Larry Moran: Vitamin C Pseudogene is Powerful Evidence

Mung, If you use a copyig machineto replicate (copy) a document, did the original self-replicate or did a copier relicate it? The point being is an art forger replicates the painting- the painting does not self-replicate. Joseph

Altering the rate from 0 to > 0 is altering the rate.

So you agree that DNA is an inhibitor and not a catalyst? Mung

DNA is a molecule that has the property of splitting and then reacting with available bases in the local environment in a manner that results in two (near-)identical molecules where before there was only one.

Wow. Where to start. So if I take some DNA out of a cell, it will split, all of it's own accord? So now I have two strands of DNA, and they with both just auto-magically match up with whatever they can find to form two nearly identical (to the original) molecules?

I would call that self-replication, but I am happy to call it something else. The property itself is what is important here.

If only DNA had that property, but alas. Mung

LoL! What do you think the “self” in self-replication means?

No need to mock, Joseph. If I am an art forger, and I manage to re-produce a Rembrandt and pass it off as an original, the original Rembrandt has most certainly self-replicated. Mung

But it is certainly a molecule DNA is a macro-molecule.

and it certainly self-replicates

It certainly does not. Mung

There is a huge difference between a template and a catalyst. And a template does not alter the rate. Joseph

Altering the rate from 0 to >0 is altering the rate. But don't let's quibble, because it doesn't affect my point. I'm happy to substitute "template" for "catalyst"> Elizabeth Liddle

EL

Nonetheless, a template fulfills your definition of a catalyst – it facilitates a reaction, but is unchanged at the end of the process.

Sorry Lizzie, not even close. NOT "facilitates a reaction"- alters the rate of a chemical reaction. shrug, sigh Joseph

EL:

Yes, I know, that, Joseph, and DNA is unchanged at the end of the chain of reactions by which the RNA complement of the DNA strand is created.

TEMPLATE, DNA is the template, not the catalyst. There is a difference- hence the two different words. Self-Sustained Replication of an RNA Enzyme by Tracey A. Lincoln and Gerald F. Joyce Notice how one RNA strand was the TEMPLATE and another CATALYZED one bond. Joseph

Yes, I know, that, Joseph, and DNA is unchanged at the end of the chain of reactions by which the RNA complement of the DNA strand is created. Without the DNA strand the reaction cannot take place (rate=0); with it it can (rate>0), yet it remains unchanged at the end of the reaction. And so it fulfils your definition of a catalyst. However, I would agree that it is an atypical catalyst, and is not normally described as an enzyme. A better (and more common) description of it is as a template. Nonetheless, a template fulfills your definition of a catalyst - it facilitates a reaction, but is unchanged at the end of the process. Elizabeth Liddle

EL:

But DNA is itself a catalyst – it facilitates chemical reactions.

Lizzie- A catalyst is a substance which alters the rate of a chemical reaction but is chemically unchanged at the end of the reaction. A deoxyRIBOZYME can do this but not just plain ole DNA. Joseph

Joseph: I completely agree that DNA requires catalysts to split. But DNA is itself a catalyst - it facilitates chemical reactions. I'm not sure what you want as a reference - this should be clear from any biology text book. Perhaps we are not using the term in the same way? Elizabeth Liddle

Interesting point, kairosfocus, and well taken, although I would, myself, say that whether you regard DNA as "inert" simply depends on your frame of reference (cf geocentricity versus heliocentricity versus a galaxy model). But I actually agree that regarding DNA as inert - as a database, if you like, is a useful way of looking at it. And indeed, if "self-replication" implies that a think self-replicates in all contexts, then I willingly concede that DNA doesn't self-replicate. What it does have, however, is the property of embodying a 2 complete specifications of itself as well as the chemical capacity, when split into those two halves, of recombining with available materials to make two editions whereas before there was one. I am reluctant to call that "inert" in any absolute sense, though - when split into single helices the molecule is far from inert - it's very reactive. But even when in double form, it's still not inert, in a chemical sense, i.e. the sense that inert gases are, because it can be split, given the presence of certain catalysts. I think you would be interested (and probably enjoy) this lecture: http://videolectures.net/eccs07_noble_psb/ I've recommended Denis Noble's book before, but the content of it is here. I think it should be required listening for all biologists! I think he's bang on, but some of his positions may surprise you (including the statement that DNA can be regarded as "inert" :)) Cheers Lizzie However Elizabeth Liddle

Folks: The metabolising, vNSR self-replicating unit is the WHOLE living cell, not part of it. DNA is essentially inert apart from the other nanomachines in the cell that act on its stored info. Indeed, without them, it would fairly rapidly corrupt itself. GEM of TKI kairosfocus

Lizzie:

However, remember that in the first context, the DNA itself catalyses the very compounds that result in the cell,

Citation please. Joseph

Lizzie:

DNA is a molecule that has the property of splitting and then reacting with available bases in the local environment in a manner that results in two (near-)identical molecules where before there was only one.

That's wrong. DNA does not have such a property. In order to split DNA requires enzymes. IOW without a hosy of oter molecule DNA wouldn't do anything by itSELF. Joseph

Joseph: I think the "self" in "self-replication" means that one thing transforms into two replicas of the original (perhaps "auto-replicate" would be a better word). It may only do so in certain contexts, but that doesn't make it not a self- (or auto-)replicator. Nothing can self-replicate unless, for example, it has the materials to hand with which to fabricate the replica. In the case of DNA, the context can be a cell, or a test-tube in which a biological catalyst has been deliberately added. However, remember that in the first context, the DNA itself catalyses the very compounds that result in the cell, and so the thing is a chain reaction, and in the second, again, after the chain reaction has begun, the DNA itself catalyses further splitting and reforming. But lest we get into a war of words about this, the important point, I think, we would agree on: DNA is a molecule that has the property of splitting and then reacting with available bases in the local environment in a manner that results in two (near-)identical molecules where before there was only one. I would call that self-replication, but I am happy to call it something else. The property itself is what is important here. Cheers Lizzie Elizabeth Liddle

Lizzie:

I didn’t say that DNA self-replicates “on its own”.

LoL! What do you think the "self" in self-replication means?

But it is certainly a molecule, and it certainly self-replicates,

No, it doesn't. You do not know what you are talking about. Self-replication means it replicates by itself- so you need to buy a vowel and then come back when you have a clue. Joseph

Joseph: I didn't say that DNA self-replicates "on its own". Many chemical reactions are contingent certain conditions, e.g. a catalyst, or even heat. But it is certainly a molecule, and it certainly self-replicates, and that's because its double helix structure means that under certain conditions it will separate into two single helices, each of which then binds to available bases to form two new doubles, identical to the first,give or take the odd glitch. It can even be done in the lab, which is why DNA "amplification" is a routine technique. http://en.wikipedia.org/wiki/Polymerase_chain_reaction And it's a chain reaction - i.e. once started, its own continuation. Elizabeth Liddle

Correction: in the above, please replace "specification" in paragraph one with "arbitrary chemical sequence which gives rise to the illusion of exquisitely organized complexity via processes which we're very close to understanding, sort of." I'll try to be more careful with loaded and intentionally misleading vocabulary in the future. material.infantacy

Yes but the specifications for producing the organelles which perform replication are themselves encoded in DNA, so hence it self-replicates. If you're going to ask me how that happened, it should be noted that self-replication introduces a significant survival advantage, and there's been a lot of advances made in the area of OOL. This is all very reasonable unless you're a creationist. material.infantacy

No, there isn't any evidence that DNA is a self-replicating molecule. DNA replicates as part of cellular repliction, but DNA on its own does nothing. Joseph

There’s no evidence that DNA is a self-replicating molecule.

There isn't? Elizabeth Liddle

I think the evidence shows that self-replicating molecules, like DNA, are capable of absorbing information from the environment and keeping a record of which variations are able to exploit that environment.

There's no evidence that DNA is a self-replicating molecule. Mung

BA77: I think we're starting to go in circles; we both keep saying the same things to each other. I think the evidence shows that self-replicating molecules, like DNA, are capable of absorbing information from the environment and keeping a record of which variations are able to exploit that environment. I think I'll just leave it there. Except to pass on a joke: What's the worst part about being a Materialist? Not being able to say "I told you so!" after you die. :-) Anyway, I hope you have a good Memorial Day (I'm assuming you live in the USA) with your friends and family. ellazimm

BA77 Your last post is excellent. One of the best posts I've seen from you, and I've seen a lot. It's a keeper. However, next time you find an opportunity to post this response, could you please provide more links to your sources if they are available online (like you normally do)? Thanks way in advance. :) CannuckianYankee

