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Prove an interpretation?

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Prove an interpretation?
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RumraketUser avatarPosts: 1175Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: Prove an interpretation?

leroy wrote:
Rumraket wrote:Why would it have to be achievable in 1 generation? Why not 2, or 5, or a hundred? The answer is that it doesn't.

Why would it have to be "positive" rather than neutral? It doesn't. It could even be slightly deleterious and still fix by drift in a small population, or substantially deleterious yet hitchike with another beneficial allele.

Why would someone have to provide a step by step path at this level of detail? Do you even have any other beliefs which are supported by such a level corroboration? Of course you don't.

Isn't it obvious you're deliberately setting the bar irrationally high? Yes, yes it is.

well by definition a step is achievable in 1 generation, with step I mean a genetic change that would be selected by natural selection and that would represent a step closer towards a modern eye.

Okay, but then your "demand" becomes vacuous, because all genetic changes that owe to a single mutation, or homologous recombination, is by definition achievable in 1 generation.

leroy wrote:If you what to proclaim that blind creatures evolved modern eyes by accumulating neutral mutations, then you would be claiming mount improbable

No. I'm obviously not claiming all of eye-evolution was achieved by genetic drift, that would be preposterous. Rather, I'm merely saying that not all of the "steps" have to be beneficial. We know for a fact that there are complex phenotypes who's evolutionary history include necessary neutral mutations that fixed by genetic drift.

For example, the evolution of chloroquine resistance in plasmodium falciparum requires multiple neutral mutations along the way.

And in the Long-Term Evolution Experiment, the cit+ phenotype requires at least one neutral, potentiating mutation.

leroy wrote:most neutral mutations are removed by genetic drift.

Yes, most, but not all.

The rate of fixation of neutral mutations is equal to the mutation rate. Neutral mutations, because most mutations are neutral, are constantly arising. The vast majority are lost again, but even so, because so many constantly crop up in every individual in the population (and this is true for all populations), there is a constant rate of fixation of neutral alleles.

http://www.nyu.edu/projects/fitch/courses/evolution/html/genetic_drift.html
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"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Thu Feb 23, 2017 9:47 am
thenexttodiePosts: 799Joined: Fri Mar 13, 2015 7:59 pm Gender: Male

Post Re: Prove an interpretation?

Nesslig20 wrote:
I have looked up some things about the ultraviolet vision of fish and some important things that contradict your statement.
1. Not all fish have ultra violet vision nor infra red - some vision of fish are much like ours.
2. Ultra violet vision in fish is linked to mate selection - not with regard to the damaging effects of UV underwater.
3. Ultra violet light is absorbed quickly by water, thus UV isn't very damaging when you are under water.
4. Many animals can see the UV light, some live on land and some live underwater, even ones that are not fish nor any other vertebrate (meaning they have different eyes without the blindspot).

Your explanation that vertebrate eyes are better suited for handling direct light on land, still doesn't work with regard to animals with vertebrates that live under water.


Yes, I have recently looked up these things too. Thank you for your constructive critazism. I think you are correct in saying that this was a poor argument which I made.

You should write a book sometime. I would buy it.

Nesslig20 wrote:
Why do ALL and ONLY vertebrates have eyes with blindspots? ....there are animals with eyes that don't have a blindspot, yet are supplied by blood.


There are no animals which depend on an oxygenated blood supply, that have non blind spot eyes. Regardless of what enviroment they are in, they would still require a hole in the eye for blood to enter to receive enough oxygen to function. Humans use iron in the blood to distribute blood oxygen throughout the body. In Mollusks, the oxygen is just freely distribute throughout the body and is not dependent on their blood supply.
Non vertebrates have a different body chemistry the vertebrates.
“..the simplest thing cannot be made clear to the most intelligent man if he is firmly persuaded that he knows already, without a shadow of doubt, what is laid before him.” Tolstoy
Thu Feb 23, 2017 7:00 pm
Nesslig20User avatarPosts: 260Joined: Wed Mar 16, 2016 6:44 pm Gender: Male

Post Re: Prove an interpretation?

thenexttodie wrote:
Nesslig20 wrote:
I have looked up some things about the ultraviolet vision of fish and some important things that contradict your statement.
1. Not all fish have ultra violet vision nor infra red - some vision of fish are much like ours.
2. Ultra violet vision in fish is linked to mate selection - not with regard to the damaging effects of UV underwater.
3. Ultra violet light is absorbed quickly by water, thus UV isn't very damaging when you are under water.
4. Many animals can see the UV light, some live on land and some live underwater, even ones that are not fish nor any other vertebrate (meaning they have different eyes without the blindspot).

Your explanation that vertebrate eyes are better suited for handling direct light on land, still doesn't work with regard to animals with vertebrates that live under water.


Yes, I have recently looked up these things too. Thank you for your constructive critazism. I think you are correct in saying that this was a poor argument which I made.

You should write a book sometime. I would buy it.


Well, thanks for the compliment.

Nesslig20 wrote:
thenexttodie wrote:Why do ALL and ONLY vertebrates have eyes with blindspots? ....there are animals with eyes that don't have a blindspot, yet are supplied by blood.


There are no animals which depend on an oxygenated blood supply, that have non blind spot eyes.

Regardless of what enviroment they are in, they would still require a hole in the eye for blood to enter to receive enough oxygen to function. Humans use iron in the blood to distribute blood oxygen throughout the body. In Mollusks, the oxygen is just freely distribute throughout the body and is not dependent on their blood supply.
Non vertebrates have a different body chemistry the vertebrates.


I am sorry, but that is simply not true.

For one thing, you can supply the eye with blood without having to puncture through the retina. The blood can simply circulate around the eye ball and supply oxygen that way. But that is not the main problem with your statement.

Mollusks have blood too and they do depend on their blood supply to distribute oxygen throughout a body. Vertebrates use iron-containing hemoglobin as the oxygen transporter, while mollusks (and arthropods) use copper-containing hemocyanin.

Wait? That is another observation similar to the occurrence of different eyes among different taxa.

All vertebrates have one type of oxygen transporter while all mollusks have another type.
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Figure 4.8 - Phylogenetic distribution of oxygen-carrier proteins: Hb, hemoglobin; Mb, myoglobin; Er, erythrocruorin; Ch, chlorocruorin; He, hemocyanin; Hr, hemerythrin.15a Reproduced with permission from K. E. van Holde and K. I. Miller, Quart. Rev. Biophys. 15 (1982), 1-129.


Although there are a couple of exceptions, though these exceptions only makes the case for evolution stronger.

There is a group of ice fish that have lost their hemoglobin (they don't need it since cold water can carry enough oxygen on its own without any oxygen carrier) and replaced it with clear blood with an antifreeze, though they still have the remnant hemoglobin pseudogenes as an evolutionary baggage of their vertebrate ancestry.


And there is a group of snails (Planorbidae) that have red blood due to a novel hemoglobin. Though having the same name, the hemoglobin protein is different than that vertebrates and it has evolved independently. And these snails still express a broken form of hemocyanin as an evolutionary baggage of their mollusk ancestry.

This doesn't make sense from a designers perspective to leave broken genes as traces of the organisms evolutionary ancestry, which shows the exact same hierarchal pattern of the occurrence of unique traits among different taxonomic groups, that evolution via common descent would produce. Isn't this odd? This is why we say that...
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"Ignorance more frequently begets confidence than does knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science."
Charles Darwin
Thu Feb 23, 2017 11:51 pm
thenexttodiePosts: 799Joined: Fri Mar 13, 2015 7:59 pm Gender: Male

Post Re: Prove an interpretation?

thenexttodie wrote:Why do ALL and ONLY vertebrates have eyes with blindspots? ....there are animals with eyes that don't have a blindspot, yet are supplied by blood.


