Posted on 09/26/2005 3:27:53 AM PDT by Crackingham
When scientists announced last month they had determined the exact order of all 3 billion bits of genetic code that go into making a chimpanzee, it was no surprise that the sequence was more than 96 percent identical to the human genome. Charles Darwin had deduced more than a century ago that chimps were among humans' closest cousins. But decoding chimpanzees' DNA allowed scientists to do more than just refine their estimates of how similar humans and chimps are. It let them put the very theory of evolution to some tough new tests.
If Darwin was right, for example, then scientists should be able to perform a neat trick. Using a mathematical formula that emerges from evolutionary theory, they should be able to predict the number of harmful mutations in chimpanzee DNA by knowing the number of mutations in a different species' DNA and the two animals' population sizes.
"That's a very specific prediction," said Eric Lander, a geneticist at the Broad Institute of MIT and Harvard, and a leader in the chimp project.
Sure enough, when Lander and his colleagues tallied the harmful mutations in the chimp genome, the number fit perfectly into the range that evolutionary theory had predicted.
SNIP
Evolution's repeated power to predict the unexpected goes a long way toward explaining why so many scientists are practically apoplectic over the recent decision by a Pennsylvania school board to treat evolution as an unproven hypothesis, on par with "alternative" explanations such as Intelligent Design (ID), the proposition that life as we know it could not have arisen without the helping hand of some mysterious intelligent force.
SNIP
"What makes evolution a scientific explanation is that it makes testable predictions," Lander said. "You only believe theories when they make non-obvious predictions that are confirmed by scientific evidence."
(Excerpt) Read more at washingtonpost.com ...
I've gone back and read some of your previous posts. You write disparaging things about others as if that contributed something positive to the discussion.
The people you disparage, whether right or wrong, write clearly and use analogies that help explain things to people lacking degrees in molecular biology.
Let me try.
Darwin thought that inheritance was a matter of fractions, continuously variable characters (traits) that would mix freely in the offspring of the parents. I.e., an orange cat might mate with a black cat to product a brown cat. Darwin was also something of a Lamarckian, in that he believed that acquired characters would be inherited by offspring. So a giraffe that stretched its neck a bit further than its parents would have offspring with longer necks.
This turns out to be wrong. Mendel discovered that characters are controlled by "genes" that are like little light switches that are either on or off. Unless a character is controlled by many genes (as sometimes happens), you either have the character or you don't. You have blue eyes or brown eyes but not some shade in between (well, hazel maybe). If you cross a black cat and a tabby orange cat, you don't get a brown cat, you might get a calico.
This was a big problem for the theory of evolution. You don't have a smooth blending of characters that Darwin supposed would happen. You don't have acquired characteristics being inherited. Instead, scientists realized, you have random mutations that appear, and if they are beneficial (usually they're neutral, neither good or bad), they spread throughout the population over hundreds of generations. The theory of this was worked out in the early to mid 20th century (the details are very mathematical; read something on "population genetics" and you'll see).
All of this happened before the fateful year of 1953 (or was it 1954?) when the structure of DNA was discovered. Now scientists were in a position to understand the exact molecular details of genetics, of inheritance, of mutations and of evolution itself. This was developed through the 1960s. The result is known as the "neo-Darwinian synthesis". That is, the synthesis of molecular biology (genetics) with evolutionary theory.
A very brief summary: most processes in an animal (or plant) body and cells are controlled by proteins. Proteins are chains of amino acids (peptides) glued together. There are 20 amino acids to choose from. DNA is a chemical code for proteins. A "gene" is a stretch of DNA that codes for a single protein. (We now know that it isn't always that simple, but never mind.) Now DNA resembles a spiral staircase, where each step ("base pair") is a mated pair of "nucleotides" whose names are abbreviated A C G or T. So we think of DNA as a chain of these four letters that occur in seemly random orders. Now it turns out that every three letters codes for one amino acid. A triple is called a "codon". There are 64 codons possible. Given that there are only 20 amino acids, it turns out some codons code for the same amino acid, but there are codons that code for no amino acid at all. These are "stop" codes on the DNA: they stop the synthesis of the protein. The protein, as I said above, is a chain of amino acids. These are assembled by an elaborate set of molecular machines which read the DNA, but they stop reading when the get to the stop code. The DNA controls other things, in particular when proteins are to be made ("gene regulation").
One spectacular discovery was made sometime in the 1980s (my knowledge here is a bit fuzzy): homeobox genes. These are the sets of genes that control how animal body plans develop. Apparently, we inherited these from the earliest segmented worms 600 million years ago or longer. All animals have these. A small change in these can result in a dramatic change in an animal's body plan. So small mutations in the right place can hasten the development of a new species in a population. I would guess this is what's going on when you see a kitten with an unusual number of toes. (A friend of mine had a cat with extra toes: he named the animal Bigfoot.) Anyone who sees a cat with extra toes shouldn't have much trouble understanding how mutations can cause harmless changes to an animal that might even prove beneficial.
I would be grateful if anyone who actually knows the molecular biology or genetics would correct or clarify what I've written (I'm only a mathematician).
paging "furball4paws".....
