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Cytochrome C - The Illusion Exposed


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#41 Guest_shpongle_*

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Posted 03 December 2008 - 01:07 PM

http://www.evolution...?showtopic=1882

http://www.evolution...topic=1878&st=0

Are you having trouble seeing the trees because of the forest? ;)


But again, none of that (at least from what I can recall in the threads) is a positive demonstration of design. You simply asked "how did X evolve" and when not presented answers to your satisfication, declared victory for design.

Imagine if you were in a contest with someone else. You were asked a question but your answer wasn't satisfactory. As a result victory was declared for the other person by default. Do you think that's a fair contest?

You can't merely assume design as a defult. You need to have some sort of positive demonstrable criteria to conclude design. From what I've seen of the ID movement, they are working on this problem but they have yet to come up with any empirical verification of their criteria thus far (unless there's been something new published within the last couple years I'm unaware of).

What is the logical cause of intellegent information and order?  :blink:


Define "intellegent information". And quantify it with respect to biological forms. Ditto with "order".

Smoke screen


You claimed branches on phylogenetic trees were "pulled out of thin air". I responded they are derived via algorthimic methods based on datasets. Where is the smokescreen? I mean, you can read all about this yourself if you don't believe me.

#42 Adam Nagy

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Posted 03 December 2008 - 01:21 PM

Indeed.  I'm not really a huge fan of astronomy or geology so if it's all right with you, I'm going to stick with biology as the topic of discussion.

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We don't have to discuss these other issues but still consider looking into them. All the evidence for an old earth and biological evolution are a package deal. They need each other to even begin to look plausible.

If you find a sunken ship and want to discover some information about when it was sank, what can you do? Well, say you're lucky enough to pull out a chest of coins. Which coins give you the proper limiting date for when it sank? the young ones or the old ones?

All the speculations about the dating of an old earth are trumped by methods that establish young ages. Before I get called on a derail, I’ll stop. :blink:

#43 Adam Nagy

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Posted 03 December 2008 - 01:35 PM

Define "intellegent information".  And quantify it with respect to biological forms.  Ditto with "order".


example - intellegent information - as found in the DNA code for all living organisms

example - order - the laws by which we can succesfully do the scientific method


You claimed branches on phylogenetic trees were "pulled out of thin air".  I responded they are derived via algorthimic methods based on datasets.  Where is the smokescreen?  I mean, you can read all about this yourself if you don't believe me.

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assumption - evolution

work - derive "proof" by fitting to the assumption of evolution

result - assumption "proved"

You purport to prove what you have assumed. I will gladly admit God as the starting assumption of my view of the world and validate this as a safe assumption. Will you admit that evolution is your starting assumption or would you rather admit that you believe circular reasoning is a-okay? This is not a false dichotomy, it’s you’re only two choices.

This is why evolutionists lose debates. They can’t admit their assumptions. Christians that can’t admit their assumptions or don’t understand what that means end up on the same losing end as well. This isn’t a mutually exclusive problem. It’s a philosophical problem.

#44 Guest_shpongle_*

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Posted 03 December 2008 - 01:49 PM

example - intellegent information - as found in the DNA code for all living organisms

example - order - the laws by which we can succesfully do the scientific method


You're going to need to be much more specific and comphrehensive in your definitions I'm afraid. Especially with respect to "intellegent information". You need to quantify your definitions if you think it's something that you can measure.

assumption - evolution

work - derive "proof" by fitting to the assumption of evolution

result - assumption "proved"


Nope, this is incorrect. While there are phylogenetic methodologies which do rely on evolutionary bases for tree construction (like maximum parsimony), the method I used (least squares) to construct the tree I did previously isn't based on any evolutionary assumptions. It was simply a statistical method based on relative similarities and differences between items in the dataset given (in this case, Cytochrome C protein sequences).

This is why I said you can apply phylogenetic tree reconstruction to things besides biology.

#45 Adam Nagy

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Posted 03 December 2008 - 01:59 PM

It was simply a statistical method based on relative similarities and differences between items in the dataset given (in this case, Cytochrome C protein sequences).


I don't think anybody here would have the slightest problem with the above statement, creationist or evolutionist.

It's when the words; "This proves the "tree of life" common decent from a single living organism, aka The Origin of Species..."

This would reveal that you either don't understand that the "facts" of evolution that you were taught in school were actually hypothetical speculations or you are willingly ignorant of your assumptions.

#46 Adam Nagy

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Posted 03 December 2008 - 02:09 PM

You need to quantify your definitions if you think it's something that you can measure.


Don't you see how crossed your wires are? You can't quantify Darwinian Evolution and yet you purport that it's been proven.

You'll say; yes it has been Quantified:

Evolution is the change of living organisms over time through mutations and natural selection.

Nobody is disputing that claim.

