The Common Ancestry Thread (page 8)

cofty

I put up some rebuttals against the articles posted and have yet to hear a satisfactory response to some of them.

The try being specific.

Here is your challenge... give us one rebuttal succintly in your own words and watch how thoroughly we respond.

Phizzy

Sound of crickets chirping, and tumble weed rolling by as yet another apologist slinks off in to the shadows, never to return.

Bye Bye Ticker

EntirelyPossible

I put up some rebuttals against the articles posted and have yet to hear a satisfactory response to some of them.

Not understanding the rebuttal doesn't mean it wasn't satisfactory.

cofty

I intend to make a few more posts on this topic to explain some of it in a bit more detail but first it might be good to briefly explain a few basics for beginners.

You may have heard it said that your DNA is like a blueprint - it isn't. In a blueprint one small part of the drawing corresponds to one specific area of the building or machine. Things are far more subtle in biology. Your DNA could better be compared with a recipe or a set of instructions on how to build you. As with a recipe a small change in one detail can make significant and surprising differences in the outcome.

The entire set of instructions is contained in the nucleus of every one of the 50 trillion cells in your body. A useful analogy is to think about your genome as being like a large book containing 23 chapters or chromosomes. In fact you have two copies of every chapter - one inherited from each parent.

The language the book is written in has only 4 letters in its alphabet - A, C, G and T which are abbreviations for four nucleotides, adenine, cytosine, guanine, and thymine. These four letters can be in any order and the entire book is approximately 3 billions letters long.

Among these 3 billion letter are instructions on making the proteins that our bodies are made from. Surprisingly only 1.5% of the genome codes for proteins. These sections of code are what we call genes and we have about 20 000 protein coding genes in total.

Of the rest of the genome 4% is regulatory DNA which identifies the start and stop locations for the genes for example.

10% is structural DNA - centromeres and telomers which compensate for a substandard copying mechanism.

21% are LINEs Long Interspersed Nuclear Elements, 13% are SINEs Short Interspersed Nuclear Elements and 3% are DNA Transposons or jumping genes. Adding these three together that makes 37% of our book that came about through copying errors. We know for an absolute certainty how they originated and why. There is no longer any mystery about these parasitic elements. More on this later.

A further 8% are ERVs Endogenous RetroViruses which have been discussed at some length above. These began as viruses, similar to HIV that got copied back into the genome in a sex cell of an ancestor.

That gives us 45% of our genome that we know for certain is parasitic. The remaining 40% is currently unknown - it is job security for another generation of geneticists. Perhaps some or all of it will prove to be functional or perhaps it will be other forms of non-coding DNA.

The point is that while creationsts like to point to functions that have been discovered for some examples of non-coding code we already know that 45% of our 3 billion letters came from and I would like to say more about LINES, SINES and TRANSPOSONS in another post shortly.

First back to how DNA makes proteins and how that provides very powerful evidence for common ancestry.

coming soon....

cofty

So first the genes, the 1.5% of the genome that codes for protein molecules. We are made of all sorts of proteins that perform a huge variety of tasks.

Proteins are macromolecules that depend for their function on their physical shape. They are made from chains of smaller molecules called amino acids.

You can think about amino acids as being like small, oddly-shaped magnets that interlock in a huge variety of ways to form the larger protein molecules. There are 20 different amino acids in living things, each with its own properties.

As we said above the alphabet of the genome contains just 4 letters, A, C, G and T. These are read off as codons which are all 3 letters long. For example the sequence, CGGATTAACGGTACTGCC would be read as the 6 codons CGG ATT AAC GGT ACT GCC.

This gives us 64 possible codons each of which code for an amino acid. With 64 codons and 20 amino acids that means there are more than one codon that will produce some amino acids.

More on the connection between DNA and amino acids in the next part, for now the almost limitless ways amino acids can fit together to make a particular protein.

Imagine we were each given a large box of lego bricks and asked to build a model house with a very specific size and shape. Each box contains the same 20 varieties of lego bricks. It is very unlikely 2 of us would build identical houses. Some may more 4x4 bricks than 8x4 without effecting the final product.

In the same way a specific protein molecule can be assembled from an almost infinite combinations of the 20 amino acids.

Earlier in the thread more than one poster mentioned the example of the protein Cytochrome C. It is essential for life and is found in all living things. For this reason it is referred to as an ubiquitous protein. It has been removed from yeast and replaced with Cytochrome C from humans, rats, pigeons and fruit flies and it worked fine.

There are a large number of ways for amino acids to fold up into the structure required for this protein. In fact there are 10 to the power 93 (10^93) different ways - that's more than all the atoms in the known universe. Since it is the physical shape of the protein that counts every one of those sequences would work equally.

