IC All The Way Down, The Grand Human Evolutionary Discontinuity, And Probabilistic Resources

_{Gil Dodgen

November 26, 2009

Intelligent Design}

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The more we learn the more it appears that almost everything of any significance in living systems is irreducibly complex. Multiple systems must almost always be simultaneously modified to proceed to the next island of function. Every software engineer knows this, and living things are fundamentally based on software.

Evolution in the fossil record is consistently characterized by major discontinuities — as my thesis about IC being a virtually universal rule at all levels, from the cell to human cognition and language, would suggest — and the discontinuity between humans and all other living things is the most profound of all. Morphological similarities are utterly swamped by the profound differences exhibited by human language, math, art, engineering, ethics, and much more.

Yes, chimps have been shown to use tools: They can pick up ants with a stick in order to eat them. But there is a big difference between this and designing and building a Cray supercomputer or an F-35 fighter aircraft. To the best of my knowledge our primitive simian ancestors did not advance beyond ant-stick technology.

I continue to be bewildered by the fact that proponents of human evolution by Darwinian mechanisms (i.e., random errors filtered by natural selection) don’t do some simple math to see that the probabilistic resources are hopelessly inadequate, even when the most optimistic assumptions are made.

Unrealistically and optimistically assume the following base-ten orders of magnitude: an average generation time of 10^1 years; an average population of 10^8; and a time frame of 10^7 years.

Do the math. With these probabilistic resources it is assumed by Darwinian theorists that their mechanism produced the most profound and stunning of all evolutionary discontinuities.

I believe that our ancient ancestors were just as smart as we are. They figured out, in their time and with what they had access to, how to make fire, bows and arrows, art, and much more. If I were to be transported back to those times, and be stripped of my current knowledge, I would probably be considered an idiot by the dudes who figured out fire and arrows.

Chimps are still picking up ants with sticks.

Something very profound happened, very suddenly, and Darwinian theory clearly does not explain it.

