Evolution and common genetics

Discussion in 'Baptist Theology & Bible Study' started by Pete Richert, Oct 27, 2005.

  1. Pete Richert

    Pete Richert
    Expand Collapse
    New Member

    Joined:
    Jul 6, 2001
    Messages:
    1,283
    Likes Received:
    0
    I would like to question the following quote to probe about its meaning. I ask that we keep this thread pure from any argueing as there are plenty of other threads ongoing where one can participate in that.

    UTEOTW , you wrote,

    I'm not sure why any such simularities in and of themselves are evidence of evolution. Indeed, one could just as well say that any simularities in genetics is proof that the "designer" was using the same building blocks.

    Lets start with Monkeys and Humans. I believe it has been said that 95% of of our genetics is indentical. But this in and of itself doesn't say we evolved from a common ancestor. It could just be as likely that God thought "Hmm, I plan on making humans and monkeys look pretty similar so I will use much of the same DNA!" To be honest, I would expect our DNA to be very similar, we look a lot alike! Our hearts and lungs and kidneys probably work in the exact same fashion so I would expect the DNA coding their constrution and DNA coding the proteins that facilitate their use would be indentical.

    But now lets go to your question. Why would we EXPECT a crocondille and a bird to be more similar (in genetic structure) then other animals. Well, we probably wouldn't expect it one way or another. I we may find this a very interesting surprise. But once again, it just would no more prove evolution then prove that God wished these two animals to share many characteristics (most of which we obviously couldn't recognize on the surface).

    Anyway, just a thought.
     
  2. just-want-peace

    just-want-peace
    Expand Collapse
    Well-Known Member

    Joined:
    Feb 3, 2002
    Messages:
    5,503
    Likes Received:
    40
    Simple; the explanation is not designed to reflect any facts save those that agree with evolution.

    Any other explanation is purely subjective and biased.

    Bet you didn't expect such a short answer did you? [​IMG]
     
  3. Pete Richert

    Pete Richert
    Expand Collapse
    New Member

    Joined:
    Jul 6, 2001
    Messages:
    1,283
    Likes Received:
    0
    I would just as well have anyone with similar off topic comments to refrain from posting from here on out.

    Thank you.
     
  4. Mercury

    Mercury
    Expand Collapse
    New Member

    Joined:
    Dec 22, 2003
    Messages:
    642
    Likes Received:
    0
    Well, let me make a prediction based on my acceptance of evolution. I think that because humans and apes are related, and because the similarities are due to heredity and not a common designer who made them as-is, that even in organs like lungs, hearts and kidneys that have the same function across these species there will be slight differences. This is because if evolution including common descent is true, mutations should cause slight differences throughout the species, not just differences in places where the other apes are functionally quite different. From what I'm aware of, there are ways that mutations can change DNA without affecting which proteins are produced, and so these mutations would not result in any functional change in the organism. These kinds of mutations should be prevalent, causing the DNA of all species of apes including humans to have variations, and the amount of those variations should roughly correspond with how long the species have supposedly diverged.

    Now, you've predicted that if the common designer hypothesis is true, then parts that work in the exact same fashion should have identical construction. I think that's a good prediction, and it does follow from that hypothesis.

    I would be interested in hearing from others whether these predictions have been tested. I may have just put my foot in my mouth or shown my scientific ignorance, but if I'm wrong I'll certainly be willing to admit it.
     
  5. Petrel

    Petrel
    Expand Collapse
    New Member

    Joined:
    Jul 13, 2005
    Messages:
    1,408
    Likes Received:
    0
    Would you expect that humans and other primates would share a gene for vitamin C synthesis? Probably so. Would you expect that gene to be broken in both? Maybe. Would you expect that the changes that break that gene would be an identical viral insert in the same exact place? Not unless you're really credulous--then I have a bridge to sell you! :D

    The similarity in "junk DNA" is more compelling than the similarity in coding DNA from a young-earth point of view, I think. After all, why would God make people and apes with broken genes? If he made them with functioning genes, how did they manage to get broken in the same way? I told another poster that if he could find a way to target one particular sequence out of the billions of bases in our DNA and modify that so specifically, he should get a Nobel prize. There is no known mechanism for inducing this change. Researchers would love to find a way to do this because it would provide a means for genetic engineering and for fighting cancer.

