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Cytochrome C - The Illusion Exposed


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#21 jamesf

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Posted 14 February 2008 - 07:45 PM

How thoughtful of you.

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I think kindness and logic is usually the best way to start when two people disagree. Too many people that disagree start with some degree of ridicule and that creates unnecessary hostility. So if I can help, I am happy to do so.

It’s not a hidden bias, it’s a clear bias that is both unscientific, and intellectually dishonest. In no way does Cyto-C allow one to build the trunk and major branches, all of which are inferences only.

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I would argue that this both represents a misunderstanding of the computer program that generated the chart as well as a misunderstanding of how science works. Most all of science is based on inference. Today, from the wobble and the intensity variations of stars we are inferring that there are planets going around those stars and inferring the size of those planets. Most all of chemistry and modern physics is based on inference. It is the heart of science. As long as you state your assumptions and work logically, you can be both scientific and honest in your conclusions.
The logic that generated the computer code is extremely simple, and as you said the biases and assumptions are clear. Of course, one's interpretation of these results depends on whether you accept the assumptions, but the assumptions are quite clear and the logic quite open and honest. I am sorry if this upsets you. Your responses to this computer program lead me to believe that you do not understand the logic that generated the chart. However, it is important to remember that it is this chart that makes the findings of Cyto-C exciting to scientists, not the similarities it produces to similar "kinds".

I felt I was very clear on this in my response to Numbers.

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I was addressing the comment you made to me, not to Numbers. In your second response, you colored all the nodes of the computer program in green and called it "dishonest" and a "fairytale". But you had referred to those same nodes and said:
"What you refuse to see is that the nodes on your tree are the same nodes creationists would have deduced by grouping them as kinds"

The nodes on this tree that are exciting to scientists are, for example, those that show reptiles and birds on a related branch. Or the one that shows that the lamprey have a separate branch from the other fish. There is part of a whole field called 'cladistics' that had previously created trees like this based on the similarities of basic features. The fact this tree with quite similar branches could be produced with such simple assumptions and logic helped settle arguments in evolutionary biology. The notion that it also provides evidence for common decent is really quite secondary. The fact that chimps and humans are similar here is also rather uninteresting to the scientists, since virtually no evolutionary biologist doubted that.


Here are the major points, again:

1) Of the 5 ‘E’s Numbers inferred correctly (the “recent ancestors”), 4 of these could also just as easily been inferred by Creationists to suggest they are of the same kind. Is it a surprise to you that us silly creationists think horses and zebras are of the same kind? Of the 4 ‘N’s where Numbers flunked (but is now equivocating on), we too as creationists would have flunked if we had tried to draw inferences from the sequence.

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Cyto-C is not a good choice when comparing animals that are "closely related" It can have an error rate of something like plus or minus 40 million years. Cyto-C is used because virtually all of life has this gene. It is so fundamental that every form of life can be placed on the chart and a simple program can deduce the nodes. I find it remarkable that with such simple logic and simple assumptions, a tree like this can be constructed from a single gene. And I am impressed that the tree that this program produces is so similar to the ancestral tree created through cladistics.

If you wants more precision, you will need to go to other genes. For example, below is a link to a chart drawn for the dog genome. Each tree uses a gene that has different resolutions. You are welcome to question the assumptions of any such chart. Such questioning is good science. However, the assumptions can be deduced from the paper and all this work is considered top rate science by the scientific community.

Here is a link to the paper it comes from
http://www.genome.or...15/12/1706#FIG1

Afraid the picture is too big when I post it, so here is a link to the dog genome chart I mention
http://www.genome.or...e/1706fig1.jpeg



2) Of the distant differences, should creationists be surprised that wheat and bananas have a much different sequence than humans? Should creationists be surprised with a mosaic sequence such as occurred with the rattlesnake? I rememberd that Denton had written about this so I just grabbed the book and dusted it off. Denton was an evolutionist who saw through the illusion and was being intellectually honest when he wrote regarding Cyto-C "No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of the other group. Transitional or intermediate classes are completely absent from the matrix". - Evolution, a Theory in Crisis, pg 280. [emphasis mine]

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I am sure you are aware how Denton is considered in field of genetics and evolutionary biology. There are plenty of critiques elsewhere so I won't repeat them. However, I do not understand the part you put in bold. It is the logic of the program that 'infers' where the nodes are, based on the number of amino acids that are aligned. Are you expecting them to put in the Cyto-C code for an archaeopteryx? Or an animal from the Cambrian?