Comments

Voice Coil, Fully develop...Joseph_{December 6, 2009
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Zachriel, Goldfish are carp.Joseph_{December 6, 2009
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Nakashima, Your referenced papaer did NOT allow the embryo to fully develop. Do you understand that?Joseph_{December 6, 2009
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Mr Joseph, Best of luck and a swift recovery to you!Nakashima_{December 5, 2009
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Mr Zachriel, That is an interesting result, and one that might help elucidate a difference in this discussion between development and heredity. Mr Joseph's claim was actually one about development, not heredity. Even if there was a chemical marker in the egg cell which was respected by the genetic cascade introduced with the nuclear DNA (and here the small distance between the two species is important, goldfish are carp after all), what would the offspring of this egg become? I don't think the new germ cells, created according to the new DNA instructions, would include that signal. Thus, I would predict that the offspring would be carp in all phases of development and adulthood, and would breed true as carp. However, the mitochondria would still have the DNA of the egg donor, so the fact that the mother was a chimera could still be proven from the children. This point has recently been proposed as the basis of a treatment path for diseases related to faults in the mitochondrial DNA of a woman.Nakashima_{December 5, 2009
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Nakashima:
We also know that if we take the DNA of one species and put it into an egg of another, if anything develops it will resemble the species of the EGG.
From what source do we “know” that?
The closest would be this case of nuclear transfer embryos of carp nuclei into goldfish eggs. The result, as expected, were carp. But the somite development were consistent with goldfish.
Sun et al., Cytoplasmic Impact on Cross-Genus Cloned Fish, Biology of Reproduction 2005. In previous studies of animal cloning, as expected, most cloned animals were identical to their nuclear donor species in phenotype. Likewise, in the present study, most development characteristics of the cloned fish were the same as those of nuclear donor common carp. But, strikingly, analysis of somite development and vertebral number led to an unexpected result: vertebral development resembled that of the cytoplasmic recipient.
Zachriel_{December 5, 2009
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Joseph:
I know we can put nuclear DNA from one “species” into another’s egg and get something to develop. But when you look the two allegedly different species are so close that it calls into question the definition of “species”.
Cow oocytes have received nuclei from the following and attained development at least to the blastocyst stage: Sheep Yak Goat Pig Horse Rabbit Mouse Rat Dog Korean Tiger Black Bear Chicken Cynomolgus monkey and Human Cite: Insterspecies Somatic Cell Nuclear Transfer and Preliminary Data for House-Cow/Mouse iSCNT Tercirlioglu, Guo, Trounsen Stem Cell Reviews Volume 2, 2006Voice Coil_{December 5, 2009
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Mr Joseph, You said, We also know that if we take the DNA of one species and put it into an egg of another, if anything develops it will resemble the species of the EGG. But the study tested the rsults and found: The derived ntES cells are human based on karyotype, isogenicity, in situ hybridization, PCR and immunocytochemistry with probes that distinguish between the various species. So passing all of these tests does not acheive "resemble the species" for you? I think you are in a very small minority. And where is the reference that supports your position?Nakashima_{December 5, 2009
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Nakashima, I will look for the reference today. I just had another knee surgery yesterday morning. However I do remeber that it was something Jonathan Wells wrote so while I am laying back I will peruse my literature and see what I can find...Joseph_{December 5, 2009
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Voice Coil, I know we can put nuclear DNA from one "species" into another's egg and get something to develop. But when you look the two allegedly different species are so close that it calls into question the definition of "species".Joseph_{December 5, 2009
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Nakashima, Just because you are incapable of following along doesn't mean I moved anything. The study referenced just shows different types of human cells can be cultivated when nuclear DNA from human somatic cells is put into a rabbit's egg. And that is only once they are isolated at a certain developmental stage. We have no idea what would develop, if anything, if left to do so. So, what needs to be done is for that new embryo to fully develop. If you are correct we should get a human. If I am correct we will get a rabbit-looking organism or nothing- ie death to the developing cells.Joseph_{December 5, 2009
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Mr Joseph, When they get a human please let me know. That defense mechanism is called "moving the goalposts". You said: We also know that if we take the DNA of one species and put it into an egg of another, if anything develops it will resemble the species of the EGG. But the study tested the rsults and found: The derived ntES cells are human based on karyotype, isogenicity, in situ hybridization, PCR and immunocytochemistry with probes that distinguish between the various species. And you said: But DNA does not determine the type of organism- at least there isn’t any scientific evidence for that. But the reference I provided was from an experiment reported in a prestigious scientific journal. Both of those statements have been proven wrong. And you haven't provided a reference to back up your position in the first of those quotes: We also know that if we take the DNA of one species and put it into an egg of another, if anything develops it will resemble the species of the EGG. From what source do we "know" that?Nakashima_{December 5, 2009
