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Author Topic:   How novel features evolve #2
New Cat's Eye
Inactive Member


Message 128 of 402 (671327)
08-24-2012 11:30 AM
Reply to: Message 127 by zi ko
08-24-2012 10:38 AM


Re: DNA sequences and Phenotype selection
Why do you ignore the third (and more propable after epigenetics and the recent immence flow of knowledge about RNA) possibility, that of information from environment causing guided mutations?
The evnironment doesn't reach the genome in order to mutate it.

This message is a reply to:
 Message 127 by zi ko, posted 08-24-2012 10:38 AM zi ko has replied

Replies to this message:
 Message 130 by zi ko, posted 08-25-2012 12:55 AM New Cat's Eye has replied
 Message 152 by zi ko, posted 09-04-2012 12:57 AM New Cat's Eye has replied

  
New Cat's Eye
Inactive Member


Message 132 of 402 (671549)
08-27-2012 10:20 AM
Reply to: Message 130 by zi ko
08-25-2012 12:55 AM


Re: DNA sequences and Phenotype selection
The evnironment doesn't reach the genome in order to mutate it.
You seem so sure.... Can you bring any evidenc for random mutations in metazoa?
DNA replication is imperfect and leads to random errors in the gemone that are referred to as mutations. Here's a paper that goes into great detail about it:
http://www.nature.com/...lication-and-causes-of-mutation-409
But that's beside the point that the photype acts as a barrier between the envoronment and the genome, and thus prevents the evironment from directly mutating the genome. Granted, you could nuke your balls in the microwave, or something like that, but I don't think that's what we're talking about.

This message is a reply to:
 Message 130 by zi ko, posted 08-25-2012 12:55 AM zi ko has replied

Replies to this message:
 Message 137 by zi ko, posted 08-31-2012 11:06 AM New Cat's Eye has replied

  
New Cat's Eye
Inactive Member


Message 136 of 402 (671621)
08-28-2012 1:18 PM
Reply to: Message 134 by zi ko
08-28-2012 12:32 PM


Re: Meaningless controvercy.
It had proved beyond any doupt that stress causes genes mutations.
...which are still random with respect to fitness. So therefore, the environment is not driving evolution by directly affecting any mutations.
So the mechanism for it exists in metazoa.
But its not a mechanism for what you are proposing.

This message is a reply to:
 Message 134 by zi ko, posted 08-28-2012 12:32 PM zi ko has not replied

  
New Cat's Eye
Inactive Member


Message 139 of 402 (671911)
08-31-2012 11:23 AM
Reply to: Message 137 by zi ko
08-31-2012 11:06 AM


Re: DNA sequences and Phenotype selection
So environment causes gene mutations!
Sure, but it really doesn't have any impact on the evolution of species. Its negligible. It doesn't really matter.
You just have your pet idea and are doing anything you can to confirm your preconceived suspicions. Far be it from me to try to convince you to do otherwise.
In that case we would have a serious evidence or not of guided mutations.
But damn do you have to be grasping at straws to even come close to thinking that!

This message is a reply to:
 Message 137 by zi ko, posted 08-31-2012 11:06 AM zi ko has not replied

Replies to this message:
 Message 141 by Percy, posted 08-31-2012 11:29 AM New Cat's Eye has replied

  
New Cat's Eye
Inactive Member


Message 142 of 402 (671916)
08-31-2012 11:39 AM
Reply to: Message 141 by Percy
08-31-2012 11:29 AM


Re: DNA sequences and Phenotype selection
Catholic Scientist writes:
So environment causes gene mutations!
Sure, but it really doesn't have any impact on the evolution of species.
I'm guessing you really meant to something about guided evolution since any mutation, regardless of ultimate cause, can have an impact on evolution.
Your right. What I meant was that environment caused mutations aren't really that important when we're considering the evolution of speices. Sure, they aren't non-existant, but do they really matter? Meh, not so much. They don't really (read: an appreciable amount) affect evolution.
Especially, that is, compared to the extent that zi ko wants to use them to claim that it opens up an avenue for there to be guided mutations through the environment. That's why I said they're negligible.
But its obvious what he's doing. He wants there to be an intelligent designer. He likes that idea that mutation are guided through the environment. So what does he do? He points to every instance of there being any affect on mutation by the environment and then wants to think that that gives room for his favorite idea... but it doesn't.

