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Author Topic:   How novel features evolve #2
zaius137
Member (Idle past 1362 days)
Posts: 407
Joined: 05-08-2012


Message 241 of 402 (674352)
09-28-2012 1:45 AM
Reply to: Message 238 by Percy
09-27-2012 2:23 PM


Re: On topic news
Percy,

So before we come up with yet another example I think you need to provide your criteria for novelty, otherwise coming up with more examples is pointless because you'll just dismiss them as "not novel" for arbitrary reasons.

From the Merriam-Webster: (Novel)

quote:
1) new and not resembling something formerly known or used
2) original or striking especially in conception or style
http://www.merriam-webster.com/dictionary/novel

I would say that this adaptation was not novel because of definition one. The adaptation “resembled” something formally known or used.


This message is a reply to:
 Message 238 by Percy, posted 09-27-2012 2:23 PM Percy has responded

Replies to this message:
 Message 242 by Percy, posted 09-28-2012 8:11 AM zaius137 has not yet responded
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Percy
Member
Posts: 17879
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


(1)
Message 242 of 402 (674372)
09-28-2012 8:11 AM
Reply to: Message 241 by zaius137
09-28-2012 1:45 AM


Re: On topic news
Zaius,

You're not being very helpful. You offer two definitions instead of one, and you don't explain how your definitions lead to the conclusion that the ability to digest citrate in the presence of oxygen is not novel while a fin becoming a leg is. The citrate example that involves the difference between life and death for an E. coli with the misfortune to be involved in the experiment certainly seems new, original and striking to everyone here but you.

--Percy


This message is a reply to:
 Message 241 by zaius137, posted 09-28-2012 1:45 AM zaius137 has not yet responded

    
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 responded

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

  
Solstice
Junior Member (Idle past 2121 days)
Posts: 3
Joined: 07-20-2012


Message 244 of 402 (674435)
09-29-2012 12:12 AM
Reply to: Message 241 by zaius137
09-28-2012 1:45 AM


Re: On topic news
quote:
From the Merriam-Webster: (Novel)

quote:
1) new and not resembling something formerly known or used
2) original or striking especially in conception or style

http://www.merriam-webster.com/dictionary/novel
I would say that this adaptation was not novel because of definition one. The adaptation “resembled” something formally known or used.

What compels you to apply that definition to evolution? Especially when considering the fact that many major morphological changes necessitate the alteration of existing features.

Edited by Solstice, : No reason given.

Edited by Solstice, : No reason given.


This message is a reply to:
 Message 241 by zaius137, posted 09-28-2012 1:45 AM zaius137 has not yet responded

    
zaius137
Member (Idle past 1362 days)
Posts: 407
Joined: 05-08-2012


Message 245 of 402 (674436)
09-29-2012 12:33 AM
Reply to: Message 243 by New Cat's Eye
09-28-2012 10:12 AM


Re: On topic news
The Catholic Scientist…

Can you offer an example of something that you would consider novel?

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).

Can a real biologist chime in….

Edited by zaius137, : A clear misspeak


This message is a reply to:
 Message 243 by New Cat's Eye, posted 09-28-2012 10:12 AM New Cat's Eye has responded

Replies to this message:
 Message 246 by Tangle, posted 09-29-2012 2:40 AM zaius137 has not yet responded
 Message 247 by New Cat's Eye, posted 09-29-2012 2:45 AM zaius137 has responded
 Message 248 by Percy, posted 09-29-2012 8:51 AM zaius137 has not yet responded
 Message 249 by herebedragons, posted 09-29-2012 10:09 AM zaius137 has responded

  
Tangle
Member
Posts: 6249
From: UK
Joined: 10-07-2011
Member Rating: 2.4


(2)
Message 246 of 402 (674443)
09-29-2012 2:40 AM
Reply to: Message 245 by zaius137
09-29-2012 12:33 AM


Re: On topic news
novel writes:

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).

Well that's a fairly typical switch, you're asked what novel is and you reply with a requirement for a second condition that has nothing to do with any definition of novel. Cute.

But never mind, what do you think would happen to a mixed population of of citrate and non-citrate eating bacteria with nothing to eat except citrate in the presence of oxygen? I'm guessing that you'd be left with a replicating population of citrate eaters only. Wouldn't you?

Edited by Tangle, : No reason given.


Life, don't talk to me about life - Marvin the Paranoid Android

This message is a reply to:
 Message 245 by zaius137, posted 09-29-2012 12:33 AM zaius137 has not yet responded

  
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 responded

Replies to this message:
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Percy
Member
Posts: 17879
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


(2)
Message 248 of 402 (674466)
09-29-2012 8:51 AM
Reply to: Message 245 by zaius137
09-29-2012 12:33 AM


Re: On topic news
Tangle pointed out that this new criteria has nothing to do with novelty, so you haven't answered the question about how you're defining novelty.