The foul comes in when the extrapolation is made that this proves "The Origin of Species"

BTW, I don't approach God through operational science. I assume God as the author of operational science. He deserves our reverence. His power is displayed every time you look into a telescope or peer into a microscope or when you simply take a breath and look out your back window.

#47 Guest_shpongle_*

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Posted 03 December 2008 - 02:11 PM

Don't you see how crossed your wires are? You can't quantify Darwinian Evolution and yet you purport that it's been proven.


Actually there are evolutionary quantifications. Look up "molecular clocks".

The key is that if you are going to try to define something like "information" as some sort of measurement with respect to DNA, you need to quantify it. Failure to do so doesn't really give it any meaning with respect to DNA.

#48 Adam Nagy

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Posted 03 December 2008 - 02:14 PM

Actually there are evolutionary quantifications.  Look up "molecular clocks".

The key is that if you are going to try to define something like "information" as some sort of measurement with respect to DNA, you need to quantify it.  Failure to do so doesn't really give it any meaning with respect to DNA.

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Here you go:

http://www.evolution...m/forum_faq.htm

I haven't looked at these specific examples but the general argument for what information is, looks right to me.

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Posted 03 December 2008 - 02:17 PM

I don't think anybody here would have the slightest problem with the above statement, creationist or evolutionist.

It's when the words; "This proves the "tree of life" common decent from a single living organism, aka The Origin of Species..."

This would reveal that you either don't understand that the "facts" of evolution that you were taught in school were actually hypothetical speculations or you are willingly ignorant of your assumptions.

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Or perhaps you don't understand the underlying meaning behind phylogenetic reconstruction and converging trees.

The point is that the tree I constructed falls remarkably in line with expectations about evolutionary history of the various taxa in that list derived from other sources of data. This was the challenge of the OP: come up with a tree without knowing the items beforehand and see what you get. It's not 100% perfect to be sure, but it's pretty darned good.

And this is the really the meat of things. Converging phylogenies is powerful evidence for evolution. To be sure, convergence is never going to be 100% perfect as there are limitations with any statistical measure, but you can get things pretty close. (Remember what I said about there being 8,000,000,000,000,000,000,000,000,000,000,000,000 possible trees based on the 30 items in the OP?).

And if things like what you suggest (about whales and bacteria last sharing an ancestor relative to other mammals), I wouldn't expect to see them clustered where they are on the tree. In fact, they should be a distant outlier along with the tomato and rattlesnake. Yet, based on this but also studied of morphology and fossils, they are more or less right where I'd expect them to be if they evolved from land dwelling mammals.

You never did answer my question, btw: why don't whales have gills like fish?

#50 Adam Nagy

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Posted 03 December 2008 - 02:21 PM

Shpongle,

We went over this topic already. Let's let the next batch of onlookers decide what to do with what's been said. ;)

#51 Guest_shpongle_*

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Posted 03 December 2008 - 02:23 PM

Shpongle,

We went over this topic already. Let's let the next batch of onlookers decide what to do with what's been said. ;)

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Right. But do you at least understand what I'm saying? I want to make sure I'm clear because if I'm not conveying this right, I want to better explain it for the benefit of you or whoever else reads this thread.

#52 Adam Nagy

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Posted 03 December 2008 - 02:33 PM

Right.  But do you at least understand what I'm saying?  I want to make sure I'm clear because if I'm not conveying this right, I want to better explain it for the benefit of you or whoever else reads this thread.

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I really think I do. You are certainly polite, passionate, and articulate and for this I commend you. The bottom line is; I'm not compelled by what you think it points to.

The question is; Does my bias color what I see when you are sharing your thoughts? The answer is a bold, Yes. I hope you stop to think about your own biases, and this is not to say that they are necessarily a bad thing but unrecognized biases can keep you from objectively examining other people’s views.

I really truly, think I follow exactly what you’re saying, without having to step out of my worldview. Peace be with you, Shpongle.

We’ll be talking. I enjoy your dialogues. ;)

#53 Guest_shpongle_*

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Posted 03 December 2008 - 05:17 PM

Adam_777,

Thanks for your candor and I just want to say I enjoy our discussions too. You're one of the more polite creationists I've debated with in quite some time.

I just hope we do understand each other's points. Often times in these debates I find a lot of contention occurs just because one side doesn't understand what the other side is saying. Even if we don't agree, understanding is important.

#54 Guest_DNAunion_*

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Posted 21 March 2010 - 12:45 AM

So let me get this right, the grey whale is more closely related to the camel than it is to the elephant seal?



This is just a single-protein comparison. As with all statistical analyses, the larger the data set, the more reliable the results.

#55 Guest_DNAunion_*

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Posted 21 March 2010 - 12:56 AM

Posted Image



What am I missing?