This message is a reply to:
 Message 141 by Percy, posted 08-31-2012 11:29 AM Percy has replied

Replies to this message:
 Message 143 by Percy, posted 08-31-2012 12:04 PM New Cat's Eye has replied

  
New Cat's Eye
Inactive Member


Message 144 of 402 (671919)
08-31-2012 12:30 PM
Reply to: Message 143 by Percy
08-31-2012 12:04 PM


Re: DNA sequences and Phenotype selection
You may be unduly minimizing the impact of environmentally caused mutations on evolution.
I may be. Hey, maybe I'll learn something!
Environmental stress can increase mutation rates.
How's that work? What's the mechanism?
A population under environmental stress and possibly facing eventual extinction has a better chance of evolving it's way out of its predicament if it has a higher mutation rate.
See, I'm under the impression that zi ko is talking about the environment directly causeing a particular mutation... not that environmental stress can increase the rate of mutations in general.
I think the current understanding is that environmentally caused mutations can matter a great deal.
But a particular mutation isn't caused by the enivronment in these cases, is it? I know it is possible for the evnironment to directly cause a mutation, but that's not the same thing as the environment increasing mutation rates. And an environmentally increased mutation rate doesn't have anything to do with guided evolution.

This message is a reply to:
 Message 143 by Percy, posted 08-31-2012 12:04 PM Percy has seen this message but not replied

Replies to this message:
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New Cat's Eye
Inactive Member


Message 155 of 402 (672154)
09-04-2012 9:51 AM
Reply to: Message 152 by zi ko
09-04-2012 12:57 AM


Re: Re:choosing the easy enemy?
The evnironment doesn't reach the genome in order to mutate it.
Can isuppose,after Percy's intervention, you agree that it is not so?
I agreed that it is not so before Percy's intervention... in a post you've replied to.
From Message 132:
quote:
But that's beside the point that the photype acts as a barrier between the envoronment and the genome, and thus prevents the evironment from directly mutating the genome. Granted, you could nuke your balls in the microwave, or something like that, but I don't think that's what we're talking about.
In the context of what you are talking about, some sort of guided evolution, the evnironment doesn't reach the genome. There are certain and specific cases where it does happen, and you could make it happen if you wanted to (nuclear tanning bed or something).... but in the context of the evolution of species in general: particular mutations are not caused by the environment directly. They're random.
That's all that matters. Your pet idea is wrong.
But far be it from me to convince you otherwise or stop you from bringing it up in every single topic that you post in.

This message is a reply to:
 Message 152 by zi ko, posted 09-04-2012 12:57 AM zi ko has not replied

  
New Cat's Eye
Inactive Member


Message 157 of 402 (672160)
09-04-2012 11:11 AM
Reply to: Message 156 by foreveryoung
09-04-2012 10:44 AM


Re: DNA sequences and Phenotype selection
taq writes:
We ignore it because the evidence doesn't support it.
Or, so you say. What if we don't have the means to find the evidence...proper technology? What if we are wrong about what true evidence should look like?
Without the ability to consider the evidence, we have no choice but to ignore it.
It might be a problem if we were finding that science didn't really work all that well, but it does... like, really well.

This message is a reply to:
 Message 156 by foreveryoung, posted 09-04-2012 10:44 AM foreveryoung has not replied

  
New Cat's Eye
Inactive Member


(4)
Message 202 of 402 (673595)
09-20-2012 1:56 PM


On topic news
quote:
Evolution is as complicated as 1-2-3
A team of researchers at Michigan State University has documented the step-by-step process in which organisms evolve new functions.
The results, published in the current issue of Nature, are revealed through an in-depth, genomics-based analysis that decodes how E. coli bacteria figured out how to supplement a traditional diet of glucose with an extra course of citrate.
...
In the Nature paper, Blount and his teammates analyzed 29 genomes from different generations to find the mutational pieces of the puzzle. They uncovered a three-step process in which the bacteria developed this new ability.
The first stage was potentiation, when the E. coli accumulated at least two mutations that set the stage for later events. The second step, actualization, is when the bacteria first began eating citrate, but only just barely nibbling at it. The final stage, refinement, involved mutations that greatly improved the initially weak function. This allowed the citrate eaters to wolf down their new food source and to become dominant in the population.
We were particularly excited about the actualization stage, Blount said. The actual mutation involved is quite complex. It re-arranged part of the bacteria’s DNA, making a new regulatory module that had not existed before. This new module causes the production of a protein that allows the bacteria to bring citrate into the cell when oxygen is present. That is a new trick for E. coli.
The change was far from normal, Lenski said.
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.
http://news.msu.edu/.../evolution-is-as-complicated-as-1-2-3

Replies to this message:
 Message 203 by zaius137, posted 09-22-2012 12:01 AM New Cat's Eye has replied

  
New Cat's Eye
Inactive Member


(1)
Message 212 of 402 (673860)
09-24-2012 11:37 AM
Reply to: Message 203 by zaius137
09-22-2012 12:01 AM