And CS pointed out that citrate digesting bacteria already fulfill your new criteria, so if you really believe this new criteria defines novelty then you have in effect just conceded that citrate digestion is an example of novelty.

I assume that wasn't your intention, so your only path out of this quandary is to introduce yet more criteria. What is it to be this time? That it can't happen in a lab? That it can't be single-celled organisms?

This thread is about how evolution produces novelty. Naturally some traits are more novel than others. There must inevitably be a spectrum from slight to extreme novelty, but there will always be novelty. Changing environments impose demands for change in organisms, and random mutations guarantee that many new traits offered up to natural selection will be novel.

Again, this thread is about how evolution produces novelty. Evolution produces change one little mutation at a time, and citrate digestion is a prime example of how this process of gradual change produces novelty. Whether or not citrate digestion is novel, the process that produced citrate digestion is the same one that produces novelty. Whatever features you eventually decide to concede are novel, they are produced in the same way as citrate digestion, one little step at a time.

By the way, I chanced across a mention in the Wikipedia article on citrate-digesting bacteria that these E. coli are larger and more rounded, so there *is* a morphological difference. This is as irrelevant as it was when you first raised it as an issue, but I just thought I'd mention that yet another of your objections has disappeared. Perhaps these morphological differences are in your mind insufficient to qualify as real differences, but in that case it would just be a further demonstration of your constant recourse to inventing criteria as you go along.

--Percy


This message is a reply to:
 Message 245 by zaius137, posted 09-29-2012 12:33 AM zaius137 has not yet responded

    
herebedragons
Member
Posts: 1483
From: Michigan
Joined: 11-22-2009


(2)
Message 249 of 402 (674480)
09-29-2012 10:09 AM
Reply to: Message 245 by zaius137
09-29-2012 12:33 AM


Re: On topic news
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.

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.


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

Replies to this message:
 Message 251 by zaius137, posted 09-30-2012 2:47 AM herebedragons has not yet responded

  
zaius137
Member (Idle past 1362 days)
Posts: 407
Joined: 05-08-2012


(1)
Message 250 of 402 (674528)
09-30-2012 12:34 AM
Reply to: Message 247 by New Cat's Eye
09-29-2012 2:45 AM


Re: On topic news
To the Catholic Scientist, but it is shaped as a general reply to several participants.

I believe I have more than met the request made that I define what I believe is a novel innovation of a new trait or novel Phenotypic Variation.

Concerning the E. coli example…

By definition, I showed that the transport of citrate trough the cell wall of E. coli was not a novel innovation because under anaerobic conditions it could already take place. Point of fact concerning the definition of novel…

quote:
1) new and not resembling something formerly known or used

This is because the transport of citrate through the cell wall under anaerobic conditions was adapted to aerobic conditions via a newly promoted recessive gene. The transport of citrate already occurred but was enhanced (adapted), in that strict sense the qualification of “resembling” was satisfied.

Now was there a novel transporter mechanism in the genome that suddenly appeared. The answer is no. The transport of citrate in aerobic conditions (Cit+) appeared because of a tandem duplication that acted as an aerobic promoter of a previous silent transporter.

quote:
The Cit+ trait originated in one clade by a tandem duplication that captured an aerobically expressed promoter for the expression of a previously silent citrate transporter. http://www.nature.com/...al/v489/n7417/full/nature11514.html

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.

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. A genome designed by a all powerful Creator.


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 Message 247 by New Cat's Eye, posted 09-29-2012 2:45 AM New Cat's Eye has not yet responded

Replies to this message:
 Message 252 by Percy, posted 09-30-2012 2:10 PM zaius137 has responded
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zaius137
Member (Idle past 1362 days)
Posts: 407
Joined: 05-08-2012


Message 251 of 402 (674532)
09-30-2012 2:47 AM
Reply to: Message 249 by herebedragons
09-29-2012 10:09 AM


New example.
(herebedragons)…

Since I have shown that E. coli using citrate is not a new novel trait, I would like to address the polar bear.

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.

Something bothers me here…

Can selective pressure cause an evolutionary like change? In the case of bears, apparently it does not, so you rightly label it as adaptation. In fact, scientific experiments have come to the same conclusions; particularly in fruit flies. Massive selective pressure has only produced adaptation (not new novel traits). In all cases, there is a limit to adaptation; in other words, there is a limit to phylogenic change in a species that never really produces a truly novel trait. Adaptation is always a better definition, as you seem to verify.

Interesting that Polar Bears and Grizzlies can and do interbreed (Pizzlys). Supposedly, the two groups diverged about 5 million years ago, about the same time as the chimp human divergence. There is an extraordinary environmental pressure rift between the two bears yet they remain bears. Awkwardly the environmental pressure on pre-human hominids is not as well defined as in bears. In one case, you call natural selection as a force for adaptation in bears but what about human evolution.

Is there a consistent expectation in the theory of evolution or is it on a case-by-case basis. If the latter is true, do you have a theory or just a philosophy?

