Summations Only

Evolution is descent with modification and natural selection. Evolution is not defined as speciation. The process of adaptation that you said was not evolution *is* absolutely evolution because it involves descent with modification and natural selection. Those E. coli best able to digest citrate and most likely to survive have progeny, who then repeat the process. If you restrict yourself to morphology and ignore the adaptation to digesting citrate then yes, under the microscope the new E. coli will look pretty much the same. Why do you wish to ignore the adaptation that was produced through a process of descent with modification and natural selection and that you yourself described? You do realize, I hope, that one will thrive on a citrate substrate and the other will die. That *is* quite a significant difference.Let me emphasize again that no one's making any claims that this is an example of speciation. The claim is that this is an example of evolution producing adaptation. Even you described it as mutations and selection producing adaptation. And what might it be that imposes that limit? And what form might that barrier take? Yes, of course this is true. But if G produces greater adaptation than A, then those organisms with G will be favored and gradually dominate the population. Of course "some types of deleterious mutations are fatal to an organism." It would be very safe to go way beyond that and say that many types of deleterious mutations are fatal to an organism. But can you describe for us and reference the research demonstrating that Hox gene mutations can play no role in speciation? Since the observation is incorrect, obviously it was appropriate for evolutionists to ignore it. This sentence appears nowhere on the Internet except here. Who are you quoting?Gene duplication followed by mutations in both copies of the gene produces entirely new genes. The genomes of organisms are filled with examples of this.--PercyEdited by Percy, : Grammar.

I posted the article because it was news that specifically pertained to the thread topic. But adaptation and evolution have something to do with each other. Hang on a second. Did you take a look at the picture of the researcher:http://news.msu.edu/...5af96-2626-404d-9b9a-32cc393bca34.jpgClick to enlarge that. Those are petri dishes behind him. Think about how much work they put into this.How much work did you or the folks at AiG put into their position? Did they even touch one petri dish? Its one thing to try to get an understanding of how mutation cause novel features to arrise by spending years doing the reseach, but to sit at a computer and type up unevidenced assertions because you're starting at a position of wanting to deny evolution isn't really something that we need to devote any attention too. Reasearchers are going to continue to make advances in the theory and progress is going to be made, and you folk are going to continue to deny it because it upsets your religious sensibilities. I'm just provinding new information about how mutations lead to novel features, the topic of this thread. This is not a 'prove evolution' thread. The magic of time!?

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Around generation 31,500 additional mutations enabled the cells to utilize citrate and grow more rapidly than cells without the adaptive mutations.

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Just to be clear: 31,500 generations of humans is on the order of a half a million years. That long ago, I'd bet that humans looked different enough for even you to consider them a different species than those of us today. Even if you must deny that we evolved and have to say that we only "adapted" since then...

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Adaptive mechanisms in bacteria work by altering currently existing genetic information or functional systems to make the bacteria more suitable for a particular environment.

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Well sure, I mean, if you want to go back far enough, all we're working with is pre-existing A, T, C, and G's. But its the combinations of those that produce genes, and the mutations to those genes which provide new and novel information that can be seen arrising in the phenotypes.From the article:

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It wasn’t a typical mutation at all, where just one base-pair, one letter, in the genome is changed, he said. Instead, part of the genome was copied so that two chunks of DNA were stitched together in a new way. One chunk encoded a protein to get citrate into the cell, and the other chunk caused that protein to be expressed.

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Two chunks of DNA stitched together. So, yeah, the chunck already existed but it was copied. You might say that that isn't really new information because the chunk was already there, but the combination of the copy is what lead to a change in the bacteria, and that was new information arrising. The bacteria gained a new ability.That is a novel feature arrising, and researchers have shown how it happens. That is the topic of this thread so do you have anything to comment on about that? How else could the new feature arrose if not this way?Edited by Catholic Scientist, : removed image tags to save bandwidth

An example of a random mutation leading to a novel and beneficial adaptation is a very strong case for evolution. Why wouldn't it be? However, the ancestral strain could not transport citrate in high oxygen environments, and now it can. This novel feature was produced by a random mutation and was selected for. This is evolution. The species concept doesn't work well with bacteria to begin with, so I really don't see how that matters. What was observed was the evolution of a novel feature which is the topic of this thread.Also, how can you have a heterozygote in a haploid organism? Compare the human and chimp genomes. The differences between those two genomes should supply many examples of mutations that led to divergent species.

