Discussion for AronRa and OFNF exclusive thread

[Inferno]

To be fair, it's hard to keep up with which paper was talked about at which point. In the original thread, an excess of 30 papers were quoted and linked to. In the debate, at least two were quoted and linked to, the peanut gallery contains another ten.

I don't know what y'all are talking about. I originally linked to the Osnabrück paper, showing those illustrations. That citation had a link at the bottom for the Full PDF. There was no subscription required for that. Then I showed that this same research was also examined in peer review at PubMed and Nature, under the title, "Inventing the dynamo machine: the evolution of the F-type and V-type ATPases". That one I didn't provide the full text to, because my point was made without that. Then I cited a second study from Upstate Med.U., and I made sure to show the accessible version of that too. I don't what you guys are confused about when you say that I didn't cite the same thing as last time.

I'm talking about "Inventing the dynamo machine: the evolution of the F-type and V-type ATPases" though and, so it seems, is everyone else. For that one you didn't provide the full text, as you acknowledged. I provided the paper both in a PM and here, as did fightofthejellyfish.

I don't what you guys are confused about when you say that I didn't cite the same thing as last time.

I believe you did. Let me explain:
You constantly link to the first paper, Mulkidjanian, A.Y., M.Y. Galperin. 2010. Evolutionary origins of membrane proteins In: Structural Bioinformatics of Membrane Proteins (D. Frishman, Ed.), Springer, Wien

However, the illustration you provided stems from the sixth paper, Mulkidjanian, A.Y., K.S. Makarova, M.Y. Galperin and E.V. Koonin. 2007. Inventing the dynamo machine: On the origin of the F-type and V-type membrane ATPases from membrane RNA/protein translocases, Nature Reviews Microbiology, 5:892-899

I think that's the whole confusion, nothing else.
In any case, we now have all of the papers as open-access versions, so we should be fine.

That being said, I did say that you might have made a mistake and I intend to discuss that.
You stated:

AronRa[/url]"]The fact that it was posted to peer review means that the scientific community recognizes this as an explanation of the evolution of the first ATP motor.

I hope I didn't quote that out of context.
The fact that it was posted to peer review does not yet mean anything at all. Creationists have had their garbage approved in reputable peer-reviewed journals as well, but that doesn't mean anything. If it passes the first round of peer-review and is actually published, it simply means that the paper meets certain criteria (language and other formal criteria top among them).
If the paper doesn't meet too much criticism, that's generally another good criterion.
If the content gets into university grade textbooks, that's usually proof that the content was really good and really valuable.

But I don't need to explain that to you, you know that already. I'm just trying to point out that you could sometimes be more careful in your phrasing. In most cases where I disagree with you, it's not because you are wrong but because you have chosen a wording that makes you seem wrong.

 

[Miracles4Real]

I'm not sure why OFNF disagrees with the giraffe thing. a neck getting longer through this "arms race" with trees in a new environment does seem like a possible adaptation. I'm looking at bones of a Palaeotragus. I don't know why he doesn't concede that one. He implies that this nerve has a reason for going all the way down a neck.

Even though it's somehow appropriate for this conversation, I think that Aron Ra's positivism philosophy displayed throughout looks somewhat naive. Does he think that there is no value in abstract ideas and principles beyond particular observable facts and relationships. Does he use empathy at all in his life and value it, and if so why? Does he think there are no necessary principles, or that we just cannot know them. "if you cannot show it then you do not know it" are you kidding me? Then there is a huge number of things that we do not and can not know to the point that I don't know if we could even work as a society.

 

[Master_Ghost_Knight]

We are discussing specifically on weather if Darwinian mechanisms can build complex systems like the eye.

I'm going to hammer this on you until you get it.
Do you mean that "it can" or do you rather mean that "it did"? Because they are 2 completely different questions, which have 2 different answers.

Then there is a huge number of things that we do not and can not know to the point that I don't know if we could even work as a society.

As I have explained before, just because you don't know something, it doesn't mean that you can't function.
And you can believe me when I tell you that scientists are not automaton, they to have feelings and beliefs about things, hopes, dreams and aspirations, they can appreciate art. It is just than in somethings they see it very objectively, but that doesn't diminish their enjoyment of life.

