Eminent Domain Stuff
New London Update (2/24/06)
Bad NLDC!
Coverage of the Rally at New London's City Hall (w/ pics)
Monday, October 25, 2004
Evolution vs. Creationism: Round 8
In my last post on this topic (Round 7), I promised to take a look at a few of the papers cited by Elsberry and friends that were not mentioned in the rebuttal written by people at the Discovery Institute. Since I've got a number of pressing things to do that pay the bills, I have had to limit my outside reading and have only gotten through one of the papers I linked to in Round 7. I'll do what I can do summarize and put the paper into context, but anyone with access to encouraged to take a look for yourself.
The paper I'll be discussing here is by Laszlo Patthy in Genetica (2003) 118: 217-231 and is entitled Modular assembly of genes and the evolution of new functions. This is a review that discusses the organization of genetic information and the resulting protein configuration across most of life. As with most scientific papers on this topic, evolution is taken for granted and ID is neither mentioned nor eluded to. However, I think that this paper provides some information that the people at the Discovery Institute would rather not discuss...and so have chosen not to.
Patthy begins by establishing the fact that the sequencing of the human genome has surprised scientists with its relatively low number of total genes. We had originally thought there must be at least 100,000 genes to make a human work, but the new estimates are closer to 30,000 (depending on whom you talk to). To put this number in context, bacteria have approximately 3,000 genes while the tiny worm, C. elegans, gets by with 19,000. Patthy goes on to point out that while the number of genes (i.e., "coding DNA" because it codes for protein) varies less than one might predict, the overall size of the genome increases at a much greater rate as one moves up the evolutionary ladder. While humans have only 10 times the number of genes compared to bacteria, our total genome (i.e., the total amount of DNA we have) is nearly 1000 times greater in size.
The significance of the different ratios of coding to noncoding DNA is significant in that there are data which suggest the noncoding DNA allows for large rearrangements of genes (i.e., "exon shuffling"). These rearrangements are obvious when sequences are compared among related proteins with different functions. So, if one takes that fact and fits it into the framework of Evolution, it is reasonable to suggest that noncoding DNA was selected for by virtue of its ability to provide the substrate of natural selection, namely: variation. The reason I mention this here is that ID proponents (specifically Meyers and his friends) would have us believe that Evolution only had a very little variation to work with...and can therefore not account for Life as we know it. I would suggest that there are actually many mechanisms by which variation can been generated aside from 'simple' mutation during DNA replication. Exon shuffling is one example, and there are more that I will not get into here.
Interestingly, I think there is a very important implication here that few (to my knowledge) have addressed. We know that bacteria can adapt much better (which is to say, faster) than we humans can. Why? The answer is that there are more of them and they reproduce faster. A bacterial population can be reduced a thousand-fold and regenerate to its initial numbers overnight (literally). A human population, on the other hand, obviously will take longer. So, it does make a certain amount of sense that if life did indeed Evolve (as opposed to ID-ed) then higher, more complex, organisms would need a way to provide variation at a great rate/generation than do bacteria. Put more simply, a bacterial population has so many members that there are bound to be a few that are well suited for whatever environmental change just occurred. Higher organisms, on the other hand, have far fewer members in a population and therefore must be able to generate variation some other way in order to survive. While this may seem like the ramblings of a pro-Evolution nutjob, I think this argument is supported by a paper by Earl and Deem entitled Evolvability is a selectable trait.
After discussing this issue of the gene-number to genome-size ratio, Platthy gets into a really interesting discussion of protein modules. Proteins are composed of strings of amino acids that fold into three-dimensional shapes. The exact shape of a protein is determined (for the most part) by its amino acid sequence (for some background see this). 'We' (structural biologists) have the ability to determine the exact three-dimensional shape of proteins. Since we can often determine the function of the same protein, we can compare the structure and function of protein A with that of protein B. In this way we begin to understand the essence of protein function.