3) I then concluded that “neither side can use Cyto-C as evidence to support their version of “common decent”.” It would be bad science to do so, since Cyto-C is just one of thousands upon thousands of sequences we can look at. Evolutionists happen to love Cyto-C because it was one of those sequences where chimps and humans come up the same. It helps sell their illusion.

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I personally haven't seen any scientific papers that use Cyto-C to compare humans and chimps. It is too crude for that. Cyto-C was chosen because virtually all life has this gene. There are hundreds of genes that are identical in humans and chimps, but that isn't the point of Cyto-C.

What I did like is that you marked in green all the most interesting parts of the chart. This is where the computer program shines. You are quite right. It is important that full trees like this be drawn using a wide range of different genes. And indeed they are (like the canine example above). However, it is amazing (to me) that it is even possible to get this tree with just a single gene (although a very important gene).

I thought your monkey was cute, but not sure how it addressed the logic of our discussion.

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I look forward to your response,'
James

p.s. I do appreciate that you allow both sides to state their argument on this site.

#22 Fred Williams

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Posted 17 February 2008 - 04:44 PM

I am sure you are aware how Denton is considered in field of genetics and evolutionary biology. There are plenty of critiques elsewhere so I won't repeat them.


This ad homenim against Denton is against forum rules (see 7th bullet). We argue the evidence presented, not who the messenger is or what his credentials are, unless it is found to be absolutely critical to the argument.

However, I do not understand the part you put in bold.


The point I’m trying to make is that there is no basis for the underlying root system and major connecting branches. Perhaps I should have emphasized the penultimate sentence - "No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of the other group. Transitional or intermediate classes are completely absent from the matrix".

What I did like is that you marked in green all the most interesting parts of the chart. This is where the computer program shines. You are quite right. It is important that full trees like this be drawn using a wide range of different genes. And indeed they are (like the canine example above). However, it is amazing (to me) that it is even possible to get this tree with just a single gene (although a very important gene).


And like I said, such a tree is pure fantasy, nothing more. Using the same Cyto-C data we get the creationist “orchard”:

http://www.nmsr.org/phylo3.jpg

Fred

(FYI, I've pinned this topic)

#23 deadlock

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Posted 17 February 2008 - 05:04 PM

Just checked the first link I posted, it went to a diagram associated with the article in question. I don't know if you noticed the link on the bottom saying "return to article" but if you missed reading the actual full article, here's where is says bats are close to the dog group Carnivora. Notice that in listing the closest groups there is no mention of Rodentia, the mouse group.


It´s interesting to notice that in the link I posted there is no mention of carnivora too.So, Who is right ? Nobody is right, It´s true to say that depending on the part of the genome one analyzes one gets different relatioships.That´s what is expected if living beings were created instead of evolved.Because , common traits are distributed according to design needs not according to common ancestor.

I've shown twice on this thread that that's not true. Could you provide a source for your claim.


I already provided the link but I´ll do it again.

Scientists at MD Anderson Cancer Center have created mice with long, slender, bat-like fingers in place of their short, stubby little paws.
Researchers created the “mouat” by simply replacing a small section of DNA from the mouse version to the bat version. This section is responsible for regulating the levels of a single protein in the developing limb—with the protein at elevated bat levels, the mouse’s fingers grew long and slender.

It means that mouse and bats have the same genes regulating the fingers size.They are so similar that they replaced the DNA code of the regulating gene of the mouse with the DNA code of the bat´s gene and it worked.


Reference

What part of that article do you think shows mice are the closest living relative to bats? All it says is that mice have one of the genes that bats do, that is not the same thing as being closer to mice than dogs.


What make one living being closer to another ? You are giving more importance to one study than the other only because it supports your point of view.Why dont they pick those 12 coding regions of the bat´s genome and replace them in the dog´s genome and see if it works ?

All this is kind of beside the point since I specifically said that bats weren't particularly close to any of the animals on the chart, and if you go back and look at the spreadsheet you can see the high spread of differences for the bat vs. all the rest of the animals.


You showed a study that Bats have some relationship with Carnivores, cetaceans, so why didnt you say that bats are related to graywhales like they are to dogs ? It´s simple, because the cytocrome C does not show that relationship.As I said, depending on the part of the genome you compare you get different relationships.

