Summations Only

I'm a senior studying Environmental Biology, is that close enough? At least I'm not a fake biologist. You have this completely backwards. You have merely defined adaptation. An example of this would be brown bears/ polar bears. White fur is an adaption of brown bears to polar conditions. The trait was there in brown bear populations but selected for when they were subject to polar conditions. The trait then became "homozygous" in the polar bear population.Which brings me to the second point: You are misusing the terms heterozygous and homozygous. Homozygous means that both copies of a gene are the same allele, heterozygous means that both gene copies are different alleles. There is no need for an entire population to be homozygous, that is a completely unrealistic expectation and sets up nothing more than a straw man. If a trait is not completely homozygous then it is not novel? Geez, that disqualifies just about everything. And I would suspect that if a trait could be shown to be completely homozygous, that still wouldn't qualify it as a novel trait, would it?Another problem is that it is often difficult to distinguish morphological features of bacteria species. What is it you are expecting? For the bacteria to grow arms or legs? To turn into a Paramecium or Euglena? Would that be novel enough? Bacteria are tiny, tiny specks even under 1000X magnification. Most of the characteristics of bacteria are microbiological in nature, you just can't expect a novel feature to produce significant morphological changes.Below is a picture of some significant morphological characteristics of cocci bacteria. Notice they are all round, small, and "still bacteria". Nothing novel here right? But the arrangement of the cells is a very morphologically significant feature and is caused by unseen, microbiological processes during replication. It allows us to separate these bacteria into different genera. So if you are looking for morphological differences in bacteria, this is about it. What about going from a cocci to a rod shape, or from short rods to long rods? Would that be novel? I think you are expecting way to much in the way of morphological changes from bacteria.In the case of citrate, yes wild-type e-coli can process citrate, what they cannot do is transport it into the cell. This mutation allows the cell to transport citrate into the cell so that it can be processed. I am not sure of the exact nature of this mechanism but, it took two mutations, one that built upon a previous mutation, to build this transport mechanism. Are you familiar with molecular transport systems? If not I suggest that you do some research on the subject. They are not simple systems, but are highly specialized molecular processes.Inventing bogus definitions of novel is not sufficient to disqualify this as a novel trait. You would have to show that this trait already existed in the parent population and was simply selected for, which is not the case.HBD

Hi zaius,I gave your post a cheer because you actually did present some evidence for your claim. However, I don't think you have made a very strong case.Here is a link to the full text version of the paper you cited: Genomic analysis of a key innovation in an experimental Escherichia coli population (Its helpful to have more than just the abstract)The very first line of the article gives a clear definition of novel features.

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Evolutionary novelties are qualitatively new traits that open up ecological opportunities and thereby promote diversification.

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The authors then go on to explain how the process is thought to give rise to these novel functions.

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These traits are thought to arise typically by the exaptation of genes that previously encoded other functions through processes such as domain shuffling, altered regulation and duplication followed by neo-functionalization. Multiple mutations may be necessary to produce the new function, and thus its potential to evolve may be contingent on subtle differences between species, populations or even genotypes.

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It is important to note that this is not just a case of duplicate an existing gene and go, but it involves multiple steps in the development of the feature. The authors refer to three steps in the evolution of this trait; actualization, potentiation and refinement. The Cit+ variant first appeared at 31,500 generations, but was very weak. But before that duplication could even be expressed, there needed to be a genetic background that allowed the new trait to function. And then the trait needed to be refined by subsequent mutations in order to be efficient.

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The evolution of citrate use also highlights that such actualizing mutations are only part of the process by which novelties arise. Before a new function can arise, it may be essential for a lineage to evolve a potentiating genetic background that allows the actualizing mutation to occur or the new function to be expressed. Finally, novel functions often emerge in rudimentary forms that must be refined to exploit the ecological opportunities. This three-step processin which potentiation makes a trait possible, actualization makes the trait manifest, and refinement makes it effectiveis probably typical of many new functions.