There are no animals which depend on an oxygenated blood supply, that have non blind spot eyes.

Regardless of what enviroment they are in, they would still require a hole in the eye for blood to enter to receive enough oxygen to function. Humans use iron in the blood to distribute blood oxygen throughout the body. In Mollusks, the oxygen is just freely distribute throughout the body and is not dependent on their blood supply.
Non vertebrates have a different body chemistry the vertebrates.


[quote="Nesslig20"] I am sorry, but that is simply not true.

For one thing, you can supply the eye with blood without having to puncture through the retina. The blood can simply circulate around the eye ball and supply oxygen that way. But that is not the main problem with your statement.

Mollusks have blood too and they do depend on their blood supply to distribute oxygen throughout a body. Vertebrates use iron-containing hemoglobin as the oxygen transporter, while mollusks (and arthropods) use copper-containing hemocyanin.[quote]

What I said about oxygenated blood and mollusks was wrong . I'm not sure why I wrote that because I did not cite any sources in any of my posts.

Nesslig, What I think I wanted to write was that because of the difference of the chemistry used to transmit oxygen, oxygen should be able to faster permeate through the wall of photo cells in mollusks than in humans. Thus mollusks have no need for a "blind spot". It would be cool if you could evaluate this statement for me because I swear I had a source for this but now I can't find it.



[quote="Nesslig20"] Wait? That is another observation similar to the occurrence of different eyes among different taxa.

All vertebrates have one type of oxygen transporter while all mollusks have another type. [quote]

Yes! This was kinda the point I was trying to make, (though I think the way taxa are defined is often arbitrary.) Why waste time comparing structures and even opsins if the type of eye a creature has might be proved to a symptom of body chemistry or metabolic trade off? Wouldn't this make things much simpler? It would be a win win situation for both of us. Fuck all the bullshit.

Thank you for taking the time to respond to my posts in such a constructive manner. I know you think this is stupid but I think there is a God and that he loves you very very much, even though we beat him and killed him very painfully.
“..the simplest thing cannot be made clear to the most intelligent man if he is firmly persuaded that he knows already, without a shadow of doubt, what is laid before him.” Tolstoy
Mon Feb 27, 2017 5:03 pm
Nesslig20User avatarPosts: 260Joined: Wed Mar 16, 2016 6:44 pm Gender: Male

Post Re: Prove an interpretation?

thenexttodie wrote:What I said about oxygenated blood and mollusks was wrong . I'm not sure why I wrote that because I did not cite any sources in any of my posts.
Nesslig, What I think I wanted to write was that because of the difference of the chemistry used to transmit oxygen, oxygen should be able to faster permeate through the wall of photo cells in mollusks than in humans. Thus mollusks have no need for a "blind spot". It would be cool if you could evaluate this statement for me because I swear I had a source for this but now I can't find it.


That is a quite different statement, I am not sure how it can be that you wanted to write this yet wrote something completely different.
The chemistry used to transmit oxygen is different, as I have noted with the oxygen carriers among different taxa. However, that has nothing to do with how oxygen permeates through the wall of cells. That happens by diffusion after the oxygen is released from the oxygen career hemoglobin or hemocyanin. Diffusion is the same as in any organism, both octopi and vertebrates.

IF your argument now turns into the difference in the chemistry used to transmit oxygen, than the problem is just moved back a step and the same pattern persists (instead of the eye it is blood chemistry). Why do all mollusks have hemocyanin and all vertebrates have hemoglobin? see my previous reply for more.

Blood is supplied to the eye by several arteries, some of which don't go through the retinal area causing the blind spot. So it is not necessary for arteries to go through the blind spot to supply the eye with blood. Also it is not just the arteries that go through the retina, it is also the nerves. The only reason that particular artery punctures the retina is that it follows the optic nerve by supplying the fibers of that nerve with oxygen and nutrients.
So the question is, why should the optic nerve make that blindspot in all vertebrates and only in vertebrates?

thenexttodie wrote:Yes! This was kinda the point I was trying to make, (though I think the way taxa are defined is often arbitrary.)


Then your point supports common ancestry. And taxonomy isn't arbitrary since it uses characteristics based definitions and now we use genetics to support or correct that classification. All humans are mammals (you've got mammary glands) and all mammals are vertebrates (you have a backbone), etc. This isn't arbitrary.

thenexttodie wrote:Why waste time comparing structures and even opsins


Because that is how (in simple terms) scientists investigate how these things evolve. And I showed the research to someone asking the very question of how the eye evolved, but ignored it, like usual.

thenexttodie wrote:if the type of eye a creature has might be proved to a symptom of body chemistry or metabolic trade off?


Does it? You have argued that, but I don't see how chemistry/metabolic trade offs are linked to the design of the eye as I have explained here.
The only reason there is that explains the occurrence of different eyes between taxa and the same eyes within taxa is their phylogenetic history. Their evolutionary ancestry determines which taxon inherits a particular design of an eye or oxygen carrier (i.e. blood chemistry).

thenexttodie wrote:Thank you for taking the time to respond to my posts in such a constructive manner. I know you think this is stupid but I think there is a God and that he loves you very very much, even though we beat him and killed him very painfully.


I do think it is stupid, but probably not for the reasons you think I do. But this is irrelevant because in either case, whether a god exists or not, whether your God (with a capital G) exists or not, it doesn't matter. We both are, in either case, evolved apes.
"Ignorance more frequently begets confidence than does knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science."
Charles Darwin
Tue Feb 28, 2017 10:23 pm
leroy
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Posts: 1765Joined: Sat Apr 04, 2015 1:30 pm

Post Re: Prove an interpretation?

Rumraket wrote:Okay, but then your "demand" becomes vacuous, because all genetic changes that owe to a single mutation, or homologous recombination, is by definition achievable in 1 generation.


granted, My request was to provide a genetic change that
1 is achievable in 1 generation
2 that would be selected by natural selection
3 that Would represent closer towards a modern eye.


in order to evolve an eye form a blind, eyeless creature you need to repeat 1,2 and 3 like millions of times, I am just asking for a small sample of all the steps that where suppose to happen.............showing a single step Would be a good start

with step I mean 1,2 and 3 all together.



No. I'm obviously not claiming all of eye-evolution was achieved by genetic drift, that would be preposterous. Rather, I'm merely saying that not all of the "steps" have to be beneficial. We know for a fact that there are complex phenotypes who's evolutionary history include necessary neutral mutations that fixed by genetic drift


granted, not all of the steps have to be beneficial, but if you what to invoke too many neutral steps you will have a serious probabilistic problem. Even in a small population of 1000 individuals, genetic drift would remove 1999 mutations for every 2,000 mutations.
.

For example, the evolution of chloroquine resistance in plasmodium falciparum requires multiple neutral mutations along the way.


no familiar with that, but granted,

And in the Long-Term Evolution Experiment, the cit+ phenotype requires at least one neutral, potentiating mutation.


well we are talking about unicelular organisms and under a controlled laboratory, in the wild and with multicellular organisms it is very hard to keep a specific neutral mutation,



The rate of fixation of neutral mutations is equal to the mutation rate. Neutral mutations, because most mutations are neutral, are constantly arising. The vast majority are lost again, but even so, because so many constantly crop up in every individual in the population (and this is true for all populations), there is a constant rate of fixation of neutral alleles.


the problem is that you need the specific neutral mutations that would represent a step closer towards modern eyes, for example is you need a point mutation in some gene in order to advance 1 step towards modern eyes the probability of keeping that mutation is 1/2N.