#24 deadlock

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Posted 17 February 2008 - 05:09 PM

So out of 17 total statements you can only find fault with 2 of them?  Without the 40 MY and 80 MY date your objections don't work because the groups end up being very distinct 5-50,50-100,100+.

just fyi, the 8,10 date is ">50" which means "greater than 50".

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Please, dont make me laugh

#25 numbers

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Posted 17 February 2008 - 08:41 PM

Because , common traits are distributed according to design needs not according to common ancestor.


That demonstrates a fundamental misunderstanding of the whole problem with differing cytochrome c for a creationist perspective. There is no functional difference between the cytochrome c of any animal on earth. They all fold into the same shape and react the same way and perform the same function. There are not multiple design needs which means a designer does not need multiple versions of cytochrome c.

Since there are somewhere around 10^90 different sequences that will make a functional cytrochrome c protein, even if a designer wanted to use different sequences for the same need the probability is essentially zero that a designer would independently arrive at the same sequence twice. That means that if there are identical sequences in different species at least one of those identical sequences was copied from the other (a.k.a common descent). There is no distinct design need that would require chimps and humans but not other animals to have the same cytochrome c sequence.

Since there's no need for them to be the same, and theres only a 1 in 1000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 chance of a designer choosing the same sequence without copying, the only explanation for them being the same is that one was copied from the other.


Scientists at MD Anderson Cancer Center have created mice with long, slender, bat-like fingers in place of their short, stubby little paws.
Researchers created the “mouat” by simply replacing a small section of DNA from the mouse version to the bat version. This section is responsible for regulating the levels of a single protein in the developing limb—with the protein at elevated bat levels, the mouse’s fingers grew long and slender.

It means that mouse and bats have the same genes regulating the fingers size.They are so similar that they replaced the DNA code of the regulating gene of the mouse with the DNA code of the bat´s gene and it worked.


Reference
What make one living being closer to another ? You are giving more importance to one study than the other only because it supports your point of view.


In a discussion about genetic closeness I'm giving weight to studies intended to investigate genetic closeness over studies intended to investigate protein regulation, not sure why you think that's a bad thing. The study you posted wasn't intended to deal with mice being closer or further away from bats than other animals so it has absolutely no relevance to this discussion.


Why dont they pick those 12 coding regions of the bat´s genome and replace them in the dog´s genome and see  if it works ?


I don't know anything about the decisions made for that study but mice are usually cheaper and easier to experiment on than other animals.

You showed a study that Bats have some relationship with Carnivores, cetaceans, so why didnt you say that bats are related to graywhales like they are to dogs ? It´s simple, because the cytocrome C does not show that relationship.As I said, depending on the part of the genome you compare you get different relationships.

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Take a look at the spreadsheet I posted back at the beginning and look at the entry for bats, the whale was one of the lower numbers of differences. If a tree was built based on that spreadsheet, whales would indeed be grouped near bats.

#26 deadlock

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Posted 18 February 2008 - 03:31 AM

That demonstrates a fundamental misunderstanding of the whole problem with differing cytochrome c for a creationist perspective.  There is no functional difference between the cytochrome c of any animal on earth.  They all fold into the same shape and react the same way and perform the same function.  There are not multiple design needs which means a designer does not need multiple versions of cytochrome c. 


I think that our knowledge about the function of cells is very small to say that the differences in Cytocrome C is not necessary to each specie.

Since there are somewhere around 10^90 different sequences that will make a functional cytrochrome c protein, even if a designer wanted to use different sequences for the same need the probability is essentially zero that a designer would independently arrive at the same sequence twice.  That means that if there are identical sequences in different species at least one of those identical sequences was copied from the other (a.k.a common descent).  There is no distinct design need that would require chimps and humans but not other animals to have the same cytochrome c sequence.  Since there's no need for them to be the same, and theres only a 1 in 1000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 chance of a designer choosing the same sequence without copying, the only explanation for them being the same is that one was copied from the other.


Your reasoning is no sense.Designer is not limited by probabilities, only random events are.

In a discussion about genetic closeness I'm giving weight to studies intended to investigate genetic closeness over studies intended to investigate protein regulation, not sure why you think that's a bad thing.


The study I posted has the intention to explain bats evolution.It´s very clear.

  The study you posted wasn't intended to deal with mice being closer or further away from bats than other animals so it has absolutely no relevance to this discussion.


Of course it is.They are trying to explain bat´s evolution.

I don't know anything about the decisions made for that study but mice are usually cheaper and easier to experiment on than other animals.