and now the last line you stated ellazimm,,, 'It’s all of them!’ You are right ellazimm, it is all of the evidences taken together that points overwhelmingly to a conclusion, but it is not the conclusion that you would prefer to be true,,, the materialistic and Theistic philosophy make, and have made, several natural contradictory predictions about what evidence we will find. These predictions, and the evidence we have found, can be tested against one another within the scientific method. Steps of the Scientific Method http://www.sciencebuddies.org/science-fair-projects/project_scientific_method.shtml For a quick overview, here are a few: 1.Materialism predicted an eternal universe, Theism predicted a created universe. - Big Bang points to a creation event. - 2. Materialism predicted time had an infinite past, Theism predicted time had a creation. - Time was created in the Big Bang. - 3. Materialism predicted space has always existed, Theism predicted space had a creation (Psalm 89:12) - Space was created in the Big Bang. - 4. Materialism predicted that material has always existed, Theism predicted 'material' was created. - 'Material' was created in the Big Bang. 5. Materialism predicted at the base of physical reality would be a solid indestructible material particle which rigidly obeyed the rules of time and space, Theism predicted the basis of this reality was created by a infinitely powerful and transcendent Being who is not limited by time and space - Quantum mechanics reveals a wave/particle duality for the basis of our reality which blatantly defies our concepts of time and space. - 6. Materialism predicted the rate at which time passed was constant everywhere in the universe, Theism predicted God is eternal and is outside of time - Special Relativity has shown that time, as we understand it, is relative and comes to a complete stop at the speed of light. (Psalm 90:4 - 2 Timothy 1:9)- 7. Materialism predicted the universe did not have life in mind and life was ultimately an accident of time and chance. Theism predicted this universe was purposely created by God with man in mind - Every transcendent universal constant scientists can measure is exquisitely fine-tuned for carbon-based life to exist in this universe. - 8. Materialism predicted complex life in this universe should be fairly common. Theism predicted the earth is extremely unique in this universe - Statistical analysis of the hundreds of required parameters which enable complex life to be possible on earth gives strong indication the earth is extremely unique in this universe. - 9. Materialism predicted much of the DNA code was junk. Theism predicted we are fearfully and wonderfully made - ENCODE research into the DNA has revealed a "biological jungle deeper, denser, and more difficult to penetrate than anyone imagined.". - 10. Materialism predicted a extremely beneficial and flexible mutation rate for DNA which was ultimately responsible for all the diversity and complexity of life we see on earth. Theism predicted only God created life on earth - The mutation rate to DNA is overwhelmingly detrimental. Detrimental to such a point that it is seriously questioned whether there are any truly beneficial mutations whatsoever. (M. Behe; JC Sanford) - 11. Materialism predicted a very simple first life form which accidentally came from "a warm little pond". Theism predicted God created life - The simplest life ever found on Earth is far more complex than any machine man has made through concerted effort. (Michael Denton PhD) - 12. Materialism predicted it took a very long time for life to develop on earth. Theism predicted life to appear abruptly on earth after water appeared on earth (Genesis 1:10-11) - We find evidence for complex photo-synthetic life in the oldest sedimentary rocks ever found on earth - 13. Materialism predicted the gradual unfolding of life to be self-evident in the fossil record. Theism predicted complex and diverse life to appear abruptly in the seas in God's fifth day of creation. - The Cambrian Explosion shows a sudden appearance of many different and completely unique fossils within a very short "geologic resolution time" in the Cambrian seas. - 14. Materialism predicted there should be numerous transitional fossils found in the fossil record, Theism predicted sudden appearance and rapid diversity within different kinds found in the fossil record - Fossils are consistently characterized by sudden appearance of a group/kind in the fossil record, then rapid diversity within the group/kind, and then long term stability and even deterioration of variety within the overall group/kind, and within the specific species of the kind, over long periods of time. Of the few dozen or so fossils claimed as transitional, not one is uncontested as a true example of transition between major animal forms out of millions of collected fossils. - 15. Materialism predicted animal speciation should happen on a somewhat constant basis on earth. Theism predicted man was the last species created on earth - Man himself is the last generally accepted major fossil form to have suddenly appeared in the fossil record. - As you can see when we remove the artificial imposition of the materialistic philosophy, from the scientific method, and look carefully at the predictions of both the materialistic philosophy and the Theistic philosophy, side by side, we find the scientific method is very good at pointing us in the direction of Theism as the true explanation. - In fact it is even very good at pointing us to Christianity: General Relativity, Quantum Mechanics, Entropy & the Shroud Of Turin - video http://www.metacafe.com/watch/5070355 bornagain77

ellazimm, you state the following as lines of evidence; 'it’s not just fossils or morphology or the geographic distribution of species or the genetic evidence. It’s all of them!' First,,, ,,,it’s not just fossils,,, yet,,, Here is a page of quotes by leading paleontologists on the true state of the fossil record: https://docs.google.com/document/pub?id=15dxL40Ff6kI2o6hs8SAbfNiGj1hEOE1QHhf1hQmT2Yg ,,,or morphology,,, yet,,, 'The differences between the creatures that suddenly appear in the Cambrian are enormous. In fact these differences are so large many of these animals are one of a kind. Nothing like them existed before and nothing like them has ever appeared again.” Dr. Raymond G. Bohlin, University of Illinois (B.S., zoology), North Texas State University (M.S., population genetics), University of Texas at Dallas (M.S., Ph.D., molecular biology). Origin of Phyla - The Fossil Evidence - Timeline Graph http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzNobjlobjNncQ&hl=en The unscientific hegemony of uniformitarianism - David Tyler - May 2011 Excerpt: Evolution has been implicitly viewed as a uniformitarian process where the rates may vary but the underlying processes, including the types of variation, are essentially invariant through time. Recent studies demonstrate that this uniformitarian assumption is false, suggesting that the types of variation may vary through time. http://www.arn.org/blogs/index.php/literature/2011/05/16/the_unscientific_hegemony_of_uniformitar Here is a graph showing a partial list of morphologically distinct fossil groups showing their sudden appearance in the fossil record- (without the artificially imposed dotted lines) - Timeline Illustration: http://www.earthhistory.org.uk/wp-content/majorgroups.jpg Punctuated Equilibrium and Patterns from the Fossil Record - Casey Luskin Excerpt: “The Cambrian Explosion is by no means the only “explosion” in the fossil record. One evolutionist concedes that for the origin of fishes, “this is one count in the creationists’ charge that can only evoke in unison from paleontologists a plea of nolo contendere [no contest].” Plant biologists have called the origin of plants an “explosion,” saying, “the … radiation of land (plant) biotas is the terrestrial equivalent of the much-debated Cambrian ‘explosion’ of marine faunas.” Vertebrate paleontologists believe there was a mammal explosion because of the few transitional forms between major mammal groups: “There are all sorts of gaps: absence of gradationally intermediate ‘transitional’ forms between species, but also between larger groups — between, say, families of carnivores, or the orders of mammals.” Another study, “Evolutionary Explosions and the Phylogenetic Fuse,” found a bird (as well as a mammal) “Early Tertiary ‘explosion’” because many bird and mammal groups appear in a short time period lacking immediately recognizable ancestral forms. Finally, others have called the origin of our own genus Homo, “a genetic revolution” where “no australopithecine (ape) species is obviously transitional” leading one commentator to call it, like others called the Cambrian Explosion, a “big bang theory” of human evolution." ,,,or the geographic distribution of species,,, yet,,, This following article reveals how evolutionists avoid falsification from the biogeographical data of finding numerous and highly similar species in widely separated locations: More Biogeographical Conundrums for Neo-Darwinism - March 2010 http://www.evolutionnews.org/2010/03/sea_monkeys_are_the_tip_of_the.html Amazing Insects Defy Evolution – October 2010 Excerpt: India spent tens of millions of years as an island before colliding with Asia. Yet the fossil record contains no evidence that unique species evolved on the subcontinent during this time, http://www.creationsafaris.com/crev201010.htm#20101026a ,,,or the genetic evidence.,,, yet,,, The Biological Big Bang model for the major transitions in evolution - Eugene V Koonin - Background: "Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable; Since evolutionists continually misrepresent the true state of the evidence for molecular sequences, here are several more comments and articles, by leading experts, on the incongruence of molecular sequences to Darwin's theory: https://docs.google.com/document/pub?id=1S5wXsukzkauD5YQLkQYuIMGL25I4fJrOUzJhONvBXe4 ,,,Thus ellazimm, since you are found severely wanting on all fronts of evidence, perhaps you can address the main issue at hand, Perhaps you can scientifically prove that purely material processes are able to generate ANY functional information whatsoever?? At least then ellazimm, if you honestly addressed this MOST important question, I would not view you as intellectually dishonest in this question of origins!!! The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html ====== Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A bornagain77

BA77: "i.e. your argument boils down to, God would not have done it that way therefore neo-Darwinism must be true. As solid proof that this ‘religion driving science’ criticism is correct, it has recently come to light, in peer review, that the strongest arguments for neo-Darwinism, in Darwin’s “Origin Of Species”, are Theological, not scientific, in their basis;" I'm not making an argument right now at all. I did ask the question of what the ID explanation for the varying genome sizes is but I was told off for that. It still is true that genome sizes and the number of chromosomes is not well understood by biologists and that is what I was saying. It's an interesting area of research. No matter what arguments Darwin used (I've not read The Origin of Species actually) my own view of the modern evolutionary synthesis comes from reading fairly current discussions. Lizzie: "and ellazimm clearly knows much more about this than I do" . . . . HAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHAHHHAHAHAHAHAHA :-) I'm very good at copying and pasting, that I will own up to. I'd also like to reiterate my statements made on other threads that it's not just fossils or morphology or the geographic distribution of species or the genetic evidence. It's all of them! All pointing in the same direction, all necessary results of common descent with modification. We don't know every twist and turn but every day a new piece of the puzzle falls into place. And I agree that most people in this controversy are being honest and speaking from the heart. BA77: Just because we do not chose to address all your links does not mean we have not now or in the past considered the arguments presented therein. The Rhizome issue you bring up, for example, is very interesting and I remember discussing it briefly elsewhere. And, if I remember correctly, one of the researchers suggested that while there may be several roots to the tree/bush/shrub of life it does not point to intelligent design. Just that things were messy when life was getting started and there was lots of genetic shuffling and swapping. ellazimm

Furthermore Elizabeth, the materialistic foundation that neo-Darwinism is based on, is shown not to be a complete description of molecular biology! https://uncommondescent.com/culture/are-the-wheels-coming-off-harvard%E2%80%99s-multi-million-endowment-to-find-the-origin-of-life/#comment-381932 ,,, Thus it is shown scientifically, not theologically (as Darwinism does), that neo-Darwinism CANNOT be a complete description of life on earth!!!! bornagain77