For a diploid population of size N and neutral mutation rate
μ {\displaystyle \mu }
, the initial frequency of a novel mutation is simply 1/(2N),

https://en.wikipedia.org/wiki/Fixation_ ... n_genetics)
"events with a zero probability happen all the time"
Wed Mar 01, 2017 8:27 pm
leroy
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Posts: 1765Joined: Sat Apr 04, 2015 1:30 pm

Post Re: Prove an interpretation?

Nesslig20 wrote:
And genetic changes in opsins (light sensitive proteins), genes involved in development of the eye (like Pax6) and crystallines (structural proteins of the lens) and more have been identified. Many changes involve the same gene duplication mechanism.

Citations:
- Metazoan opsin evolution reveals a simple route to animal vision
- Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup
- Deep homology of eye development and the parallel evolution of animal eyes.
- Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish
- Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants
- Evolution of crystallins for a role in the vertebrate eye lens



Well what i would call a step requires 3 things

1 a genetic change achievable in 1 generation (like a gene duplication for example)

2 it has to be beneficial (something that would be selected by natural selection)

3 it has to represent a step closer towards modern eyes


does any of your articles provide an example of a step (1,2 and 3)?......if yes can you please copy_paste the exact portions of the article that show 1 2 and 3?



Fallacy of shifting the burden of proof. You made two claims:



:lol: :lol: :lol: why is it that atheist never what to accept their burden.

I am the skeptic, and I was told by he_who_is_nobody that skpetics don't have to prove anything


1. each of those steps requires multiple independent genetic changes,
and
2. even a small benefit requires multiple independent genetic changes

These are the claims that you made so you have the burden.[/quote]
I am just saying that 1 are 2 are probably true, I am not claiming that I know it........I am the skeptic, you are the one who is claiming that there is a step by step path from eyeless to modern eyes.



Of course, that is not what you mean. You mean that we don't understand this at all, which we don't. We do understand more about this than you want to admit. The details are still discussed among experts, but they all share the general conclusion that yes, opsins, crystallines, and other elements involved in the function and structure of the eye have all evolved and we do have a damn good understanding of how they did. Again read the citations.


What I meant is that in reality we don't know, we don't have enough understanding on how eyes work at a genetic level and what genes and genetic changes are required to evolve eyeless to modern eyes. therefore we don't know if there is a viable step by step path.
"events with a zero probability happen all the time"
Wed Mar 01, 2017 9:01 pm
he_who_is_nobodyBloggerUser avatarPosts: 3338Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Prove an interpretation?

leroy wrote:
Fallacy of shifting the burden of proof. You made two claims:



:lol: :lol: :lol: why is it that atheist never what to accept their burden.

I am the skeptic, and I was told by he_who_is_nobody that skpetics don't have to prove anything

[...]

These are the claims that you made so you have the burden.

I am just saying that 1 are 2 are probably true, I am not claiming that I know it........I am the skeptic, you are the one who is claiming that there is a step by step path from eyeless to modern eyes.


I did say that. Guess what? Nesslig20 provided you with the evidence (you even left it in your response). How did you retort?

leroy wrote:Well what i would call a step requires 3 things

1 a genetic change achievable in 1 generation (like a gene duplication for example)

2 it has to be beneficial (something that would be selected by natural selection)

3 it has to represent a step closer towards modern eyes


does any of your articles provide an example of a step (1,2 and 3)?......if yes can you please copy_paste the exact portions of the article that show 1 2 and 3?


Thus, you went from skeptic to denialist. The evidence is right there at your fingertips and you refuse to look at it. Now, stop being lazy and read the sources he provided.
_BONES AND FOSSILS = LOVE_
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Wed Mar 01, 2017 9:39 pm
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Nesslig20User avatarPosts: 260Joined: Wed Mar 16, 2016 6:44 pm Gender: Male

Post Re: Prove an interpretation?

First things first, let's put the context back to see what happened.
leroy wrote:that is what I am talking about...No one is saying that those proto eyes would be useless, sure a proto eye that can detect light is better than nothing in an environment where detecting light represents a selective benefit.
The point is and has always been that each of those steps requires multiple independent genetic changes, even a small benefit requires multiple independent genetic changes

Then I pressed you on these claims you have made here.
Nesslig20 wrote:Fallacy, argument from assertion and incredulity. What makes you think that multiple mutations are needed to result in benefits and what makes you think multiple independent mutations producing beneficial effects cannot happen. [or what makes you think that small benefits requires multiple independent genetic changes] Though the later maybe a straw man, but if you do agree that multiple independent mutations that produce beneficial effects can occur than you don't have an objection anymore.

Then you tried to shrug of the burden to backup these claims.
leroy wrote:well you are the one who proclaims evolution, you are the one who has the burden, if you think that each of these steps is possible with 1 genetic change feel free to prove it.

Here I pointed out the fallacies you have made.
Nesslig20 wrote:Fallacy of shifting the burden of proof. You made two claims:
1. each of those steps requires multiple independent genetic changes,
and
2. even a small benefit requires multiple independent genetic changes
These are the claims that you made so you have the burden.

I didn't claim that each step is possible with 1 genetic change - straw man fallacy.


Now comes the latest butt hurt reaction.

leroy wrote:Why is it that atheist never what to accept their burden.
I am the skeptic, and I was told by he_who_is_nobody that skpetics don't have to prove anything


If you are just being a skeptic, then you wouldn't have a burden of proof of course, but that is NOT what you were doing. Once you make claims and tried to avoid backing them up despite being called out on by many different people repeatedly (which I will point out latter), you've stopped being a skeptic and become someone who is dishonestly spouting BS he cannot defend while pretending to be "just a skeptic" and the next comment demonstrates this.

leroy wrote:
Nesslig20 wrote:Fallacy of shifting the burden of proof. You made two claims:
1. each of those steps requires multiple independent genetic changes,
and
2. even a small benefit requires multiple independent genetic changes
These are the claims that you made so you have the burden.

I am just saying that 1 are 2 are probably true, I am not claiming that I know it........
I am the skeptic, you are the one who is claiming that there is a step by step path from eyeless to modern eyes.


Saying that those statements are probably true is STILL a claim, no matter how soft you want to make it out to be by weaseling.
Stop pretending that you are a skeptic, you ain't one.

leroy wrote:
Nesslig20 wrote:And genetic changes in opsins (light sensitive proteins), genes involved in development of the eye (like Pax6) and crystallines (structural proteins of the lens) and more have been identified. Many changes involve the same gene duplication mechanism.
Citations:
- Metazoan opsin evolution reveals a simple route to animal vision
- Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup
- Deep homology of eye development and the parallel evolution of animal eyes.
- Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish
- Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants
- Evolution of crystallins for a role in the vertebrate eye lens

Well what i would call a step requires 3 things
1 a genetic change achievable in 1 generation (like a gene duplication for example)
2 it has to be beneficial (something that would be selected by natural selection)
3 it has to represent a step closer towards modern eyes
does any of your articles provide an example of a step (1,2 and 3)?......if yes can you please copy_paste the exact portions of the article that show 1 2 and 3?


Turns out I have been validated to be right again, when I said this to someone else:
Nesslig20 wrote:
thenexttodie wrote:Why waste time comparing structures and even opsins

Because that is how (in simple terms) scientists investigate how these things evolve. And I showed the research to someone asking the very question of how the eye evolved, but ignored it, like usual.


Now you have not only stopped being a skeptic, you have gone into complete denial. I have given you the citation, that you can CLICK on right to the articles that answer your question. And to make matters worse, even though you are asking me to copy paste portions of the article, that is exactly what I have already done previously with one citation, SEVERAL times!!

And your three requirements have been refuted before by others, especially number 2.