Thank you for demonstrating that the intelligent design hypothesis is untestable, and therefore cannot be science.
You are in good company. The one big problem is that nature has a way of eating the evidence.
"Let me try."
And I'll give your request a try too. Let me say that I am a microbiologist, so my knowledge of molecular biology of animals is somewhat less deep.
"Darwin thought that inheritance was a matter of fractions, continuously variable characters (traits) that would mix freely in the offspring of the parents. I.e., an orange cat might mate with a black cat to product a brown cat. Darwin was also something of a Lamarckian, in that he believed that acquired characters would be inherited by offspring. So a giraffe that stretched its neck a bit further than its parents would have offspring with longer necks."
Other than the reference to Lamarck, this appears to be OK.
"This turns out to be wrong. Mendel discovered that characters are controlled by "genes" [Mendel discovered the laws of genetics, but he had absolutely no idea what a gene was] that are like little light switches that are either on or off. Unless a character is controlled by many genes (as sometimes happens), you either have the character or you don't. You have blue eyes or brown eyes but not some shade in between (well, hazel maybe). If you cross a black cat and a tabby orange cat, you don't get a brown cat, you might get a calico."
OK, eye color is controlled by multiple genes and people with one blue eye and one brown one (like a particular breed of cats) are not rare. I have blue eyes, but one is about 1/3 brown. There is a "smear" on some traits. Some genes show dominance/recessivity some show partial dominance (say white/pink/red flowers).
"This was a big problem for the theory of evolution. You don't have a smooth blending of characters that Darwin supposed would happen. You don't have acquired characteristics being inherited. Instead, scientists realized, you have random mutations that appear, and if they are beneficial (usually they're neutral, neither good or bad), they spread throughout the population over hundreds of generations. The theory of this was worked out in the early to mid 20th century (the details are very mathematical; read something on "population genetics" and you'll see)."
This looks good, but I don't think genes were a problem for evolution, they explained so much. However, they did require adjustment to the theory.
"All of this happened before the fateful year of 1953 (or was it 1954?) when the structure of DNA was discovered. Now scientists were in a position to understand the exact molecular details of genetics, of inheritance, of mutations and of evolution itself. This was developed through the 1960s. The result is known as the "neo-Darwinian synthesis". That is, the synthesis of molecular biology (genetics) with evolutionary theory."
OK
"A very brief summary: most processes in an animal (or plant) body and cells are controlled by proteins. Proteins are chains of amino acids (peptides)[scratch this word - it doesn't fit] glued together. There are 20 amino acids to choose from. DNA is a chemical code for proteins. A "gene" is a stretch of DNA [doesn't have to be contiguous] that codes for a single protein. (We now know that it isn't always that simple, but never mind.) Now DNA resembles a spiral staircase, where each step ("base pair") is a mated pair of "nucleotides" whose names are abbreviated A C G or T. So we think of DNA as a chain of these four letters that occur in seemly random orders. Now it turns out that every three letters codes for one amino acid. A triple is called a "codon". There are 64 codons possible. Given that there are only 20 amino acids, it turns out some codons code for the same amino acid, but there are codons [3] that code for no amino acid at all. These are "stop" codes on the DNA: they stop the synthesis of the protein. The protein, as I said above, is a chain of amino acids. These are assembled by an elaborate set of molecular machines which read the DNA, but they stop reading when the get to the stop code. The DNA controls other things, in particular when proteins are to be made ("gene regulation"). [although most gene regulation happens at the level of DNA, it is mediated by small(er) molecules]"
"One spectacular discovery was made sometime in the 1980s (my knowledge here is a bit fuzzy): homeobox genes. These are the sets of genes that control how animal body plans develop. Apparently, we inherited these from the earliest segmented worms 600 million years ago or longer. All animals have these. A small change in these can result in a dramatic change in an animal's body plan. So small mutations in the right place can hasten the development of a new species in a population. I would guess this is what's going on when you see a kitten with an unusual number of toes. (A friend of mine had a cat with extra toes: he named the animal Bigfoot.) [this is a trait called polydactyly and is controlled by a single recessive gene in humans. I think this is also the case in most mammals.] Anyone who sees a cat with extra toes shouldn't have much trouble understanding how mutations can cause harmless changes to an animal that might even prove beneficial. "
"I would be grateful if anyone who actually knows the molecular biology or genetics would correct or clarify what I've written (I'm only a mathematician)."
You did pretty good, mega. Related to Bacillus megatherium?
However, the creationoid will not be satisfied with your answer.
I know Eichler personally, but my question was about a statement of yours. I'm sorry if you chose to misunderstand it, but it still stands.
YEC INTREP
"And another funny thing is earlier on this thread someone said the coding regions show 99%."
I think I posted that. From the original paper, the coding regions were 99% identical (this is from memory, maybe it was 98.6%?). The 96% figure was for the whole genome including the non-coding regions.
What's the problem? Most of our genes are identical to the chimps, the non-coding regions, which we are just beginning to understand, is where the major differences are.
What do you want? "This is the Chimp/Human transformation gene." Turn it on and you get js1138; turn it off and you get Bozo?