Elizabeth, you simply have no basis for your Theological argument: For instance, I provided several links, and can provide several more, that show the evidence from phylogenetics is not nearly as conducive to neo-Darwinian thought as you believe. But you ignore all that evidence and focus only on the studies that were construed to arrive at your desired conclusion. Do Molecular Clocks Run at All? A Critique of Molecular Systematics - Jeffrey H. Schwartz, Bruno Maresca Abstract: Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states (synapomorphies), the latter is not the case. Rather, molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”.. For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central … http://www.mitpressjournals.org/doi/abs/10.1162/biot.2006.1.4.357 A Primer on the Tree of Life - Casey Luskin - 2009 Excerpt: The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified. http://www.discovery.org/a/10651 Pattern pluralism and the Tree of Life hypothesis - 2006 Excerpt: Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about process, is unlikely to be broadly true. http://www.pnas.org/content/104/7/2043.abstract A New Model for Evolution: A Rhizome - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html bornagain77

bornagain77: I think it's very easy to think that people who have adopted a different position than the one you yourself think is "obvious" are being dishonest. One of the reasons I appreciate being here is the opportunity to find out why people who think otherwise from the way I do, do so. That's because I actually believe that most people are not, actually, fundamentally dishonest - most people try to carve out a worldview that makes sense to them. What you call "neo-Darwinism" makes sense to me, and, more importantly, in my view makes sense of the data. You may disagree with my view, but I think you are making a mistake if you think that people like me are being dishonest, and I think people like me are also making a mistake when they think people like you are being dishonest (and they do). I think the most productive approach, myself, is to try to find out why the "other side" thinks the way they do - remaining open, of course, always, to the possibility that they may have a good case! Or, at least, that they may have an important point, or of course that one may have completely misunderstood what they actually think. Science isn't science if it isn't open to rethinking its current models, but that works both ways. A good start, I think, is taking what the "other side" is saying in good faith, at least until there is clear evidence of dishonesty. Mere disagreement isn't that evidence :) Cheers Lizzie Elizabeth Liddle

Mung: yes, I actually agree - common descent is "assumed at the outset", and phylogenies are constructed based on that assumption. However, if it were an invalid assumption, then, I suggest, we would not see either consistent, or highly nested, phylogenies, and phylogenies constructed from different sets of data would not tend to map on to each other. This is what I meant when I said that it is the distribution of characters (e.g. the broken GULO gene, but also anatomical features) that supports common descent, because when those distributions are used to generate a phylogeny, the tend to produced trees that are both deeply nested and consistent across datasets. I would certainly argue (and ellazimm clearly knows much more about this than I do) that "distribution" is not simply "a fancy way of saying they are there or they aren’t", and I struggle to suppress a sense of irony that point being put forward by a pro-ID person! It is because observed characters of living things have a non-random distribution that we can infer that there is some kind of pattern to be inferred,and the pattern that is consistently inferred is a nested hierarchical structure - the structure of a family tree. Linnaeus spotted this, and subsequent data supports it. However, there are processes other than family trees that can produce nested hierarchical patterns, so even the inference (the valid inference, I would argue) of a nested hierarchy does not necessarily allow us to infer common descent. It could, for example, imply a certain kind of design process. But the inference of the pattern it seems to me to be extremely well-founded. And of course, I subscribe to the view that common descent is the most likely explanation for the pattern :) At least partly because it is supported by the spatial distribution of fossils in the geological column. And also of course by longitudinal studies of heritability. @bornagain77: Thank you for your diligent efforts to keep me right! As I said earlier, we really are going to have to agree to disagree on this. You wrote:

Let’s try one more time here Elizabeth,,, you state;

So would finding organisms with the characteristics of a clade with a node at 100 billion years ago(sic) in a stratum dating from 200 billion years ago(sic).,, ‘So disconfirmatory evidence is certainly possible.’

Let’s just see how ‘certainly possible’ this is for you??? How about a ‘precambrian rabbit’ 635 million years ago???

Yes, I think a fossilised "precambrian rabbit" 635 million years would present a major problem for the Theory of Evolution. However, as we don't have one, we don't actually have the problem :) And I confess I don't see anything in your excerpted links that persuades me otherwise. Cheers Lizzie Elizabeth Liddle

ellazimm, whether you like the shallowness of neo-Darwinism being made fun of or not, whether you find it offensive or not that I would make play of this shallowness that would be laughed out of any other rigorous scientific discipline, The plain fact of the matter is that, whether neo-Darwinists know it or not, it always comes down to deception being told (sold), in the name of science, by those committed to the neo-Darwinian framework just to protect their 'preferred' religion of atheistic materialism. In fact you yourself ellazimm have, instead of addressing the evidence honestly to see if it offers solid support for your neo-Darwinian conjectures, made Theological arguments in regards to varying chromosome/gene number (c-value enigma), and you do this whether you realize it or not. i.e. your argument boils down to, God would not have done it that way therefore neo-Darwinism must be true. As solid proof that this 'religion driving science' criticism is correct, it has recently come to light, in peer review, that the strongest arguments for neo-Darwinism, in Darwin's "Origin Of Species", are Theological, not scientific, in their basis; Charles Darwin, Theologian: Major New Article on Darwin’s Use of Theology in the Origin of Species – May 2011 Excerpt: “Charles Darwin’s use of theology in the Origin of Species,” BJHS 2011, argues that Darwin used theology throughout his 1859 masterwork to argue for the truth of his theory of descent with modification by natural causes. Darwin’s theology was not merely negative, entertaining the assumptions of his creationist opponents as hypotheses simply to contradict those assumptions with evidence. Rather, Dilley argues, Darwin employed theology in a positive fashion, as support for his own position. “In the Origin,” Dilley writes, “Darwin used a specific theological view of God’s relationship to natural laws in order to argue for evolution and against special creation.” The Origin supplies abundant evidence of theology in action; as Dilley observes,, http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html further note: From Philosopher to Science Writer: The Dissemination of Evolutionary Thought – May 2011 Excerpt: The powerful theory of evolution hangs on this framework of thought that mandates naturalism. The science is weak but the metaphysics are strong. This is the key to understanding evolutionary thought. The weak arguments are scientific and the strong arguments, though filled with empirical observation and scientific jargon, are metaphysical. The stronger the argument, the more theological or philosophical. http://darwins-god.blogspot.com/2011/05/from-philosopher-to-science-writer.html I think Michael Behe does an excellent job, in this following debate, of pointing out that denying the overwhelming evidence for design in biology makes the science of biology ‘irrational’. As well Dr. Behe makes it clear that materialistic evolutionists themselves, by their own admission in many cases, are promoting their very own religious viewpoint, Atheism, in public schools, and thus are in fact violating the establishment clause of the constitution: Should Intelligent Design Be Taught as Science? Michael Behe debates Stephen Barr - 2010 - video http://www.isi.org/lectures/flvplayer/lectureplayer.aspx?file=v000355_cicero_040710.mp4&dir=mp4/lectures Evolution Is Religion--Not Science by Henry Morris, Ph.D. Excerpt: Evolution is promoted by its practitioners as more than mere science. Evolution is promulgated as an ideology, a secular religion—a full-fledged alternative to Christianity, with meaning and morality,,, Evolution is a religion. This was true of evolution in the beginning, and it is true of evolution still today. Darwinian atheist Michael Ruse - Prominent Philosopher http://www.icr.org/article/455/ This following video, at about the 6:45 minute mark, is very interesting, for in it you see ‘Darwinian Theology’ been played out to its fullest, and most absurd, extent. The Anthropic Principle – Fine Tuning Of The Universe – Michael Strauss PhD. http://www.metacafe.com/watch/4323661/ Some may say the example in the video of 'Darwinian Theology' being played out to its fullest extent is 'overkill' as to the point, but is not that 'extreme extent' what it all really boils down to??? i.e. in final analysis, Does neo-Darwinism not all boil down to the fact that man wants to become his own god, playing by his own rules, instead of giving glory and honor that belongs to almighty God alone? ===================== bornagain77

Also, the number of chromosomes varies dramatically, sometimes even within a species!! From the Wikipedia entry on Karyotype: "A spectacular example of variability between closely related species is the muntjac, which was investigated by Kurt Benirschke and his colleague Doris Wurster. The diploid number of the Chinese muntjac, Muntiacus reevesi, was found to be 46, all telocentric. When they looked at the karyotype of the closely related Indian muntjac, Muntiacus muntjak, they were astonished to find it had female = 6, male = 7 chromosomes. "They simply could not believe what they saw... They kept quiet for two or three years because they thought something was wrong with their tissue culture... But when they obtained a couple more specimens they confirmed [their findings]" Hsu p73-4[14] The number of chromosomes in the karyotype between (relatively) unrelated species is hugely variable. The low record is held by the nematode Parascaris univalens, where the haploid n = 1; the high record would be somewhere amongst the ferns, with the Adder's Tongue Fern Ophioglossum ahead with an average of 1262 chromosomes. Top score for animals might be the shortnose sturgeon Acipenser brevirostrum at a mere 372 chromosomes. The existence of supernumerary or B chromosomes means that chromosome number can vary even within one interbreeding population; and aneuploids are another example, though in this case they would not be regarded as normal members of the population." An 'average' number of chromosomes? Sometimes I'm just glad to be alive to be able to see all this being discovered and studied. ellazimm

JGuy: "Why waste resources making more “junk” genes?" I think that is an issue of genomic studies: at what point is carrying around lots of genomic material become a liability in itself? It seems to be a high threshold though; humans have roughly 3.2 billion base pairs in their genome whereas Pieris japonica (Japanese-native, pale-petal) has roughly 150 billion base pairs. And Polychaos dubium ("Amoeba" dubia) might have as much as 670 billion base pairs. There's some dispute over that I guess. The variety within similar creatures is also staggering: Tetraodon nigroviridis (type of puffer fish) has 385 million base pairs in its genome while Protopterus aethiopicus (marbled lungfish) has 130 billion. Three orders of magnitude difference between two species of fish? Very weird but very interesting. ellazimm

Seems to me if it was a broken vitamin C gene from many common anscestors ago, that the "junk" would have been selected out. Why waste resources making more "junk" genes? Perhaps, evolution was too busy trying to figure out how to select the rare unselectable slightly beneficial mutations to notice. :P JGuy

BA77: Sorry for being short and sharp. I know you've thought about all this a lot and it frustrates you at times that what seems crystal clear to you is not to others. ellazimm

Supports of non-design common descent with modification are accused of being liars, part of a conspiracy to block real science and ignorant of evidence and the failings of their own theories. Makes me feel very welcome.