Re: On topic news
I suppose why you are using E. coli adaptation in this thread is because you believe it is a case for evolution.
I posted the article because it was news that specifically pertained to the thread topic.
The adaptation of E. coli has nothing to do with evolution and everything to do with adaptation.
But adaptation and evolution have something to do with each other.
E. coli could already transport citrate into the cell and partially use it in wild, but under low oxygen conditions. There is but a few allowed mutations to take place to refine the process to allow full utilization of citrate as a food source. The mechanism was present in E. coli and only needed to adapt in controlled ways to accommodate full utilization.
Hang on a second. Did you take a look at the picture of the researcher:
http://news.msu.edu/...5af96-2626-404d-9b9a-32cc393bca34.jpg
Click 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.
Now are you up to separating designed adaptation from the dogma of evolution? Alternatively, are you claiming evolution is adaptation that leads to speciation?
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.
If so, you need a real example of a speciation event, and please do not invoke the magic of time.
The magic of time!?
quote:
Around generation 31,500 additional mutations enabled the cells to utilize citrate and grow more rapidly than cells without the adaptive mutations.
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...
quote:
Adaptive mechanisms in bacteria work by altering currently existing genetic information or functional systems to make the bacteria more suitable for a particular environment.
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:
quote:
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.
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

This message is a reply to:
 Message 203 by zaius137, posted 09-22-2012 12:01 AM zaius137 has replied

Replies to this message:
 Message 216 by zaius137, posted 09-25-2012 1:48 AM New Cat's Eye has replied

  
New Cat's Eye
Inactive Member


(1)
Message 218 of 402 (673963)
09-25-2012 10:26 AM
Reply to: Message 216 by zaius137
09-25-2012 1:48 AM


The answer to how mutations lead to novel features (adaptations) firmly fits in the Creation mindset.
Okay, so within that Creation mindset: How do novel features come about? How do they change?
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.
Um, I don't think so. I think that would take a lot more mutations than it took in this research.
Let us see, if there was as little change to humans as in the E. coli;
Wait, what? There was a huge change 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?
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.
This experiment only illustrates a morphological stasis in both E. coli and humans.
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.
isn’t really new information and was new information Could not characterize your confusion better.
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.
Two ways we know something, either by speculation or revelation. Given the availability of the two choices, I chose the revelation.
That's your loss. I choose learning from science.

This message is a reply to:
 Message 216 by zaius137, posted 09-25-2012 1:48 AM zaius137 has not replied

  
New Cat's Eye
Inactive Member


Message 230 of 402 (674193)
09-27-2012 1:41 AM
Reply to: Message 229 by zaius137
09-27-2012 1:20 AM


So were you unable to speculate or did you lack the revelation to actually respond to that?

This message is a reply to:
 Message 229 by zaius137, posted 09-27-2012 1:20 AM zaius137 has not replied

  
New Cat's Eye
Inactive Member


Message 240 of 402 (674296)
09-27-2012 5:49 PM


A novel feature's a novel feature
No matter how small

  
New Cat's Eye
Inactive Member


Message 243 of 402 (674380)
09-28-2012 10:12 AM
Reply to: Message 241 by zaius137
09-28-2012 1:45 AM


Re: On topic news
I would say that this adaptation was not novel because of definition one. The adaptation resembled something formally known or used.
Can you offer an example of something that you would consider novel?

This message is a reply to:
 Message 241 by zaius137, posted 09-28-2012 1:45 AM zaius137 has replied

Replies to this message:
 Message 245 by zaius137, posted 09-29-2012 12:33 AM New Cat's Eye has replied

  
New Cat's Eye
Inactive Member


(2)
Message 247 of 402 (674444)
09-29-2012 2:45 AM
Reply to: Message 245 by zaius137
09-29-2012 12:33 AM


Re: On topic news
A novel adaptation would have to include an entire population where that population becomes homozygous to that trait.
Isn't that what happened to the bacteria with the citrate? The ones who had the mutations to be able to digest it survived and the ones who couldn't died. Therefore, the entire population that survived had that homozygous trait. As a whole, that population became heterozygous to what it was.
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.
The population is made up of individuals, so the trait has to start somewhere. When it spreads to the population that survives the condition, i.e. citrate, and then the ones who don't have it die, then you end up with just individuals who have the novel trait. This is Evolution 101.
That is the heterozygosity completely being cleansed in the resulting genome (a classic sweep in evolution).
Right, by the lethality of the citrate killing off all the individuals who don't have the novel trait.
Can a real biologist chime in.
Nigga please. This is high school level stuff.

This message is a reply to:
 Message 245 by zaius137, posted 09-29-2012 12:33 AM zaius137 has replied

Replies to this message:
 Message 250 by zaius137, posted 09-30-2012 12:34 AM New Cat's Eye has not replied

  
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