No, it´s because mouse has the same genes regulating finger´s size.If dog had it they would have used dog.


Take a look at the spreadsheet I posted back at the beginning and look at the entry for bats, the whale was one of the lower numbers of differences.  If a tree was built based on that spreadsheet, whales would indeed be grouped near bats.

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So, Why didnt you put it ?

#27 numbers

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Posted 19 February 2008 - 05:55 PM

I think that our knowledge about the function of cells is very small to say that the differences in Cytocrome C is not necessary to each specie.

Our understanding of cytochrome c is quite robust actually. The cytochrome c in every animal is the same shape, does the same thing, and reacts the same way.

http://www.bio.mtu.e...401lec10p1.html
First, we find that all cytochrome c proteins from eukaryotic organisms have the same 3-D shape and they all bind heme-Fe in the same way and are found in mitochondria. However, while there are about 100 AAs in all these cytochrome c proteins, only about 30 of the AAs are exactly the same in all of them.


Cytochrome c between very different species is interchangeable. Here's a link to an abstract of a study where rat cytochrome c was put into yeast.

http://links.jstor.o...TOR-enlargePage

"Therefore, the rat polypeptide, when expressed at normal physiological levels, is recognized by the yeast machinery involved in the multiple steps required for the processing and transport of an active cytochrome c as well as its functional interaction with the respiratory apparatus"

It would be an interesting research project for creationists if they could find a reason for cytochrome c to be different in different species. Right now there is no reason except random divergence from a common ancestor.


Your reasoning is no sense.Designer is not limited by probabilities, only random events are.


You aren't understanding the problem. We know a designer didn't use the same sequence in each animal even though he could have. That means a designer must have wanted different sequences in different species. There are for all practical purposes a nearly infinite number of sequences that will work. Since the designer selected different sequences from a extremely large range of options we can use probability to determine if the selections were related to one another.

Think of it this way. I ask you to select 4 numbers from a range of 1-100000 and you give me 1,1,2,3. No one would believe that the any of the selections were made without thinking of the other selections. Each of your selections was either copied or used as a basis for an additional selection.

Similarly, with such a wide range of cytochrome c sequences available to chose from, when we see selections that are identical or only have a couple of differences we can be certain that the sequences were copied or built off of each other.

Not only that but when we plot out the differences in the sequences we get pretty good matches of prior expectations of evolutionary relationshihps. Such as the correct identification of a large difference between bats and mice (look at the spreadsheet to see the high number of differences compared to most of the other mammals).

The study I posted has the intention to explain bats evolution.It´s very clear.


They wanted to see if a single regulatory region can affect limb length, which is related to bat evolution. So they copied that region into another animal to see if that animal exhibited different limb length. The experiment worked, they confirmed that a single regulatory region could have significant morphological impact.

We copy human genes into mice all the time, that doesn't mean mice and humans are more closely related than other animals.

No, it´s because mouse has the same genes regulating finger´s size.If dog had it they would have used dog.


Where are you getting the idea that the experiment wouldn't work similarly with a dog?
Why on earth would they use a more expensive, harder to work with animal when a easier, cheaper alternative is available?

It sounds like you think they had to use a close ancestor to a bat for the experiment to work, but nothing in that article implies any such thing.


It's getting kind of repetitive trying to show you bats aren't related to mice so I'm going to try a different approach.

Here's 5 different sources saying mice aren't related to bats

http://www.batsnorth...c_bat_FAQs.html
http://www.ucmp.berk...chiroptera.html
http://www.batsgaute...a/BatPhobia.htm
http://science.howst...ks.com/bat1.htm
http://rainforest.mo...mmals/bats.html

Please come up with one, just 1, source that says "bats are related to mice","bats have a close ancestor to mice" or any variation of those words. I don't want you to post a study that you think sort of implies that bats are related to mice, I am asking for a source that says point blank "bats and mice are related" at any level closer than they are both mammals. If you can't find one either admit you are wrong about mice and bats being related or I'm going to have to conclude that you are simply unwilling to accept evidence that contradicts your opinions.

So, Why didnt you put it ?

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I posted the spreadsheet and explained how to read it. If you read my original post on this topic I explained that I was only writing statements for the lowest number for each animal.

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Posted 29 November 2008 - 12:32 AM

I realize the discussion in this thread is about 9 months old, but since it was pinned I figured it's fair game.

Anyway, the challenge the OP presented piqued my interest, and since no one had actually done a phylogenetic reconstruction, I figured it was worth trying.