 

[he_who_is_nobody]

To be fair, it's hard to keep up with which paper was talked about at which point. In the original thread, an excess of 30 papers were quoted and linked to. In the debate, at least two were quoted and linked to, the peanut gallery contains another ten.

I don't know what y'all are talking about. I originally linked to the Osnabrück paper, showing those illustrations. That citation had a link at the bottom for the Full PDF. There was no subscription required for that. Then I showed that this same research was also examined in peer review at PubMed and Nature, under the title, "Inventing the dynamo machine: the evolution of the F-type and V-type ATPases". That one I didn't provide the full text to, because my point was made without that. Then I cited a second study from Upstate Med.U., and I made sure to show the accessible version of that too. I don't what you guys are confused about when you say that I didn't cite the same thing as last time.

So than I was not wrong after all.

 

[AronRa]

I don't what you guys are confused about when you say that I didn't cite the same thing as last time.

I believe you did. Let me explain:
You constantly link to the first paper, Mulkidjanian, A.Y., M.Y. Galperin. 2010. Evolutionary origins of membrane proteins In: Structural Bioinformatics of Membrane Proteins (D. Frishman, Ed.), Springer, Wien

However, the illustration you provided stems from the sixth paper, Mulkidjanian, A.Y., K.S. Makarova, M.Y. Galperin and E.V. Koonin. 2007. Inventing the dynamo machine: On the origin of the F-type and V-type membrane ATPases from membrane RNA/protein translocases, Nature Reviews Microbiology, 5:892-899

I think that's the whole confusion, nothing else.

No sir. The image came from the http://www.macromol.uni-osnabrueck.de/ATP_synthase.php]Osnabrück[/url] site that I listed the first time.

In any case, we now have all of the papers as open-access versions, so we should be fine.

That being said, I did say that you might have made a mistake and I intend to discuss that.
You stated:

AronRa[/url]"]The fact that it was posted to peer review means that the scientific community recognizes this as an explanation of the evolution of the first ATP motor.

I hope I didn't quote that out of context.
The fact that it was posted to peer review does not yet mean anything at all. Creationists have had their garbage approved in reputable peer-reviewed journals as well, but that doesn't mean anything. If it passes the first round of peer-review and is actually published, it simply means that the paper meets certain criteria (language and other formal criteria top among them).
If the paper doesn't meet too much criticism, that's generally another good criterion.
If the content gets into university grade textbooks, that's usually proof that the content was really good and really valuable.

But I don't need to explain that to you, you know that already. I'm just trying to point out that you could sometimes be more careful in your phrasing. In most cases where I disagree with you, it's not because you are wrong but because you have chosen a wording that makes you seem wrong.

I showed the article in PubMed, Nature, and Wikipedia to counter OFNF's attempt to say that ATP had not been and could not be explained by science. Obviously ATP falls into the same category as the bacterial flagellum and the blood-clotting cascade and everything else Intelligent Design websites said were irreducibly complex and inexplicable without evoking magick.

 

[Inferno]

No sir. The image came from the Osnabrück site that I listed the first time.

Oh come now Aron, are you going to be like that?
Read what it says immediately underneath the image:

Proposed evolution of the F- and V-type membrane ATPases. The figure is taken taken from [6]

The original picture came from reference six, agreed?
However, you cited reference one, agreed?

I showed the article in PubMed, Nature, and Wikipedia to counter OFNF's attempt to say that ATP had not been and could not be explained by science. Obviously ATP falls into the same category as the bacterial flagellum and the blood-clotting cascade and everything else Intelligent Design websites said were irreducibly complex and inexplicable without evoking magick.

I never stated otherwise, my point of contention was another one.
Also, kudos on using "magick" instead of "magic".

 

[Isotelus]

No sir. The image came from the Osnabrück site that I listed the first time.

Oh come now Aron, are you going to be like that?
Read what it says immediately underneath the image:

Proposed evolution of the F- and V-type membrane ATPases. The figure is taken taken from [6]

The original picture came from reference six, agreed?
However, you cited reference one, agreed?

