are all those hox and other regulatory genes capable of forming by chance in so short a time. I don't think so.jerry
March 5, 2009
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In #24 maddoc asked:
"Which storybook did you find this in?"
Peterson, K., McPeek, M., and Evans, D. (2005) "Tempo and mode of early animal evolution: Inferences from rocks, Hox, and molecular clocks." In Vrba, E. & Eldredge, N. (2005) Macroevolution: Diversity, Disparity, Contingency; Essays in Honor of Stephen Jay Gould, The Paleontological Society, vol. 31, no. 2, ISBN #1891276492, pp. 36-55Allen_MacNeill
March 5, 2009
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It seems to that that many of the traits we are most knowledgeable about when it comes to microbes are genes/proteins related to pathogenicity. Clearly, if evolved, they would not have evolved until a host was present (a Type Three Secretion System is of little use unless there is a host to secrete you virulence factors into). So my question is, given the extreme complexity of many of these virulence systems, along with things like quorum sensing which allows bacteria to talk to each other when they are in large groups (like infecting the gut), what is the basis for a 'large-scale' evolutionary change talked about? Must it only be metabolic?Winston Macchi
March 5, 2009
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Re:Allen McNeill "These new cell types (and multicellular organisms) had to wait until the “snowball Earth” melted enough to allow sunlight to penetrate to sufficient depths in the epicontinental oceans to allow for macrophytic photosynthesis, which set the stage for macrophagy and the evolution of the metazoa." Which storybook did you find this in? Oh! This one: "*However, science fiction author Hal Clement (Harry Clement Stubbs) published a novel in 1980......." TEE HEEmad doc
March 5, 2009
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Collin #8 I seem to have stayed logged in all day...I don't think I've logged in for days actually.pharmgirl
March 4, 2009
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And another BTW: My comment above would have to do with an atheistic world view. If you're a believer of a creator of the universe, and even believe in evolution, the questions don't so much apply. Nor am I suggestion that evolutionists claim that evolution has anything to do with the universe (although Richard Dawkins has actually suggested there is some sort of Darwinian mechanism for the reason the universe is the way it is.) In fact, Richard Dawkins would do good to honestly evaluate my above questions...Domoman
March 4, 2009
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I wonder: why there is light, and life can just so happen to see? I do not mean, that life could not have evolved eyes (although, I honestly do not believe it could by chance), but rather, why is it such that properties exist within the universe that specifically allow life to have eyes? For that matter, why can life hear? And why can it eat substances to maintain its existence? Why can it recycle the substances it eats? I'm not looking at evolution as a possible answer. This is already assuming that evolution could create life as it is (even though I highly doubt unguided evolution). This is asking why life can specifically be the way it is, period. Is it not strange that light, sounds waves, availability of substances to eat, to recycle substances, and to touch (to give a few examples) can even exist? Would it not, given a chance creation of a universe, be more likely to have light but not the ability of life to see (that is, it may be, for instance, physically impossible to see)? Or sound waves without ears? Or mouths without edible substances? Or, even differently, why do we not have ears and yet only have light and a complete lack of sound waves? Or vise versa-eyes but only sound waves? Seems to me that chance isn't even a reasonable answer. This is a bit of philosophical approach to the reason why existence is exactly what it is, rather than scientific, but I've been thinking about it lately. Seems to put evolutionary just-so stories in perspective... BTW: Platonist, enjoy your date!Domoman
March 4, 2009
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And yes, there is no single-rooted "tree of life". It's a mangrove, with its roots in the muddy water of the Archaeon Eon.Allen_MacNeill
March 4, 2009
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As to the question of why bacteria have not evolved much in the past two billion years, the question reveals a basic misunderstanding of cellular evolution. Yes, no new major metabolic pathways have evolved since the nitrogen-fixing and nitrifying bacteria evolved about two billion years ago. However, that's because there is no new element (that is necessary for life) that has a reservoir in the Earth's atmosphere. All four of the major elements necessary for life – hydrogen, oxygen, nitrogen, and carbon – participate in biogeochemical cycles that have a major reservoir in the atmosphere (and, in some cases, the ocean). Once bacteria had evolved the two major nitrogen metabolic pathways, there were no new major metabolic niches to exploit.* In other words, once the four major (HONC) biogeochemical cycles had evolved, the only "new" ecological niches available were for new types of cells (and, eventually, multicellular organisms), not new metabolic pathways. These new cell types (and multicellular organisms) had to wait until the "snowball Earth" melted enough to allow sunlight to penetrate to sufficient depths in the epicontinental oceans to allow for macrophytic photosynthesis, which set the stage for macrophagy and the evolution of the metazoa. *However, science fiction author Hal Clement (Harry Clement Stubbs) published a novel in 1980 in which he proposed that a widely distributed oceanic bacterium evolved the ability to combine the nitrogen and oxygen in the atmosphere, thereby depleting virtually all free atmospheric oxygen (O2) and leaving mostly nitrogen (N2), with traces of water, nitrogen oxides and carbon dioxide in the atmosphere. This would leave the ocean as a dilute solution of nitric acid, and would, of course, kill almost all forms of life on the planet. This has happened once before, when non-cyclic photosynthesis evolved among the cyanobacteria, releasing a corrosive, explosively reactive, toxic gas into the atmosphere... ...oxygen (O2).Allen_MacNeill