    First, no, Mercury, there is no foot in your mouth. ;)

    Interestingly, their function is the same, but their gene sequence is not identical. To digress a bit, this very fact proves problematic for those young earth creationists who say that mutation is always detrimental and always results in loss of specificity. Having a single exact sequence is not required to retain enzyme activity. Indeed, it's been shown in a variety of species that a protein that is an orthologue (a protein from a different species with the same origin but a slightly different sequence) of one of the creature's own proteins can correct an absence of that protein. Obviously, then, having a slightly different protein sequence is not necessarily going to cause you to keel over and die.

    So since having a single exact sequence is not critical, we would expect that on occasion a mutation would arise that does not result in a loss of function for that protein. After a long period of time, we would be able to look at the gene sequence and see that it is significantly different than it was at the beginning. With enough time we might even be able to recognize certain parts of the gene sequence that remain the same because those amino acids are critical for the protein. We would be able to calculate the rate of mutation, and from that we would be able to calculate the time in the past when two populations of that creature were separated and their gene sequences began to diverge.

    Interestingly, young earth creationists generally do accept genetic similarity as evidence of relatedness--but only as long as they feel comfortable with the amount of change that has happened. For instance, most young earth creationists think that all of the species alive came from some original kinds that God made, which then evolved and speciated into the species we see now. Thus all maples came from an original maple, all cats came from an original cat, and all doglike canids came from an original doglike canid. These kinds can supposedly be detected by the member species' ability to hybridize within the kind.

    Unfortunately apparently all frogs did not come from one original frog, even though most can hybridize, because frogs produce a staggering variety of antimicrobial peptides with different sequences and lengths, which can be specific down to the species level. Since young earth creationists deny the ability of creatures to produce new genes coding for new proteins or peptides, that means that all of these frogs must have come from their own kind--in spite of the evidence that mechanisms such as duplication of existing genes and mutation can result in the production of new proteins or peptides. And again, there must have been multiple original kinds of foxes, since the foxes vary greatly in their number of chromosomes and most are incapable of interbreeding. Once again, this ignores the evidence that chromosome changes such as merging or splitting can result in a decrease or increase in the number of chromosomes, so likely the ancestral fox was capable of interbreeding with other canids. But I digress!

    At any rate, I'm sure most educated young earth creationists would agree that dogs are more closely related to wolves than to the other members of the group based upon gene evidence and morphology. But if we can conclude from genetic evidence that dogs are related to wolves, what logical reason can we have for then ignoring other evidence of genetic relatedness because it disagrees with prior assumptions?

    I'm going to go ahead and post again some about the evolution of the Volvicide algae and a single cell to multicellular transition:

    Chlamydomonas reinharditii are phytoflagellates, tiny unicellular biflagellated photosynthesizing protists. They reproduce asexually (sexual reproduction is present as well, but it is chiefly a method to produce dormant spores to survive difficult times) by multiple fission, in which the cell increases its size 2^n times and then divides n times into 2^n number of daughter cells, n being 2, 8, 4, 16. The daughter cells formed are enclosed inside the mother cell's cell wall, which then bursts to release the daughter cells, which swim off on their own. However, it has been reported on several occasions that the Chlamydomonas daughter cells do not swim off separately because their cell walls are linked together at points and their cytoplasm is continuous. This produces a little "colony" of Chlamydomonas cells similar to Gonium.

    Gonium is a colonial biflagellated phytoflagellate occuring in groups of usually 8 or 16 cells. The cells are joined at points and the cytoplasm is continuous among the cells. However, sometimes when cells of the species Gonium dispersum undergo multiple fission and release the daughter cells, they are unjoined and swim away separately remarkably like Chlamydomonas. Indeed, genetic studies of Chlamydomonas and Gonium show similarities in both coding and noncoding regions (see papers below and this link), with Chlamydomonas reinharditii being most closely related to Gonium, most likely a direct descendant of the original ancestor.