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SO these are the reasons that people that have done the research on this are calling it "novel." You can dismiss it as not being novel if you choose, but it really misses the point altogether. This is not an instance of the cell deciding it needed to be able to utilize citrate and simply duplicated its "pre-existing" components. How can you even make this claim? How do you know it has never been "pruned" by evolution? You are really stretching the facts far beyond what you actually know. How so? This is simply jumping to a conclusion and avoids the issue at hand. Why is this not a novel trait? Even if it was "front-loaded", it still meets the definition of novel. The trait was not there before and now it is and it promotes diversity and exploitation of a new ecological opportunity. It is not simply a case of turning a switch on, it is a whole series of changes that result in something new; or in other words ... novel.HBD

Is the following representative of what you would consider a novel mutation?(letters indicate gene sequences and associated codes)Original organism: A B C D E F G H I JOrganism after mutation: A B C D E K F G H I JYou do realize this is how creation ex nihilo works, not evolution, don't you? Evolution uses existing materials to develop new features and new functions for existing features. It doesn't create something from nothing. If you wonder how the information got there in the first place, that is a different subject. This topic is discussing how evolution creates novel features using existing information.Essentially you are committing the straw man fallacy, but with a unique twist; instead of setting the straw man up and beating on it (which is the common way this fallacy is executed), you set the straw man up and say that he can kick the ass of the current theory. So those here that are arguing against you, end up beating on your straw man that you yourself set up. Even if "new information" dropped from the sky and fell right into a cell, it would still require an energy input. So in your opinion, the only way to generate "new information" is ex nihilo creation. Your whole perception of "information theory" shows a complete lack of understanding about how genetic information works and is utilized.HBD

I don't see how changing the terms changes anything. So should we change the discussion to how does adaptation produce novel features? Oh and let's change "novel" to "different".So now the question is: How does "adaptation" produce "different" features. Does that correct the "errors" in terminology? The question may indeed beg the answer, but that is not what the thread is about. Biological evolution (notice the forum we are in) assumes preexisting material. Do you assume that new features are created ex nihilo on the fly. Or that all creatures are essentially the same as they were when they were first created? You can't actually believe this. Lol! The debate hasn't even begun! I don't know what you mean by "novel" or "evolution" or "species" or "adaptation" or "scientifically" or just about anything else you have said. I do use the Word of God to navigate my life. So if I use it to navigate my life and within my life I engage in science, then I am using the Word of God to "navigate science." Other than that I don't know how else I should be using it to "navigate science." How would you apply the Bible to the issue we have been discussing, the "adaptation" of citrate utilization in e-coli?But if by success you mean "denying reality", I just can't accept that as success.If the whole point you are trying to make is that the "adaptation" of citrate utilization cannot be extrapolated to the sort of evolution that results in changing an arm into a wing, you may have a valid argument. But you are not going to advance that argument by equivocating on definitions, denying clear facts and submitting baseless assertions.HBD

Welcome mindspawn ... Here is an article about new functional sex genes in Drosophila. They discuss three ways that new genes arise and give examples of each. Tandem Duplication:

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This type of duplication typically includes the entire coding region of a gene, along with its flanking regulatory sequences.

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The new genes then specialize and the alternate splicing functions change and new protien producing genes are formed. Retrotransposons occasionally mRNA is reverse transcribed and stuck back into the parent DNA in a random position. It then relies on regulatory sequences that flank the new gene sequence. De novo gene evolution this one is rather interesting. A formerly non-coding section of DNA can be altered so that it begins to function.(Examples of the specific genes that were studied are given in the article.) This is just plain wrong. Do you have a source that supports this? So I take it you are thinking of genetic entropy?HBD