Maybe he meant that he took the image from the webpage he listed, and is not referring to where the image itself originated?

 

[Inferno]

Maybe he meant that he took the image from the webpage he listed, and is not referring to where the image itself originated?

Absolutely, I agree that's what he meant. However, the sixth reference is (IMO) the more important one, so why sideline it?

In any case, this is a minor matter. I agree that there shouldn't be this much fuss about it.

 

[Miracles4Real]

As I have explained before, just because you don't know something, it doesn't mean that you can't function.
And you can believe me when I tell you that scientists are not automaton, they to have feelings and beliefs about things, hopes, dreams and aspirations, they can appreciate art. It is just than in somethings they see it very objectively, but that doesn't diminish their enjoyment of life.

I agree with you, scientists are not automatons. They do enjoy beauty, many of them are convinced there is a God and they have faith in things they have no hope of ever showing a scrap of empirical evidence for. They know that scientific questions are not the only valuable questions and they don't allow science alone to run their lives because it's unable to answer anything that isn't testable, observable or falsifiable. So I guess we agree that "Everything I know I can back up with evidence." sounds naive.

I'm thinking now though it is just a tactic to deal with this particular debate. It can't actually be the way he thinks, it just somehow rubs me the wrong way.

 

[he_who_is_nobody]

Why do I need to understand the mind of God in order to propose it as the most elegant answer with greater explanatory power and greater explanatory scope? It accounts for things without us needing to tie ourselves up in knots to explain it, and it does so simply and intuitively.

Well, I would not say that you need to know the mind of a god(s), but it would be nice to have evidence for one before you proposed it as an explanation. One cannot posit something as an answer without first showing it exists.

As I said earlier, you are answering an unknown with another unknown and believing that it solves the problem. However, the difference is that the unknown you are proposing is infinitely more complex than the phenomenon you are trying to explain. Thus, your answer is not elegant, nor does it have any explanatory power. You are simply answering a question with an “I do not know”, but making the mistake of believing you have actually answered it. Essentially, sitting back and saying GodDidIt, as you are proposing is not a real answer.

 

[dandan]

So plain and simple, can any of you provide any scientific papers that actually proves that Darwinian mechanisms are responsible for the evolution of the eye, the ATP Motor or any other organ or system that creationists typically consider complex?

Yes. I already provided several articles for the eye and Aron provided several for ATP. Others have posted several articles as well. I can post them again, but you won't read them and dismiss them without thought.

The Eye:
Trevor D. Lamb, Shaun P. Collin & Edward N. Pugh (2007) Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup, Nature Reviews Neuroscience 8, 960-976 (December 2007)

Nilsson DE, Pelger S. (1994) A pessimistic estimate of the time required for an eye to evolve. Proc Biol Sci. 1994 Apr 22;256(1345):53-8.

Also, here's PBS's quick guide: Video

ATP:
Mulkidjanian - ATP synthase

The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio

I even found the Nature-paper open-access: Inventing the dynamo machine: the evolution of the F‑type and V‑type ATPases

So can you please copy-paste the exact portion of any of the articles where the author proves that the eye (or the ATP MOTOR) was build trough Darwinian mechanisms?
I suspect I will ask this question like 10 times and won´t receive an answer.

 

[dandan]

To hold a spirit of reciprocity, I will provide peer reviewed evidence for any of the so called “creationists claims” (just one per person) it could be any creationists claim, ether related or unrelated to this topic. If I can´t provide such article I will honestly and unambiguously admit that I can´t provide such article

I suggest you return to this thread and start citing sources that back the assertions you have made there.

I´ll try to catch up in the other threads in a few weeks

 

[dandan]

I'm going to hammer this on you until you get it.
Do you mean that "it can" or do you rather mean that "it did"? Because they are 2 completely different questions, which have 2 different answers.

]

I mean CAN if you can prove that it can do it i will accept evoluton

 

[dandan]

To be fair, it's hard to keep up with which paper was talked about at which point. In the original thread, an excess of 30 papers were quoted and linked to. In the debate, at least two were quoted and linked to, the peanut gallery contains another ten.