    Gonium is a simple colonial organism, and there is no division of labor among the cells. However, there are a variety of more complicated organisms in the same order, Volvocida, that have been shown by genetic testing to be related. The most complicated of these is Volvox, a colonial organism in which some thousands of somatic cells in a globe surround germ cells on the inside of the colony. Asexual reproduction in Volvox involves multiple fission of one of the germ cells to produce a tiny daughter colony. The somatic cells undergo programmed cell death at only four days old, releasing the daughter colonies.

    While Gonium is a flattened disc, all of the other Volvocida members are globular. This is important because the initial colony embryos have the flagella pointing in towards the center of the globe, making them useless for locomotion. In order to function, they must invert. This inversion is carried out by the action of InvA, a novel kinesin, which acts on the microtubules at the cytoplasmic bridges to bend the sheet of cells. This protein is required in Gonium as well, where it switches the concavity of the colony so that the flagella are on the convex side. InvA is coded for by the gene invA. Chlamydomonas, Gonium, Pandorina, Eudorina, and Pleodorina all have a gene that is a orthologue of invA, and the gene in Chlamydomonas, IAR1, has been inserted into an inversion-incapable invA Volvox mutant, enabling inversion. This is yet another instance of novel use of a pre-existing protein (also demonstrated in another case by the ability of the Chlamydomonas orthologue of gls to return asymmetric cell division to a Volvox gls mutant).

    The next major hurdle after cytoplasmic continuity and embryonic inversion is germ-stroma division of labor in Volvox. This is caused by two gene expression regulators, regA, which represses chloroplast protein synthesis in somatic cells (required for germ cells to pass on chloroplasts, stalling the usual transition from biflagellated stage to nonflagellated reproductive stage), and lag, which keeps germ cells from developing somatic features like flagella and eyespots. It currently is unclear whether these genes are new inventions in Volvox or if they are present in ancestors but not used for this purpose.

    The close genetic and morphological similarity among the Volvocida members show that they have a common ancestry and are closely related. The genetic and morphological similarity between Chlamydomonas reinharditii and Gonium show that these two have a relatively recent common ancestor. This demonstrates an evolution from a single-celled "lifestyle" to a multicellular colonial one.


    Coleman A. W.; Mai, J. C. "Ribosomal DNA ITS-1 andITS-2 sequence comparisons as a tool for predicting genetic relatedness." J Mol. Evol. 1997, 45:168–177.

    Kirk, David L. "Volvox as a Model System for Studying the Ontogeny and Phylogeny of Multicellularity and Cellular Division." J. Plant Growth Regul. 2000, 19:265-274.

    Kirk, David L. "Seeking the Ultimate and Proximal Causes of Volvox Multicellularity and Cellular Division." Integ. Comp. Biol. 2003, 43:247-253.

    Cole, Douglas; Reedy, Mark. "Algal Morphogenesis: How Volvox Turns Itself Inside-Out." Current Biol. 2003, 13:R770-R772.

    Kirk, David L. "A twelve-step program for evolving multicellularity and a divsiton of labor." BioEssays 2005, 27:299-310.

    Liss, Michael; Kirk, David; Beyser, K.; Fabry, S. "Intron sequences provide a tool for high-resolution phylogenetic analysis of Volvocine algae." Curr. Genet. 1997, 31:214-227.

    Nozaki, H.; Itoh, R.; Sano, H.; Uchida, M.; Watanabe, M.; Kuroiwa, T. "Phylogentic relationships within the colonial Volvocales (Chlorophyta) inferred from rbcL gene sequence data." J. Phycol. 1995, 31:970-979.
     
  6. Pete Richert

    Pete Richert
    Expand Collapse
    New Member

    Joined:
    Jul 6, 2001
    Messages:
    1,283
    Likes Received:
    0
    That is a very good observation. I would be interested in the answer.
     
  7. Mercury

    Mercury
    Expand Collapse
    New Member

    Joined:
    Dec 22, 2003
    Messages:
    642
    Likes Received:
    0
    Wow, that was quick Petrel. I take it you just added the reference to me after writing that, right? Either that, or you're the speediest poster I know! :D

    Also, lest anyone think my prediction was not in good faith, I should be clear that I was already aware of the vitamin C similarities, and that added to my confidence in making that prediction. However, I'd still love to know if there are particular studies comparing genes that serve the same purpose in the apes (not non-functional genes), yet have minor variations including ones not affecting function, and variations that fit the pattern predicted by common descent (more variations in those species supposedly further removed).
     