Think of it as Darwinism in action. You'll come up with something that allows you to cope, or you won't. Me, I've reached an agreement with BA77 that I would pretty much ignore his posts unless they were directed at something I had written. I feel your pain. honestly. If you recall, I even tried to stick up for you. Consider the death of the following thread: https://uncommondescent.com/intelligent-design/the-spirituality-of-physics/ I tried to warn you. Mung

I have nothing to add to what Lizzie had to say; I think she stated the case very well. And I think the debate is getting a bit . . . . unrestrained. I don't know how to respond to statements like: "Got to love this theory, it is strong evidence except when it is not strong evidence,,, frankly this theory is best thing since sliced bread for science,, no real pesky falsifiability criteria to deal with, like actually having to demonstrate that purely material, neo-Darwinian, processes can actually produce completely novel functional genes,,, NO Sir, that is beneath the dignity of neo-Darwinism,, Man all you got to do is wait for the evidence to come to you and make up whatever story you want, with as many big words as possible, collect your paycheck from the taxpayers, and laugh all the way to the bank." In fact, if that's the thanks Lizzie gets for spending lots of time answering your questions and trying to explain then should she even bother in the future? Supports of non-design common descent with modification are accused of being liars, part of a conspiracy to block real science and ignorant of evidence and the failings of their own theories. Makes me feel very welcome. ellazimm

Elizabeth Liddle @45:

Neither shared nor unshared genes indicate common descent or infirm common descent.

Nearing the truth. Common descent is assumed to be true. Therefore, it does not require confirmation or dis-confirmation. What is not assumed is the various phylogenies, iow, what a specific pattern of decent with modification looks like. Now I can accept that as science. Hypothetical phylogenies can be tested. Common descent can't, because it's assumed from the outset. As an interesting aside, phylogenies are inferred. There's got to be a connection there to ID and inference to the best explanation (iow, some phylogenies explain the evidence better than others). Personally, I would admit that shared characters are evidence for descent from a common ancestor and the lack of those shared characters mitigate against a common ancestor. I don't see what's so controversial about that. The alternative, as BA77 points out, is to make the theory look like it can't be tested and is therefore not scientific, as it is not subject to falsification.

That’s why I said that the distribution of the similarities and differences is what is important.

But isn't "distribution" just a fancy way of saying they are there or they aren't? ;) But really, do what extent to these phylogenies take into account what isn't present? So it's the similarities that matter, isn't it? Can we build a phylogeny based on stuff that's missing? Is it done very often? Grr... I don't wanbt o have to haul out my books on phylogenetics, lol. Is this covered in Sober's Evidence and Evolution? I have that handy.

If the broken gene was scattered haphazardly through the primate phylogeny, i.e. in paraphyletic groups it would bring the original phylogeny into question.

Would it really? I don't think it would. I think it just would not confirm the original phylogeny. I think it would only bring the original phylogeny into question if it suggested an alternative phylogeny.

On the other hand, non-shared genes aren’t as interesting from the point of view of establishing relatedness.

Is it reasonable to ask why not? Why is one set of data to be preferred over another? Is it because the first set conforms to the picture we want to establish as the consensus while the other doesn't? I'd really like to understand why the two aren't equally important. I hope you don't have to work tomorrow Lizzie! Overall you've been a great debate partner. Thanks. You too ellazimm, if you're lurking. I love bouncing ideas around. It's such an un-natural thing to do. Mung

Let's try one more time here Elizabeth,,, you state; So would finding organisms with the characteristics of a clade with a node at 100 billion years ago(sic) in a stratum dating from 200 billion years ago(sic).,, 'So disconfirmatory evidence is certainly possible.' Let's just see how 'certainly possible' this is for you??? How about a 'precambrian rabbit' 635 million years ago??? More Questions for Evolutionists - August 2010 Excerpt: First of all, we have 65% of the gene number of humans in little old sponges—an organism that appears as far back as 635 million years ago, about as old as you can get [except for bacteria]. This kind of demolishes Darwin’s argument about what he called the pre-Silurian (pre-Cambrian). 635 mya predates both the Cambrian AND the Edicarian, which comes before the Cambrian (i.e., the pre-Cambrian) IOW, out of nowhere, 18,000 animal genes. Darwinian gradualism is dealt a death blow here (unless you’re a ‘true believer”!). Here’s a quote: “It means there was an elaborate machinery in place that already had some function. What I want to know now is what were all these genes doing prior to the advent of sponge.” (Charles Marshall, director of the University of California Museum of Paleontology in Berkeley.) I want to know, too! https://uncommondescent.com/intelligent-design/more-questions-for-evolutionists/ ================= The new animal phylogeny: Reliability and implications: Excerpt: "The new molecular based phylogeny has several important implications. Foremost among them is the disappearance of "intermediate" taxa between sponges, cnidarians, ctenophores, and the last common ancestor of bilaterians or "Urbilateria."...A corollary is that we have a major gap in the stem leading to the Urbilataria. We have lost the hope, so common in older evolutionary reasoning, of reconstructing the morphology of the "coelomate ancestor" through a scenario involving successive grades of increasing complexity based on the anatomy of extant "primitive" lineages." From Proceedings of the National Academy of Sciences, USA, in 2000 - http://www.pnas.org/content/97/9/4453.full.pdf?ijkey=USJfrrxyih/gM A New Model for Evolution: A Rhizome - May 2010 Excerpt: Thus we cannot currently identify a single common ancestor for the gene repertoire of any organism.,,, Overall, it is now thought that there are no two genes that have a similar history along the phylogenic tree.,,,Therefore the representation of the evolutionary pathway as a tree leading to a single common ancestor on the basis of the analysis of one or more genes provides an incorrect representation of the stability and hierarchy of evolution. Finally, genome analyses have revealed that a very high proportion of genes are likely to be newly created,,, and that some genes are only found in one organism (named ORFans). These genes do not belong to any phylogenic tree and represent new genetic creations. http://darwins-god.blogspot.com/2010/05/new-model-for-evolution-rhizome.html bornagain77

Elizabeth you state: 'Neither shared nor unshared genes indicate common descent or infirm common descent.' But alas you had just argued for the whole thread that vitamin c gene was 'strong' evidence for common descent. Got to love this theory, it is strong evidence except when it is not strong evidence,,, frankly this theory is best thing since sliced bread for science,, no real pesky falsifiability criteria to deal with, like actually having to demonstrate that purely material, neo-Darwinian, processes can actually produce completely novel functional genes,,, NO Sir, that is beneath the dignity of neo-Darwinism,, Man all you got to do is wait for the evidence to come to you and make up whatever story you want, with as many big words as possible, collect your paycheck from the taxpayers, and laugh all the way to the bank. bornagain77

No, bornagain77, it doesn't predict "exactly opposite things", and I didn't say it did! Neither shared nor unshared genes indicate common descent or infirm common descent. It is the distribution of those genes that strongly suggest a specific phylogeny. In the case of the GULO gene, it supports a phylogeny in which the haplorrhini primates form a single clade, which is interesting, because independent data suggest the same, so we have independent data leading to the same conclusion. If they suggested different phylogenies, then that would be a real problem for the theory that haplorrhini primates share a more recent ancestor than all primates do. As for pond scum: what evolutionary theory predicts is that populations will move towards fitness peaks, then stay there. So the similarity of billion year old pond scum and modern scum again neither confirms nor infirms evolutionary theory but is perfectly consistent with it. What would seriously infirm common descent would be genetic phylogenies that were wildly at odds with phylogenies constructed from other characteristics. So would finding organisms with the characteristics of a clade with a node at 100 billion years ago in a stratum dating from 200 billion years ago. So disconfirmatory evidence is certainly possible. Elizabeth Liddle

Man you got to love a theory that predicts exactly opposite things and is still considered true without the bat of an eye! shared = common descent not shared = common descent Thanks for clearing that up Elizabeth. Man this evolutionary science stuff is a breeze, find billion year old pond scum that looks exactly like modern scum, no problem, make a story up and wa la, evolution predicts that, find completely unique genes not found in any other species, no problem, make another story up and wa la, evolution predicts that too. bornagain77

Ah, thanks. But I think I got that. That's why I said that the distribution of the similarities and differences is what is important. If, for example, phylogenetic analyses indicate that primates share a common ancestor, and haplorrhini primates share a more recent common ancestor, and the GULO gene is found to be broken in all haplorrhini primates, but not on others, then that is confirmatory evidence in support of the original phylogeny. If the broken gene was scattered haphazardly through the primate phylogeny, i.e. in paraphyletic grups it would bring the original phylogeny into question. On the other hand, non-shared genes aren't as interesting from the point of view of establishing relatedness. Obviously non-interbreeding populations (i.e. pairs of species) will have a substantial set of non-shared genes each. It doesn't tell you much more than that they are not the same species, which you already know (by definition). The don't mean "not common descent", they just mean "different lineage". Elizabeth Liddle

His point is that if the presence of some "gene," say the Vitamin C pseudogene, counts as evidence for common descent due to the fact that it is shared with other species, why does not the absence of genes (by his count at least 1000 such) not count as evidence against common descent with those same other species by virtue of the fact that they are not shared? It's really a simple question. The simplicity sort of gets lost in all the quotes and links. If shared = common descent then ought not shared mean not common descent? Or is there no disconfirming evidence against common descent? Mung

Well, what it argues for is a distinct lineage. But then we know we are a distinct lineage anyway! So I'm not getting your point. Clearly we differ from our closest primate relatives in a large number of ways, and those differences must be genetic (because clearly we inherit them!) But equally clearly we share a large number of features (including our inability to synthesize vitamin C) and that is reflected in the degree of genotypic similarity. Elizabeth Liddle

correction ; Moreover Elizabeth, why does the fact that we have found over 1000 completely genes within humans NOT count against common descent? bornagain77

