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Cytochrome C - The Illusion Exposed


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#81 believer55

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Posted 09 October 2011 - 02:05 PM

Using Ad Homs against members of this forum (especially the owner) is frowned on, strictly. You did not address the O.P. except to ask that corrections were made to a quote that wasn't even his. If you don't have any empirical science to add except that his isn't, then I would consider you an evobabbler and not a YEC.

Fair Warning


ok you are right. let's just stay on topic. so please if you can put even just the amino acid sequence so that i can copy it (i don't need the coding sequence) then i will try to make an allignement according to clustal or uniprot and see what kind of phylogenetic tree the program pukes out.
you can use the the aas you put in the first post, with the birds, the apes, the sheep, the lama and so on

#82 jason777

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Posted 09 October 2011 - 02:19 PM

ok you are right. let's just stay on topic. so please if you can put even just the amino acid sequence so that i can copy it (i don't need the coding sequence) then i will try to make an allignement according to clustal or uniprot and see what kind of phylogenetic tree the program pukes out.
you can use the the aas you put in the first post, with the birds, the apes, the sheep, the lama and so on


Thank you for cooperating with the forum rules. Sometimes things may seem wrong, but it can be handled with a proper attitude anyway with a P.M. to any Admin. of this forum.

I doubt if anyone is going to spend all of the time and effort to redo a topic that isn't sufficiently answered to start with (i.e. Numbers predicted a recent common ancestor for an organism that theory predicts evolved over 50 million years ago, etc.).




Enjoy.

#83 ikester7579

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Posted 09 October 2011 - 02:56 PM

anyway i will leave this forum. i first thought that there are people who constructively support their theories and try to understand how things are
but all i see is people trying to discredit the whole science at all costs. because all scientist are stupid puppets for you.
you are always trying to find one wrong claim out of a million claims made by one person, in order to prove that they are all stupid.
and the funny thing is that you always miserably fail.



You take things to personally. Free thinkers also allow others to free think as well. Unless it's one sided?

#84 OmneVivumExVivo

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Posted 10 October 2011 - 11:19 AM

You may not realise it, but you're actually making a testable claim here, and let me flesh it out for you.
If Cytochrome C is designed, and, as you say, the similarities/differences in protein sequences correspond to similarities/differences in morphology and physiology, then you should be able to predict - with a reasonable degree of certainty - the Cytochrome C sequence of a particular animal given the morphological and physiological requirements of that animal.

Alright. Even though I am not as well qualified for such predictions as I would like to be, I will do my best.

So, hop to it! List any morphological or physiological attributes you like, and tell me how they each affect the sequence. There are a few examples in particular that your criteria must explain:

1. Why is the dog CYC sequence 99% identical to the seal sequence?

Both are hypercarnivores who require great stamina, the former due to its cusorial mode of hunting, the latter due to its aquatic habitat.

2. Why is the whale CYC sequence identical to the camel sequence?

I will admit that this is much more difficult question. I tentatively cite the fact that both the whale and the camel have large repositories of fat, the former in the form of blubber, and the latter in the form of its hump. I admit the explanation is somewhat weak, but I would definitely say it is on firmer ground than the recent common ancestor hypothesis.

Anyways, isn't the whale supposed to be more closely related to the hippo than it is to the other members of artiodactylamorpha?

Or, I could just tell you how it will pan out: no such set of morphological or physiological criteria exists. What you will end up with is multiple contingent criteria that describe that animal uniquely, and then say that it maps to a specific sequence in its entirety. Surely you could see why that is meaningless ...

Seems like a better idea than constructing phylogenic trees saying that birds are more closely related to us than walabies are, or that the guineapig's closest relative is the kangaroo.


We'll see how reasonable it is to assume that after you try to test your claim.

I have neither the materials nor the tools to "test" anything I say in the scientific sense. For the time being, I am completely reliant on the research of others.

#85 OmneVivumExVivo

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Posted 10 October 2011 - 01:01 PM

Well no, you need to learn how to assess these trees against the consensus tree; you do this by counting the minimum number of changes you would need to make it match the consensus tree.

The concensus tree is based on the assumption of common descent, which in its turn is based on the inherently flawed naturalistic paradigm.

And in this case, you only need to make one change, and that is to move the wallaby to the next node to the right.

Of course, when the data doesn't fit the paradigm, find out how to correct the data. That's kind of backwards, don't you think?

This will cause the bird group to fall back in with the reptiles, and it will place the wallaby as precursor to the mammals.