This is rather disingenuous of you don't you think? You asked for specific examples of duplications adding additional functional genes. You were given several examples (by myself and Taq) but apparently that was not what you were really looking for.1. We observe duplications in laboratory populations of Drosophila
2. Duplications have effects that are expressed in the phenotype of laboratory populations of Drosophila
3. We make observations of populations of different species of Drosophila
4. We observe the types of duplication events that were observed in the lab and they are part of what makes these species different from each other.
5. By experimentation, we can determine the function of these duplicated regions
6. By comparing the different regions, we can determine what changes caused these different functions
7. This strongly suggests that a duplication event and subsequent divergence that led to speciationIs this proof that this is actually what happened? No, of course not. But it strongly implies it. Does it exclude these other possibilities? No, any of these three possibilities could have happened, but which option does the evidence suggest?You also ignored the other questions in my post. Why do you think that duplications reduce fitness? It seems as if you are basing your thinking on the idea of genetic entropy. Is that the case? Polyploidy is rather common in plants (although it does occur in some animals) and is the duplication of entire chromosomes and even the entire genome. Sometimes the genome has undergone multiple polyploidy events, there are even examples of dodecaploids (12 copies of the chromosomes). So not only duplication of one or two proteins, but many, many proteins with no reduction in fitness. In fact, it is common for polyploids to be more successful than their predecessors.I don't want to convince you to be an evolutionist (I don't actually consider myself to be one) or an atheist (I am not), but we need to be able to have sincere discussions about these things. If you are going to be one who simply dismisses evidence, things won't get very far and this will be nothing but an exercise in futility.HBD

* Since we have additional 100 msgs in this thread, I can take the time to ask this Is citrate utilization an identifying characteristic of e-coli? I looked at an older version of the Enterotube and cit - is one of the identifying characteristics of e-coli, with 0% showing cit +. However, a newer version appears to have some more leeway as to the citrate test in identification of e-coli.With you doing this on a daily bases, is cit - a characteristic you would use to identify e-coli? Do you use Enterotube for diagnostic purposes?HBDEdited by herebedragons, : clarification

When referring to humans, yes. Humans seem especially sensitive to major genetic changes. I am not sure exactly why this is or if it even has any statistical significance. It may just be that we are more aware of genetic defects and subsequent loss of fitness in humans. But humans are less than ideal genetic models. It is considered unethical to do genetic manipulations in humans. We study those defects that present phenotypic expression that causes disease. We don't look for genetic "defects" when someone is healthy. So anyway, to study genetic mutations we use "model organisms" such as Drosophila, Arabidopsis, Saccharomyces and Caenorhabditis to name a few. If you review studies on these organisms you will find many duplications that increase fitness or have other useful functions to the organism. You are oversimplifying the situation. There is much more going on than just protein production. The situation is much, much more complicated than that. It involves gene interactions, not just in the duplicated genes, but with genes on other chromosomes as well. It also depends heavily on what the gene product does. Some proteins can be overexpressed with little or no effect, some cause severe problems and others provide a benefit. Such generalized statement as these really don't have any significance.Again, if you look only at the human genome, then yes, you will probably find this to be the case most of the time. But not so for other organisms. You just need to do a little research on the topic. I have already mentioned polyploidy in plants. Turns out polyploidy can be very beneficial to plants. Many of our food crops are polyploids.Here is an example of overexpression providing a benefit

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Overexpression of TaSnRK2.8 resulted in enhanced tolerance to drought, salt and cold stresses, further confirmed by longer primary roots and various physiological characteristics, including higher relative water content, strengthened cell membrane stability, significantly lower osmotic potential, more chlorophyll content, and enhanced PSII activity.

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Unfortunately, science doesn't quite work this way; proof is an unrealistic goal. The best we can do is collect evidence and make the most of it. Do we need to make some assumptions? Yes. Do we make inferences? Of course. But to think those are things that hinder proper scientific investigation is just not realistic. We have to do the best we can with the information at hand. If there is evidence that contradicts the assumptions and inferences that have been made, then the conclusions will be overturned. But as long as the evidence points in a certain direction, conclusions are drawn from that. Then wouldn't it also be true that a decrease in protein production would decrease fitness?

Thanks Malcolm. I wanted to point this out to zaius but couldn't confirm the specifics. If citrate utilization is a diagnostic feature of E coli, then a positive result is unusual to say the least. But hey, its still a bacteria huh? It didn't evolve into a puppy ... so not novel. HBD