So I did. First a pre-amble with a couple caveats:

1) I had to transcribe things by hand, since the original data in the OP was an image file. I expediated the process by transcribing one sequence then trying to carryover differences. Also, it's not clear in the OP, but the bird sequences differ more than is highlighted, so I had to go back and double check those to make sure I had the differences correct. Otherwise, the tree would have been very odd. That said, there still could be some transcription errors. Human error and all that.

2) I tried to do some statistical weighting for individual sites based on relative divergences and similarities in the OP. This was all ball-park stuff based on a cursory examination of the highlighted differences, so again, judgement and error is going to be introduced. I could probably do more rigorous analysis, but for this purpose I don't see the point.

3) The method I used was a distance matrix method and least squares to build the tree. There are various methods, both for distances and tree construction, which can give slightly different results. This is why real phylogenetic reconstruction tends to take a lot more work (usually building multiple trees, doing tree comparison, etc). I just did one for simplicity.

4) I initially labelled everything with "Animal 1, Animal 2, etc", but it made it really hard to cross reference, so I went back and labelled everything properly.

5) I included tomato sequence to have an outlier. I chose something very distinct based on the given sequences, and since they were all animals, I figured a plant was a safe bet. This was to avoid weird tree reconstruction that could have resulted in using a different outlier. I suppose the rattle snake sequence would have worked too, but I went for a safer bet by using a plant.

6) Software used was PHYLIP, free phylogenetic reconstruction software anyone can download and use. Anyone wants the raw text file data I used, PM me.

'nuff said, here's the tree:

Posted Image

Discussion: This is more or less ballpark for what I expected based on an examination of the sequences in the OP. There are some oddities, like murids (mouse and rats) located where they are. Hippos are placed a bit odd too, but the closest nodes are so close sequence-wise that it's pretty ballpark. This is something where relative weighting can also play a big role in determining nesting. Kangaroos are also odd, but again, given the data and assumptions, I'm not surprised there are oddities.

Bottom line, I think it's a decent tree with oddities to be expected given the limited data set and base assumptions going in. Obviously tree refinement would require better overall analysis and probably more than a singular dataset (especially for sequences that are very closely related).

Unfortunately for the OP, this tree does not confirm their premise.

#29 Adam Nagy

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Posted 01 December 2008 - 09:31 PM

Posted Image


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

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Posted 01 December 2008 - 11:36 PM

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

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Actually yes (and this is even based on more comprehensive phylogenetic studies).

Whales are part of the Cetartiodactyla clade along with other species like pigs, camels, sheep, deer, etc.

Elephants seals are part of the order Carnivora and actually most closely related to dogs in this list (and based on other phylogenetic studies).

That said, I wouldn't read too much into this particular phylogenetic tree, however, since there is so much sequence similarity in Cytochrome-C for many of the animals in the list (particularly for those in the Cetartiodactyla clade), that resolving precise phylogenetic relationships is problematic. A better approach would be to use a more comprehensive data set with multiple sequence alignments.

My approach was very basic here and just to illustrate that yes, you can build a reasonable if imprecise phylogenetic tree from the data given in the OP.

#31 Adam Nagy

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Posted 02 December 2008 - 07:57 AM

Actually yes (and this is even based on more comprehensive phylogenetic studies).

Whales are part of the Cetartiodactyla clade along with other species like pigs, camels, sheep, deer, etc.

Elephants seals are part of the order Carnivora and actually most closely related to dogs in this list (and based on other phylogenetic studies).

That said, I wouldn't read too much into this particular phylogenetic tree, however, since there is so much sequence similarity in Cytochrome-C for many of the animals in the list (particularly for those in the Cetartiodactyla clade), that resolving precise phylogenetic relationships is problematic.  A better approach would be to use a more comprehensive data set with multiple sequence alignments.

My approach was very basic here and just to illustrate that yes, you can build a reasonable if imprecise phylogenetic tree from the data given in the OP.

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You have got to be kidding me. Everything you said about similarities, based on diet and other commonalities are just that. However, the things that you say are the same are mocked by the wild mechanical differences between these animals.

When someone concludes that camels and whales have a common ancestor they truly are religious about their beliefs.

Okay, let’s stick a pin in the genetics for one moment. What would the common ancestor of the whale and camel look like?

Hey I found it...

Posted Image

It's the Great, Great, Great, Great, Great, Great, Great, Great, Great, Grandpa of the Camel and Whale!