So what does a comparison between the amino acids sequences of Cytochrome C of various species reveal?

If evolution is true then we are closely related to chimpanzees, more distantly related to mice, even less closely related to birds and very distantly related to yeast and we would expect to see that reflected in a comparison of Cytochrome C.

If special creation is true we are not related to anything and we would expect a ubiquitous protein like Cytochrome C to either be identical in every living thing or perhaps quite different in every species.

What we find is powerful evidence for the common ancestry of all living things in precisely the way that evolution already predicted. There are between 100 and 104 amino acids in the protein. Chimps have an identical sequence. W hen you compare human Cytochrome C to that of other mammals, you find that there is only about 10 amino acids difference between them and if you compare human Cytochrome C with the organism the least related to us, outside of bacteria, you find that there’s only about 51 amino acids difference between us. The chance of this happening without shared heredity is about 1 in 10^25.

For more info see Evolution 101 by Dr Zach Moore.

(Please don't speed-read this, google Cytochrome C and copy-paste some BS answer from Ken Ham)

Next - an even more incredible comparison of Cytochrome C and DNA sequence.

cantleave

For those that don't like to read and prefer visual presentations, here is a video that may help you understand the concepts we have been talking about. From 9.:30 it talks about genetic proofs but prior to that it brilliantly explains the phylogenetic tree another proof of common ancestry. phylogenetic tree

http://www.youtube.com/watch?v=JgyTVT3dqGY

Please watch the video in its entirety.

The reason I want to post this video on this thread is because every source is quoted.

Sources: Gilbert, S. F. (1997) Developmental Biology. Fifth edition. Sinauer Associates.
Carroll, R. L. (1988) Vertebrate Paleontology and Evolution. New York, W. H. Freeman and Co.
Futuyma, D. (1998) Evolutionary Biology. Third edition. Sunderland, Mass., Sinauer Associates.
Gould, S. J. (1990) "An earful of jaw." Natural History 3: 12-23.
Kardong, K. V. (2002) Vertebrates: Comparative Anatomy, Function, Evolution. Third ed. New York: McGraw Hill.
Rubin, G. M. et al. (2000) "Comparative Genomics of the Eukaryotes." Science 287: 2204-2218. [PubMed]
Schmid, K. J., and Tautz, D. (1997) "A screen for fast evolving genes from Drosophila." Proc. Natl. Acad. Sci. USA. 94: 9746-9750. http://www.pnas.org/cgi/content/full/94/18/9746
Sereno, P. C. (1999) "The Evolution of Dinosaurs." Science 284: 2137-2147. [PubMed]
Smit, A. F. A. (1996) "The origin of interspersed repeats in the human genome." Current Opinion in Genetics and Development 6: 743-748. [PubMed]
Thornhill, R. H., and Ussery, D. W. (2000) "A classification of possible routes of Darwinian evolution." Journal of Theoretical Biology 203: 111-116. [PubMed]
Voet, D., and Voet, J. (1995) Biochemistry. New York, John Wiley and Sons.
Williams, G. C. (1992) Natural Selection: Domains, Levels, and Challenges. New York, Oxford University Press.
Scarpulla, R. C., and Nye, S. H. (1986) "Functional expression of rat cytochrome c in Saccharomyces Cerevisiae." Proc Natl Acad Sci 83: 6352-6. [PubMed]
Shimamura, M., et al. (1997) "Molecular evidence from retroposons that whales form a clade within even-toed ungulates." Nature 388: 666. [PubMed]
Smit, A. F. A. (1996) "The origin of interspersed repeats in the human genome." Current Opinion in Genetics and Development 6: 743-748. [PubMed]
Stewart, C. B. and Disotell, T. R. (1998) "Primate evolution - in and out of Africa." Current Biology 8: R582-588. [PubMed]
Svensson, A. C., N. Setterblad, et al. (1995) "Primate DRB genes from the DR3 and DR8 haplotypes contain ERV9 LTR elements at identical positions." Immunogenetics 41: 74. [PubMed]
Sverdlov, E. D. (2000) "Retroviruses and primate evolution." BioEssays 22: 161-171. [PubMed

SunnyDays

Cofty, you said

I intend to make a few more posts on this topic to explain some of it in a bit more detail but first it might be good to briefly explain a few basics for beginners.

That would be lovely. This topic is like a breath of fresh air. I was beginning to fear this forum could very well be used as a case to prove the regression of man. Thank you, gentlemen.

:)

Sunny

The Common Ancestry Thread

cofty

Phizzy

EntirelyPossible

cofty

cofty

cantleave

SunnyDays

bohm

cantleave

cofty

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