March 4, 2009
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Like the term "germ", the term "microbe" has no technical definition. It means (roughly) "something so small you need a microscope to see it". So yes, both bacteria and some unicellular eukaryotes qualify as "microbes". There are no bacterial cells (indeed, no prokaryotes) large enough to be seen as single cells without a microscope. Yes, colonies of bacteria can be seen with the unaided eye, but such colonies contain millions or even billions of individual cells. By contrast, there are many eukaryotic cells that can be seen without a microscope. Currently, the largest eukaryotic cell is an unfertilized ostrich's egg (some dinosaur eggs were bigger). However, most of the unicellular Protista can be seen without a microscope, and of course almost all of the multicellular eukaryotes are visible with the naked eye.Allen_MacNeill
March 4, 2009
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Neither Penny's hypothesis about the origin of eukaryotes nor the evidence upon which it is based (which is very thin and ambiguous) are widely accepted by most evolutionary biologists. On the contrary, most of the evidence (especially at the genomic level) points to the conclusion that prokaryotes (i.e. bacteria and archaea) preceded the appearance of eukaryotes by at least two billion years. By the way, the name for the period of time between the origin of nitrogen metabolism in bacteria and the origin of eukaryotic cells is the Proterozoic Eon. And one answer to the question "why did eukaryotes 'wait' until the end of the Proterozoic?" is that there is very good evidence that the entire Earth was covered with glacial ice for about 215 million years. This happened during the Cryogenian Period, which lasted from 850 to 635 million years ago. The Cryogenian Period was the second geologic period of the Neoproterozoic Era, and there is mounting evidence that the "defrosting" of the "snowball Earth" (combined with the increase in atmospheric oxygen and the concomitant increase in oceanic calcium carbonate) during the Archaean and Proterozoic Eons set the stage for the origin of the eukaryotes, and especially the metazoa.Allen_MacNeill
March 4, 2009
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The Darwinian tree of life is bogus. There have been many posts on the site about that. Lets be optimistic. Universal common ancestry, macroevolution is toast. All the best everyone. I got a date tonight.Platonist
March 4, 2009
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magnan: "They call it the period during which Eucaryotic single-celled organisms evolved..." What, single-celled eucaryotes are not microbes? I thought all single-celled organisms were microbes.bFast
March 4, 2009
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Collin (#8): "The emperor is nekked." If so, why do you accept microevolution or even common ancestry? Is the Emperor, in fact, partially clothed? Michael Behe doesn't accept a naked Emperor. RayR. Martinez
March 4, 2009
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Collin- I believe the article is only referring to archaea and bacteria, which are prokaryotes. (I could be wrong though.) However, his point is moot if eukaryotes really evolved first as suggested by the article Joseph linked us to in "Questioning the Role of Gene Duplication-based Evolution in Monarch Migration". http://www.msnbc.msn.com/id/12853798/ “Can evolution make things less complicated? Instead, the data suggest that eukaryote cells with all their bells and whistles are probably as ancient as bacteria and archaea, and may have even appeared first, with bacteria and archaea appearing later as stripped-down versions of eukaryotes, according to David Penny, a molecular biologist at Massey University in New Zealand. Penny, who worked on the research with Chuck Kurland of Sweden’s Lund University and Massey University’s L.J. Collins, acknowledged that the results might come as a surprise. “We do think there is a tendency to look at evolution as progressive,” he said. “We prefer to think of evolution as backwards, sideways, and occasionally forward.””pharmgirl
March 4, 2009
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"“For microbes, it appears that almost all of their major evolution took place before we have any record of them, way back in the dark mists of prehistory,”" Well that sure is convenient. If we have no record of the major evolution of bacteria then how can people be so sure they did evolve ? Am I missing something here ? Do I just lack the appropriate Magica... I mean ... "scientific" perspective ?Jason Rennie
March 4, 2009
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magnan, I don't see how to reconcile your comments about Eucaryotic single celled organisms evolving and Buicks claim that the evolution of single cell organisms was essentially completed 2.5 million years ago. What am I missing here?Collin
March 4, 2009
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"What do they call the period of time between 2.5 bya and 0.5 bya, the evolutionary dark ages?" They call it the period during which Eucaryotic single-celled organisms evolved, containing a nucleus and organelles like mitochondria. Including single celled animals like protists, and single celled fungi like yeast. These had to come about in order to build multicellular animals and plants. It seems to me it is unclear how the long-ago end to major evolution of bacteria relates to ID. It could be argued that the structural and biochemical potentials of the bacterial form had been exhausted. I.E. maybe the next step available to the basic system was to jump to a much larger single cell with organelles. That did happen. The issue is how did it happen.magnan
March 4, 2009
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“All microbes are amazing chemists compared to us.” Buick said This is like that one guy who told us that Darwinism is true by using the analogy of the evolution of automobiles. Incredible!Collin
March 4, 2009
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The emperor is nekked. By the way, how long does wordpress keep the rest of you logged on? It seems like I have to re-sign in all the time.Collin
March 4, 2009
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