It's the Whalecamel Bacteria from Mars.

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Posted 02 December 2008 - 01:03 PM

You have got to be kidding me. Everything you said about similarities, based on diet and other commonalities are just that. However, the things that you say are the same are mocked by the wild mechanical differences between these animals.


I'm not kidding you. And yes, they have some gross mechanical differences, but the underlying anatomy shows a lot of similarity. There's more in common between whales and other mammals than, say, whales and fish. Which is not what you would expect if these organisms were engineered seperately.

Same with development and same with genetics. It all converges on the same pattern of evolutionary ancestry. Why is that?

When someone concludes that camels and whales have a common ancestor they truly are religious about their beliefs.


Nope. It's all about the data.

Okay, let’s stick a pin in the genetics for one moment. What would the common ancestor of the whale and camel look like?


Probably something along these lines:

Posted Image

It's the Great, Great, Great, Great, Great, Great, Great, Great, Great, Grandpa of the Camel and Whale!

It's the Whalecamel Bacteria from Mars


I know you're just kidding around, but in all seriousness, if whales were as genetically divergence from bacteria as other species, then I would expect them to be equally distant from snakes, tomatos, birds, humans, hippos, seals, etc.

But of course, the actual evidence does not support this idea at all.

#33 Adam Nagy

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Posted 02 December 2008 - 08:26 PM

Probably something along these lines:

Posted Image

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Shpongle, I do admire your zeal but you're investing a lot of faith into a data set and a certain conclusion that doesn't have the convincing power that you want it to.

I know at this point you would advise me to get deeper into the technical end but I don't see how I would find this compelling at all. You are straining at this with great intensity. Let's just say your way was the right way to draw conclusions from the data. The moment you turn around and look at the other road blocks that God stuck in front of you, this data interpretation looks really week, friend.

You told me that you had tried to get opinions from YEC groups in the past. Have you tried the Discovery institute?

http://www.discovery.org/

I’m sure you’re familiar with them. I wonder what they have to say about your conclusions. They aren’t a YEC group but that would actually make their response interesting to analyze. Let us know what you find if you decide to pursue it.

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Posted 02 December 2008 - 09:55 PM

Just curious. I notice when you quoted me you didn't include the phrase I wrote just prior to, "But of course, the actual evidence does not support this idea at all.". Was that deliberate? Just wondering...

Shpongle, I do admire your zeal but you're investing a lot of faith into a data set and a certain conclusion that doesn't have the convincing power that you want it to.

I know at this point you would advise me to get deeper into the technical end but I don't see how I would find this compelling at all. You are straining at this with great intensity. Let's just say your way was the right way to draw conclusions from the data. The moment you turn around and look at the other road blocks that God stuck in front of you, this data interpretation looks really week, friend.


I think phylogenetics is incredibly compelling, especially when you understand the sheer number of possibilities in phylogenetic tree reconstruction. In the case of the OP, we're looking at 30 different species. That means there are about 8,000,000,000,000,000,000,000,000,000,000,000,000 possible trees (that's 8 followed by 36 zeros). Yet, the resulting tree based on phylogenetic analysis is remarkable convergent with what we'd expect if those species (or more specifically Cytochrome C genes) evolved via common ancestors.

And this is true whether you construct trees based on different genetic sequences, morphological characteristics between different species, fossil characteristics. They all show remarkable convergence despite the sheer possible number of variations. And as I said before, a designer would not be constrained in this way.

The only possible explanations are: a) Modern life forms share common ancestry with each other. b ) Modern life formed were created to look like they share common ancestry with each other.

Either way, life just looks like it evolved.

You told me that you had tried to get opinions from YEC groups in the past. Have you tried the Discovery institute?

http://www.discovery.org/

I’m sure you’re familiar with them. I wonder what they have to say about your conclusions. They aren’t a YEC group but that would actually make their response interesting to analyze. Let us know what you find if you decide to pursue it.

View Post


I haven't emailed the DI about this, but mainly because I don't expect them to disagree with any of it. While views of DI members can be sometimes difficult to figure out with respect to evolution, I know people like Behe, Meyer, and Denton have in the past indicated they accept evolutionary common descent. They just disagree with the mechanisms.

I was mainly curious as to how people who explicity deny evolutionary common descent (like AiG and ICR) would react. I was disappointed they were (and still are) completely silent on the issue.