  8. Petrel

    Petrel
    Expand Collapse
    New Member

    Joined:
    Jul 13, 2005
    Messages:
    1,408
    Likes Received:
    0
    No, Mercury, I'm prescient. :D

    Actually when I write a really long post I typically check to make sure no one replied during the composition.

    Well, I have a book with a chapter on divergent molecular evolution of New World primates lying on my desk right now, but unfortunately that does not help very much. I'll go look for free articles. However, I can't help but think that (*cue dramatic drumroll*) this sounds like a job for--UTEOTW!! But in his absence I will go check.

    In my searching I did run across [this extremely intriguing article]--another case proving that mutations are not always detrimental and how a foreign gene introduced into an organism or a duplicate gene can evolve to serve an entirely new purpose!

    The archae are not vulnerable to penicillin-like drugs, so they do not produce beta-lactamases. The researchers sampled multiple archae genes and transfected them into E. coli. One of the genes coincidentally conferred some resistance to ampicillin, which was then improved by continued selection pressure from ampicillin treatment.
     
  9. Petrel

    Petrel
    Expand Collapse
    New Member

    Joined:
    Jul 13, 2005
    Messages:
    1,408
    Likes Received:
    0
    Here are some other articles. Unfortunately none of them are as exhaustive as I'd like (they target one particular gene instead of a variety of genes), but that's why books are written!

    Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates

    Reduction of two functional gamma-globin genes to one: An evolutionary trend in New World monkeys (infraorder Platyrrhini)

    Origins and antiquity of X-linked triallelic color vision systems in New World monkeys

    Genomic evolution of MHC class I region in primates

    (Oops--I didn't limit to apes, as you can see.)
     
  10. UTEOTW

    UTEOTW
    Expand Collapse
    New Member

    Joined:
    May 8, 2002
    Messages:
    4,087
    Likes Received:
    0
    "I'm not sure why any such simularities in and of themselves are evidence of evolution. Indeed, one could just as well say that any simularities in genetics is proof that the "designer" was using the same building blocks."

    Good question Pete and one which is obvious to ask.

    The answer lies in the pattern of these similarities. You have read the logic that I gave for birds and crocodiles so you should have some idea of where I am coming from. In that case, there is a set of observations ranging from similarity in structures through fossils recording change in the animals in question that leads to the conclusion that birds evolved from dinosaurs and that dinosaurs share a common ancesotor with crocodiles that is more recent that the shared ancestor of crocodiles and any living reptile. So we expect the genes to reflect this and they do.

    You are right in that this does not prove anything by itself. But it is moving towards something.

    Now think about what you would expect if a common designer were reusing genetic parts to make new animals. I, personally, would expect that the similarities would be closest between animals that resmebled one another the most. A reasonable assumption. So if you were to look at crocodiles, surely they would be most genetically similar to something like a lizard or a snake. You would not expect it to be a bird. It is odd. But if common descent is true, it is just what you would expect.

    I am going to start my next thought in a new post.
     
  11. UTEOTW

    UTEOTW
    Expand Collapse
    New Member

    Joined:
    May 8, 2002
    Messages:
    4,087
    Likes Received:
    0
    When you look at the genome, there are a few things to notice.

    First off, most of the genome is full of useless junk. Long repeats of the same sequence over and over. Copies of genes which have been duplicated but then a copy mutated until it did nothing useful. Inserted bits of viral DNA from infections in past ancestors. And all sorts of other oddities.

    Now it must be said that a small amount of what was consider junk has found to have a regulatory role, but that does not quantitatively affect our discussion.

    Now there are many things that can be learned from the junk. One is shared, specific mutations. A common example is Vitamin C. Most animals use a very specfic set of four genes to make four enzymes to make vitatim C. But in all primates, one of the genes has been broken. Not only that, but in all primates it is the same gene and they are broken by the same mutation. By itself, this does not prove anything. But you can begin to see the logic involved. Why would an intelligent common designer use the same broken building block over and over. If he did, then why would it be specifically reserved for one heirarchy of animals?