I don't know what y'all are talking about. I originally linked to the Osnabrück paper, showing those illustrations. That citation had a link at the bottom for the Full PDF. There was no subscription required for that. Then I showed that this same research was also examined in peer review at PubMed and Nature, under the title, "Inventing the dynamo machine: the evolution of the F-type and V-type ATPases". That one I didn't provide the full text to, because my point was made without that. Then I cited a second study from Upstate Med.U., and I made sure to show the accessible version of that too. I don't what you guys are confused about when you say that I didn't cite the same thing as last time.

To be honest, I think the actual problem is that you are not unambiguously presenting your proof for evolution. It´s not clear for me if any of those papers represent your actual proof for evolution, or if these papers are just part of OFNF´s education.

For example is your last paper is supposed to prove that the ATP motor evolved from "somethign simple" through random genetic changes + natural selection (and maybe genetic drift)?

I am honestly just expecting a YES/No answer

 

[Inferno]

So can you please copy-paste the exact portion of any of the articles where the author proves that the eye (or the ATP MOTOR) was build trough Darwinian mechanisms?
I suspect I will ask this question like 10 times and won´t receive an answer.

I think it was Aron who said it first:
How can I point to one specific portion when the whole article is about that?
If you give me a book "Computers for dummies", I would be a fool to ask you for a specific section that shows how a computer works or how I can operate one. You need the context of the whole.

However:

Subsequent studies have shown how the roles of several key sites have altered during evolution (94–97), and have defined the molecular characteristics of the different classes of opsin (98–105).

To be honest, I think the actual problem is that you are not unambiguously presenting your proof for evolution. It´s not clear for me if any of those papers represent your actual proof for evolution, or if these papers are just part of OFNF´s education.

Both. Obviously OFNF needs an education, but they are also continuing proof for evolution.

For example is your last paper is supposed to prove that the ATP motor evolved from "somethign simple" through random genetic changes + natural selection (and maybe genetic drift)?

Yes, and it does just that.

 

[AronRa]

To be honest, I think the actual problem is that you are not unambiguously presenting your proof for evolution. It´s not clear for me if any of those papers represent your actual proof for evolution, or if these papers are just part of OFNF´s education.

For example is your last paper is supposed to prove that the ATP motor evolved from "somethign simple" through random genetic changes + natural selection (and maybe genetic drift)?

I am honestly just expecting a YES/No answer

If you want a yes or no answer, ask a yes or no question. For example, I do not consider evolution to be "something simple". As my citations have shown, it can be quite complex.

However the problem is that I am trying to present unambiguous proof, and OFNF is trying to side-track in order to prevent me from doing that. That's why he keeps trying to change the subject, and why he has to dodge the questions which are the focus of this discussion. He calls them 'rabbit trail' questions, but they are what this whole discussion is all about. They have to be addressed in order to achieve my objective, and he can't address them. He can't admit that he didn't understand protein-folding, for example; he can't refute college level classes on cell biology, but he can't admit his ignorance either; neither can he correct himself. So what can he do? Wait a few days and think up some other boastful excuse to evade the inevitable.

 

[Rumraket]

Dandan it seems to me you've skipped the latest batch of replies to you, from me and a few others.

 

[Miracles4Real]

Why do I need to understand the mind of God in order to propose it as the most elegant answer with greater explanatory power and greater explanatory scope? It accounts for things without us needing to tie ourselves up in knots to explain it, and it does so simply and intuitively.

Well, I would not say that you need to know the mind of a god(s), but it would be nice to have evidence for one before you proposed it as an explanation. One cannot posit something as an answer without first showing it exists.

As I said earlier, you are answering an unknown with another unknown and believing that it solves the problem. However, the difference is that the unknown you are proposing is infinitely more complex than the phenomenon you are trying to explain. Thus, your answer is not elegant, nor does it have any explanatory power. You are simply answering a question with an “I do not know”, but making the mistake of believing you have actually answered it. Essentially, sitting back and saying GodDidIt, as you are proposing is not a real answer.

Does proposing "Dark energy" without knowing what it is exactly, in order to account for the expansion rate of the universe- have all the same "problems" you mentioned?

