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.
How thoughtful of you.
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.
ItÃ¢â‚¬â„¢s not a hidden bias, itÃ¢â‚¬â„¢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.
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.
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 Ã¢â‚¬ËœEÃ¢â‚¬â„¢s Numbers inferred correctly (the Ã¢â‚¬Å“recent ancestorsÃ¢â‚¬Â), 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 Ã¢â‚¬ËœNÃ¢â‚¬â„¢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.
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
Afraid the picture is too big when I post it, so here is a link to the dog genome chart I mention
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]
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 Ã¢â‚¬Å“neither side can use Cyto-C as evidence to support their version of Ã¢â‚¬Å“common decentÃ¢â‚¬Â.Ã¢â‚¬Â 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.
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.
I look forward to your response,'
p.s. I do appreciate that you allow both sides to state their argument on this site.