    The viral inserts are another example I like. There are some types of virus, called a retrovirus, that inserts some of its DNA into its host during infection. Now occasionally a virus will infect a sperm or an egg cell and insert a DNA seqence randomly into the genome of that cell. Even more rare is that the cell is actually used for reproduction, passing on the insertion. Even more rare will be when that insertion then gets passed around until every member of the population has it.

    Despite that, a few percent of your genome is old retroviral inserts. Now when you look at humans, you see that they share the same essential set of inserts. Now, as it turns out, you can find the almost exact same set of inserts in the other apes. But not the same exact set. As it turns out, when you look at which inserts are shared between the various apes, you can map out the relationships between the species. And these relationships among the apes as determined from retroviral inserts matches the relationships as determined by other means.

    Now, because of the huge size of the genome and the randomness of the insertion, to find two species wit hthe exact same insert at teh exact same location is considered to be incontrovertible proof of common ancestry. Humans and the other apes share many such insertions.
     
  12. UTEOTW

    UTEOTW
    Expand Collapse
    New Member

    Joined:
    May 8, 2002
    Messages:
    4,087
    Likes Received:
    0
    Now there is another thing to be known about the genome. There are four letters in the alphabet of the genome. These four letters are used to spell three letter words called codons.

    Now the codons usually call for a specific amino acid or do other things like single then end of a gene.

    As it turns out, the positions are not equal. Very often, a change to the third letter in a codon will either result in the exact same amino acid or one that is very similar. In this manner, silent mutations can accumulate in the genes.

    But this gives us a means to compare between the species. When you compare the patterns of these silent mutations, you once again get the same kinds of patterns of relationship as you do with other kinds of evidence.

    If an intelligent designer was re-using spare parts, it would not make sense to over and over and over make tiny changes to the parts that did not affect the performance, but which would show a pattern of relationship.
     
  13. Pete Richert

    Pete Richert
    Expand Collapse
    New Member

    Joined:
    Jul 6, 2001
    Messages:
    1,283
    Likes Received:
    0
    You guys have given me an aweful lot to think and honesty, have gone way beyond my understanding. I'm going to need to study molecular biology and genetics before I can fairly continue on with this conversation.

    Thanks for the help.
     
  14. Petrel

    Petrel
    Expand Collapse
    New Member

    Joined:
    Jul 13, 2005
    Messages:
    1,408
    Likes Received:
    0
    I just ran across something that is relevant to the above discussion while reading through an article about antimicrobial peptides.

    Rachel Dommett, Matthias Zilbauer, John T. George, Mona Bajaj-Elliott, "Innate immune defence in the human gastrointestinal tract." Molecular Immunology, 2005, 42, 903-912.

    These two paragraph demonstrate many of the things that we have been talking about. Firstly, the enzyme lysozyme has only a 73% sequence homology between humans and chickens. This demonstrates once again that the innaccuracy of the premise that all mutations are detrimental because they are a change away from a pinnacle ideal gene sequence. Bacteriophage (viral) lysozyme is another example of enzymes that retain three-dimensional structure shared with a distantly related homologue while having an almost completely different sequence. Secondly, while the enzyme is present in a wide variety of organisms, it does not have the exact same role in all. This is another demonstration of the ability of organisms to adapt existing enzymes to new functions. Finally, the diversification of lysozyme is illustrative of the ability of organisms to add information to their genomes when genes are copied and the extraneous copies then subjected to mutation and natural selection.

    All of this tied up in two little paragraphs!
     
  15. robycop3

    robycop3
    Expand Collapse
    Active Member

    Joined:
    Jul 31, 2000
    Messages:
    7,573
    Likes Received:
    10
    Here are some observations made by my HS biology teacher long before DNA & many of today's well-known archaeological discoveries were made:

    (Inexact quotes from the late Dr. Lyle Plymale, Huntington, WV)
    "For a bird to have evolved from a lizard is to ask a lot of the lizard. First, note that we're asking it to change its bony jaws & teeth into a beak made of materials very dissimilar to bone. However, the archaeopteryx, the earliest-known bird, had teeth...but some mammals have beals or bills!