 

[dandan]

To be honest, I think the actual problem is that you are not unambiguously presenting your proof for evolution. It´s not clear for me if any of those papers represent your actual proof for evolution, or if these papers are just part of OFNF´s education.

For example is your last paper is supposed to prove that the ATP motor evolved from "somethign simple" through random genetic changes + natural selection (and maybe genetic drift)?

I am honestly just expecting a YES/No answer

If you want a yes or no answer, ask a yes or no question. For example, I do not consider evolution to be "something simple". As my citations have shown, it can be quite complex.

However the problem is that I am trying to present unambiguous proof, and OFNF is trying to side-track in order to prevent me from doing that. That's why he keeps trying to change the subject, and why he has to dodge the questions which are the focus of this discussion. He calls them 'rabbit trail' questions, but they are what this whole discussion is all about. They have to be addressed in order to achieve my objective, and he can't address them. He can't admit that he didn't understand protein-folding, for example; he can't refute college level classes on cell biology, but he can't admit his ignorance either; neither can he correct himself. So what can he do? Wait a few days and think up some other boastful excuse to evade the inevitable.

So yes or no.

Does your article represents your proof for evoluton? or is this article just part of OFNF education?

*this is the article I am talking about
http://www.sciencedirect.com/science/article/pii/S0014579304010841

The evolution of A-, F-, and V-type ATP synthases and ATPases: reversals in function and changes in the H+/ATP coupling ratio



Aronra

First you asked me, "What evidence do you have that there is a biochemical pathway to create such a motor, such that each mutation provides a beneficial advantage?" So I showed the illustration, answering that question. The link I gave you to A. Mulkidjanian, Osnabrück had another link at the bottom for the Full PDF. There was no subscription required.

Yes or No…
Are you saying that this article provides the beneficial mutations required to evolve an ATP Motor?

 

[Darkprophet232]

sheesh! then why knit pick?
What they DID believe is that they had discovered evidence for God. Though I'm not sure we agree with that.

Hold up the wrong train here. My problem with your assertion was that you were assuming the motivations for scientists, not if they had found evidence for a god, which none of the quotes support either. That you would conflate a scientist saying, “I believe that what I perceive to be order in the universe is evidence that it was created by a god,” with “My motivation for studying science is to understand the mind of my god,” is very telling. You are doing the same thing you asked me not to do:

Lets do eachother a favor and try not to make assumptions about one another by reading between the lines.

You’ve done just that with these scientists. You’re assuming things they have not said, and you don’t even have the basis of their actions, like I did for you, to justify your assumptions. Can you honestly read any of those quotes and tell me they speak to motivation? That a theist has deluded himself to ignore what evidence he does have in order to hold onto the beliefs he was raised with is not motivation. Furthermore, that they think “order” is evidence for a designer does not make it evidence. It’s the same as if I came across a beach and said that sand is constructed too orderly to be random chance, thus the order of sand is evidence for a designer. I wouldn’t be making such an unsupported and dubious claim if I didn’t start from the position that there must be a designer and then use whatever I can to support that belief.

I never realized that our current understanding of the universe included God not being real.

It’s not the inclusion of god not being real, but that a god is not necessary. Our current understanding of all of these fields of science is that all of their subjects occurred naturally without the need for a designer. You are saying that understanding is wrong because you feel it is wrong.

I feel like there is a designer- yes. This cannot be totally scientifically verified. Many important questions are unfalsifiable and untestable and unscientific.
What is more important, the rights of the individual or the rights of the society?
What is the best use of your time on earth?
What does it feel like to be a cow, a bat, an onion?
You can't scientifically verify questions like these, so is coming to conclusion on these questions by using other means at our disposal (philosophy, epistomoloigy, noetics, intuition, logic, empathy.) "dishonest"?

These are not scientific questions, they are philosophical. You are saying that because science can’t answer philosophical questions, we can interject philosophy, specifically theology, into science. It’s a non sequitur. Science isn’t concerned with the best use of our time. It concerns itself with endeavors like ending diseases, which if we had allowed theology to answer that question, we would still be treating schizophrenia with exorcisms.

logical positivism, philosophical naturalism and scientism do not seem to be helpful worldviews, or even functional. I don't think anyone really uses them if they are honest with themselves. We do use intuition and feelings to learn things all the time and they are often right even if they are not as perfect and verifiable as science. Science doesnt have all the answers. it is incapable of having all the answers. Even answers that you need in order to function as a healthy conscious soul.