Moreover Elizabeth, why does the fact that we have found over 1000 completely genes within humans count against common descent? Human Gene Count Tumbles Again – 2008 Excerpt: Scientists on the hunt for typical genes — that is, the ones that encode proteins — have traditionally set their sights on so-called open reading frames, which are long stretches of 300 or more nucleotides, or “letters” of DNA, bookended by genetic start and stop signals.,,,, The researchers considered genes to be valid if and only if similar sequences could be found in other mammals – namely, mouse and dog. Applying this technique to nearly 22,000 genes in the Ensembl gene catalog, the analysis revealed 1,177 “orphan” DNA sequences. These orphans looked like proteins because of their open reading frames, but were not found in either the mouse or dog genomes.,,, Alternatively, the genes could have been more ancient creations — present in a common mammalian ancestor — that were lost in mouse and dog lineages yet retained in humans. If either of these possibilities were true, then the orphan genes should appear in other primate genomes, in addition to our own. To explore this, the researchers compared the orphan sequences to the DNA of two primate cousins, chimpanzees and macaques. After careful genomic comparisons, the orphan genes were found to be true to their name — they were absent from both primate genomes. (The 1,177 ORFan genes in humans are completely unique to our lineage) http://www.sciencedaily.com/releases/2008/01/080113161406.htm In fact it turns out that the authors of the preceding ‘kick the ORFans out in the street’ paper actually did know that there was clear and unbiased evidence strongly indicating the ORFan genes encoded proteins but chose to ignore that strong evidence in favor of their preconceived evolutionary bias of forcing the genetic sequences of chimps and humans to be as similar as possible. That is EXACTLY how you ARE NOT suppose to practice science!!!: https://uncommondescent.com/intelligent-design/proteins-fold-as-darwin-crumbles/#comment-358547 Moreover new ORFan genes are found to be just as essential as older genes: Age doesn't matter: New genes are as essential as ancient ones - December 2010 Excerpt: "A new gene is as essential as any other gene; the importance of a gene is independent of its age," said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. "New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked." http://www.sciencedaily.com/releases/2010/12/101216142523.htm New Genes in Drosophila Quickly Become Essential - 2010 https://wiki.brandeis.edu/twiki/pub/Bio/MolGenJCSchedule/ChenScience.pdf As well, a large percentage of completely unique ORFan genes are found in each new genome sequenced: ORFan Genes Challenge Common Descent - Paul Nelson - video with references http://www.vimeo.com/17135166 I would like to reiterate that evolutionists cannot even account for the origination of even one unique gene or protein, much less over one thousand completely unique ORFan genes: Could Chance Arrange the Code for (Just) One Gene? “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).” http://www.creationsafaris.com/epoi_c10.htm “Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: – Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences.” http://www.mendeley.com/research/estimating-the-prevalence-of-protein-sequences-adopting-functional-enzyme-folds/ Stephen Meyer - Functional Proteins And Information For Body Plans - video http://www.metacafe.com/watch/4050681/ Poly-Functional Complexity equals Poly-Constrained Complexity http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMjdoZmd2emZncQ etc.. etc.. etc.. The whole point being Elizabeth, is that the evidence for over 1000 completely unique ORFan genes in humans was severely distorted simply because of the researchers preconceived bias that dictated what the evidence should look like. It is just such blatant and prejudiced, bias that IDists continually fight against bornagain77

Elizabeth, while you ignore the fact that you have no rigorous basis to make your common decent argument in the first place, since you have not shown that evolution can even produce a gene in the first place, your evidence, which you refuse to question yourself, is not nearly as strong as you think it is, for example,,, 'It would seem from the evidence of a potential human pseudogene for L-gulono-?-lactone and the presence of the other enzymes necessary for synthesizing vitamin C that humans have lost the ability to make vitamin C. However, there is more to this story. There are only four exons for the gene encoding L-gulono-?-lactone in humans. Two-thirds of the homologous rat gene is completely missing. Most pseudogenes represent 90% of the entire functional gene. This DNA sequence, labeled as a pseudogene, might have an entirely different function than the rat gene. Stating that only the last enzyme is missing for the pathway to convert glucose to vitamin C might imply to the untrained individual that there is a biochemical pathway that leads to a dead end. Actually, the biochemical pathway that leads to the synthesis of vitamin C in rats also leads to the formation of five-carbon sugars in the pentose phosphate pathway present in virtually all animals (Linster and Van Schaftingen 2007). There are several metabolic intermediates in this pathway illustrating that these substances can be used as precursors for many compounds in the cell. In the pentose phosphate pathway, five-carbon sugars are made from glucose (a six-carbon sugar) to be used in the synthesis of DNA, RNA, and many energy producing substances such as ATP and NADPH (Garrett 1999). Animals that synthesize vitamin C can use both pathways illustrated in the simplified diagram below. Humans and the other animals "less fortunate" than rats only use the pentose phosphate pathway.' http://www.icr.org/article/adam-eve-vitamin-c-pseudogenes/ bornagain77

What is evidence for common descent is not the broken GULO gene by itself, but a) its pattern of distribution (it tends to be found within members of a clade, established from other data and b) the patterns of mutations found in pseudo-genes tend to match within those clades, again established from other data. Elizabeth Liddle

Elizabeth; once again you simply do not have the evidence to back up your 'assumptions'!!! For all evidence we have shows loss of information for 'sub-speciation' events; In fact that is the main argument for ID, in that neo-Darwinists have absolutely ZERO concrete evidence for purely material, neo-Darwinian, processes creating ANY functional information WHATSOEVER. And yet you, in your very own post, have 'intelligently' produced more functional information than can reasonably be expected by the entire material processes of the universe over the ENTIRE history of the universe. This is no small matter Elizabeth, you can imagine this or that as what may have happened in the history of life, but the brute fact is that when the rubber meets the road and a thorough search is made for a credible 'consistent' source for functional information, neo-Darwinian processes fail miserably, whereas Intelligence fits the bill perfectly. bornagain77

you hold sequence similarity as evidence for common descent, yet ‘horrendously different’, similarity, as one researcher described the Y chromosome study, does not count against common descent. Elizabeth, it is completely disingenuous for you to view the evidence in such a biased manner.

I disagree. Common descent accommodates both. If both similarities and differences did not co-exist we'd not even be talking about common descent. Take the Vitamin C gene, for example. Say there were no Vitamin C pseudogenes. And all Mammals had this Vitamin C gene. That would be strong evidence of common descent. Say further that not all mammals had this vitamin C gene, that some do and some do not. This also is strong evidence for common descent. Say further, that we have another group of mammals that do not have this Vitamin C gene, but have something that looks remarkably similar. Call it a pseudogene. That too, is strong evidence for common descent. See? Mung

bornagain77, we really are going to have to agree to differ here, I think. We seem to share so few assumptions! For a start, you use the term "subspeciation" which I don't in fact recognise - as I said, ALL speciation starts as "sub-speciation", and must - because every species starts as the bifurcation of an existing single population which, if it is one that human beings know about, we have given a "species" name. Then, in brackets, you imply that this "sub-speciation" is, in brackets, equivalent to "loss of information". Again, I profoundly disagree. When a population, over time, divides into two non-interbreeding populations, each occupying a different occupational niche, I do not regard net information has having been "lost". For example, if a population that inhabits one island is divided by a geological catastrophe that splits it into two, the two halves of the original population may well, over time, evolve down different routes that result in the inability of individuals from each to breed with the other. And it may be that on one island, the environment is rockier than on the other, which is more like the original island. The rocky inhabitants may lose the "information" required to survive in a lush environment and instead "gain" information required to survie in a harsher environment (thicker skin, for instances, a different beak size). Both genotypes possess whatever "information" is required to build phenotypes that can survive in the local conditions. At any rate, be that as it may - that's my model! And I'd claim substantial evidential support for it. However, it's off topic for this OP, and in any case I wish you well. Thanks for sharing your thoughts with me :) Cheers Lizzie PS: to return to the OP, I do, of course, agree,that when the GULO gene was broken, information was lost as to how to synthesise vitamin C. The gene wasn't weeded out, however, probably because the population happened to have access to a vitamin-C diet (it's speculation of course, but primates today tend to inhabit environments where vitamin-C bearing food is abundant). So I'm not saying that useful information, once gained, can never be lost. It can, and deleterious mutations can spread through a population simply through drift. Elizabeth Liddle

Elizabeth, you simply don't have the evidence to back up your assertions!!! You state: 'I am simply making the argument that the evidence does support a “tree of life” in which a single “trunk”, over time, diversified both laterally (into many species) and longitudinally (changes over time).' Deepening Darwin's Dilemma - Jonathan Wells - The Cambrian Explosion - video http://www.metacafe.com/watch/4154263 Jonathan Wells - Cambrian Explosion - video http://www.cross.tv/55196 The unscientific hegemony of uniformitarianism - David Tyler - 2011 Excerpt: The summary of results for phyla is as follows. The pattern reinforces earlier research that concluded the Explosion is not an artefact of sampling. Much the same finding applies to the appearance of classes. http://www.arn.org/blogs/index.php/literature/2011/05/16/the_unscientific_hegemony_of_uniformitar Fossil Finds Show Cambrian Explosion Getting More Explosive - May 2010 Excerpt: Cephalopods, which include marine mollusks like squid, octopus, and cuttlefish, are now being reported in the Cambrian explosion fossils. http://www.evolutionnews.org/2010/05/fossil_finds_show_cambrian_exp.html The Cambrian Explosion Just Got More Explosive - August 2010 - audio http://intelligentdesign.podomatic.com/player/web/2010-08-11T10_49_02-07_00 If this abrupt appearance for all these completely different and unique phyla in the Cambrian was not bad enough for materialists, the fossil record shows there was actually more variety of phyla by the end of the Cambrian explosion than there are today due to extinction. Of Note: "Phyla are broad categories of classification. All fish, amphibians, reptiles, birds and mammals are in the same phylum. Squid, octopi, oysters, clams and snails are in another phylum. Lobsters, crayfish, insects, and millipedes are in still another." Ray Bohlin PhD “A simple way of putting it is that currently we have about 38 phyla of different groups of animals, but the total number of phyla discovered during the Cambrian explosion (including those in China, Canada, and elsewhere) adds up to over 50 phyla. (Actually the number 50 was first quoted as over 100 for a while, but then the consensus became 50-plus.) That means there are more phyla in the very, very beginning, where we found the first fossils, than exist now.” “Also, the animal explosion caught people's attention when the Chinese confirmed they found a genus now called Yunnanzoon that was present in the very beginning of the Cambrian explosion. This genus is considered a chordate, and the phylum Chordata includes fish, mammals and man. An evolutionist would say the ancestor of humans was present then. Looked at more objectively, you could say the most complex animal group, the chordates, were represented at the very beginning, and they did not go through a slow gradual evolution to become a chordate.” Dr. Paul Chien PhD., chairman of the biology department at the University of San Francisco http://www.discovery.org/scripts/viewDB/index.php?command=view&isFellow=true&id=52 etc.. etc.. Elizabeth, I can assure you with 100% certainty, the reality of how life appeared on earth, is far, far, different from what you have pictured in your imagination of gradualness bornagain77