No self respecting evolutionist should be caught calling marsupials precursors to mammals. Slip of the tounge?

So how big is this change, and why are we justified in making it?

It's not the only problem with the tree. The tree as a whole would appear to indicate that the primates belong in the group Fereuungulata, having diverged only recently from the mangled clade that contains both the Perissodactyls and the Suinamorphs.

You'll notice that in the COX1 tree I posted above, the names of the animals do not line up nicely at the right hand side. That is because I happened to tell the software to make use the "branch lengths", rather than make a nice pretty diagram. The horizontal branch lengths correlate to the differences in the hypothetical sequences from one node to the next. So you can see from the diagram that to move the wallaby to the next node to the right is only a couple of pixels. Who knows, maybe it corresponds to changing the wallaby sequence at only one or two residues (out of 500 odd) to make it appear in the correct position. So from here, surely you can appreciate that with a stochastic process like mutation, it is statistically certain that there will be occasions when particular residues are the same when they did not come about through common descent.

What you are suggesting, while in and of itself rather small, has been similarly used with ALL the evidence upon which the theory of common descent rests. Alone, none of these "white lies" are significant. Taken together, however, they obliterate the foundation for the theory of evolution.



I'm sure you're aware that humans have a fused chromosome, meaning we once had 48 as well ...

You assume that we once had 48 chromosomes. What evidence, other than the fact that it "must have happened" because we are supposedly the progeny of apes, do you have for that fact? And how do you suggest such fusion occured without turning the creature who suffered from it into a disabled freak, unfit by any definition?

just like orangutans, chimpanzees and gorillas. I believe I asked why the humans should be EXCLUDED from the primate group, not reasons why they should be grouped together :)

So you're saying that DIFFERENT chromosome number means that humans should be INCLUDED with the apes?

#86 jason777

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Posted 14 October 2011 - 12:44 PM

I will admit that this is much more difficult question. I tentatively cite the fact that both the whale and the camel have large repositories of fat, the former in the form of blubber, and the latter in the form of its hump. I admit the explanation is somewhat weak, but I would definitely say it is on firmer ground than the recent common ancestor hypothesis.


According to the morphological evidence there is evidence to suggest you are correct, but there is other evidence that strongly suggest that whales and camels do not share a recent common ancestor. So, this may be another strike for cyto-c comparisons with reasons why they should be similar by creation and no reason why they should be similar if they have different common ancestors.

"Researchers who learn how living animals are related by studying their DNA have tended to group cetaceans ... with even-toed ungulates, or artiodactyls. By some analyses, hippos are the closest living whale relatives. But to paleontologists, who study fossils, that conclusion has long been anathema. Instead they contend that cetaceans descended from an extinct hyena-like mammals called "mesonychians" [which were NOT artiodactyls]."
"...Thewissen thinks the morphological evidence, although mixed, opens the door to some kind of relation between the whales and the ungulates. He adds that there is now "considerable doubt" that cetaceans are closely related to mesonychians. That conclusion got a thumbs up from paleontologists at the meeting. For example, John Allroy of the National Museum of National History in Washington, D.C, says pulling the mesonychians out of the picture makes a closer cetacean-artiodactyl link plausible. But O'Leary says "it's [still] difficult to connect hippos with whales in the fossil record." The molecular camp, for its part, viewed Thewissen's conclusion as just a first step toward ultimate vindication. As Norihiro Okada, a molecular biologist at Tokyo Institute of Technology, put it: "I think paleontologists may discover more [features common to early cetaceans and early hippos] in the near future."
(Normile D., "New Views of the Origins of Mammals," Science, Vol 281, 7 August 1998, pp.774-775)

Roohif,

just like orangutans, chimpanzees and gorillas. I believe I asked why the humans should be EXCLUDED from the primate group, not reasons why they should be grouped together


A Creationist put them there, so you'll have to find a better quibbling point than that. An order is a huge classification and you'll have to provide the reason why humans should be considered apes.

The differences include:

1) Curved fingers and toes for brachiation.

2) No nasal ridge.

3) Semicircular canals that balance during knuckle walking.

4) Opposable toes for grasping.

5) Longer arms than legs.

6) A baculum.

7) Shoulder blades that fully rotate for reaching over the head without pivoting the arm.(Pectoral Girdle)

8) Nuchal crests.

9) No chin.

10) Spread out iliac blades of the pelvis.