    Now, the changes become more complex.A lizard's limbs bend same as ours, while most birds' limbs bend the opposite way. This calls for a 'missing link' with limbs that bent both ways, in which case I don't see how it could move except to flop around.

    Next, we're asking the lizard to change its scales into feathers. That's asking the missing link to have had fales or sceathers, which couldn't do the job of either scales or feathers. Different species of lizards have scales specialized for their 'lifestyles', while birds likewise have specialized feathers.

    And finally, here's the most difficult of all changes...from cold-blood physiology to that of warm blood. It's simply impossible for there to have been a 'halfway' physiology, as the chemistry differences between cold blood & warm blood are so radically far apart. There are many specifics within each physiology that simply MUST be there to sustain life.

    Contrary to popular belief, cold-blooded is NOT more primitive than warm-blooded! Cold blood is ideal for environments where the climate changes very little, and we all know that in temperate climates many reptiles & amphibians hibernate in winter, while many species of fish continue to function over a wide temperature range.

    The greatest advantage of cold blood over warm is that the cold-blooded creature requires only 1/10 the amount of food that a warm-blooded creature of the same weight requires.

    Therefore I entirely disbelieve the theory that entirely-different creatures evolved from each other."
     
  16. Helen

    Helen
    Expand Collapse
    <img src =/Helen2.gif>

    Joined:
    Aug 29, 2001
    Messages:
    11,703
    Likes Received:
    1
    Thanks, robycop3 -- while they are trying to overwhelm folk with the little tiny molecular stuff, it's nice to have a little common sense material that people can see for themselves and realize evolution in terms of the changes of kind to kind is not just impossible but ridiculous. God bless.
     
  17. UTEOTW

    UTEOTW
    Expand Collapse
    New Member

    Joined:
    May 8, 2002
    Messages:
    4,087
    Likes Received:
    0
    "Here are some observations made by my HS biology teacher long before DNA & many of today's well-known archaeological discoveries were made:"

    I am glad you noted that the material is old.

    "For a bird to have evolved from a lizard is to ask a lot of the lizard. First, note that we're asking it to change its bony jaws & teeth into a beak made of materials very dissimilar to bone. However, the archaeopteryx, the earliest-known bird, had teeth...but some mammals have beals or bills!"

    Except that archy did not have a beak, it had jaws with teeth. I guess you could argue instead that archy was justa feathered, flying dinosaur which happened to have some birdlike qualities.

    It should also be noted that the "bill" of a platypus is only superficially like that of a bird. It is made from different materials and serves a different purpose.

    " Now, the changes become more complex.A lizard's limbs bend same as ours, while most birds' limbs bend the opposite way. This calls for a 'missing link' with limbs that bent both ways, in which case I don't see how it could move except to flop around."

    There is not enough detailed information here for me to know what specifically is being discussed, but archy has a pelvis which is intermediate between that of reptiles and birds with features of each so it sounds like it addresses the concerns.

    " Next, we're asking the lizard to change its scales into feathers. That's asking the missing link to have had fales or sceathers, which couldn't do the job of either scales or feathers. Different species of lizards have scales specialized for their 'lifestyles', while birds likewise have specialized feathers."

    No "sceathers" needed.

    This is one area in which there has been a lot of recent discovery. In the fossil arena, we have found numerous feathered dinosaurs running the gaunlet from a downy covering to a plume of tail feathers to the marvelous Microraptor which is a small dinosaur with fully formed flight feathers coving both its arms and legs. It was a four winged gliding machine. On the genetic side, we have discovered the cascade of regulatory genes which control the development of feathers.

    " And finally, here's the most difficult of all changes...from cold-blood physiology to that of warm blood. It's simply impossible for there to have been a 'halfway' physiology, as the chemistry differences between cold blood & warm blood are so radically far apart. There are many specifics within each physiology that simply MUST be there to sustain life."

    Yet we can turn back to the platypus for an example of an animal with what many consider to be a physiology halfway or so to warm blooded.

    Returning to the fossils, we see that some dinosaurs had the four chambered heart and pneumatic bones that are associated with birds. And there is also some evidence from the bones of dinosaurs which support warm blooded dinos.
     