It would seem to me that you should have a problem with every single theory in science since all of them incorporate time as a process. Why does milk spoil? Over time, the number of microorganisms increases. Over time, these microorganisms metabolize the nutrients in the milk. According to you, we should abandon the germ theory of milk spoilage because it requires time. What is wrong with the mechanisms we already have? Each human is born with 50 to 100 mutations plus a few indels. Are you saying that we are not allowed to state that in 100 generations that you will have an accumulation of 5,000 to 10,000 mutations and 100 times the number of indels as that found in a single generation? Why would that be?It would seem to me that you need to invent new physics and chemistry in order to keep mutations from accumulating from generation to generation.

There are many different species of bacteria with that morphology. You can have speciation and still keep the same morphology. Given the fact that species that are around today are viable it would seem that this barrier has not been crossed. This barrier you speak of is not a barrier for producing the biodiversity we see today from a single ancestral population. Doesn't change the fact that mutations lead to novel phenotypes. The differences in HOX gene sequence between species shows that you are wrong. They can change, and they are responsible for differences in morphology. You are arguing against reality on this one. Yes there is. It is called mutation.

My friend the Catholic Scientist. Your question should first ask how much money was spent supporting this research. Years of doing research means money for the lab, personnel, equipmentYou folk are going to continue spending money in fruitless dead ends where every discovery forces a scramble to Grok the evidence to a dead theory.Evolution is wrong because it is bad science and tenable only as a weak philosophy. Let us try spending money on research that recognizes the genome is designed and not thrown together by chance. The answer to how mutations lead to novel features (adaptations) firmly fits in the Creation mindset. I assume you are saying this thread is not concerned with the un-provability of evolution. Given an assumed generation of 20 years for humans, that is 630,000 years to be exact. A change in food source for E. coli would probably parallel humanity switching from total plant eaters to eating meat and plants in 630,000 years. Let us see, if there was as little change to humans as in the E. coli; how on earth would there be enough changes in a hominid 5.5 million years ago (~8.7x longer) to produce a human from a supposed chimp human divergence?This experiment only illustrates a morphological stasis in both E. coli and humans. isn’t really new information and was new information Could not characterize your confusion better.Two ways we know something, either by speculation or revelation. Given the availability of the two choices, I chose the revelation.

Taq, Even accepting there are many species of bacteria with the same morphology (dubious claim). You can claim speciation only when biologists use 24 separate definitions of a species not necessarily dependent on aligning morphology. The only question is if the phenotypes are front loaded. Give me an example Single point mutations are not new gene sequences. I did not make this up, it is a recognized observation.

Okay, so within that Creation mindset: How do novel features come about? How do they change? Um, I don't think so. I think that would take a lot more mutations than it took in this research. Wait, what? There was a huge change in the E. coli. In 275,000 generations? There's plenty of change to be had in that many generations. And it doesn't really take that much change. Our DNA isn't too terribly different from the chimps. No, it does not. It doesn't even illustrate morphological stasis at all, that's a complete non-sequitor. And it does illustrate other things: that is how novel features evolve. Actually, it shows the confustion of the Creation mindset. Think of it this way: There's only 27 letters in the alphabet. All words are just going to be combinations of those pre-existing letter. No new letters come about so according to the Creation mindset; no new information can ever be created. A new book comming out tomorrow with totally novel ideas cannot be considered new information, according to the Creation mindset, because its just using already existing words and letters so no new information is really created.But that's bullshit. Of course new information can come out by combining pre-existing words and letters to form new ideas. Just like new information can come about from mutations to DNA that re-arrange the ATCG's into new combinations. The Creation mindset is just plain wrong about that. That's your loss. I choose learning from science.