Your understanding of science is lacking. As has been pointed out to before, scientists are not automatons. We can experiment. Often, when we think of doing something by intuition and then do it, we are experimenting. If we keep track of the results of our actions and use prior results to influence future actions, we are using a form of methodological naturalism. If you know that taking a certain route to your workplace is faster than the other ones because you have driven them, and not because of car-enhancing pixies that only operate on a certain road, you are using naturalism. Not all science is done in sterilized laboratories by old men in lab coats. The only reason these may seem to be unhelpful for you is that you don’t realize that you utilize them in your day-to-day life.

These worldviews that you deem unhelpful are the reason why we can get clean water to drought-stricken parts of Africa, find cures for diseases, launch satellites into space that allow us to use GPS directions, and yes, even have discussions online using electricity and computers.

Also, please explain, in unambiguous terms, what a soul is, what it does for us, and how you know this.

I'm not saying "yeah that's good enough" I'm here to learn. I don't know how you missed this as I've said it many times. I just have the courage to state my current opinion (an opinion which I admit could be wrong)

Yet you’re fighting science at every step. This is talking out of both sides of your mouth. You may say you are here to learn, but you are actively fighting against our current understanding of science so that you can keep your god. You have shown no intention to learn in your posts, other than just asserting that you are. If you are here to learn, may I suggest that you stop asking leading questions, read what others have said, and stop trying to force a philosophical view of god into science?

Can you even have an opinion, or are you a scientific droid?
What if someone asks you who you think will win in a Lakers game? because you do not have the available statistics on every player in each team and cannot at that moment calculate with peer reviewed accuracy the trajectory of each shot and its statistical likelihood of making a basket do you believe it is dishonest to say anything other than "I don't know"?

If I know that the game is in LA and the Pistons are currently on an away losing streak, and that the Lakers are dominating at home, I would be justified in saying, “I'm confidant the Lakers will win.” In fact, I have many opinions that aren’t based in science. But I am not offering my opinions as EVIDENCE. That is what you are doing, as you’ve time and time again conflated feelings, even a scientists, for evidence. This isn't a dichotomy, where either we understand nothing or we understand everything. Stop trying to force science into something its not, which I can only assume you're doing because its easier to dismiss than what the science actually says.

In everyday life I do not find myself talking to androids. So yeah I usually share my *cringe* feelings.
live long and prosper.

I’m not saying you can’t have opinions and feelings. I’m saying that it’s disingenuous to say that the evidence we have is wrong because of your opinions and feelings.

I won't pretend to know what God's goals are or why he creates a universe with warts and all.
one that includes suffering, beauty, morality and parasitic microbes.
Maybe a few different spiritual gurus had something of an insight into Gods plan. If I had to speculate (again not 100% scientifically peer reviewed on this) I'd say it has something to do with loving one another, not taking anything for granted and being free to express ourselves. Maybe Jesus was onto something, maybe Gandhi and Buddha were too.

You have an issue where you say a lot, but don’t actually engage with what is being said. I don’t care about what guru have to say about “god’s plan.” You, Miracles4Real, are positing that everything in the universe is designed. I’m telling you that a consequence of this assertion is that this designer created pain and violence, where neither were needed, as the only means for creating new life for dozens of life forms. These consequences must be justified if your feelings are true. That you would push this responsibility onto someone else, and won't fully explore what your feelings lead to screams to me that you don’t actually care about learning about the evidence, just putting science down.

Maybe no one has any insight into it at all, but it sure seems designed. at least, to me.

Do you have anything to back up your assertion? You keep making it, but you never justify it. It the equivalent of my saying “I think the universe is made of pudding, and all biological life forms are just different kinds of pudding. Why do I think this? It’s just seems to be made of pudding to me, and any evidence presented to the contrary I’ll dismiss out of hand and accuse others of being lifeless husks for not feeling the world is made of pudding either, but I’m here to learn!”