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A passage from the above cited article indicates that several assumptions underlie the research and many questions remain. Note in the last sentence how the assumptions are to be tested and the questions answered:
As previously mentioned, nuclear transfer (NT) experiments that employ oocytes and donor cells from two different species are defined as interspecies or interspecies nuclear transfers (iSCNT) (Figure 1). The two main assumptions required for iSCNT are that early developmental events and mechanisms are evolutionarily conserved among mammals and that molecules that regulate these events in mammalian oocytes are capable of interacting with nuclei from another species. The validity of these assumptions, however, deserves vigorous scrutiny. Although most mammalian embryos follow a very similar pattern of ontogenic development, significant differences in many aspects of the process do exist among evolutionarily divergent taxonomic groups (Gilbert and Bolker, 2001). Temporal regulation of developmental events—such as cell-cycle progression, embryonic genome activation (EGA), blastocyst formation, implantation, and organogenesis—differs from species to species. One wonders, therefore, how these developmental processes are regulated in an embryo reconstructed using an oocyte and a donor cell from different species. What constituent of this unusual embryo drives the development? Is there crosstalk between the donor nucleus and the recipient cytoplasm? What developmental program is executed—the oocyte’s, the donor’s, or both? Are the interspecies cybrid cells functional and viable? Is the resulting embryo/fetus viable? Are any live offspring produced, and, if so, are they fertile? These are some of the most important questions that need to be, and can be, addressed by interspecies cloning experiments.
Few of the methods sections of these experiments will note the use of armchairs.Voice Coil_{December 5, 2009
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As of a 2007 review (cite below) 40 studies involving the transfer of nuclei from one species into oocytes of another had been performed. Success varies with interspecies distance. Around 30 studies report attaining embryonic development to the blastula stage, 11 studies attained implantation, and five yielded live offspring. All embryos reflect the donor nucleus, of course. The authors of this study observe that his process can succeed at all only because of highly evolutionarily conserved mammalian developmental mechanisms. Molecules that regulate these events in recipient mammalian oocytes are capable of interacting with nuclei from other species only due to their common ancestry and that high degree of conservation. Success all the way to live birth has been most probable in the most closely related species. See: Interspecies Nuclear Transfer: Implications for Embryonic Stem Cell Biology Zeki Beyhan,1 Amy E. Iager,1 and Jose B. Cibelli Cell Stem Cell 1, November 2007 Sorry, no link, as the article is behind institutional walls. Here is the abstract:
Accessibility of human oocytes for research poses a serious ethical challenge to society. This fact categorically holds true when pursuing some of the most promising areas of research, such as somatic cell nuclear transfer and embryonic stem cell studies. One approach to overcoming this limitation is to use an oocyte from one species and a somatic cell from another. Recently, several attempts to capture the promises of this approach have met with varying success, ranging from establishing human embryonic stem cells to obtaining live offspring in animals. This review focuses on the challenges and opportunities presented by the formidable task of overcoming biological differences among species.
Voice Coil_{December 5, 2009
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Human stem cells but not humans. Got it. When they get a human please let me know.Joseph_{December 5, 2009
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Mr Joseph, IOW try cloning a human using human DNA and a rabbit’s egg. If you are correct we should get a human. This is exactly what that experiment confirmed happens. The stem cells were not an input to the experiment. A nucleus from a human body cell was the input. The egg cell from which the nucleus was removed was from a rabbit. Human DNA + rabbit egg = ?? You say the outcome should have tested as a rabbit. It turns out you are wrong. Human DNA + rabbit egg = human stem cell The derived ntES cells are human based on karyotype, isogenicity, in situ hybridization, PCR and immunocytochemistry with probes that distinguish between the various species. The ntES cells maintain the capability of sustained growth in an undifferentiated state, and form embryoid bodies, which, on further induction, give rise to cell types such as neuron and muscle, as well as mixed cell populations that express markers representative of all three germ layers. Thus, ntES cells derived from human somatic cells by NT to rabbit eggs retain phenotypes similar to those of conventional human ES cells, including the ability to undergo multilineage cellular differentiation.Nakashima_{December 5, 2009
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Nakashima, Your "reference" doesn't even address what I am saying. There is a huge difference between taking stem cells and using only the DNA. We are only discussing the DNA. Take all the nuclear DNA from a human and put it into an egg of a rabbit and see what happens. IOW try cloning a human using human DNA and a rabbit's egg. If you are correct we should get a human.Joseph_{December 5, 2009
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We also know that if we take the DNA of one species and put it into an egg of another, if anything develops it will resemble the species of the EGG.
Wrong. From the abstract: "It was thus verified that due to selection, chondriome components could be transferred from a N. sylvestris donor into a cybrid having all the phenotypic features controlled by the nucleus of the recipient fusion partner (S. tuberosum)." Note that "chondriome components" = cytoplasm. In this study, the cytoplasm of a tobacco cell was fused with the nucleus of a potato cell. The cybrids possessed tobacco cytoplasm and potato nuclei, and the cells grew into potato plants.Arthur Hunt_{December 4, 2009