Claim CB144. Human and chimp genomes differ by more than one percent.
For years, evolutionists have hailed the chimpanzee as "our closest living relative" and have pointed out that the DNA is 98 to 99 percent identical between the two. Scientists now say the difference is 4 percent, double what they have been claiming for years.
Source:
DeWitt, David A. 2005. Chimp genome sequence very different from man.
http://www.answersingenesis.org/docs2005/0905chimp.asp
Response:
1. The difference between chimpanzees and humans due to single-nucleotide substitutions averages 1.23 percent, of which 1.06 percent or less is due to fixed divergence, and the rest being a result of polymorphism within chimp populations and within human populations. Insertion and deletion (indel) events account for another approximately 3 percent difference between chimp and human sequences, but each indel typically involves multiple nucleotides. The number of genetic changes from indels is a fraction of the number of single-nucleotide substitutions (roughly 5 million compared with roughly 35 million). So describing humans and chimpanzees as 98 to 99 percent identical is entirely appropriate (Chimpanzee Sequencing 2005).
2. The difference measurement depends on what you are measuring. If you measure the number of proteins for which the entire protein is identical in the two species, humans and chimpanzees are 29 percent identical (Chimpanzee Sequencing 2005). If you measure nonsynonymous base pair differences within protein coding regions, humans and chimps are 99.45 percent identical (Chen et al. 2001). Whatever measure is used, however, as long as the same measurement is used consistently, will show that humans are more closely related to chimpanzees (including the bonobo, sister species to the common chimpanzee) than to any other species.
References:
1. Chen, F.-C., E. J. Vallender, H. Wang, C.-S. Tzeng, and W.-H. Li. 2001. Genomic divergence between human and chimpanzee estimated from large-scale alignments of genomic sequences. _Journal of Heredity_ 92(6): 481-489.
2. Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. _Nature_ 437: 69-87.
Thank you very much for finding this. I hope it clears up things for our little tempest in a teapot.
I am not being argumentitive. I'm trying to find out what point tallhappy is trying to make. Is 99% good for evolution or bad? Is 96% good or bad? Is the problem in some technical detail of the argument?
I read through some of his earlier posts, and he was complaining that we were oversimplifyiing molecular biology. Well golly, why would anyone oversimplify molecular biology on a forum where maybe three people are qualified to lecture on it?
My point has been, if there is a problem, it is possible to explain it to bright people.
Great post. That sums it up in a nutshell.
I'm very flattered -- thank you very much for the interesting clarifications!
My namesake is a giant ground sloth. No relation to Bacillus.
I suppose you're right about creationoids. The problem is that evolution is easy to describe on a superficial level in such a way that intelligent lay people think they have a good enough understanding to argue against it. Phillip Johnson (Darwin on Trial) comes to mind. But it's all so unnecessary -- there is nothing in a mature understanding of Christianity that requires disbelief in evolution. (I am a conservative Episcopalian; we do not believe in "verbal plenary inspiration".) At this point I recommend the book Finding Darwin's God by the well-known biologist Kenneth Miller, who is also Roman Catholic.
Source? (one of the things I have learned reading these threads - always get a source for a 'fact'.)
It's as if your exam paper in school were 96% the same as the guy who was sitting in front of you, including his wrong answers, and including his crazy answers. There's wouldn't be much doubt where you got your answers from.
Ok, maybe a little doubt for me. The guy in front copied? The guy behind copied? Or, maybe they both got the answers from another source...
Maybe not exactly all specifically molecular theory of evolution (but background and relevant).
This: The DNA controls other things, in particular when proteins are to be made ("gene regulation").
Would be better stated protein-DNA interactions gene regulation -- but then your last part about homeobox genes talked about just that.
I'd add the experiments of Hershey and Chase and Oswald Avery that showed nucleic acid to be the genetic material.
A book, The Monk in the Garden, does a nice job in describing this early history in presenting biography of Morgan, Bateson and others who are called "re-discoverers" of Mendel.
As an aside, one of the three re-discoverers became quite a strong Nazi eugenicist.
furball, your points about eye color were apt. There are examples of "blending" (note the quotes). Mendel was lucky to have picked the traits he did -- or more likely just knowledgeable about the plants (his children).
I did not misunderstand. Are you saying you do not know or understand the argument put forth in the t.o. tract that was linked to?
The appeal to pure randomness in element event formation upon which the t.o. tract is based is turning out not to be true. The Chimp geneome analysis is just one more case where it is seen. Eichler's hotspots of de novo duplication (as he calls it), observation of elements not common in every extant ancestor -- particulary missing in humans on multiple occasions -- dates the argument, strong as it ostensibly sounds.
It seems you are just playing games which is beneath you.
The findings in that paper are exciting, and as Eichler points out, unexpected. They are also exciting and intriguing in terms of their implications for understanding certain genetic diseases.
Come on, man. Put aside your socio-political based biases and defense mechanisms and talk about science for the pure joy of science and discovery.
Accuracy and coherence.
I was simply correcting mistakes. The 98 - 99 % figure applies not just to the coding region where of course there would be a higher level of homology due to the need to conserve function, but the whole genome shows this high number as well.
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