Apes share all of the above characters in common and I'm sure there are more than that.



Enjoy.

#87 sjl197

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Posted 22 October 2011 - 11:10 PM

Ok, i'd like to answer and follow on, but i'd like to first clarify please..

A Creationist put them there, so you'll have to find a better quibbling point than that. An order is a huge classification and you'll have to provide the reason why humans should be considered apes.

The differences include:

1) Curved fingers and toes for brachiation.




About "A Creationist put them there, "

Do you mean you got this info from somewhere/ someone else? Can you tell me your source please/where to find this?

and "The differences include: 1 ,2, etc"

Is this list supposed to be ape+human synapomorphies you are wishing to argue against, or human autapomorphies ?

If you dont know these terms, please look them up, plenty of great resources freely on the web. I ask you to do this otherwise its almost impossible to make clear and meaningful discussion on the merits or pitfalls of mainstream phylogenic theory and techniques without us sharing a basic understanding these basic terms and definitions. [also useful to lookup symplesiomorphy, monophyly, paraphyly, etc]

#88 OmneVivumExVivo

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Posted 24 October 2011 - 11:24 AM

Ok, i'd like to answer and follow on, but i'd like to first clarify please..




About "A Creationist put them there, "

Do you mean you got this info from somewhere/ someone else? Can you tell me your source please/where to find this?


Carl Linnaeus classified humans as primates. He also placed something he called "Homo troglodytes" in our genus. It was partially based on myth and partially based on orangutans and chimpanzees.

and "The differences include: 1 ,2, etc"

Is this list supposed to be ape+human synapomorphies you are wishing to argue against, or human autapomorphies ?


Synapomorphies- Traits that two taxa and a common ancestor share, but the ancestor's ancestor doesn't share(?)

Autapomorphies- Traits that a taxa has that are neither present in a common ancestor, nor in a close relative(?)


Well, since Jason's a YEC, I guess the second one would be closer to what he's getting at. Overall, his point is that humans and apes DON'T HAVE a common ancestor, so neither one quite goes far enough. His point is that calling humans apes would, in the strict common-ancestor sense of the term, make apes a polyphyletic (spelling?) group.

#89 jason777

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Posted 26 October 2011 - 04:54 PM

Ok, i'd like to answer and follow on, but i'd like to first clarify please..



Is this list supposed to be ape+human synapomorphies you are wishing to argue against, or human autapomorphies ?

If you dont know these terms, please look them up, plenty of great resources freely on the web. I ask you to do this otherwise its almost impossible to make clear and meaningful discussion on the merits or pitfalls of mainstream phylogenic theory and techniques without us sharing a basic understanding these basic terms and definitions. [also useful to lookup symplesiomorphy, monophyly, paraphyly, etc]



If you don't understand my list, then you may need some help. :P


Usually, when someone is refuted and has no answer they will begin to quibble over terms. That's not happening is it? :rolleyes:




Enjoy.

#90 jason777

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Posted 26 October 2011 - 04:56 PM

Carl Linnaeus classified humans as primates. He also placed something he called "Homo troglodytes" in our genus. It was partially based on myth and partially based on orangutans and chimpanzees.



Excellent history. I thought that I would be the only person on this forum that knew that. B)




Enjoy.

#91 xbox

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Posted 04 November 2011 - 11:45 AM

According to the morphological evidence there is evidence to suggest you are correct, but there is other evidence that strongly suggest that whales and camels do not share a recent common ancestor. So, this may be another strike for cyto-c comparisons with reasons why they should be similar by creation and no reason why they should be similar if they have different common ancestors.

"Researchers who learn how living animals are related by studying their DNA have tended to group cetaceans ... with even-toed ungulates, or artiodactyls. By some analyses, hippos are the closest living whale relatives. But to paleontologists, who study fossils, that conclusion has long been anathema. Instead they contend that cetaceans descended from an extinct hyena-like mammals called "mesonychians" [which were NOT artiodactyls]."


Mesonychids are the sister group of artiodactyls.