#35 Adam Nagy

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Posted 03 December 2008 - 07:23 AM

Just curious.  I notice when you quoted me you didn't include the phrase I wrote just prior to, "But of course, the actual evidence does not support this idea at all.".  Was that deliberate?  Just wondering...


That was a goof on my part. I didn't want the quote underneath included. Maybe a mod will fix that for us.

I think phylogenetics is incredibly compelling, especially when you understand the sheer number of possibilities in phylogenetic tree reconstruction.  In the case of the OP, we're looking at 30 different species.  That means there are about 8,000,000,000,000,000,000,000,000,000,000,000,000 possible trees (that's 8 followed by 36 zeros).  Yet, the resulting tree based on phylogenetic analysis is remarkable convergent with what we'd expect if those species (or more specifically Cytochrome C genes) evolved via common ancestors.


Chance has an important role for evolution but not for Creation. I think the data that Fred Williams shared is a perfect example of how these trees are mostly fairytales (I especially like how that little slithery branch of bacteria sneaks up behind the tree):

Posted Image

And this is true whether you construct trees based on different genetic sequences, morphological characteristics between different species, fossil characteristics.  They all show remarkable convergence despite the sheer possible number of variations.  And as I said before, a designer would not be constrained in this way.


Well, a designer not constrained, is a non-starter and what the designer has done is obvious. You’re staring at His magnificence every time you do the work.

The only possible explanations are:  a) Modern life forms share common ancestry with each other.


Let me fix that: Modern life forms share a common Designer with each other.

b ) Modern life formed were created to look like they share common ancestry with each other.


When you compare genes and are compelled that camels and whales are closely related, you have some blinders on. This argument is the same as, if God wanted us to believe the earth was young why do our interpretations of our selected evidence show an old earth?

Either way, life just looks like it evolved.


I think knives, forks, and spoons look like they're evolved:

Q6I6dEhKSPA

Why would silverware manufacturers be so deceptive in the manufacturing of their goods?

If you haven’t done so, watch the whole H*vind verses Rainbow debate. It’s really good because at the end Rainbow has the humility to start asking for advice. Rainbow’s background is biology so this debate is right up your alley:

H*vind vs Rainbow

I haven't emailed the DI about this, but mainly because I don't expect them to disagree with any of it.  While views of DI members can be sometimes difficult to figure out with respect to evolution, I know people like Behe, Meyer, and Denton have in the past indicated they accept evolutionary common descent.  They just disagree with the mechanisms.


This is why their response would be interesting.

I was mainly curious as to how people who explicity deny evolutionary common descent (like AiG and ICR) would react.  I was disappointed they were (and still are) completely silent on the issue.

View Post


I think the picture above shows how YECs generally view these trees. This whole thread answers the questions of how we view the gene sequencing and the fairytales derived from it.

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Posted 03 December 2008 - 11:50 AM

That was a goof on my part. I didn't want the quote underneath included. Maybe a mod will fix that for us.


Oh okay. That's fine, I just hoped you weren't trying to make it sound like I was contradicting myself.

Chance has an important role for evolution but not for Creation. I think the data that Fred Williams shared is a perfect example of how these trees are mostly fairytales (I especially like how that little slithery branch of bacteria sneaks up behind the tree):


What data? I'm not sure where you are getting this idea from. I mean, yes, he drew the word "Fairytale" on a chart. But I'd be a lot more impressed if he could demonstrate some sort of gross violation of common descent. That would be remarkable.

Well, a designer not constrained, is a non-starter and what the designer has done is obvious. You’re staring at His magnificence every time you do the work.


Unfortunately saying "what the designer has done is obvious" doesn't give one a path for scientific inquiry into what the designer did.

We can come up with things we might expect to find if a designer created life individually (like genetic chimeras), but we don't find any of those. So no, it's not so obvious.

Let me fix that: Modern life forms share a common Designer with each other.


So? Demonstrate it. Nested hierarchies in phylogenetic analysis point to common descent not common design. Completely random phylogenies and genetic chimeras would point to common design. But the latter doesn't happen. Why is that?

When you compare genes and are compelled that camels and whales are closely related, you have some blinders on. This argument is the same as, if God wanted us to believe the earth was young why do our interpretations of our selected evidence show an old earth?


Because the Earth looks old. Heck, even Kurt Wise admits this (and he's a YEC!).

I think the picture above shows how YECs generally view these trees. This whole thread answers the questions of how we view the gene sequencing and the fairytales derived from it.