Rumraket wrote:Why would it have to be achievable in 1 generation? Why not 2, or 5, or a hundred? The answer is that it doesn't.
Why would it have to be "positive" rather than neutral? It doesn't. It could even be slightly deleterious and still fix by drift in a small population, or substantially deleterious yet hitchike with another beneficial allele.
Why would someone have to provide a step by step path at this level of detail? Do you even have any other beliefs which are supported by such a level corroboration? Of course you don't.
Isn't it obvious you're deliberately setting the bar irrationally high? Yes, yes it is.
......................
No. I'm obviously not claiming all of eye-evolution was achieved by genetic drift, that would be preposterous. Rather, I'm merely saying that not all of the "steps" have to be beneficial. We know for a fact that there are complex phenotypes who's evolutionary history include necessary neutral mutations that fixed by genetic drift.
For example, the evolution of chloroquine resistance in plasmodium falciparum requires multiple neutral mutations along the way.
And in the Long-Term Evolution Experiment, the cit+ phenotype requires at least one neutral, potentiating mutation.

hackenslash wrote:
thenexttodie wrote:each change (or at least most of them) would have to be beneficial

This is simply not true, and the fact that it isn't true has been pointed out six ways from Sunday.
You're operating from an entirely false premise. Not only are they not required to be beneficial, they're not even required to be beneficial in the context of their environment. There's no sense in which your contention isn't fundamentally wrong.


And you admitted that requirement #2 isn't necessary.
thenexttodie wrote:granted, not all of the steps have to be beneficial.

So why include that requirement again? Suffer from short term memory? From looking at old discussions between you and others and from my own experience by arguing with you, I think you do.
You frequently bring up points back even though they have been refuted before, like that Bat/Dolphin echolocation thing that you brought back some time later after I have shown that to be flawed. Stop using PRATTS.

thenexttodie wrote:
Of course, that is not what you mean. You mean that we don't understand this at all, which we don't. We do understand more about this than you want to admit. The details are still discussed among experts, but they all share the general conclusion that yes, opsins, crystallines, and other elements involved in the function and structure of the eye have all evolved and we do have a damn good understanding of how they did. Again read the citations.

What I meant is that in reality we don't know, we don't have enough understanding on how eyes work at a genetic level and what genes and genetic changes are required to evolve eyeless to modern eyes. therefore we don't know if there is a viable step by step path.


You are wrong and you would know that if yo are willing to click on any of the links I provided to you.
And just because you are too lazy to click on links and I am such a nice guy, I will make it easy for you, as long as you won't complain about the length of this post. I know that being buried by mountains of scientific literature that proves you wrong is uncomfortable for you, but you asked for it.

This first one I have provided to you previously.
Origin of opsins wrote:Opsins, and their major divisions (25) arose very early in metazoan evolution. In this article the term ‘opsin’ will refer only to ‘Type 2 animal opsins’, and not to the ‘Type 1 microbial opsins’ of bacteria or the ‘channelrhodopsins’ of algae, both of which are unrelated and appear to have arisen by convergent evolution. The phylogeny of ciliary opsins will be considered in Sections 5 and 6 for chordates generally, and for the vertebrate retina, but for now the questions are: How did the ancestral opsin originate? and What were the initial stages in its diversification?. In addressing these questions, important clues have been obtained through analysis of a number of cnidarian opsin sequences that have become available since 2007 (12, 26-31).

Animal opsins evolved from within the eponymous ‘Rhodopsin family’ of the ‘GRAFS’ superfamily of G-protein coupled receptors (GPCRs), and it is known that this superfamily originated in an ancient eukaryote that existed prior to the divergence of fungi (32)). Recently, Feuda et al (30)) analyzed the phylogeny of opsins and proposed a scheme for the early origin of opsins. They showed that the closest relatives of the opsins are found in the lineage that includes the vertebrate receptors for melatonin. However, for the corresponding GPCRs in invertebrates the ligand has not yet been identified, and so it is not clear what the ancestral ligand might have been at the time that the opsin lineage diverged.

One potential problem with the analysis of Feuda et al (30) is its reliance on the (unproven) existence of R-opsins in cnidaria, but that issue appears to have been resolved by an independent and nearly simultaneous study of opsins from a coral (31), that clearly identified the existence of an R-opsin. The following scenario for the early origin of animal opsins, illustrated in Figure 2B builds on the report of Feuda et al (30), and is presented here as the first in a series of scenarios/hypotheses for the events that gave rise to photoreceptors:

A-1) The forerunner of the first opsin arose through duplication of a GPCR in an ancient metazoan, at a time prior to the divergence of the amoeba-like placozoans.

A-2) That forerunner protein did not possess the retinal-binding lysine (‘K296′) in the seventh transmembrane helix (30); this suggests that retinaldehyde ligand occupied the internal cavity by means of non-covalent binding, as for ligands in conventional GPCRs, and in Figure 2B this pre-opsin is termed a ‘retinaldehyde receptor’. The placozoan Trichoplax has a homolog of opsin (dubbed placopsin by Feuda et al, 2012), that likewise is devoid of the retinal-binding lysine residue.

A-3) Acquisition of an appropriately situated lysine residue within the seventh transmembrane segment of that receptor allowed the retinaldehyde ligand to bind covalently. Initially, the Schiff base bond is likely to have been unprotonated, so that the molecule would have absorbed in the UV. Acquisition of an appropriately located negatively charged residue (e.g. E181) permitted the bond to be protonated, thereby creating the ancestral opsin, and enabling the absorption peak to be shifted into the ‘visible’ spectrum.

A-4) As for most opsins (though not for vertebrate visual opsins), the activated metarhodopsin state of this opsin was thermally stable and could undergo photoreversal to the rhodopsin state. Hence this protein probably did not require a source of 11-cis retinal and could instead utilize all-trans retinal perfectly well.

A-5) Subsequently, two duplications of that earliest opsin occurred, during the relatively short interval between the divergence of placozoa and the divergence of cnidarians from bilaterians. Thus, all of the duplications indicated in Figure 2B took place shortly prior to the first of the numbered branchings shown in Figure 1 (i.e. prior to #1).

an other independent genetic that produces something that connects the cells with the brain, an other independent genetic change that produces a reaction when light is detected.

Image
Figure 2. Origin of opsins, and their possible association with membrane type. A, Opsin phylogeny. Cnidarians have orthologs of each bilaterian opsin subfamily; i.e. the C-, R-, and RGR/Go-opsin subfamilies. Numbers indicate support values (Bayesian PPs) for key nodes. From Feuda et al (2012). B, Hypothesized duplications of ancestral opsin and its precursors, and suggested association with membrane type. An ancient GPCR (related to extant vertebrate melatonin receptors) duplicated, and its ligand became retinaldehyde, which bound non-covalently; this is denoted as ‘Retinaldehyde receptor’. After the divergence of the amoeba-like placozoans (~711 Mya), this GPCR evolved a lysine residue in its seventh transmembrane segment and a negatively charged residue (counterion) so that retinaldehyde bound covalently via a protonated Schiff base linkage; this form is denoted ‘Ancestral opsin’. Within a relatively short interval (prior to the divergence of cnidarians, ~700 Mya), this opsin duplicated twice, giving rise to three major families of opsins: C-opsins, R-opsins, and RGR/Go-opsins. It is proposed that these three opsins preferentially associated with ciliary membrane, microvillar membrane, and the membranes of intracellular organelles, respectively. Note that all these events occurred just prior to the starting point of Fig. 1.

Hypothesized association between opsin type and membrane type . A contributory factor in the co-evolution of opsin classes and photoreceptor classes may have been a preferential association of the different opsins with different regions of membrane, as indicated in Figure 2B. Accordingly, the hypothetical scenario for the early evolution of opsins is extended as follows:

A-6) The two variants of opsin that emerged after the first duplication event may have trafficked preferentially to the membrane of sub-cellular organelles and to surface membrane. Those variants would have given rise to the RGR- division and the C-/R- division, respectively, of modern opsins.