Elizabeth you state: 'But speciation (I’d submit that ALL speciation starts as “sub-speciation” just as even great forks in great trees started as a pair of bifurcating twigs),' Which is exactly what evolutionists must hold to since they can't pass this simple test: Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 Thank Goodness the NCSE Is Wrong: Fitness Costs Are Important to Evolutionary Microbiology Excerpt: it (an antibiotic resistant bacterium) reproduces slower than it did before it was changed. This effect is widely recognized, and is called the fitness cost of antibiotic resistance. It is the existence of these costs and other examples of the limits of evolution that call into question the neo-Darwinian story of macroevolution. http://www.evolutionnews.org/2010/03/thank_goodness_the_ncse_is_wro.html ,, But Elizabeth, even we grant your baseless assertion that sub-speciation (loss of information) must precede primary speciation (gain in functional information, and we test for it, as Lenski has done, here is what we find: These following articles refute Richard E. Lenski's 'supposed evolution' of the citrate ability for the E-Coli bacteria after 20,000 generations of the E-Coli from his 'Long Term Evolution Experiment' (LTEE) which has been going on since 1988: Multiple Mutations Needed for E. Coli - Michael Behe Excerpt: As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1) Other workers (cited by Lenski) in the past several decades have also identified mutant E. coli that could use citrate as a food source. In one instance the mutation wasn’t tracked down. (2) In another instance a protein coded by a gene called citT, which normally transports citrate in the absence of oxygen, was overexpressed. (3) The overexpressed protein allowed E. coli to grow on citrate in the presence of oxygen. It seems likely that Lenski’s mutant will turn out to be either this gene or another of the bacterium’s citrate-using genes, tweaked a bit to allow it to transport citrate in the presence of oxygen. (He hasn’t yet tracked down the mutation.),,, If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell. http://behe.uncommondescent.com/2008/06/multiple-mutations-needed-for-e-coli/ Michael Behe's Quarterly Review of Biology Paper Critiques Richard Lenski's E. Coli Evolution Experiments - December 2010 Excerpt: After reviewing the results of Lenski's research, Behe concludes that the observed adaptive mutations all entail either loss or modification--but not gain--of Functional Coding ElemenTs (FCTs) http://www.evolutionnews.org/2010/12/michael_behes_quarterly_review041221.html Lenski's e-coli - Analysis of Genetic Entropy Excerpt: Mutants of E. coli obtained after 20,000 generations at 37°C were less “fit” than the wild-type strain when cultivated at either 20°C or 42°C. Other E. coli mutants obtained after 20,000 generations in medium where glucose was their sole catabolite tended to lose the ability to catabolize other carbohydrates. Such a reduction can be beneficially selected only as long as the organism remains in that constant environment. Ultimately, the genetic effect of these mutations is a loss of a function useful for one type of environment as a trade-off for adaptation to a different environment. http://www.answersingenesis.org/articles/aid/v4/n1/beneficial-mutations-in-bacteria Lenski's work actually did do something useful in that it proved that 'convergent evolution' is impossible because it showed that evolution is 'historically contingent'. This following video and article make this point clear: Lenski's Citrate E-Coli - Disproof of Convergent Evolution - Fazale Rana - video (the disproof of convergence starts at the 2:45 minute mark of the video) http://www.metacafe.com/watch/4564682 The Long Term Evolution Experiment - Analysis Excerpt: The experiment just goes to show that even with historical contingency and extreme selection pressure, the probability of random mutations causing even a tiny evolutionary improvement in digestion is, in the words of the researchers who did the experiment, “extremely low.” Therefore, it can’t be the explanation for the origin and varieity of all the forms of life on Earth. http://www.scienceagainstevolution.org/v12i11f.htm The loss of 'convergent evolution', as a argument for molecular sequence similarity, is a major blow to neo-Darwinian story telling: Implications of Genetic Convergent Evolution for Common Descent - Casey Luskin - Sept. 2010 Excerpt: When building evolutionary trees, evolutionists assume that functional genetic similarity is the result of inheritance from a common ancestor. Except for when it isn't. And when the data doesn't fit their assumptions, evolutionists explain it away as the result of "convergence." Using this methodology, one can explain virtually any dataset. Is there a way to falsify common descent, even in the face of convergent genetic similarity? If convergent genetic evolution is common, how does one know if their tree is based upon homologous sequences or convergent ones? Critics like me see the logic underlying evolutionary trees to be methodologically inconsistent, unpersuasive, and ultimately arbitrary. http://www.evolutionnews.org/2010/09/implications_of_genetic_conver037841.html Origin of Hemoglobins: A Repeated Problem for Biological Evolution - 2010 Excerpt: When analyzed from an evolutionary perspective, it appears as if the hemoglobins originated independently in jawless vertebrates and jawed vertebrates.,,, This result fits awkwardly within the evolutionary framework. It also contradicts the results of the Long-term Experimental Evolution (LTEE; Lenski) study, which demonstrated that microevolutionary biochemical changes are historically contingent. http://www.reasons.org/origin-hemoglobins-repeated-problem-biological-evolution bornagain77

Hi, bornagain77:

Elizabeth, you simply do not have the evidence to back your assertion for ‘vertical evolution’. Sub-speciation in fact explains the evidence much better than evolution since information is lost in the sub-speciation events, as well it agrees with the overall pattern we find in the fossil record; i.e. abrupt appearance and Disparity of major lifeforms precedes diversity of sub-species within the novel major lifeforms:

I'm not quite sure what you are calling "vertical evolution" but I assume you mean where one population changes over time without diverging, and you seemed to agree that this occurs in an oscillatory fashion in, for example, Galapagos finches, yes? So is your point that you think we do not have evidence for lower frequency changes? Again, let me make it clear that I am not making an anti-ID argument here - ID is perfectly compatible (as Mung rightly reminded me in another thread) with gradual evolutionary change over time (albeit enhanced or directed by Intelligent processes). But I would point to, for example, various transitional series in the fossil record in which incremental changes over time amount to large changes between the beginning and end of the series, as evidence for "vertical evolution" (in the broadest sense of "evolution". But speciation (I'd submit that ALL speciation starts as "sub-speciation" just as even great forks in great trees started as a pair of bifurcating twigs), is indeed a hugely important part of the picture, and is what explains contemporaneous diversity, as opposed to longitudinal diversity. So I won't attempt, here, to make the argument that such changes are a result of "Darwinian" processes, as opposed to "ID" processes (although I am persuaded that they are). I am simply making the argument that the evidence does support a "tree of life" in which a single "trunk", over time, diversified both laterally (into many species) and longitudinally (changes over time). That, it seems to me, is clearly what the data support, which is essentially the pattern formalised by Linnaeus, and is, indeed, what Darwin sought to explain. Behe, for example, disagrees with Darwin's explanation, but he and I assume many other IDists (Mung?) agree on the explanandum. Elizabeth Liddle

Elizabeth, as well, you hold sequence similarity as evidence for common descent, yet 'horrendously different', similarity, as one researcher described the Y chromosome study, does not count against common descent. Elizabeth, it is completely disingenuous for you to view the evidence in such a biased manner. bornagain77

Mung - it's powerful evidence for common descent. I don't see that it is particularly powerful evidence for evolution by means of replication with variance and natural selection. Elizabeth Liddle

Elizabeth, you simply do not have the evidence to back your assertion for 'vertical evolution'. Sub-speciation in fact explains the evidence much better than evolution since information is lost in the sub-speciation events, as well it agrees with the overall pattern we find in the fossil record; i.e. abrupt appearance and Disparity of major lifeforms precedes diversity of sub-species within the novel major lifeforms: The unscientific hegemony of uniformitarianism - David Tyler - May 2011 Excerpt: Evolution has been implicitly viewed as a uniformitarian process where the rates may vary but the underlying processes, including the types of variation, are essentially invariant through time. Recent studies demonstrate that this uniformitarian assumption is false, suggesting that the types of variation may vary through time. http://www.arn.org/blogs/index.php/literature/2011/05/16/the_unscientific_hegemony_of_uniformitar Here is a page of quotes by leading paleontologists on the true state of the fossil record: https://docs.google.com/document/pub?id=15dxL40Ff6kI2o6hs8SAbfNiGj1hEOE1QHhf1hQmT2Yg ================ Elizabeth, for you to stay scientific, you must demonstrate a method that can generate functional information over and above what was already in the parent species, that does not include intelligence. By the way Elizabeth, there is a million dollar prize for demonstrating a purely material process that is capable of producing functional information: "The Origin-of-Life Prize" ® (hereafter called "the Prize") will be awarded for proposing a highly plausible natural-process mechanism for the spontaneous rise of genetic instructions in nature sufficient to give rise to life. The explanation must be consistent with empirical biochemical, kinetic, and thermodynamic concepts as further delineated herein, and be published in a well-respected, peer-reviewed science journal(s). http://lifeorigin.info/ The Law of Physicodynamic Insufficiency - Dr David L. Abel - November 2010 Excerpt: “If decision-node programming selections are made randomly or by law rather than with purposeful intent, no non-trivial (sophisticated) function will spontaneously arise.”,,, After ten years of continual republication of the null hypothesis with appeals for falsification, no falsification has been provided. The time has come to extend this null hypothesis into a formal scientific prediction: “No non trivial algorithmic/computational utility will ever arise from chance and/or necessity alone.” http://www.scitopics.com/The_Law_of_Physicodynamic_Insufficiency.html bornagain77