  18. UTEOTW

    UTEOTW
    Expand Collapse
    New Member

    Joined:
    May 8, 2002
    Messages:
    4,087
    Likes Received:
    0
    But this leads directly to a topic for which YEers owe an explanation. It has to do with birds and genetics.


    There are a number of homologies that have been discovered between birds and dinosaurs. Current ideas on birds are that they evolved from a group of dinosaurs, often called theropods, which include tyrannosaurs.

    So it should not be surprising that when well preserved t-rex blood vessels were examined that they have similarities to the blood vessels in some birds.

    There have been many finds in recent years of feathered dinosaurs. Some of the these finds have included fully formed flight feathers on theropod dinosaurs. Microraptor is an example. It had fully formed flight feathers on both it front arms / wings and on its legs. Even tyrannosaurs have been found with downy feathers. And I think I remember reading that at least one Archaeopteryx fossil was at first misidentified as a dinosaur.

    Dinosaur fossils have been found that indicate that they, too, had four chambered hearts, not the three chambered hearts of most other reptiles. Interestingly, it seems that crocodiles and their relatives have a four chambered heart. This is an interesting homology because dinosuars and crocodiles are both thought to have evolved from the archosaur branch of reptiles.

    Speaking of which, recent discoveries have shown that the theropod reproduction system is intermediate between that of crocodiles and that of birds. Just what you would expect.

    For a while, it has been observed that theropods, like birds, have air sacs in some of their bones. More recently, it has even been found that the basal theropods possessed these air sacs and the flow through system of respiration of birds.

    There is a tissue, known as the medullary bone, that is only found in extant female birds which has also been found in fossil tyrannosaurs.

    There are even developmental homologies. One would be easiest to see in Vargas & Fallon, The digits of the wing of birds are 1, 2, and 3. a review, J Exp Zoolog B Mol Dev Evol. 2005 May 15;304(3):198-205.

    There are many, many more physical homologies that can be shown between birds and dinosaurs. But I want to move to a different piece of evidence that ties these all together.

    Different researchers looking and different genes have found that birds and crocodiles are very closely related to one another. In a recently and separately created "kinds" paradigm, I am at a loss as to why anyone would expect that birds and crocodiles SPECIFICALLY would be expected to be very closely related to one another. Shouldn't crocs group more closely to other reptiles? Not according to the expectations of common descent and not according to the actual testing.

    LARHAMMAR, D., and R. J. MILNER. 1989. Phylogenetic relationship of birds with crocodiles and mammals, as deduced from protein sequences. Mol. Biol. Evol. 6:693-696.

    HEDGES, S. B. 1994. Molecular evidence for the origin of birds. Proc. Natl. Acad. Sci. USA 91:2621-2624.

    KUMAZAWA, Y., and M. NISHIDA. 1995. Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Mol. Biol. Evol. 12:759-772.

    And from Axe Janke and Ulfir Amason, The Complete Mitochondrial Genome of Alligator mississippiensis and the Separation Between Recent Archosauria (Birds and Crocodiles)

    It is a question that deserves a testible answer. If all of the evidence that leads to the conclusion that birds are dinosaurs is wrong, then why to we see the particular genetics that are observed? If there is an alternate to why birds and crocodiles specifically should be so closely related to one another, could someone present what it is and how we can test that idea especially with regard to differentiating the explanation from that provided by common descent.
     
  19. UTEOTW

    UTEOTW
    Expand Collapse
    New Member

    Joined:
    May 8, 2002
    Messages:
    4,087
    Likes Received:
    0
    Pete

    I do not know if you have had time to digest some of the things from above, but I would like to give you another topic on which to dwell.

    In some of the previous posts, I and other have scratched the surface of some of the ways in which DNA is used to track common ancestry. Things such as different animals with the exact same genes broken by the exact same mutation and animals sharing the same viral insertions in their DNA. We also scratched the surface on how this genetic data generally confirms the expectations from other types of data like fossils.

    What I want to introduce is the idea that you can trace how specific genes evolved by the evidence that is in the genome. It is often claimed by YEers that all mutations cause harm or decrease "specificity" or something else asserting that a series of mutations could not build up the life that we see. One of the common answers is that duplication and mutation are powerful means of creating new genes which can be used to evolve new features. I think Petrel actually gave you some links that discussed this very thing.