As 'we' have solved the structure and determined the functions of a lot proteins it has become clear that many proteins with very different functions share common three-dimensional shapes (i.e., 'folds'). The folds that have been found to be common over and over again can be called 'modules' because they exist as little building blocks in multiple proteins. So, just as proteins are composed of a string of building blocks called amino acids, we can also think of proteins as composed of building blocks called 'modules' (which are, in turn, made up of specific sequences of amino acids). The interesting thing, is that many of these modules are found across nearly all multicellular life. To be specific, these modules appear with increasing frequency as one moves up from the relatively simple worm (C. elegans) to humans.
So, what I take away from Patthy's discussion of protein modules is that (again, within the framework of Evolution) as Life evolved from simple multicellularity to complex multicellularity this change was mediated by an increase in preexisting protein modules. This, to some extent, helps provide a simplifying explanation as to how increasingly complex cell-cell interactions may have come to be.
The question still remains as to how one goes from the single celled bacteria to 'higher' multicellular organisms. I think that this issue has been a bit misrepresented...mostly due to a lack of scientific knowledge.
For the majority of the time microorganisms have been studied, it has been assumed that bacteria live solitary lives. This assumption has been put to the test in recent years with the discovery of biofilms. Biofilms are made of sticky molecules that are released by bacteria and function to hold them onto a surface (Cystic Fibrosis is a good but tragic example of biofilms' usefulness). Additionally, bacteria have been shown to communicate with each other and work in collaboration with one another (sometimes even across species lines). So, the idea that some truly 'new thing' had to develop in order for cell-cell interactions to take place is somewhat misplaced. However, since this post is getting a little long we'll have to save that discussion for another time.
I hope I have managed to provide a bit of information that makes the process of Evolution seem more plausible that it did before. In summary, proponents of ID have suggested that Evolution could not possibly have produced Life as we know it because there is no way the necessary variation could have been generated for Nature to select. I would argue that the IDers have misrepresented the actual range of variation-generating-processes that are known to exist. Additionally, protein diversity is not dependent only on slow, nucleotide by nucleotide, mutation of DNA. Rather, independently folding amino acid modules can be "shuffled" to produce proteins with novel overall structure and function by modular rearrangement.
I hope anyone interested in this topic will check back both here at MuD&PHuD and at A Physicist's Perspective in the near future for lots more fun.
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The paper I'll be discussing here is by Laszlo Patthy in Genetica (2003) 118: 217-231 and is entitled Modular assembly of genes and the evolution of new functions. This is a review that discusses the organization of genetic information and the resulting protein configuration across most of life. As with most scientific papers on this topic, evolution is taken for granted and ID is neither mentioned nor eluded to. However, I think that this paper provides some information that the people at the Discovery Institute would rather not discuss...and so have chosen not to.
Patthy begins by establishing the fact that the sequencing of the human genome has surprised scientists with its relatively low number of total genes. We had originally thought there must be at least 100,000 genes to make a human work, but the new estimates are closer to 30,000 (depending on whom you talk to). To put this number in context, bacteria have approximately 3,000 genes while the tiny worm, C. elegans, gets by with 19,000. Patthy goes on to point out that while the number of genes (i.e., "coding DNA" because it codes for protein) varies less than one might predict, the overall size of the genome increases at a much greater rate as one moves up the evolutionary ladder. While humans have only 10 times the number of genes compared to bacteria, our total genome (i.e., the total amount of DNA we have) is nearly 1000 times greater in size.
The significance of the different ratios of coding to noncoding DNA is significant in that there are data which suggest the noncoding DNA allows for large rearrangements of genes (i.e., "exon shuffling"). These rearrangements are obvious when sequences are compared among related proteins with different functions. So, if one takes that fact and fits it into the framework of Evolution, it is reasonable to suggest that noncoding DNA was selected for by virtue of its ability to provide the substrate of natural selection, namely: variation. The reason I mention this here is that ID proponents (specifically Meyers and his friends) would have us believe that Evolution only had a very little variation to work with...and can therefore not account for Life as we know it. I would suggest that there are actually many mechanisms by which variation can been generated aside from 'simple' mutation during DNA replication. Exon shuffling is one example, and there are more that I will not get into here.