View Post


Oh I know YECs dismiss common ancestry, but the problem for you guys is you have yet to find anything that would be a demonstrable violation of common descent. Genetic chimeras would be a HUGE violation of common descent. I mean, if you found a whale with gills and the resulting genetic structure to produce them that was extremely similar to say, a shark, then that would turn evolution on its ear. But no one finds things like that in nature.

Just out of curiosity, why do you think whales have lungs and have to breath air? Why would a designer not give them gills like fish have?

#37 Adam Nagy

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Posted 03 December 2008 - 12:25 PM

What data?  I'm not sure where you are getting this idea from.  I mean, yes, he drew the word "Fairytale" on a chart.  But I'd be a lot more impressed if he could demonstrate some sort of gross violation of common descent.  That would be remarkable.

View Post


I want to ask you...What data?

Evolutionists draw the branches that are just pulled out of thin air (marked “fairytale” in above chart). Tell me how the bacteria branch is demonstrated through the scientific method or operational science. You are the one excited about applied science. Well, apply it and stop pretending that evolutionists have accomplished something that they haven’t.

I'd be a lot more impressed if he could demonstrate some sort of gross violation of common descent.


This is a classic example of shifting the burden of proof. Have you ever studied the Oort Cloud? The Oort Cloud is supposed to be a shell of comets 50,000au away from us. When Christians demand evidence for its existence, evolutionists will say; "You can’t prove it’s not there…" (Do you know what embarrassing problem the Oort cloud is supposed to cover up?) I’ll start a new thread if this is a topic of interest.

If I told you that falling trees don’t make any noise when people or testing devices aren’t present, how would you prove me wrong?

Because the Earth looks old. Heck, even Kurt Wise admits this (and he's a YEC!).


I'll even admit it looks old but we have proof that the appearence of age can happen rapidly. Look up Surtsey Iceland:

Posted Image

Again this is off topic, so I'll be glad to start another thread.

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Posted 03 December 2008 - 12:42 PM

I want to ask you...What data?

Evolutionists draw the branches that are just pulled out of thin air (marked “fairytale” in above chart). Tell me how the bacteria branch is demonstrated through the scientific method or operational science. You are the one excited about applied science. Well, apply it and stop pretending that evolutionists have accomplished something that they haven’t.


The branches are not "pulled out of thin air". Saying so is grossly misunderstanding how phylogenetic trees are constructed.

Phylogenetic trees are constructed based on algorithmic methods (and there are quite a number of them which I won't go into here) which analyze an underlying dataset to create hierarchical trees of relationships based on the dataset.

You can construct phylogenetic trees based on almost anything. For example, you could if you wanted to use it on human designed things like cars or washing machines or books. All you need is an input dataset. In the case of biology, scientists use datasets typically derived from morphologies or genetics.

If fact, I think it would be incredibly interesting to create phylogenies based on things like cars to see if you could get any sort of convergence at all, or if the results would be more or less random depending on the dataset used.

This is a classic example of shifting the burden of proof.


Of course it's shifting the burden of proof. If you guys are going to claim design, you guys have to demonstrate it. Simply saying "evolution can't have happened" does not demonstrate design.

Have you ever studied the Oort Cloud? The Oort Cloud is supposed to be a shell of comets 50,000au away from us. When Christians demand evidence for its existence, evolutionists will say that we can’t be proven it’s not there… (Do you know what embarrassing problem the Oort cloud is supposed to cover up?) I’ll start a new thread if this is a topic of interest.


I'm not extremely familiar with the Oort Cloud, but my understanding is that its existence is inferred based on the composition and trajectories of comets, as opposed to being directly observed.

But this is all off topic. We are talking about inferring biological design in organisms.

Again this is off topic, so I'll be glad to start another thread.

View Post


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.

#39 Adam Nagy

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Posted 03 December 2008 - 12:51 PM

So?  Demonstrate it.


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

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

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

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

Before you say; "Well where does God come from?"

Watch this:

Qsymb6UxWM0

#40 Adam Nagy

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Posted 03 December 2008 - 12:56 PM

Phylogenetic trees are constructed based on algorithmic methods (and there are quite a number of them which I won't go into here) which analyze an underlying dataset to create hierarchical trees of relationships based on the dataset.


Smoke screen

I'm not extremely familiar with the Oort Cloud, but my understanding is that its existence is inferred based on the composition and trajectories of comets, as opposed to being directly observed.


Smoke screen




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