A-7) Following the duplication event that created the distinction between C- and R-opsins, these two variants trafficked to ciliary and microvillar membrane, respectively. In Figure 2B this duplication is shown as having occurred subsequent to the duplication mentioned in the previous point, but at present one cannot reliably distinguish the order in which this pair of duplication events occurred.

A-8) Subsequently, cells expressing the C- and R-opsin classes became distinct from each other, through a process termed ‘division of labor’ (5, 33), leading to (a) ciliary photoreceptors that possessed C-opsins and (b) microvillar photoreceptors that possessed R-opsins; see next Section. The third variant of opsin, RGR-opsin, tended to be expressed in the membranes of intracellular organelles, possibly as an additional opsin in the first two classes of photoreceptors.

A-9) Later in evolution, further division of labor occurred, so that (for example) RGR-opsin could be expressed in separate cells. This would explain how it is possible, on the one hand, for squid photoreceptors to contain an R-opsin in their microvillar membranes as well as retinochrome (an RGR-opsin) in their intracellular organelles, and, on the other hand, for vertebrate cones and rods to contain only a C-opsin in their outer segments whereas RPE cells contain only RGR-opsin in their endoplasmic reticulum.


Metazoan opsin evolution reveals a simple route to animal vision wrote:We found that the Placozoa have opsins, and that the opsins share a common ancestor with the melatonin receptors. Further to this, we found that all known neuralian opsins can be classified into the same three subfamilies into which the bilaterian opsins are classified: the ciliary (C), rhabdomeric (R), and go-coupled plus retinochrome, retinal G protein-coupled receptor (Go/RGR) opsins. Our results entail a simple scenario of opsin evolution. The first opsin originated from the duplication of the common ancestor of the melatonin and opsin genes in a eumetazoan (Placozoa plus Neuralia) ancestor, and an inference of its amino acid sequence suggests that this protein might not have been light-sensitive. Two more gene duplications in the ancestral neuralian lineage resulted in the origin of the R, C, and Go/RGR opsins. Accordingly, the first animal with at least a C, an R, and a Go/RGR opsin was a neuralian progenitor.
Image
Synopsis of opsin evolution. This figure represents a gene tree embedded within a species tree illustrating the evolutionary history of the opsins and MLT receptors in Metazoa. It shows that only three duplications and no deletions are necessary to explain opsin evolution.


Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup wrote:Proposed sequence of events involved in the evolution of the vertebrate eye
Image
Stage 1: bilateral ancestor (>580 million years ago (Mya))

Animals with bilateral symmetry exist2.
Numerous families of genes exist22.
A range of G-protein-coupled signalling cascades exist146.
A primordial opsin has evolved into three major classes: rhabdomeric opsins, photoisomerase-like opsins and ciliary opsins147.
A rhabdomeric-type photoreceptor has evolved, using a Gq-based signalling cascade with a rhabdomeric opsin9.
A ciliary-type photoreceptor has evolved, using a variant opsin (the stem ciliary opsin) that probably coupled to a Go-based signalling cascade8,61,92,148.

~580 Mya
Protostomes separate from our line (deuterostomes).

Stage 2: protochordates (580–550 Mya)

The ciliary photoreceptor and ciliary opsin continue to evolve, becoming similar to those in extant amphioxus and ascidian larvae57,58,62,67.
A primordial RPE65-like isomerase evolves62,65.
These protochordates had ciliary photoreceptors with a ciliary opsin and a hyperpolarizing response, and were able to regenerate 11-cis retinal in darkness.

~550 Mya
Cephalochordates and tunicates separate from our line (chordates).

Stage 3: ancestral craniates (~550–530 Mya)

A ciliary photoreceptor evolves that has well organized outer-segment membranes, an output synapse close to the soma and a synaptic specialization appropriate for graded signal transmission42,86.
Ciliary photoreceptors make synaptic contact onto projection neurons that might have been descendants of rhabdomeric photoreceptors9,69.
The eye-field region of the diencephalon bulges to form lateral ‘eye vesicles’149.
These lateral vesicles invaginate, bringing the proto-retina into apposition with the proto-retinal pigment epithelium149.
A primordial lens placode develops, preventing pigmentation of the overlying skin145.
The resulting paired lateral photoreceptive organs would have resembled the ‘eyes’ of extant hagfish, lacking any image-forming apparatus and subserving non-visual functions.

~530 Mya
Myxiniformes (hagfish) separate from our line (vertebrates).

Stage 4: lamprey-like ancestors (~530–500 Mya)

Photoreceptors develop cone-like features:
- Highly-ordered sac/disc membranes evolve81.
- Mitochondria become concentrated within the ellipsoid region of the inner segment81.
- Coloured filter material is incorporated into the inner segment for spectral tuning83.
- Ribbon synapses evolve in the synaptic terminal78.
- Genome duplications give rise to multiple copies of the phototransduction genes23,24,28,29.
- Cell classes diverge to give five separate cone-like photoreceptors, each with its own ciliary opsin and with isoforms of transduction proteins38,90,93,108.

Retinal computing power increases:
- Cone bipolar cells evolve, either from proto-neurons or from photoreceptors114,150.
- The bipolar cells insert into the pathway from photoreceptors to ganglion cells, through the retraction of photoreceptor processes and the incorporation of new contacts114,126.
- Bi-plexiform ganglion cells develop37.
- A highly organized three-layered neuronal structure with two intervening plexiform layers develops50,51.

Ganglion-cell axons project to the thalamus44,45.
The optics evolve (the lens, accommodation and eye movement):
- The lens placode invaginates and develops to form a lens151.
- The iris develops and a degree of pupillary constriction becomes possible84.
- Innervated extra-ocular muscles evolve152.
The resulting eye and visual system would have resembled that in extant lampreys and would have provided spatial vision at photopic intensities and over a broad wavelength range.

~500 Mya
Petromyzoniformes (lampreys) separate from our line.

Stage 5: jawless fish (~500–430 Mya)

Myelin evolves and is incorporated throughout the nervous system153.
Rod photoreceptors evolve:
- Rhodopsin evolves from cone opsin38,93.
- Rod isoforms of most transduction cascade proteins arise90,108.
- Free-floating discs pinch off within the plasma membrane.
Rod bipolar cells evolve, possibly from rod photoreceptors114.
The scotopic rod pathway evolves, with a new subset of amacrine cells (AII) providing input into the pre-existing cone pathway154,155.
A highly contractile iris evolves that can adjust light levels156.
Intrinsic eye muscles develop that permit accommodation of the lens157.

This eye possessed a duplex retina that contained both rods and cones, together with retinal wiring that closely resembled that of jawed vertebrates, with colour-coded photopic pathways and a dedicated scotopic pathway; it was probably similar to that found in many extant fish.

~430 Mya
The last jawless fish separate from our own line (gnathostomes).

Stage 6: gnathostomes (<430 Mya)

In the case of tetrapods:
- The lens develops an elliptical shape to compensate for the added refractive power that is provided by the cornea in air158.
- The dermal component of the split cornea is lost and the eyelids evolve149.
- Certain opsin classes are lost, for example, SWS2 and Rh2 in mammals, under extended nocturnal conditions159.