So the Vitamin C pseudogene is powerful evidence for evolution and common descent, until it isn't. What a wonderful theory. So accommodating. Mung

Well, bornagain77, I should make my position clear: I don't "believe in Design", in the sense that you probably mean it. I agree with IDists that certain phenomena have a signature "complexity" that indicates something special about their origins, but I don't think that special something is what is normally meant by "intelligence". So I'm not an IDist. But unlike some, perhaps, I think that intelligence and design are perfectly amenable to scientific investigation, not surprisingly as I am a cognitive neuroscientist interested in the neural substrates of decision-making! Regarding the Y chromosome argument - I'm not entirely sure what you are saying - are you saying that because chimp Y chromosomes are very different from human Y chromosomes that they can't have a shared ancestor? Why? Obviously there are genetic differences between chimps and humans - why shouldn't these inclued the (very small number of) genes on the Y chromosome? Regarding speciation: ALL speciation is from a "parent lineage". That's what speciation is. And shortly after the speciation process (i.e. when what was a single population has diverged into two non-interbreeding populations) the two daughter populations will be very similar, and one may be more similar to the parent population than the other. And, as you agree, that has been observed. But that is ALL that is postulated by standard biological models of speciation, there isn't another "type of speciation that neo-Darwinists need to make their case" - what alternate "type of speciation" did you have in mind? The speciation of populations into separate non-interbreeding populations that occupy different ecological niches is exactly what standard models of evolution propose. In addition (and perhaps this is what you were referring to), a single population may evolve adaptively over time, without speciating (i.e. without diverging into two populations) by means of changing selection pressures acting on variation, but again, this has been observed in both the field and the lab (what is sometimes called "microevolution". Sure, over the short term, this will tend to be cyclical (as with the Galapagos finches you refer to), but high frequency oscillations do not preclude low-frequency drift, which indeed is what you would predict - if, for example, climate change in the future increases the frequency of el Nino events in the Galapagos, then you'd expect finch beak sizes to cease oscillating and instead drift to a new mean. Wouldn't you? Elizabeth Liddle

Well Elizabeth, You are correct on Behe and if you believe in Design great, but as more evidence accumulates the common ancestry argument is nowhere near as stong as it once was. In fact, as was pointed out, using the very same line of reasoning on Y chromosome, produces a completely different conclusion. Thus you cannot make the argument consistently, which is a very 'suspect' thing as to rigorous methodology you are applying!!! As to this statement of yours;

'in other words it is strong evidence for the process of speciation. Which, indeed, has been actually observed.'

I'm sorry Elizabeth, that is simply not true, unless you mean SUB-speciation from a parent lineage, which is not the type of speciation that neo-Darwinists need to make their case! At one of her many public talks, she [Lynn Margulis] asks the molecular biologists in the audience to name a single unambiguous example of the formation of a new species by the accumulation of mutations. Her challenge goes unmet. Michael Behe - Darwin's Black Box - Page 26 Natural Selection and Evolution's Smoking Gun, - American Scientist - 1997 “A matter of unfinished business for biologists is the identification of evolution's smoking gun,”... “the smoking gun of evolution is speciation, not local adaptation and differentiation of populations.” Keith Stewart Thomson - evolutionary biologist “The central question of the Chicago conference was whether the mechanisms underlying microevolution can be extrapolated to explain the phenomena of macroevolution. At the risk of doing violence to the position of some people at the meeting, the answer can be given as a clear, No.” Roger Lewin - Historic Chicago 'Macroevolution' conference of 1980 Evolution - Tested And Falsified - Don Patton - video http://www.metacafe.com/watch/4036803 All examples of speciation put forth by materialists all turn out to be trivial examples of reproductive isolation: "The closest science has come to observing and recording actual speciation in animals is the work of Theodosius Dobzhansky in Drosophilia paulistorium fruit flies. But even here, only reproductive isolation, not a new species, appeared." from page 32 "Acquiring Genomes" Lynn Margulis. Selection and Speciation: Why Darwinism Is False - Jonathan Wells: Excerpt: there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another.” http://www.evolutionnews.org/2009/05/selection_and_speciation_why_d.html Wired Science: One Long Bluff - Refuting a recent finch speciation claim - Jonathan Wells - Nov. 2009 Excerpt: "Does the report in Wired Science mean that “biologists have witnessed that elusive moment when a single species (of Galapagos finch) splits in two?” Absolutely not." http://www.evolutionnews.org/2009/11/wired_science_one_long_bluff.html This following study is very interesting for the researcher surveyed 130 DNA-based evolutionary trees to see if the results matched what 'natural selection' predicted for speciation and found: Accidental origins: Where species come from - March 2010 Excerpt: If speciation results from natural selection via many small changes, you would expect the branch lengths to fit a bell-shaped curve.,,, Instead, Pagel's team found that in 78 per cent of the trees, the best fit for the branch length distribution was another familiar curve, known as the exponential distribution. Like the bell curve, the exponential has a straightforward explanation - but it is a disquieting one for evolutionary biologists. The exponential is the pattern you get when you are waiting for some single, infrequent event to happen.,,,To Pagel, the implications for speciation are clear: "It isn't the accumulation of events that causes a speciation, it's single, rare events falling out of the sky, so to speak." http://www.newscientist.com/article/mg20527511.400-accidental-origins-where-species-come-from.html?page=2 As well, materialists never mention the fact that the variations found in nature (such as peppered moth color and finch beak size) which are often touted as solid proof of evolution are always found to be cyclical in nature. i.e. The variations are found to vary around a median position with never a continual deviation from the norm. This blatant distortion/omission of evidence led Phillip Johnson to comment in the Wall Street Journal: "When our leading scientists have to resort to the sort of distortion that would land a stock promoter in jail, you know they are in trouble." bornagain77

Hi, bornagain77. Thankyou for your long and informative post. Well, as I said, I wasn't making a anti-design case from the broken GULO story, I was making a shared-ancestry case. I had understood that at least a substantial proportion of the ID community accepted common ancestry of at least fairly large subsets of modern populations, and I'd submit that the fact that the broken GULO gene is found in a primate clade (haplorrhini) defined by independent data is powerful evidence that haplorrhini primates share a common ancestor, even if that common ancestor was Intelligently designed and set down on earth a comparatively short (in conventional geological terms) time ago. Yes, indeed, the guinea pig also has a broken GULO gene, but as guinea pigs cannot be accommodated in the haplorrhini clade (they are not even primates), we must postulate a different ancestral breakage event for the guinea-pig version. Ditto for breakage in various species of passerines and also bats. The interesting thing is the distribution of these pseudogenes which tend to affect complete clades (as derived from independent data). This kind of evidence is the evidence that leads us to infer family tree for living things that includes, at its twigs, different species, in other words it is strong evidence for the process of speciation. Which, indeed, has been actually observed. That seems to me to be extremely well-established, but of course on its own is not an argument for Darwinian evolution, merely for common ancestry and speciation events, which presumably could also be accounted for in ID terms. So we are going to have to agree to differ on the issue of common ancestry! But as I understand it, common ancestry, per se, is no threat to ID, and I believe a number of ID proponents (including Behe, I think) embrace it. Elizabeth Liddle

Good point Smidlee, Elizabeth, if, in your line of reasoning, small 'cherry picked' sequences nail the case shut for you for common descent, why in the world does not the entire Y chromosome, using your very same lime of reasoning, completely blow a hole in your common descent reasoning??? ========== Recent Genetic Research Shows Chimps More Distant From Humans,,, - Jan. 2010 Excerpt: A Nature paper from January, 2010 titled, "Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content," found that Y chromosomes in humans and chimps "differ radically in sequence structure and gene content," showing "extraordinary divergence" where "wholesale renovation is the paramount theme.",,, “Even more striking than the gene loss is the rearrangement of large portions of the chromosome. More than 30% of the chimp Y chromosome lacks an alignable counterpart on the human Y chromosome, and vice versa,,," http://www.evolutionnews.org/2010/04/recent_genetic_research_shows.html A False Trichotomy Excerpt: The common chimp (Pan troglodytes) and human Y chromosomes are “horrendously different from each other”, says David Page,,, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.” https://uncommondescent.com/intelligent-design/a-false-trichotomy/ Chimp and human Y chromosomes evolving faster than expected - Jan. 2010 Excerpt: "The results overturned the expectation that the chimp and human Y chromosomes would be highly similar. Instead, they differ remarkably in their structure and gene content.,,, The chimp Y, for example, has lost one third to one half of the human Y chromosome genes. http://www.physorg.com/news182605704.html The evolutionary scientists of the preceding paper offered some evolutionary 'just so' stories of 'dramatically sped up evolution' for why there are such significant differences in the Y chromosomes of chimps and humans, yet when the Y chromosome is looked at for its rate of change we find there is hardly any evidence for any change at all, much less the massive changes the evolutionists are required to explain. CHROMOSOME STUDY STUNS EVOLUTIONISTS Excerpt: To their great surprise, Dorit and his associates found no nucleotide differences at all in the non-recombinant part of the Y chromosomes of the 38 men. This non-variation suggests no evolution has occurred in male ancestry. http://www.reasons.org/interpreting-genesis/adam-and-eve/chromosome-study-stuns-evolutionists bornagain77