Interestingly, I think there is a very important implication here that few (to my knowledge) have addressed. We know that bacteria can adapt much better (which is to say, faster) than we humans can. Why? The answer is that there are more of them and they reproduce faster. A bacterial population can be reduced a thousand-fold and regenerate to its initial numbers overnight (literally). A human population, on the other hand, obviously will take longer. So, it does make a certain amount of sense that if life did indeed Evolve (as opposed to ID-ed) then higher, more complex, organisms would need a way to provide variation at a great rate/generation than do bacteria. Put more simply, a bacterial population has so many members that there are bound to be a few that are well suited for whatever environmental change just occurred. Higher organisms, on the other hand, have far fewer members in a population and therefore must be able to generate variation some other way in order to survive. While this may seem like the ramblings of a pro-Evolution nutjob, I think this argument is supported by a paper by Earl and Deem entitled Evolvability is a selectable trait.
After discussing this issue of the gene-number to genome-size ratio, Platthy gets into a really interesting discussion of protein modules. Proteins are composed of strings of amino acids that fold into three-dimensional shapes. The exact shape of a protein is determined (for the most part) by its amino acid sequence (for some background see this). 'We' (structural biologists) have the ability to determine the exact three-dimensional shape of proteins. Since we can often determine the function of the same protein, we can compare the structure and function of protein A with that of protein B. In this way we begin to understand the essence of protein function.
As 'we' have solved the structure and determined the functions of a lot proteins it has become clear that many proteins with very different functions share common three-dimensional shapes (i.e., 'folds'). The folds that have been found to be common over and over again can be called 'modules' because they exist as little building blocks in multiple proteins. So, just as proteins are composed of a string of building blocks called amino acids, we can also think of proteins as composed of building blocks called 'modules' (which are, in turn, made up of specific sequences of amino acids). The interesting thing, is that many of these modules are found across nearly all multicellular life. To be specific, these modules appear with increasing frequency as one moves up from the relatively simple worm (C. elegans) to humans.
So, what I take away from Patthy's discussion of protein modules is that (again, within the framework of Evolution) as Life evolved from simple multicellularity to complex multicellularity this change was mediated by an increase in preexisting protein modules. This, to some extent, helps provide a simplifying explanation as to how increasingly complex cell-cell interactions may have come to be.
The question still remains as to how one goes from the single celled bacteria to 'higher' multicellular organisms. I think that this issue has been a bit misrepresented...mostly due to a lack of scientific knowledge.
For the majority of the time microorganisms have been studied, it has been assumed that bacteria live solitary lives. This assumption has been put to the test in recent years with the discovery of biofilms. Biofilms are made of sticky molecules that are released by bacteria and function to hold them onto a surface (Cystic Fibrosis is a good but tragic example of biofilms' usefulness). Additionally, bacteria have been shown to communicate with each other and work in collaboration with one another (sometimes even across species lines). So, the idea that some truly 'new thing' had to develop in order for cell-cell interactions to take place is somewhat misplaced. However, since this post is getting a little long we'll have to save that discussion for another time.
I hope I have managed to provide a bit of information that makes the process of Evolution seem more plausible that it did before. In summary, proponents of ID have suggested that Evolution could not possibly have produced Life as we know it because there is no way the necessary variation could have been generated for Nature to select. I would argue that the IDers have misrepresented the actual range of variation-generating-processes that are known to exist. Additionally, protein diversity is not dependent only on slow, nucleotide by nucleotide, mutation of DNA. Rather, independently folding amino acid modules can be "shuffled" to produce proteins with novel overall structure and function by modular rearrangement.
I hope anyone interested in this topic will check back both here at MuD&PHuD and at A Physicist's Perspective in the near future for lots more fun.
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