The last common ancestor (LCA) to all currently living organisms, from eubacteria to archae to eucaryotes, already had the universal genetic code. The current organisms that lack the universal genetic code (mitochondria, certain ciliates, mycoplasma bacteria) are secondary changes in that code. But there was a time and a 'life' before the LCA. It is during that time that the genetic code and much else in the basic biochemistry of life differentiated. There may even have been a time with more than one alternative genetic code, of which only our current one remains via some combination of selection and chance. Pax-6/eyeless regulates six3/sine oculis in both insects and invertebrates. Pax-6 is a gene that plays a key role in the development of eyes in animals as diverse as Cephalopods, Vertebrates, and Arthropods. The amino acid sequence identity between the Pax-6 of humans and the equivalent possesed by the fly is 94 percent. And there are other proteins that have a higher identity (histones, for instance), and many others with much lower values. So? Do you think there is one magic number that is supposed to be fixed for all proteins for each pair of organisms? It seems strange that this gene would have remained unchanged, since the last shared ancestor between us and the fly would have existed around one-half billion years ago. It isn't unchanged. 6% of the amino acids are different; a much larger percentage of the nucleotide sequence is different. Functional constraint is usually the reason given for this retardation of evolution, but Pax-6 would seem to be no more important, to an animals survivability then hemoglobin, whose amino acid sequence can vary 50 percent between Vertebrates. Did someone forgot to wind the molecular clock for Pax-6? What makes it so special? Didn't Mayr in the late 1970's find enough anatomical differences between eyes in the animal kingdom to surmise tha they had evolved separately dozens of times? Why would the exact same gene, that seems to sit relatively high on the hierarchies of some very different developmental sequences, have been selected again and again and have experienced no variation since the early Cambrian? Does anyone have an EC (evolutionarily correct) answer for this? Sure. Look at what the gene does. Hemoglobin is a big, complex molecule which can tolerate a fair amount of variation -- that variation modulates the function of the molecule to a lesser or greater degree. Look at the oxygen binding characteristics of hemoglobin from different vertebrates and you'll see differences of a magnitude that parallel the differences in sequence. Now look at Pax-6, a smaller molecule with a much more constrained function it binds specific DNA sites. Unlike hemoglobin, a large protein that binds a small molecule, pax-6 is a small protein that binds a large molecule (a DNA sequence). Not surprisingly, a larger percentage of the smaller protein is crucial to its function. Change Pax-6, and you don't get a graded change, or a minor deviation in timing or degree of response--you get a discretely different specificity in a gene that is near the top of a long cascade of regulatory events. Small changes in Pax-6 get amplified into huge changes in the development of the organism. Rather than being an end of pathway, pax-6 is the begining of an amplified pathway. As for why Pax-6 gets recruited into eye evolution repeatedly -- there is a simple idea you have to get into your head. Pax-6 is not an "eye" gene. It does not specify the form or characteristics of the eye. Pax-6 is a regulatory gene that controls the level of expression of a suite of other genes. Many of these other genes seem to be involved in activating neuronal fates. These regulatory properties of Pax-6 are essential for normal development of the animal in ways other than formation of the eye, accounting for its conservation. In addition, as has been determined experimentally, accidental misexpression of this gene in the periphery takes you a long way towards the formation of an eye. Taking advantage of the fortuitous properties of an existing gene sounds a lot more like the expected behavior of an EC system than the behavior of a designed one, don't you think? Not that a designer couldn't recycle old designs, but I would think that if you are looking for evidence for design you would be trying to show us systems that look more custom-built and planned and optimized for a specific purpose. And there are other proteins that have a higher identity (histones, for instance), and many others with much lower values. So? Do you think there is one magic number that is supposed to be fixed for all proteins for each pair of organisms? It seems strange that this gene would have remained unchanged, since the last shared ancestor between us and the fly would have existed around one-half billion years ago. It isn't unchanged. 