Deep homology of eye development and the parallel evolution of animal eyes. wrote:Image
A route for the evolution of photoreceptor cell types and different forms of eyes. a, The cnidarian–bilaterian ancestor had photoreceptors that expressed c-opsin and PAXB. b, Rhabdomeric photoreceptors, r-opsins and PAX6 evolved in ancestral-stem bilaterians, after the split between the cnidarian and bilaterian lineages. c, The last common ancestor of all bilaterians (Urbilateria) probably had two types of light-sensing organ: a prototypical eye and a brain photo-clock, which are both found in the annelid Platynereis dumerilii. d, The photoreceptor types established in the Urbilateria were then incorporated in different ways in the parallel evolution of different eyes in various phyla. Rhabdomeric photoreceptors were the foundation for the evolution of compound and camera-type eyes in arthropods and molluscs, respectively. Both types of photoreceptor were incorporated into the vertebrate eye, with ciliary receptors carrying out phototransduction and rhabdomeric receptors being transformed into ganglion cells and functioning in image processing. Pigment cells are not shown. e, The ciliary camera-type eyes of box jellyfish are also proposed to have evolved in parallel in the cnidarian lineage. f, Cladogram depicting the evolutionary relationships of the taxa shown in a–e. (Panels a–e courtesy of L. Olds (University of Wisconsin, Madison); panel f courtesy of K. Monoyios (University of Chicago, Illinois).)


Flexibly deployed Pax genes in eye development at the early evolution of animals demonstrated by studies on a hydrozoan jellyfish wrote:Image
In our present model, gene duplications that gave rise to distinct subfamilies occurred most likely before the separation of poriferans and eumetazoans (1 in Fig. 5), as suggested by the statistical tests in refs. 4 and 22. We cannot, however, completely eliminate the possibility that some (or all) of these duplications postdate the poriferans–eumetazoans split (dashed line in Fig. 5) (4) until more sponge Pax genes that do not belong to the Pax-2/5/8 subfamily are found. When the ancestral animal eye evolved in the common ancestor of cnidarians and bilaterians, Pax genes may have been recruited as components of the gene network responsible for eye development (2 in Fig. 5). We assume that, at this stage, several classes (corresponding to subfamilies) of Pax genes were redundantly involved in this network. After the divergence of bilaterians and cnidarians on one hand, and hydrozoans and cubozoans on the other hand, the three distinct animal lineages selected different classes of Pax genes for the roles in eye development and/or maintenance (3 in Fig. 5). Such molecular-level opportunism is often observed in evolution (e.g., lens crystallins) (47). Interestingly, formation of some bilaterian eyes seems to be Pax-6 independent (ref. 14 for review). This suggests that the gene network directing eye development can be anomalously modified, making Pax-6 dispensable for eye development in some bilaterian lineages (4 in Fig. 5).


Cephalopod eye evolution was modulated by the acquisition of Pax-6 splicing variants wrote:Acquisition of the Pax-6 variants in eye formation
Image
As found in several bilaterian species, the basic function of animal Pax-6 appears to involve the regulation of the anterior part of the head and the initiation of photoreceptor formation, regardless of the photoreceptor cell type. In insect Pax-6, ey has at least three additional variants generated through gene duplication. The duplicates are thought to have originated in a pancrustacean ancestor (insect + crustacea), although the exact origin remains uncertain9. The roles of two of these duplicates, toy and eyg, have diverged in the compound eye formation processes of the fly and beetle27,28, and functional changes in toy and eyg have significantly contributed to the evolution of the size and shape of the eyes in the beetle27. These results indicate that the diversification of the Pax6 isoforms by duplication is required for eye development in insects. Diversification of Pax-6 variants is also found in vertebrates. However, the acquisition of variations in Pax-6 is completely distinct between these two taxa; vertebrate Pax-6(5a) originated from the alternative splicing of the locus, whereas insect eyg originated from gene duplication29. Pax-6(5a) shows functional similarity to the Drosophila eyg, which also lacks the PD required for HD function30. In mice, another type of protein variation, protein sumoylation onto the Pax-6 splicing variants, is expressed in the embryonic optic and lens vesicles and shows different DNA-binding and transcriptional activities from the authentic protein3. The bilaterian common ancestor (UBA) is considered to have had a Pax-6 gene for the development of photoreceptors (Figure 4). Thus, eye development has been achieved by alternative splicing or gene duplication, either of which leads to variations in the protein isoforms.


Evolution of crystallins for a role in the vertebrate eye lens wrote:The camera eye lens of vertebrates is a classic example of the re-engineering of existing protein components to fashion a new device. The bulk of the lens is formed from proteins belonging to two superfamilies, the α-crystallins and the βγ-crystallins. Tracing their ancestry may throw light on the origin of the optics of the lens. The α-crystallins belong to the ubiquitous small heat shock proteins family that plays a protective role in cellular homeostasis. They form enormous polydisperse oligomers that challenge modern biophysical methods to uncover the molecular basis of their assembly structure and chaperone-like protein binding function. It is argued that a molecular phenotype of a dynamic assembly suits a chaperone function as well as a structural role in the eye lens where the constraint of preventing protein condensation is paramount. The main cellular partners of α-crystallins, the β- and γ-crystallins, have largely been lost from the animal kingdom but the superfamily is hugely expanded in the vertebrate eye lens. Their structures show how a simple Greek key motif can evolve rapidly to form a complex array of monomers and oligomers. Apart from remaining transparent, a major role of the partnership of α-crystallins with β- and γ-crystallins in the lens is to form a refractive index gradient. Here, we show some of the structural and genetic features of these two protein superfamilies that enable the rapid creation of different assembly states, to match the rapidly changing optical needs among the various vertebrates.
"Ignorance more frequently begets confidence than does knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science."
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Thu Mar 02, 2017 5:46 pm
he_who_is_nobodyBloggerUser avatarPosts: 3338Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Prove an interpretation?

Nesslig20 wrote:
thenexttodie wrote:granted, not all of the steps have to be beneficial.

So why include that requirement again? Suffer from short term memory? From looking at old discussions between you and others and from my own experience by arguing with you, I think you do.
You frequently bring up points back even though they have been refuted before, like that Bat/Dolphin echolocation thing that you brought back some time later after I have shown that to be flawed. Stop using PRATTS.


Have you read the debate he had with Inferno? That was back when he was still going by dandan. Note the date, how much effort dandan/leroy and Inferno put into their posts, and how many times things have to be repeated to him.
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RumraketUser avatarPosts: 1175Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: Prove an interpretation?

Holy shit, I had not seen that debate before. Dandan performed the most incompetent and utterly braindead attempt at arguing against phylogenetics I have ever seen. Rarely have I seen anyone so thoroughly out of his depth, persist as if under the belief he has a clue. What a total travesty. :lol:
"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Fri Mar 03, 2017 10:57 am
hackenslashLime TordUser avatarPosts: 2379Joined: Mon Feb 23, 2009 3:43 pm Gender: Cake

Post Re: Prove an interpretation?

Spectacular, isn't it?
Fri Mar 03, 2017 11:01 am
Nesslig20User avatarPosts: 260Joined: Wed Mar 16, 2016 6:44 pm Gender: Male

Post Re: Prove an interpretation?

he_who_is_nobody wrote:
Nesslig20 wrote:So why include that requirement again? Suffer from short term memory? From looking at old discussions between you and others and from my own experience by arguing with you, I think you do.
You frequently bring up points back even though they have been refuted before, like that Bat/Dolphin echolocation thing that you brought back some time later after I have shown that to be flawed. Stop using PRATTS.


Have you read the debate he had with Inferno? That was back when he was still going by dandan. Note the date, how much effort dandan/leroy and Inferno put into their posts, and how many times things have to be repeated to him.


Me when I read Inferno's posts
Image
Me when I read dandan/Leroy's posts
Image
"Ignorance more frequently begets confidence than does knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science."
Charles Darwin
Fri Mar 03, 2017 8:39 pm
he_who_is_nobodyBloggerUser avatarPosts: 3338Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Prove an interpretation?