"...Thewissen thinks the morphological evidence, although mixed, opens the door to some kind of relation between the whales and the ungulates. He adds that there is now "considerable doubt" that cetaceans are closely related to mesonychians. That conclusion got a thumbs up from paleontologists at the meeting. For example, John Allroy of the National Museum of National History in Washington, D.C, says pulling the mesonychians out of the picture makes a closer cetacean-artiodactyl link plausible. But O'Leary says "it's [still] difficult to connect hippos with whales in the fossil record." The molecular camp, for its part, viewed Thewissen's conclusion as just a first step toward ultimate vindication. As Norihiro Okada, a molecular biologist at Tokyo Institute of Technology, put it: "I think paleontologists may discover more [features common to early cetaceans and early hippos] in the near future."
(Normile D., "New Views of the Origins of Mammals," Science, Vol 281, 7 August 1998, pp.774-775)



Whales originated from aquaticartiodactyls in the Eocene epoch of India
J. G. M. Thewissen, Lisa Noelle Cooper1,2, Mark T. Clementz3, Sunil Bajpai4 & B. N. Tiwari5

"Although the first ten million years of whale evolution are documented by a remarkable series of fossil skeletons, the link to the ancestor of cetaceans has been missing. It was known that whales are related to even-toed ungulates (artiodactyls), but until now no artiodactyls were morphologically close to early whales. Here we show that the Eocene south Asian raoellidartiodactyls are the sister group to whales. The raoellid Indohyus is similar to whales, and unlike other artiodactyls, in the structure of its ears and premolars, in the density of its limb bones and in the stable-oxygen-isotope composition of its teeth.We also show that a major dietary change occurred during the transition from artiodactyls to whales and that raoellids wereaquatic waders. This indicates that aquatic life in this lineage occurred before the origin of the order Cetacea."

This is from 2007. What a difference 9 years makes.

The differences include:

1) Curved fingers and toes for brachiation

2) No nasal ridge.

3) Semicircular canals that balance during knuckle walking.

4) Opposable toes for grasping.

5) Longer arms than legs.

6) A baculum.

7) Shoulder blades that fully rotate for reaching over the head without pivoting the arm.(Pectoral Girdle)

8) Nuchal crests.

9) No chin.

10) Spread out iliac blades of the pelvis.



1) Toes are not used in brachiation. There is some evidence that the curvature results from physiological stresses.

2) There are human populations with flattened nasal ridges.

3) This appears to be a common YEC-website classic, but it is premised on faulty information/misinterpretation. The work of Fred Spoor is most commonly cited among creationists when this issue comes up, and Spoor himself wrote:

"It is concluded that any link between the characteristic dimensions of the human canals and locomotion will be more complex than a simple association with the broad categories of quadrupedal vs. bipedal behavior." (Spoor and Zonneveld 1998)"

4) They are toes nonetheless.

5) Granted.

6) Granted.

7) Here primate shoulder blades (scapulae):Posted Image

Perhaps you can tell which is which? Our pectoral girdle allows one to reach over one's head without "pivoting" the arm as well. Not sure where you got that one from.


8) The nuchal crest is a common structure in non-bipeds. It reflects the greater stresses put on the occipital bone by the neck extensors. It is a physiological response, not a genetic one. Juvenile and infant chimps, for example, do not have nuchal crests.

9) 'Chin' is a rather ambiguous term.

10) I think you mean that the ilia lie in a different plane, yes they do.

Apes share all of the above characters in common and I'm sure there are more than that.

I'm sure of it. I am also sure that an even longer list can be made laying out the traits that humans and the other apes share


I'm sure you're aware that humans have a fused chromosome, meaning we once had 48 as well ...

You assume that we once had 48 chromosomes. What evidence, other than the fact that it "must have happened" because we are supposedly the progeny of apes, do you have for that fact?

What evidence?

Here is some very good evidence:

Origin of human chromosome 2: an ancestral telomere-telomere fusion
J W IJdo, A Baldini, D C Ward, S T Reeders, and R A Wells
Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06510.

Abstract

We have identified two allelic genomic cosmids from human chromosome 2, c8.1 and c29B, each containing two inverted arrays of the vertebrate telomeric repeat in a head-to-head arrangement, 5'(TTAGGG)n-(CCCTAA)m3'. Sequences flanking this telomeric repeat are characteristic of present-day human pretelomeres. BAL-31 nuclease experiments with yeast artificial chromosome clones of human telomeres and fluorescence in situ hybridization reveal that sequences flanking these inverted repeats hybridize both to band 2q13 and to different, but overlapping, subsets of human chromosome ends. We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.


Here is some more:

Chromosome Res. 1994 Sep;2(5):405-10.
The origin of human chromosome 2 analyzed by comparative chromosome mapping with a DNA microlibrary.
Wienberg J, Jauch A, Lüdecke HJ, Senger G, Horsthemke B, Claussen U, Cremer T, Arnold N, Lengauer C.