    Now I want to give one example here. I am doing this from memory, so please forgive any errors. But I think the general gist is correct.

    The hemoglobin that carries oxygen in your blood is made up of four globins, two are called alpha globins and two are called beta globins. The alpha globins are made by two genes from a group of 7 genes called the alpha cluster. The betas are in a cluster of 6.

    Each cluster also contains about 4 other copies of similar genes that are not functional because of mutations. The seventh alpha is called zeta and is used in the fetus only.

    Now an individual gene is generally broken into pieces. The pieces are called exons and must be connected to one another to make the final gene. The bits inbetween are called introns, these must be spliced out. When looking at the clusters, it becomes obvious that the various genes were made by duplicating an existing DNA segment.

    (Please note that this next bit is something I might have looked up first to confirm, but it is late. It is what I remember. Someone will correct me if I get it wrong.) How do we know they were made by duplication? Well, close examination will show that each individual gene in each cluster is broken into exons in the same way and that the introns, or bits of junk seperating them, are mostly the same. One original alpha was copied and copied, eventually making 7 individual genes.

    Now these copies were able to mutate. A couple became useful enough to be the ones actually incorporated into hemoglobin. Others mutated themselves into uselessness. But the pattern shows that the most likely explanation is that the useful genes of today were created through a process of duplication and mutations.

    YEers are free to step in here and tell us why, instead, we have this pattern. Surely we were not created with defective and unused genes. Surely we did not once have all of them working in some unusual system and we have all lost the same functional genes in the same manner through time.

    Let's take this a step further. If you look around, life can be grouped in a hierarchal manner into larger and larger groups. Evolutionarily, you would expect that members of a goups would be likely to share a common ancestor.

    Now if you look around at other apes, you will see that they share the same division of alpha and beta globins. So do primates. So do all mammals. So so all tetrapods (mammals, reptiles, birds, amphibians). So do most fish. You have to move to larger and larger groups before you find that the grouping that would include lampreys and hagfish with the rest of the animals mentioned above before you find animals without the division into alpha and beta globins. They have only one.

    This allows you to tie down with some confidence where in the past the duplication that gave us the alpha and beta genes happened. You may have already made the connection back to our other topics. By comparing many different genes and their patterns in the genomes of life, you can use such techniques to tie down many different relationships.

    If you take a look, you will also see what I have described here repeated over and over. Most genes have been found to belong to so called gene families where members of each family appear to have been made through repeated duplication events.

    You will also see another recurring theme if you dig. If I remember correctly, the globins that we use for oxygen transport are very similar to proteins that some more primitive organisms use to bind to NO (nitrous oxide). Evolution has a habit of often reusing old parts for new functions and of rarely requiring true novelty.
     
  20. UTEOTW

    UTEOTW
    Expand Collapse
    New Member

    Joined:
    May 8, 2002
    Messages:
    4,087
    Likes Received:
    0
    I am going to give another example, but I am going to be a bit shorter on details.

    There are segments of DNA called retroposons which are easily duplicated and inserted into the genome at diverse places. In humans and other primates there is a particular family of these called Alu sequences. There are very, very many Alu insertions in the human genome. It is possible for these Alu inserts to mutate until they present the proper genetic sequence to mark them as an exon. They can then be spliced into genes potentially making novel and useful genes.

    The paper here discusses a particular Alu insertion that occurred all the way back in the basal ancestor of anthropoid primates. The changes that happened to the Alu sequence through time is then charted by looking at the same sequence in various descendents. Eventually mutation caused the sequence to become an exon which was then used in a novel gene p75TNFR in the ancestor of old world monkeys and apes.

    This case is of particular problem for YEers because we see a useless insert spread throughout the primates and as various lineages split off, we can trace its change to something useful.

    Singer SS, Mannel DN, Hehlgans T, Brosius J, Schmitz J., From "junk" to gene: curriculum vitae of a primate receptor isoform gene, J Mol Biol. 2004 Aug 20;341(4):883-6.
    http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15328599&query_hl=1
     

Share This Page

Loading...