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Mr Joseph, We also know that if we take the DNA of one species and put it into an egg of another, if anything develops it will resemble the species of the EGG. If you were right it should resemble the species from which the DNA was taken. Can you provide a reference for that? Here's a reference that says the opposite. Embryonic stem cells generated by nuclear transfer of human somatic nuclei into rabbit oocytes To solve the problem of immune incompatibility, nuclear transplantation has been envisaged as a means to produce cells or tissues for human autologous transplantation. Here we have derived embryonic stem cells by the transfer of human somatic nuclei into rabbit oocytes. The number of blastocysts that developed from the fused nuclear transfer was comparable among nuclear donors at ages of 5, 42, 52 and 60 years, and nuclear transfer (NT) embryonic stem cells (ntES cells) were subsequently derived from each of the four age groups. These results suggest that human somatic nuclei can form ntES cells independent of the age of the donor. The derived ntES cells are human based on karyotype, isogenicity, in situ hybridization, PCR and immunocytochemistry with probes that distinguish between the various species. The ntES cells maintain the capability of sustained growth in an undifferentiated state, and form embryoid bodies, which, on further induction, give rise to cell types such as neuron and muscle, as well as mixed cell populations that express markers representative of all three germ layers. Thus, ntES cells derived from human somatic cells by NT to rabbit eggs retain phenotypes similar to those of conventional human ES cells, including the ability to undergo multilineage cellular differentiation.Nakashima_{December 4, 2009
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Yes DNA accounts for heritable differences in bacteria but it does not account for the bacteria. Do you understand the difference? Note 13 on page 68 refers to HGT. There isn't anything in "Signature in the Cell" that says the DNA is the blueprint for the type of organism to be developed. What does Denton mean by "influence"? Geez I have only given you example after example. Here is another- tinker with fruit fly genes and you can get a leg where an antennae should be. You can get one without eyes. However no matter how much we tinker with fruit fly DNA we never get anything but a fruit fly or nothing! And according to you we should start seeing something different. IOW Nakashima you don't have any evidence and what you have provided demonstrates you are wrong.Joseph_{December 4, 2009
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Nakashima, Yes DNA carries heritable information. Blue eyes, sickle-celled anemia, hair color- as geneticist Giuseppe Sermonti says:
All those and hundreds of other alterations have their basis in DNA;
We also know that if we take the DNA of one species and put it into an egg of another, if anything develops it will resemble the species of the EGG. If you were right it should resemble the species from which the DNA was taken. Then there is the fact that every cell in our bodies has the SAME DNA yet the cells are not all the same. A caterpillar and it's butterfly counterpart? SAME DNA. If you want the difference between different colored roses, sure look in the DNA. But you will not find the information for "flower" there. Research the "Altenberg 16"- these guys were/ are looking for "form" and have yet to find it. So the bottom line is yes DNA has the information for making proteins, enzymes and various RNAs. And these molecules can influence development- hair color, eye color, color vision, etc. But DNA does not determine the type of organism- at least there isn't any scientific evidence for that. If there were then scientists should be able to point to the DNA sequences that were altered in order to change a knuckle-walking primate into a fully upright bipedal primate. Not they I expect you to understand any of that...Joseph_{December 4, 2009
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"I mean to point out that there is no evidence for a non-physical basis for heredity." Now you are saying something that I believe everyone in ID would agree with. Also from before, you said about my comments. "I also did note that you had correctly hedged your comments." You can call it hedging but maybe you are reading an accurate assessment of the situation in my comments. My conclusion about this are two fold: The origin of life, the process of organism building (embryo and throughout life) and especially the origin of these processes as well as the appearance of complex novel capabilities is a MYSTERY. That I believe is the position of Michael Behe, William Dembski and most other ID people and should be the position of any reasonable person. We learn more each month but we are still far from any definitive understanding. The second thing is that there is no known naturalistic process that could account for either the origin of life or the origin of complex novel capabilities. That also should be the position of any reasonable person. To believe otherwise is really an act of faith and is no different than belief that it was the Judeo Christian God that was the origin of the these processes. Maybe future science understanding will explain it but as of now there is nothing, especially to support gradualistic changes over time as the mechanism. I especially say gradualistic changes over time have failed because such processes would leave a trail, not just one trail but millions of trails and we have found none. Certainly gradualistic process work to change populations over time but there is no evidence that they have routinely built anything of consequence (I use routinely because I am sure one can find the occasional example of something new appearing through naturalistic processes.) So I believe a reasonable person would concur with what I just said. Allen MacNeill has said that a lot of evolutionary biologists have come to the same conclusions but still hold out hope for naturalistic processes such as his 47+ engines of variation. But they have no proof or even suggestive data as of the present to justify their beliefs but will denounce in extremely vitriolic terms anyone who suggests that an Intelligence was involved. I hope I am clear enough and do not need further parsing of what I mean.jerry_{December 4, 2009
