|
Register | Sign In |
|
QuickSearch
Thread ▼ Details |
|
Thread Info
|
|
|
Author | Topic: How novel features evolve #2 | ||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined:
|
Can a real biologist chime in. I'm a senior studying Environmental Biology, is that close enough? At least I'm not a fake biologist.
A novel adaptation would have to include an entire population where that population becomes homozygous to that trait. An individual organism variation would not constitute a novel trait, in other words that trait must be fixed in a population and homozygous to all individuals with new trait substituting into the original genome of the species. That is the heterozygosity completely being cleansed in the resulting genome (a classic sweep in evolution). 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. HBDWhoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined:
|
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.
quote: The authors then go on to explain how the process is thought to give rise to these novel functions.
quote: 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.
quote: 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.
It is noteworthy that this silent transporter was in the genome all along never being pruned by evolution. If you can explain this please do. 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.
Rather than being an example of evolution producing a new and novel trait this research only shows that there is front loading of adaptation in the genome. 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. HBDWhoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined:
|
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 J Organism after mutation: A B C D E K F G H I J You 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.
SNP’s and inversions do not make new information. They simply rearrange or disrupt the existing background for adaptation to new functionality. If you have a single example of spontaneous entropy decrease now is the time to present it. 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 Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined:
|
Since evolution is speculation, you must replace it with adaptation. 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 begging an answer is where the "features" that existed beforehand came from if not from a creator. 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?
But adaptation will never change one species into another. You can't actually believe this.
You are losing the debate because you are simply in the wrong. 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.
Try using the word of God to navigate science and you will enjoy the same rate of success I do. 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 Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined:
|
Welcome mindspawn ...
But how do you add an extra functional gene? 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:
quote: 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.)
Whenever an added gene produces proteins the duplication of the proteins damages fitness to an organism. This is just plain wrong. Do you have a source that supports this?
Yes deletions can change a species into a new one, disabling of a gene too. So I take it you are thinking of genetic entropy? HBDWhoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined:
|
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 Drosophila2. 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 speciation Is this proof that this is actually what happened? No, of course not. But it strongly implies it. Does it exclude these other possibilities?
1) The extra region could have evolved 2) The missing region could have devolved complexity 3) Both species could be designed like that (intelligent design) 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. HBDWhoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined: |
We're a diagnostic lab, so we don't define what the species are, we just identify bacteria and what antibiotics are effective so doctors can treat the patient. * 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? HBD Edited by herebedragons, : clarificationWhoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined:
|
So the likelihood of an entire gene being duplicated without damage to an organism is small, that's why i need proof that this was a duplication and not a deletion. 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.
My reason is that when you duplicate the proteins produced you normally get a less fit organism because of the excess proteins causing imbalance in the organism. The proteins required for each function are very precise and even a slight increase in protein production through insertions within a gene can decrease fitness (Huntington's disease). Major duplications of entire chromosomes cause major loss of fitness as in Down's syndrome. So the likelihood of an entire gene being duplicated without damage to an organism is small 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
quote: Without the proof that the original population was devoid of the duplicates, the whole point is meaningless. 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.
The proteins required for each function are very precise and even a slight increase in protein production ... Then wouldn't it also be true that a decrease in protein production would decrease fitness? Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
||||||||||||||||||||||||||||||||||||||||
herebedragons Member (Idle past 883 days) Posts: 1517 From: Michigan Joined: |
I've not used Enterotube but looks like the same principle as Biomerieux's API system we've used, which also lists E.coli as 0% citrate positive. 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. HBDWhoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca "Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
|
|
|
Do Nothing Button
Copyright 2001-2023 by EvC Forum, All Rights Reserved
Version 4.2
Innovative software from Qwixotic © 2024