Do you have any evidence to separate this flight of your imagination from fantasy?Please realize that claims offered without evidence can be dismissed without evidence. If all you provide is your opinion and nothing else then you've given us nothing. If I were to try to convince someone else of your point of view and they asked me why I believe this, all I could say is that Zaius thinks so. You're making an invalid comparison, for more than one reason. First, humans can't really be compared very effectively with bacteria, but more importantly, gaining the ability to digest citrate is pretty significant, while humans already had the ability to digest meat 630,000 years ago (otherwise they wasted a heck of a lot of time making spears and arrows).Regarding the entire array of changes between the chimp/human common ancestor and us, some were likely as complex as the citrate-digesting change in bacteria, but many changes were rather minor.Also realize that the amount of change in DNA can be very tiny but still have a very significant impact on the organism. As an analogy, a small hole punched in your car's fender will have a negligible effect on performance, but a small hole punched in the radiator, well... To use an analogy again, to believe this you would have to think that since the morphological difference between the 4 and 8 cylinder versions of the same car model is nil that it makes no difference which one you drive in a race. The citrate-digesting ability is very significant. It's an example of the kind of novelty that is the topic of this thread. Pretending it's of no consequence is a kind of obvious fault in your argument. I think you must have misinterpreted what CS wrote. To rephrase and add a little more info, he said that though it might be argued that a copied segment of DNA isn't really new information, it provided a slate upon which to modify the copied information, and these modifications represent new information that was responsible for the new ability. You really think knowledge is only gained through speculation or revelation? You might want to reconsider this position. Just using yourself as an example, think back through your life and identify how many things you know that you didn't learn by observation. You either saw it or heard it or felt it or smelt it or tasted it in order to add it to your store of knowledge, but your didn't speculate it and revelate it.--Percy

Well no it doesn't. Thinking of genetic inheritance in terms of heterozygous or homozygous is fine for humans and pea plants since they are diploid organisms, but bacteria only have a single chromosome.Traditionally bacteria have been categorised into species by their morphology but also by the biochemical reactions they can perform including which sugars they can ferment/assimilate. We can use this method because it is fairly stable what chemical reactions different species of bacteria can perform, which is what makes the Lenski experiment so significant.Of course now with more widespread use of genetics to profile bacterial species we are seeing that, although what we define as a species are very closely related at the genetic level, there is still significant divergence, sometimes enough to identify different species. So for example you get the Enterobacter cloacae complex or Burkholderia cepacia complex, each thought to be a single species but now shown to be several species sharing the same biochemistry i.e. the same phenotype.So you can see there's a lot more to bacterial species than just morphology. You look at E.coli under the microscope and you'll see gram negative bacilli, but if look at Pseudomonas or Bacteroides they are also gram negative bacilli. Would you therefore regard those organisms as all pretty much the same thing?By comparison a great deal of the diversity we see in metazoa is not a result of novel mutations, but instead can be accounted for simply by changes in gene expression during development. You bring up the transition of a leg to a fin, yet during development a limb is already fairly fin like, it just requires genes to be expressed at the right time to control cell death between what will become fingers and toes. And for the record hox genes don't define how a limb develops, they lay out the body plan in the early stages of development so that other genes involved in limb development know where to be expressed. It's not as straight forward as a gene missing a few mutations to get from anaerobic uptake to aerobic uptake of citrate. As I understand it for citrate to be utilised it requires a cofactor such as glucose or glycerol as a reducing agent. Therefore the presence of oxygen interferes with this reaction, which is why it only occurs in anoxic conditions.{Started writing this reply a couple of days ago, so sorry to Taq and Catholic Scientist for repeating some of their points}

Malcolm You may be right when talking about heterozygosity in diploids but heterozygosity per capita is also expressible in general populations of bacteria. This is not strange to biology, as I understand it (I am not a biologist though). Here is an example study of such a usage.