Institut für Anthropologie und Humangenetik, Universität München, Munich, Germany.

Abstract
Fluorescence in situ hybridization (FISH) of microlibraries established from distinct chromosome subregions can test the evolutionary conservation of chromosome bands as well as chromosomal rearrangements that occurred during primate evolution and will help to clarify phylogenetic relationships. We used a DNA library established by microdissection and microcloning from the entire long arm of human chromosome 2 for fluorescence in situ hybridization and comparative mapping of the chromosomes of human, great apes (Pan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus) and Old World monkeys (Macaca fuscata and Cercopithecus aethiops). Inversions were found in the pericentric region of the primate chromosome 2p homologs in great apes, and the hybridization pattern demonstrates the known phylogenetically derived telomere fusion in the line that leads to human chromosome 2. The hybridization of the 2q microlibrary to chromosomes of Old World monkeys gave a different pattern from that in the gorilla and the orang-utan, but a pattern similar to that of chimpanzees. This suggests convergence of chromosomal rearrangements in different phylogenetic lines.


FEBS Lett. 2000 Jun 23;475(3):167-9.
Newly identified repeat sequences, derived from human chromosome 21qter, are also localized in the subtelomeric region of particular chromosomes and 2q13, and are conserved in the chimpanzee genome.
Park HS, Nogami M, Okumura K, Hattori M, Sakaki Y, Fujiyama A.

RIKEN Genomic Sciences Center, c/o Kitasato University, Sagamihara, Kanagawa 228-8555, Japan.

Abstract

Subtelomeric regions have been a target of structural and functional studies of human chromosomes. Markers having a defined structure are especially useful to such studies. Here, we report 93 bp tandem repeat sequences found in the subtelomeric region of human chromosome 21q. They were also detected in the telomeric region of several other chromosomes. Interestingly, the repeat was also found in the 2q13 region which is known to be a position of chromosomal fusion, a major difference between the human and chimpanzee karyotypes. To the best of our knowledge, this repetitive sequence is a new member of human subtelomeric interspersed repeats.


Chromosome Res. 2000;8(8):727-35.
Comparative FISH mapping of the ancestral fusion point of human chromosome 2.
Kasai F, Takahashi E, Koyama K, Terao K, Suto Y, Tokunaga K, Nakamura Y, Hirai M.

Department of Biological Sciences, Graduate School of Science, University of Tokyo, Japan.

Abstract
It is known that human chromosome 2 originated from the fusion of two ancestral primate chromosomes. This has been confirmed by chromosome banding and fluorescence in-situ hybridization (FISH) with human chromosome-2-specific DNA libraries. In this study, the order of 38 cosmid clones derived from the human chromosome region 2q12-q14 was exactly determined by high-resolution FISH in human chromosome 2 and its homologous chromosomes in chimpanzees (Pan trogrodydes, 2n=48) and cynomolgus monkeys (Macacafascicularis, 2n = 42). This region includes the telomere-to-telomere fusion point of two ancestral ape-type chromosomes. As a result of comparative mapping, human chromosome region 2q12-q14 was found to correspond to the short arms of chimpanzee chromosomes 12 and 13 and cynomolgus monkey chromosomes 9 and 15. It is noted that no difference was detected in the relative order of the cosmid clones between human and chimpanzee chromosomes. This suggests that two ancestral ape-type chromosomes fused tandemly at telomeres to form human chromosome 2, and the genomic organization of this region is thought to be considerably conserved. In the cynomolgus monkey, however, the order of clones in each homologue was inverted. In addition to cosmid mapping, two chromosome-2-specific yeast artificial chromosome (YAC) clones containing the fusion point were identified by FISH.



There is lots more, but I wouldn't want to be accused of "elephant hurling."

And how do you suggest such fusion occured without turning the creature who suffered from it into a disabled freak, unfit by any definition?

And how do you suggest such fusion would necessitate the production of a 'disabled freak'?


just like orangutans, chimpanzees and gorillas. I believe I asked why the humans should be EXCLUDED from the primate group, not reasons why they should be grouped together

So you're saying that DIFFERENT chromosome number means that humans should be INCLUDED with the apes?

Different karyotyopes are not as important as many seem to think. There are mammal species that maintain differing karyotypes in their populations. There are mammal species that can form fertile hybrids with related species of different karyotypes. The gene content is probably more important than mere chromosome number.




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