6% of the amino acids are different; a much larger percentage of the nucleotide sequence is different. It is rather strange that Myers' always tends to answer Nielson's posts, and by coincidence be well informed about the issue at hand, like say the Kauffman book. Could it be Rex Nielson is a Myers' stooge created solely for the purpose of making Myers look good? And there are other proteins that have a higher identity (histones, for instance), and many others with much lower values. So? Do you think there is one magic number that is supposed to be fixed for all proteins for each pair of organisms? It seems strange that this gene would have remained unchanged, since the last shared ancestor between us and the fly would have existed around one-half billion years ago. It isn't unchanged. 6% of the amino acids are different; a much larger percentage of the nucleotide sequence is different. Functional constraint is usually the reason given for this retardation of evolution, but Pax-6 would seem to be no more important, to an animals survivability then hemoglobin, whose amino acid sequence can vary 50 percent between Vertebrates. Did someone forgot to wind the molecular clock for Pax-6? What makes it so special? Didn't Mayr in the late 1970's find enough anatomical differences between eyes in the animal kingdom to surmise that they had evolved separately dozens of times? Why would the exact same gene, that seems to sit relatively high on the hierarchies of some very different developmental sequences, have been selected again and again and have experienced no variation since the early Cambrian? Does anyone have an EC (evolutionarily correct) answer for this? Why would there be homologies at the organizational level between compound and single lens eyes when they are completely different in anatomy and development. Because it's essentially the same factor, binding the same DNA sequences and interacting with the same components of transcriptional machinery. Same here means orthologous, all right? The difference in manifestation of this regulation is in the genes recruited to this pathway through their regulatory DNA sequences and secondary regulators. That is the reason why a) mouse Pax-6 (Sey) works in drosophila and b) the eye structures induced by mouse regulatory protein in drosophila are that of a fly and not of the mouse. And it is not the only example - nitrogen metabolism in many eukaryotes is regulated by the GATA-type Zn finger transcriptional factors, so bloody what? No one looses sleep over that. Other mouse developmental regulators (like HoxB6) also work in Drosophila in factor- but not species-specific fashion. BTW, exactly as expected from conserved proteins of any kind. The functioning in heterologous environment (like a different species) depends not on the value assigned to the protein by someone called Rex Nielson but on the exact molecular interactions. That's why yeast Gal4 works as transcriptional activator in mouse (and drosophila cells), whereas mouse Rpb1 (the largest subunit of the enzyme DNA-dependent RNA polymerase II) can complement the absence of its homolog in yeast. "Homology in some singular molecular components of eyes seems interesting but unsurprising; homology in complex genetic and developmental pathways for building eyes (as has been discovered) was both unexpected under usual views of evolution and downright revisionary in forcing a rethinking of many previous certainties." (p.16) Gould, S.J. "Common Pathways of Illumination" _Natural History_ Dec. 1994: 10-20. Gould is by no means a saint or a prophet in evolutionism although he enjoys a great deal of publicity. What is more relevant he is not an expert on protein evolution. What may look surprising for him might appear less revolutionary for a person with more exposure to the field. Why did you choose him over the discoverer of the Pax-6 genes, Walter Gehring? Not because Gehring in his review on the subject (Genes to Cells, 1996, 1:11-15) wrote: ...Since the various types of eyes foundin the animal kingdom are morphologically very different and also develop differently, it has been proposed that photoreceptors have originated independently in at least 40, but possibly up to 65 oe more different phyletic lines (Salvini-Plawen and Mayr, 1961)...There is at least one key gene that is shared by the photoreceptors of all the phyla -...rhodopsin...The finding that ey (pax-6) is the master control gene for eye morphogenesis in Drosophila and that a homologous gene is found in mammals raises the possibility that it is a universal master control gene for eye morphogenesis and evolution of the eye. Than he describes the testing of this hypothesis by induction of ectopic eyes in drosophila by mouse and squid genes - both quite functional in drosophila and concludes with: ...Since Pax-6 homologs have been now found in vertebrates, tunicates, echinoderms, arthropods, nematodes, nemertines and flatworms, the hypothesis that Pax-6 is a universal master control gene has