Wasn't the point of the OP that no evolutionist could get any kind of a decent phylogenetic tree out of the cytochrome C data without using preconceived notions about evolutionary relationships to manipulate the tree towards a desired outcome?

But here is software that knew nothing about preconceived notions of relationships between the animals, and used only the genetic data to construct the tree: and it is, for a single-protein tree, an overall good match to the accepted evolutionary relationships.

#56 Adam Nagy

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Posted 21 March 2010 - 03:01 AM

But here is software that knew nothing about preconceived notions of relationships between the animals, and used only the genetic data to construct the tree: and it is, for a single-protein tree, an overall good match to the accepted evolutionary relationships.

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What are 'accepted evolutionary relationships'? Never mind, I know. We're all related somehow someway so all phylogenetic trees are good because we know that all organisms are related through biological evolution, right?

The bottom line is that evolutionists aren't often (but they are sometimes) honest about the huge contradictions left when comparing morphological data to DNA data.

#57 Guest_DNAunion_*

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Posted 21 March 2010 - 04:50 AM

What are 'accepted evolutionary relationships'?


Note how in the diagram the primates all group together, at the exclusion of all other organisms in the comparison, and that within the primates, humans are most closely related to chimps, then to rhesus monkey, then to spider monkey. Then leaving the primate cluster, humans are most closely related to non-primate mammals, then to birds, and last to tomato. Note also how all the mammals are grouped together (none are found mixed in with the birds, the snake, or the tomato ... or vice versa). Note also how all of the birds group together, at the exclusion of other organisms. Note also how the horse, donkey, and zebra group together, as do rats and mice. These all agree with the accepted evolutionary relationships among the animals listed.

For a comparison based on a single-protein, the tree is a good overall match to accepted evolution relationships, and the tree was constructed without any preconceived notions of how the organisms should be linked together to construct the tree.

So contra the OP's implication, preconceived notions of evolutionary relatedness are not required to construct a decent phylogenetic tree from the raw cytochrome C data.

#58 PhilC

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Posted 14 June 2010 - 03:25 AM

Here are the questions that need to be answered:

1. Did that software have a built in bias towards the theory of evolution?

2. If not, what can explain the results that have come out of this?

If the theory of evolution was not assumed by the software then the way that these organisms have been placed into that tree requires an explanation.

Obviously, as it seems like the theory of evolution wasn't assumed, we can use this as evidence for the theory of evolution without being accused of circular reasoning.

#59 AFJ

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Posted 09 January 2011 - 06:36 AM

I just wanted to make a comment. Fred's point that the evolutionists skew the data by picking the evidence to show us, is completly valid. As we have seen in this thread, there are other ways to skew the numbers.

For instance, it is hard to see all the letters, so I'm not sure what some of the respective amino acids are, but in columns 15 and 89 we have a line of primates with the same amino acid as birds, but different than all the other mammals. Those mammals all share another a.a. Column 89 has a bit more varitation in the other mammals than 15, but the same thing is going on, birds to humans.

The evolutionists give an inconclusive case. This grid does not give the genetic sequence, but rather the sequence of the protein. Since the amino acids each have a group of codons (up to 4) this would be inconclusive for a genetic copy case.

And most importantly, if there is alot variation, it is just "selection at work." But if it's the same it's a "conserved protein." Let them take another enzyme in the electron transport chain, Kreb's cycle, or glycolysis, and see if the numbers match in the "common descent" arguement. You will se this reasoning pop out like a sore thumb. Fred is right, you can't falsify it. It's like trying to put a hole in liquid. They pride themselves on following the data, but they run ahead with their assumptions so much, it's hard to know what is actually data and inconclusive unfinished research. That is why we see so many "may be's" and "could be's" in evolutionary articles.

Finally, as in being found in science to simply list a sequence with it's differences and or commonlities is oversimplification. There are other unknown factors as to why there would be a difference--namely in regulation, free energy needs, and pleitropic enzymes. This a branch of research, and new biochemical discoveries are being made.

One example alone is phosphorylation. Each nucleotide has a ribose and phosphate that makes up the "back" of the DNA or RNA strand. This interacts with ATP AMP and other molecules in phophate signaling. This is not only in DNA, but in many biochemical cascades and processes. Who knows the full ramifications of these differences in the DNA?

#60 guillxer

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Posted 17 April 2011 - 07:43 PM

First note: I'm not an expert in Biology (don't have a Phd. in Bio/ or years of self study)

This aspect of science is not well understood. If someone claims that animals can be grouped by analysis of a single protein, I'm going to have to call their bluff.

That said, if you want to do some of your own analysis have at this website.

http://www.pdb.org/pdb/home/home.do

FYI. Even if you don't believe in evolution you can still still get use out of DNA/protein sequencing for development of drugs, predicting reactions, targeting certain viruses etc.

- agnostic




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