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Mr Jerry, Perhaps you would express this differently: There isn’t any scientific data which demonstrates the DNA is the blueprints. Experiments from Avery onward demonstrate that heredity is based on DNA - its properties or something physically attached to it. When I say, there is no elan vital, I mean to point out that there is no evidence for a non-physical basis for heredity.Nakashima_{December 4, 2009
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"There is no elan vital." Again who said or implied such a thing? Also I have not read Joseph's comments here closely since I come and go as I find time and interest. But usually I agree with all that he says. Just that we express it differently. What in Joseph's comment leads you to your comments.jerry_{December 4, 2009
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Mr Jerry, I did your message closely, and noted that your comments were directed to issues of what, not where. I also did note that you had correctly hedged your comments. But you bring up an important point. There are other channels of information besides the sequence of bases in the DNA. For example, there is the twist of the DNA, is it a or b form? There are changes to the histones, methylation marks, etc. The overarching feature is that these are all material forms of information storage, properties of DNA or physically attached to DNA. There is no elan vital. Your comments on knockout experiments is silly. It implies that someone thinks the DNA has no effect and that is so far from the truth. Who believes that? You'll have to take that question up with Mr Joseph. I don't understand his position either.Nakashima_{December 4, 2009
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"The question is not what the instructions are, but where they are located. If they are not in the physical structure of the DNA molecule, why did Avery’s experiment succeed? Why do knockout and knockin experiments succeed? Why do scientists spend so much time and effort trying to understand DNA? Why is so much effort spent proclaiming that junk DNA isn’t junk?" You really do have to read more closely. First of all I didn't say where all the instructions were or implied nothing was in the DNA. I said they didn't know where everything was and are far from pinpointing how the process unfolds. There is good reason to believe that some of the information is somehow contained outside the DNA. Second there is lots of data that says that there are compounds attached to the DNA that modify its effects. Some have high hopes for all the DNA to have function and in time they may be correct or not correct. Your comments on knockout experiments is silly. It implies that someone thinks the DNA has no effect and that is so far from the truth. Who believes that?jerry_{December 4, 2009
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That is like saying the information for the type of house resides in the building materials.
Don't you think there is a slight difference? The only building materials used in biology are cells. inside each sell reside the complete code, both for building the body, for all the various structures and types of cell required, and even all the code that the cell needs for the job it shall do for the rest of it's life.Cabal_{December 4, 2009
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Mr Jerry, The question is not what the instructions are, but where they are located. If they are not in the physical structure of the DNA molecule, why did Avery's experiment succeed? Why do knockout and knockin experiments succeed? Why do scientists spend so much time and effort trying to understand DNA? Why is so much effort spent proclaiming that junk DNA isn't junk?Nakashima_{December 4, 2009
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Mr Joseph, There isn’t any scientific data which demonstrates the DNA is the blueprints. I referred you to Signature in the Cell. Not in the peer reviwed literature, but still adequate to answer your question. The work of Avery identifying DNA as the part of the cell carrying the heritable information (AKA the blueprints for the rest of the cell) is described on pp. 66-68 of Chapter 3, The Double Helix. Have you read it? Have you noticed note 13 on p 68? Have you turned to the back of the book, to the Notes section? Have you looked on p. 515 for note 13 of Ch. 3? Have you Googled "Avery Macleod McCarty", the authors of the study cited? Have you followed the links to their original 1944 paper which appeared in the peer reviewed Journal of Experimental Medecine? Have you read that paper? I would have to guess that the answer to all these questions is No. Go figure. Mr Joseph, I can remember spoonfeeding my children. I can remember changing their diapers. Conversing with you provides a powerful feeling of nostalgia, or perhaps deja vu. But I digresseth. Lets ask the question another way. Mr Joseph, why do you think, and I use the term broadly, that Dr Meyer wrote a book about DNA? A haiku, dedicated to Mr Joseph, autumn leaves are gone, reading the words, keen lips move; crickets are chirping Is it because DNA holds up the roof of the cell? No. Is it because DNA keeps the cell from leaking when it rains? No. Does DNA provide the plumbing for the cell? No. The wiring? No. The subfloor? No. The Spandrels of San Marcos? No. Is this one of those questions you can't answer? What is your education? What does Denton mean by "influence"? Do I have to add another question to this list, Mr Joseph? Go figure.Nakashima_{December 4, 2009
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As far as I know Joseph is correct. The instructions on how to use all the proteins and modify the various facilitators and inhibitors have not been identified as of yet especially during development and even afterwards. From what I understand they do not fully understand what causes growth or changes in organisms after initial formation. What is so hard to understand. Very interesting questions but in the scheme of things not a contentious issue in the evolution debate. Sometimes I think people just pick arguments for drill. When they do it makes them less credible as you get the feeling that is all they are about.jerry_{December 4, 2009
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