Rumraket wrote:Holy shit, I had not seen that debate before. Dandan performed the most incompetent and utterly braindead attempt at arguing against phylogenetics I have ever seen. Rarely have I seen anyone so thoroughly out of his depth, persist as if under the belief he has a clue. What a total travesty. :lol:


You had not seen that before? Than who is this this guy in the peanut gallery?
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RumraketUser avatarPosts: 1175Joined: Fri Jun 25, 2010 7:49 am Gender: Male

Post Re: Prove an interpretation?

he_who_is_nobody wrote:
Rumraket wrote:Holy shit, I had not seen that debate before. Dandan performed the most incompetent and utterly braindead attempt at arguing against phylogenetics I have ever seen. Rarely have I seen anyone so thoroughly out of his depth, persist as if under the belief he has a clue. What a total travesty. :lol:


You had not seen that before? Than who is this this guy in the peanut gallery?

Well, since that's obviously me I think the only explanation is that I had completely forgotten ever reading that debate. Even seeing that post I still don't remember having read it before.
"Nullius in verba" - Take nobody's word for it. https://en.wikipedia.org/wiki/Nullius_in_verba
Extraordinary claims require extraordinary evidence.
Sun Mar 05, 2017 10:22 pm
he_who_is_nobodyBloggerUser avatarPosts: 3338Joined: Tue Feb 24, 2009 1:36 amLocation: Albuquerque, New Mexico Gender: Male

Post Re: Prove an interpretation?

Rumraket wrote:
he_who_is_nobody wrote:You had not seen that before? Than who is this this guy in the peanut gallery?

Well, since that's obviously me I think the only explanation is that I had completely forgotten ever reading that debate. Even seeing that post I still don't remember having read it before.


It could be The Mandaellah Effekt.
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leroy
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Post Re: Prove an interpretation?

[

from a source provided by Nessling
Metazoan opsin evolution reveals a simple route to animal vision wrote:
We found that the Placozoa have opsins, and that the opsins share a common ancestor with the melatonin receptors. Further to this, we found that all known neuralian opsins can be classified into the same three subfamilies into which the bilaterian opsins are classified: the ciliary (C), rhabdomeric (R), and go-coupled plus retinochrome, retinal G protein-coupled receptor (Go/RGR) opsins. Our results entail a simple scenario of opsin evolution. The first opsin originated from the duplication of the common ancestor of the melatonin and opsin genes in a eumetazoan (Placozoa plus Neuralia) ancestor, and an inference of its amino acid sequence suggests that this protein might not have been light-sensitive. Two more gene duplications in the ancestral neuralian lineage resulted in the origin of the R, C, and Go/RGR opsins. Accordingly, the first animal with at least a C, an R, and a Go/RGR opsin was a neuralian progenitor.


Lest keep things simple.

remember when I said....
Well what i would call a step requires 3 things
1 a genetic change achievable in 1 generation (like a gene duplication for example)
2 it has to be beneficial (something that would be selected by natural selection)
3 it has to represent a step closer towards modern eyes

1+2+3= what I would call a step

the article that you quoted, provided 1 and 3 quite successfully, ............al you have to do is prove that any of this duplications had a beneficial efecto that would be selected by natural selection...........al you have to do is prove 2

If you do that you would prove that at least 1 of the millions of steps needed to evolve an eye is viable trough Darwinian mechanisms, this would be far from disproving the claim on irreducibly complexity, but it would be a good start.

nessling
So why include that requirement again? Suffer from short term memory? From looking at old discussions between you and others and from my own experience by arguing with you, I think you do

the requirement being beneficial mutations...

the point that I was trying to make is that you cant include too many neutral mutations in the process of evolving an eye, because you would have a serious probabilistic problem.
"events with a zero probability happen all the time"
Mon Mar 06, 2017 7:55 pm
Nesslig20User avatarPosts: 260Joined: Wed Mar 16, 2016 6:44 pm Gender: Male

Post Re: Prove an interpretation?

:facepalm: 4 days and a response of less than 200 words (not including quotes from me) and none of those add anything new to the conversation. You have simply repeated the same question you have asked before with your 3 requirements (which were shown to be bogus). I have answered your question, I even have copy pasted sections from ALL the citations I provided to you (just like you asked me to do). But it seems it wasn't good enough for you. So let's go through this AGAIN.

leroy wrote:
Nesslig20 wrote:Metazoan opsin evolution reveals a simple route to animal vision wrote:
We found that the Placozoa have opsins, and that the opsins share a common ancestor with the melatonin receptors. Further to this, we found that all known neuralian opsins can be classified into the same three subfamilies into which the bilaterian opsins are classified: the ciliary (C), rhabdomeric (R), and go-coupled plus retinochrome, retinal G protein-coupled receptor (Go/RGR) opsins. Our results entail a simple scenario of opsin evolution. The first opsin originated from the duplication of the common ancestor of the melatonin and opsin genes in a eumetazoan (Placozoa plus Neuralia) ancestor, and an inference of its amino acid sequence suggests that this protein might not have been light-sensitive. Two more gene duplications in the ancestral neuralian lineage resulted in the origin of the R, C, and Go/RGR opsins. Accordingly, the first animal with at least a C, an R, and a Go/RGR opsin was a neuralian progenitor.

Lest keep things simple.


:lol: :lol: :lol: Why? Intimidated by to much details? That is what you get when you ask me to copy paste peer reviewed articles that you are too lazy to look at on your own.

leroy wrote:remember when I said....
Well what i would call a step requires 3 things
1 a genetic change achievable in 1 generation (like a gene duplication for example)
2 it has to be beneficial (something that would be selected by natural selection)
3 it has to represent a step closer towards modern eyes

1+2+3= what I would call a step


And that is the thing, that is what YOU would call a step, but the expectations you have of evolution just shows your ignorance about the subject. Rumraket and Hackenslash have called you out on that before and you have admitted that step 2 is not necessary.

leroy wrote:the article that you quoted, provided 1 and 3 quite successfully, ............al you have to do is prove that any of this duplications had a beneficial effect that would be selected by natural selection...........al you have to do is prove 2


No I don't, since you have admitted that 2 isn't necessary. I have the quote in which you have admitted that. However, to make it even worse for your position, I will explain both what the benefits are and the unencessity of a benefit later on.

leroy wrote:If you do that you would prove that at least 1 of the millions of steps needed to evolve an eye is viable trough Darwinian mechanisms,


So do you want me to demonstrate all millions of steps? I thought you wanted to keep this simple?
We don't need to explain ALL the steps that happened. As I said we don't know everything about any subject. We know enough what happened. Eyes evolved and we (the scientists) know the big picture that shows how they evolved and I have the citations to demonstrate this.

leroy wrote:this would be far from disproving the claim on irreducibly complexity, but it would be a good start.


Irreducible complexity has already been refuted by the scientific community and disproved during the dover trial in 2005. During that trial, every example that the ID proponents (i.e. creationists trying to disguise themselves) came up with as their "best" examples of an IC structure have been shown to be NOT irreducible and scientists had already published numerous articles and textbooks chapters providing evolutionary explanations for these structures. Also, to add insult to injury, irreducible complexity was predicted over a century ago by nobel prize winning scientist Hermann Joseph Muller to be an inescapable product of evolution, NOT intelligent design.

To this date, NO sound example of the ID concept of Irreducible complexity have ever been demonstrated.
Irreducible complexity is a point that has been refuted a thousand times.

leroy wrote:
nesslig20 wrote:So why include that requirement again? Suffer from short term memory? From looking at old discussions between you and others and from my own experience by arguing with you, I think you do

the requirement being beneficial mutations...the point that I was trying to make is that you cant include too many neutral mutations in the process of evolving an eye, because you would have a serious probabilistic problem.


Now you are being dishonest
Saying "it has to be beneficial" as you have said previously is not the same as saying "You can't have too many neutral mutations"
Fallacy of moving the goal post.