The trait then became "homozygous" in the polar bear population.

You did not mention the classic sweep (an important omission).

I do not think you have a grasp on what I am actually claiming…. For the record:

“There is no evolution, only adaptation.” Therefore, when you say, “you have it completely backwards” I say to you that you miss the point.

…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….

I addressed this in a previous post… Heterozygous in terms of per capita… I will let you figure that one out.


This message is a reply to:
 Message 249 by herebedragons, posted 09-29-2012 10:09 AM herebedragons has not yet responded

Replies to this message:
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Percy
Member
Posts: 17879
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


(2)
Message 252 of 402 (674559)
09-30-2012 2:10 PM
Reply to: Message 250 by zaius137
09-30-2012 12:34 AM


Re: On topic news
Hi Zaius,

You're failing to engage what anyone is telling you, e.g.:

I believe I have more than met the request made that I define what I believe is a novel innovation of a new trait or novel Phenotypic Variation.

No one else thinks so, so why are you ignoring their requests for clarification?

By definition, I showed that the transport of citrate trough the cell wall of E. coli was not a novel innovation because under anaerobic conditions it could already take place.

Everyone else is telling that the novelty is the ability to do this is the presence of oxygen, so why are you ignoring this? Why don't you explain to us how transportation in the absence of horses was not an innovation since stuff was already being transported anyway?

Now was there a novel transporter mechanism in the genome that suddenly appeared? The answer is no.

Evolution frequently works by taken advantage of what is already there. If you disallow these types of innovations then indeed novel differences will never emerge in experiments that can actually be performed. All you're doing now is insisting on a definition of novelty so large and significant that it would require several human lifetimes even using rapidly reproducing bacterial species.

This doesn't change the facts of how novel features evolve, which is one little evolutionary step at a time. That thirty some thousand generations of the Lenski experiment produced insufficient novelty for your criteria doesn't change the fact that it is a perfect illustration of how evolution produces novelty, for certainly if allowed to continue for a number of human generations the novelty would be so considerable as to be acceptable as novelty to anyone.

Anyway, the important point is that you still haven't provided a definition of novelty that we can use. How would we use your definition of novelty to decide whether a fin evolving into a leg is sufficiently innovative?

--Percy


This message is a reply to:
 Message 250 by zaius137, posted 09-30-2012 12:34 AM zaius137 has responded

Replies to this message:
 Message 254 by zaius137, posted 10-01-2012 12:53 AM Percy has responded

    
Percy
Member
Posts: 17879
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


(1)
Message 253 of 402 (674567)
09-30-2012 2:43 PM
Reply to: Message 251 by zaius137
09-30-2012 2:47 AM


Re: New example.
zaius137 writes:

I do not think you have a grasp on what I am actually claiming…. For the record:

“There is no evolution, only adaptation.”

Now you're repeating earlier mistakes. Is that to be your strategy, just cycling through your errors until the thread ends.

Again, adaptation is what evolution does. Is it perhaps speciation that you're thinking of and not evolution?

--Percy

Edited by Percy, : Fix typos.


This message is a reply to:
 Message 251 by zaius137, posted 09-30-2012 2:47 AM zaius137 has not yet responded

    
zaius137
Member (Idle past 1362 days)
Posts: 407
Joined: 05-08-2012


Message 254 of 402 (674612)
10-01-2012 12:53 AM
Reply to: Message 252 by Percy
09-30-2012 2:10 PM


Re: On topic news
Percy,

Anyway, the important point is that you still haven't provided a definition of novelty that we can use. How would we use your definition of novelty to decide whether a fin evolving into a leg is sufficiently innovative?
--Percy

The definition you “can use” does not exist. Fins evolving into legs are complete and utter fantasy. Now you need to make scientific arguments that support your speculation. The science is clearly on my side while wild speculation seems to be your only arguments.


This message is a reply to:
 Message 252 by Percy, posted 09-30-2012 2:10 PM Percy has responded

Replies to this message:
 Message 255 by Tangle, posted 10-01-2012 3:27 AM zaius137 has responded
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 Message 260 by Taq, posted 10-01-2012 1:37 PM zaius137 has not yet responded

  
Tangle
Member
Posts: 6249
From: UK
Joined: 10-07-2011
Member Rating: 2.4


(2)
Message 255 of 402 (674618)
10-01-2012 3:27 AM
Reply to: Message 254 by zaius137
10-01-2012 12:53 AM


Re: On topic news
Zauis writes:

The definition you “can use” does not exist

So your contribution to this entire thread has been a sham. You've ruled out all changes as impossible before you even started.


Life, don't talk to me about life - Marvin the Paranoid Android

This message is a reply to:
 Message 254 by zaius137, posted 10-01-2012 12:53 AM zaius137 has responded

Replies to this message:
 Message 259 by zaius137, posted 10-01-2012 1:36 PM Tangle has responded

  
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