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We established experimental cultures of long-term stationary phase (LTSP) Escherichia coli to test whether per capita heterozygosity varies with resource concentration, and, if so, whether population sizes associated with different resource concentrations contributed to these patterns. Diversification Rates Increase With Population Size and Resource Concentration in an Unstructured Habitat - PMC

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In addition, you might note that the plasmid or plasmids within the E. coli retains its diversification per capita in a general population of E. coli. If you know if that was directly addressed by the Lenski experiment please elaborate (I would like additional information on this). I believe you are building a straw man out of this E. coli as a species is identifiable. Although, no longer very reliably by its citrate uptake. About the hox gene not being involved in limb development, I believe you need to be specific about which hox you are talking about. Generally global statements like yours are inevitably wrong.

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In order to directly test the function of Hox genes in vertebrate limb development, we have employed a replication-competent retroviral vector to express the genes ectopically in developing chick limb buds. It has been hypothesized that the sum of all Hox genes expressed in a developing region forms a "Hox code" which determines the fate of structures arising from that region. When the Hox code of the of the anlage of the chicken hind limb digit I is altered to match that of digit II, the resulting foot has two similar toes both resembling digit II in morphology. This suggests that the misexpressed gene, Hox-4.6, plays a role in controlling digit morphological identity. Other phenotypes observed in the proximal parts of the hind limb and in similar experiments in the wing also lend support to this interpretation. The retroviral vector system used in these experiments provides a powerful approach for testing the function of genes in limb development. The role of Hox genes in limb development - PubMed

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If you read some of the citations, some gene block rearrangements provided the functionality (no new gene material spontaneously appeared). I would be curious to know if you accept that this new functionality was something other than an improvement upon existing genes (beneficial adaptation of an existing mechanism).If so, please provide some reasoning

Malcolm my friendP.S. your statement Reminds me of Ernst Haeckel and his falsified embryos. I hope you are not going to claim, ontogeny follows phylogeny. Please.

My friend Percy Actually I did not make the comparison, Catholic Scientist did. I merely expanded on that participant’s over generalized statement. I could dump on you my calculation for chimp human divergence and show that there are not enough mutations to cause a divergent hominid to produce a human. It is defiantly off point my friend.As I stated before E. coli could already utilize citrate to a degree. It was no major advance in the specie. I could see your point if revelation is used in the strictest sense.By definition
a. The act of revealing or disclosing.
b. Something revealed, especially a dramatic disclosure of something not previously known or realized.

My friend Zaius, But CS was simply using human evolution to highlight your mistaken reliance upon morphology for species identification. You went off in a completely different direction with claims about how much humans could change based upon E. coli information. It made no sense, as Malcolm also explained. And as I and several others stated before, the ability to digest citrate in the presence of oxygen is the novelty, and Malcolm described why this was no small matter genetically.You're simply trimming back the details to where there's no difference. "Oh, you can show E. coli evolving the ability to digest citrate in the presence of oxygen? But that's not novelty, the ability to digest citrate was already there."Or, "Oh, you can show some of the genetic changes that might have led to a fin evolving into a leg? But that's not novelty, they're still both limbs."Eventually you'll reach the point where you'll be saying, "Oh, you can show how an ancient land animal evolved into a whale? But that's not novelty, they're still both mammals."Your strategy of denying that any demonstrated novelty isn't really novel is kind of embarrassingly obvious, my friend. Ah, I see. So when you read a biology paper, that's revelation to you. My good friend, could you perhaps use words in the same way everyone else in this thread is using them?CS and I both explained one way in which new information is created in the genome, hopefully this "revelation" has removed your confusion.--Percy

Percy my friend, Every experiment to induce this type of macro change fails. There is no universally accepted transitional forms in the fossil record, over one hundred and fifty years of study and discovery of fossils have only turned up a handful of these much disputed examples. Studies in fruit flies have turned up the same stasis in the genome as E. coli illustrates. Scientific evidence does not support a limb to fin transition but speculation does. You can speculate all you want but it is not scientific.Those are the facts.I Answered Malcolm and await this participants return.