And I bet you cannot even define what counts as "too many" which is also prone to moving the goal post fallacy, but that is irrelevant anyway, because as I said, duplications have benefits and benefits are not necessary.

Mutations that change a necessary function a gene would be harmful if there was only one of it, but duplications negate this harmful effect, thereby allowing the copy to freely mutate without any harm to the organism.
This has (at least) two implications. The copy can change its function to fulfill a novel role which is beneficial. Of course this is an indirect benefit of a mutation that creates the potential for some future mutation to be beneficial (which would still count as beneficial). But this alone would probably not be enough, so what direct benefits has. It creates redundancy. Organisms that have many duplicated forms of their genes don't suffer from the harmful effects of mutations as much. A mutation that occurs within one organism that has only one copy of each gene would be more likely to be harmful compared to a mutation that occurs with an organism that has many copies of each gene. There are many duplications that have been lost as a result of being redundant, we have 49 duplicated Cytochrome C pseudogenes for example.
Another way is that duplication provide gene dosage which amplifies the effect of a gene (which may or may not be beneficial), thus duplications can be favored if increase in gene dosage is beneficial.

Thus duplications are beneficial (in many different ways) and thus provide a clear advantage that can be favored by natural selection.

If you want a citation for that here it is, don't be scared, I will keep it simple ;)
Loss of Genetic Redundancy in Reductive Genome Evolution wrote:Biological systems evolved to be functionally robust in uncertain environments, but also highly adaptable. Such robustness is partly achieved by genetic redundancy, where the failure of a specific component through mutation or environmental challenge can be compensated by duplicate components capable of performing, to a limited extent, the same function. Highly variable environments require very robust systems. Conversely, predictable environments should not place a high selective value on robustness. Here we test this hypothesis by investigating the evolutionary dynamics of genetic redundancy in extremely reduced genomes, found mostly in intracellular parasites and endosymbionts. By combining data analysis with simulations of genome evolution we show that in the extensive gene loss suffered by reduced genomes there is a selective drive to keep the diversity of protein families while sacrificing paralogy. We show that this is not a by-product of the known drivers of genome reduction and that there is very limited convergence to a common core of families, indicating that the repertoire of protein families in reduced genomes is the result of historical contingency and niche-specific adaptations. We propose that our observations reflect a loss of genetic redundancy due to a decreased selection for robustness in a predictable environment.


Evolution of genetic redundancy wrote:Genetic redundancy means that two or more genes are performing the same function and that inactivation of one of these genes has little or no effect on the biological phenotype. Redundancy seems to be widespread in genomes of higher organisms1, 2, 3, 4, 5, 6, 7, 8, 9. Examples of apparently redundant genes come from numerous studies of developmental biology10, 11, 12, 13, 14, 15, immunology16,17, neurobiology18,19 and the cell cycle20,21. Yet there is a problem: genes encoding functional proteins must be under selection pressure. If a gene was truly redundant then it would not be protected against the accumulation of deleterious mutations. A widespread view is therefore that such redundancy cannot be evolutionarily stable. Here we develop a simple genetic model to analyse selection pressures acting on redundant genes. We present four cases that can explain why genetic redundancy is common. In three cases, redundancy is even evolutionarily stable. Our theory provides a framework for exploring the evolution of genetic organization.


Selection in the evolution of gene duplications wrote:The results of this analysis indicate that recently duplicated paralogs evolve faster than orthologs with the same level of divergence and similar functions, but apparently do not experience a phase of neutral evolution. We hypothesize that gene duplications that persist in an evolving lineage are beneficial from the time of their origin, due primarily to a protein dosage effect in response to variable environmental conditions; duplications are likely to give rise to new functions at a later phase of their evolution once a higher level of divergence is reached.


But why doesn't there have to be a benefit, since drift can fix duplicated genes too. And we don't have a "probabilistic problem" even then. If you calculate the probability of you being born by taking the factors of independent assortment of chromosomes and crossing over, which makes each gamete cell of your parents unique. You will get a probability that is so small you are more likely to win a lottery in which there are as many tickets as there are atoms in the universe and only one winning ticket.

Does that mean everyone of us has a "probabilistic problem" according to the theory of sexual reproduction and we should instead go with the stork theory?? No, astronomically improbable event happen all the time and once they have occurred the probability of them occurring is 1 in 1. Once you are born the probability of you being born is 1 in 1 and we can calculate based on the comparison of your genomes to the ones of your parents that the probability of you not being the offspring of your parents is less then 1% (since paternity tests are often >99% accurate). There is no probabilistic problem.

Speaking of probability, Douglas Theobald calculated using computer models and statistical methods that the probability of the three domains of life (eukaryotes, Archaea and Bacteria) being unrelated, meaning they don't share any evolutionary ancestry, is

1 in 10 to the 2,680th power

And the probability of humans having an independent origin, not biologically related to any other extant species, is

1 in 10 to the 6,000th power

http://news.nationalgeographic.com/news ... -ancestor/
http://www.nature.com/nature/journal/v4 ... 09014.html
How is that for a probabilistic problem??
"Ignorance more frequently begets confidence than does knowledge: it is those who know little, and not those who know much, who so positively assert that this or that problem will never be solved by science."
Charles Darwin
Mon Mar 06, 2017 11:59 pm
leroy
Online
Posts: 1765Joined: Sat Apr 04, 2015 1:30 pm

Post Re: Prove an interpretation?

Nesslig20 wrote::

Speaking of probability, Douglas Theobald calculated using computer models and statistical methods that the probability of the three domains of life (eukaryotes, Archaea and Bacteria) being unrelated, meaning they don't share any evolutionary ancestry, is

1 in 10 to the 2,680th power

And the probability of humans having an independent origin, not biologically related to any other extant species, is

1 in 10 to the 6,000th power

http://news.nationalgeographic.com/news ... -ancestor/
http://www.nature.com/nature/journal/v4 ... 09014.html
How is that for a probabilistic problem??


I will make a reply on the rest of your post within a few days.


That comment is irrelevant since Behes concern has nothing to do with common ancestry, as far as I know Behe accepts common ancestry, his only concern is that according to him Darwinian mechanisms (mutations and natural selection) cant account for the diversity and complexity of life that we have.

the comment is also a straw man because those who deny common ancestry do not claim that the similarities between humans and other species are a product of chance.


But why cant I simply use the anthropic principle (multiverse theory for example) to explain that probability? .............if we wouldn't have 97% similarities with chimps we wouldn't be wondering why chimps and humans have a 97% similarity. ..........in other words observers that ask this question can only exist in universes where chimps and humans have a 97% similarity.

I am not accusing you in particular, but many atheist (Dawkins for example) use the anthropic principle to get away with the probabilities that theist provide, so why cant I do the same?..........this is really an honest question, I really what to know about your thoughts on the anthropic principle and on weather if we should use it or not to explain away probabilistic problems.
"events with a zero probability happen all the time"
Wed Mar 08, 2017 12:11 am
hackenslashLime TordUser avatarPosts: 2379Joined: Mon Feb 23, 2009 3:43 pm Gender: Cake

Post Re: Prove an interpretation?

leroy wrote:That comment is irrelevant since Behes concern has nothing to do with common ancestry, as far as I know Behe accepts common ancestry,


Boohoo speak with forked tongue. You can't accep[t common ancestry and not accept evolution.

his only concern is that according to him Darwinian mechanisms (mutations and natural selection) cant account for the diversity and complexity of life that we have.


Darwinian? Even your use of this word tells everybody everything they need to know about where you're getting your information from. Darwin's been dead for many years, and the theory is now something that Darwin wouldn't even recognise.

I know more about evolution than you do. Fuck, Michael Boohoo does, and he knows fuck all.

Evolution is a fact that's been observed occurring at every level predicted by the theory.
Wed Mar 08, 2017 1:35 am
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