gained considerable support. This suggests that the prototypic eye originated only once in evolution and various eye types arose from the same origin, which is much more compatible with Darwin's theory. After all, Darwin was right again. - here he refers to a specific proposal by Darwin of a hypothetic simple protoeye. I know that Pax-6 isn't an "eye" gene, it plays a role in the development of other organs like the brain and olfactory bulbs and that it is even expressed in some animals that don't have eyes (Though the speculation that Pax-6 is intimately associated with the development of sensory systems is interesting). But if, as according to Mayr, eyes evolved dozens of separate times, Pax-6 each time would have had to have been recruited from a previous role. How could it have remained so relatively unchanged during those alternative roles and through all its subsequent recruitments. Cytochrome C, for example, has been performing its same crucial task all along and it shows more variation between phyla then Pax-6. A protein "being recruited to perform another function". *closely related* function , not *any* function. All enzymes and binding proteins (curent and ancestral) perform secondary functions and can utilize and bind to secondary sites. These activities (or novel combinations of activities obtained by combining existing moieties from two proteins) are the initial 'hook' which selection can then work upon and mold to a new function. It is not "pure" chance that the proteins that perform similar functions usually have an apparently similar structure. The reason is that the secondary function of the original provides a hook which allows selection to "see" and work on its duplicate. That is why proteins performing similar functions show common ancestry rather than novel solutions. Some 'functionally' novel portions of proteins (in the range of, say, 10-20 amino acids) may occassionally be due purely to chance changes in non-crucial regions in a protein occupied in an unrelated function. But that is not typical. Nearly all enzymatic activities are due to modification and specialization of proteins that perform similar functions. Random mutation (typically a duplication or transposition) produces the initial form and random mutation (typically point mutation) produces the specializing modifications. But which mutations get retained and which mutations get lost is not random at all. That (the mutational changes that mold the initial protein into its current form) is shaped and specified by the environment the organism resides within. Changes that make the organism more successful in the particular local environment are retained. Those that make the organism worse in the local environment tend to get lost. Those that are neutral in the local environment drift in frequency. So in a sense, a protein is 'designed' by its environment. 6% of the amino acids are different; a much larger percentage of the nucleotide sequence is different. m-built and planned and optimized for a specific purpose. ====== Much "junk DNA" in mammalian genomes is comprised of medium-sized repeats, such as Alu sequences in primates. Some "young" Alus are even transcribed (by Pol III). Others are not transcribed and show evidence of having drifted away from the young, transcribed sequences (in particular, the creation of CpG islands and hypermethylation). So, yes, there is information there. Yes, it is junk, because it isn't used. No, it isn't a problem for selection because it is posited that it was once used but no longer is. In the case of pseudogenes, they were probably once useful to the organism. In the case of mid-range repeats, they are likely the remains transposable or retrotransposable/viral sequences and were probably never "useful" to the organism at all. These sequences exist in a pattern consistent with common descent. If they do nothing useful (esp. useful in terms of their specific sequences, which negates "spacing" arguments), then they are not a specific prediction of creation all at once by an omnipotent God. Yep. See if you can find a copy of John Romer's "Testament". Its an excellent read. According to Romer, who spent some 25 years puttering around digs in the middle east and restoring the tombs of the pharaohs, not only is there no evidence in Egyptian writings of such a large enslavement, but the Egyptians simply didn't *do* that kind of thing. Conquered people were generally assimilated, not enslaved. Egyptians were meticulous record-keepers. How do you suppose the enslavement of an entire culture (600,000 people, according to some accounts) escaped their attention? "Testament" - John Romer - Henry Holt and Company, Inc. ISBN 0-8050-0939-6 (hardback) ISBN 0-8050-2962-4 (An Owl Book - softback) Welcome to a troll. Where the hell is the reference for this bullshit? And you guys (yes, you! Howard, I could expect it from anyone, but from you to buy so easily into this troll?!!