Elizabeth, you can't explain the origination of the GULO gene in the first place, nor can you even explain the origination of one protein by purely materialistic, neo-Darwinian, processes, which makes any conjecture you make as to common descent completely pointless as to you having a rigorous scientific foundation in which to make such claims!! But just to suppose you had any leg to stand on, scientifically, so as to make this conjecture, let's see how strong your evidence actually is compared to how strong you merely 'think' it is: Pseudogenes and the Origin of Humanity: A Response to the Venema Critique of the RTB Human Origins Model, Part 7 - Vitamin C refutation Excerpt: Yet, as biologist Peter Borger points out, fifty percent of the mutations in the primate and guinea pig exon X sequence are identical. In addition, the guinea pig exon X region shows a mutation at position 97, the location in the primate genomes where a deletion took place. These shared features could not have resulted because guinea pigs and primates shared a common ancestor. Instead, they must reflect nonrandom, reproducible changes. http://www.reasons.org/pseudogenes-and-origin-humanity-response-venema-critique-rtb-human-origins-model-part-7 Daniel Fairbanks Cherry Picks Data On Pseudogenes To Prop Up Common Descent - March 2011 Excerpt: What is particularly astonishing about Fairbanks’ citation is that the paper also documents the presence of shared deletions and substitutions in the GULO (Vitamin C) pseudogene of both humans and guinea pigs! Given that humans and guinea pigs are thought to have diverged at the time of the common ancestor with rodents, if the mutations are truly random, a mutational difference between the rat and guinea pig should not be shared by humans. But many mutational differences were shared by humans. Inai et al. argued that this was indicative of mutation hotspots where certain types of mutations occur with a greater frequency. The paper calculates the likelihood of these same substitutions in both humans and guinea pigs to be 1.87 x 10^-12. https://uncommondescent.com/intelligent-design/daniel-fairbanks-cherry-picks-data-on-pseudogenes-to-prop-up-common-descent/ Thus Elizabeth, we find upon a little closer inspection this 'cherry picked' sequence does not provide rigor as to support your claim. Even if you had the right to make the claim towards common ancestry in the first place!!! Further notes: Primate Phylogenetics Challenge Darwin's Tree of Life - Casey Luskin - Excellent Summary Level Audio Podcast http://intelligentdesign.podomatic.com/player/web/2011-05-09T16_32_00-07_00 Why Darwin was wrong about the (genetic) tree of life: - 21 January 2009 Excerpt: Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts - also known as tunicates - are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. "Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another," Syvanen says. . "We've just annihilated the tree of life. It's not a tree any more, it's a different topology entirely," says Syvanen. "What would Darwin have made of that?" http://www.newscientist.com/article/mg20126921.600-why-darwin-was-wrong-about-the-tree-of-life.html Genetic Discoveries Uproot Darwin's Tree Of Life https://docs.google.com/document/d/1S5wXsukzkauD5YQLkQYuIMGL25I4fJrOUzJhONvBXe4/edit?hl=en_US# Widespread ORFan Genes Challenge Common Descent – Paul Nelson – video with references http://www.vimeo.com/17135166 Could Chance Arrange the Code for (Just) One Gene? "our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236)." http://www.creationsafaris.com/epoi_c10.htm "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds” 2004: - Doug Axe ,,,this implies the overall prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 10^77, adding to the body of evidence that functional folds require highly extraordinary sequences." http://www.mendeley.com/research/estimating-the-prevalence-of-protein-sequences-adopting-functional-enzyme-folds/ ================= Embryonic development is now found to be unique for each mammalian species as well i.e. Chimps and humans have unique developmental pathways during embryogenesis!!!: The mouse is not enough - February 2011 Excerpt: Richard Behringer, who studies mammalian embryogenesis at the MD Anderson Cancer Center in Texas said, “There is no ‘correct’ system. Each species is unique and uses its own tailored mechanisms to achieve development. By only studying one species (eg, the mouse), naive scientists believe that it represents all mammals.” http://www.the-scientist.com/news/display/57986/ As well Elizabeth, the fossil record does not support you! Evolution of the Genus Homo - Annual Review of Earth and Planetary Sciences - Tattersall, Schwartz, May 2009 Excerpt: "Definition of the genus Homo is almost as fraught as the definition of Homo sapiens. We look at the evidence for “early Homo,” finding little morphological basis for extending our genus to any of the 2.5–1.6-myr-old fossil forms assigned to “early Homo” or Homo habilis/rudolfensis." “Dr. Leakey produced a biased reconstruction (of 1470/ Homo Rudolfensis) based on erroneous preconceived expectations of early human appearance that violated principles of craniofacial development,” Dr. Timothy Bromage Man is indeed as unique, as different from all other animals, as had been traditionally claimed by theologians and philosophers. Evolutionist Ernst Mayr When we consider the remote past, before the origin of the actual species Homo sapiens, we are faced with a fragmentary and disconnected fossil record. Despite the excited and optimistic claims that have been made by some paleontologists, no fossil hominid species can be established as our direct ancestor. Richard Lewontin - Harvard Zoologist “Something extraordinary, if totally fortuitous, happened with the birth of our species….Homo sapiens is as distinctive an entity as exists on the face of the Earth, and should be dignified as such instead of being adulterated with every reasonably large-brained hominid fossil that happened to come along.” Anthropologist Ian Tattersall (curator at the American Museum of Natural History) bornagain77

@ post 16 I would think that not only you could trace the individual ancestor from the broken GULO gene but also by the man's Y chromosome. If the tribe had broken GULO gene but very different Y chromosomes (like man vs chimps) then I would think this would put serious doubts the broken gene came from the same man. Smidlee

FMU Hunter point is they want to accept incredible odds when it's in their favor yet dismiss them when it's not. If the odds of two species have some of the same "deactivating mutations" of the Vitamin C gene separately are bad then how bad are the odds of creating this gene the start with? Smidlee

That is your opinion. However you cannot support that with genetic data linking to the transformations required.

Well, we can have a decent shot at constructing a phylogeny from genetic data. But I can't support it personally, because it's not my field.

Do you really expect a broken gene to stay intact enough over thousands and thousands of generations all the while form-altering mutations are taking place?

No, like you, I'd expect a lot of mutations, and I'd predict, specifically, that the closer we think other haplorrhini primates are related to us (chimps and bonobos being closer than squirrel monkeys) the more similar their GULO genes to ours would be, and vice versa. That's one of the things that makes pseudogenes so useful in genetics - they accumulate mutations that aren't eliminated by selection. So I'd expect that a phylogeny based on DNA similarities in the GULO gene in happlorhini primates to map closely on to phylogenies constructed from other data. Indeed, that's a direct testable prediction arising from your premise, as I'm sure you agree. And as far as I know, it's supported by evidence. I'll try to look up the research later, gotta go to the post office right now! Cheers Lizzie Elizabeth Liddle

OK, thanks:

Not required. 1- Perhaps it was never a useful gene in all organisms- meaning it could have some other function 2- It was useful but then became disabled in several populations- mutational hot spots exist and a mutation via a common mechanism similarly disabled the working genes. Only populations that could supplement their diet (epigenetics) survived.

Well, those are testable hypotheses, so,cool. But common ancestry of haplorrhini is also a very viable hypothesis, and supported by a large amount of evidence. But sure, it's always good to look at alternative theories, which is why:

...we can make up any story we want to as long as it supports our cause

and as long as we then develop it into a testable hypothesis that we then test. Oh, and it doesn't have to support "our cause" unless, as I assume is the case for both of us, our cause is getting closer to truth about the world :)

Got it…

Yup :) Elizabeth Liddle

The broken GULO gene is not (direct) evidence of universal common ancestry, but it IS evidence for the common ancestry of a large subset of primates, including ourselves, i.e. that human beings descended from an ancestor whose descendents also included squirrel monkeys.

That is your opinion. However you cannot support that with genetic data linking to the transformations required. Do you really expect a broken gene to stay intact enough over thousands and thousands of generations all the while form-altering mutations are taking place? Joseph

Joseph, yes I know my example was from the same, well not species (we are not the same primate species as squirrel monkeys!), but clade, and that was my (fairly simple) point. The broken GULO gene is not (direct) evidence of universal common ancestry, but it IS evidence for the common ancestry of a large subset of primates, including ourselves, i.e. that human beings descended from an ancestor whose descendents also included squirrel monkeys. And as I said, I'm not arguing that all broken genes are harmless (and an intact GULO gene would have saved thousands of sailors from scurvy). That wasn't my point at all - it was simply a point about common ancestry. As for Huntington's - yes, bearers of that gene might well "survive in the wild" long enough to rear young, so selective pressure against it would probably be weak. Conceivably it might even be positive (genes that result in early death of post-infant-rearing individuals my actually benefit their descendents by liberating precious resources). But that's not really the point - the point is not that the Vitamin C gene is evidence for positive selection - it isn't, if anything it's the opposite. What it is evidence for is common ancestry of a very large group of primates that includes ourselves. Elizabeth Liddle

(And we can furthermore assume the individual in question lived in a fruit-rich environment, and so was able to flourish, despite the broken gene)

Sure we can make up any story we want to as long as it supports our cause. Got it... Joseph

I don’t see how “common design” explains it – why would a designer disable a useful gene in a particular subset of species?

Not required. 1- Perhaps it was never a useful gene in all organisms- meaning it could have some other function 2- It was useful but then became disabled in several populations- mutational hot spots exist and a mutation via a common mechanism similarly disabled the working genes. Only populations that could supplement their diet (epigenetics) survived. Joseph

Do you really expect a broken gene to stay intact enough over thousands and thousands of generations all the while form-altering mutations are taking place? Ya see your example is from the SAME species- ie LIMITED common descent. Do you think people with Huntington’s chorea would survive in the wild? Joseph

Well, common descent explains it,because, just as a broken gene in a Dutch South African settler means that his (I think it was a man) descendants inherited the allele for Huntington's chorea, and that all people with Huntington's can trace their ancestry to that individual, it seems likely that all the individuals with a broken GULO gene can trace their ancestry to a common individual. And as those individuals include all members of the Haplorrhini ("dry-nosed") primates,to which we belong, it seems likely, does it not,that we haplorrhini can trace our ancestry back to a common ancestor in whom the first GULO gene was broken? (And we can furthermore assume the individual in question lived in a fruit-rich environment, and so was able to flourish, despite the broken gene). I don't see how "common design" explains it - why would a designer disable a useful gene in a particular subset of species? Elizabeth Liddle

How does common descent expalain it? It just does? Do you really expect a broken gene to stay intact enough over thousands and thousands of generations all the while form-altering mutations are taking place? Common design explains it. There that is all I have to say because apparently that is all that is required. Joseph

OK, thanks - so presumably you are suggesting that primates do not share a common ancestor, yes? That they were all created at some time, in some manner, with unbroken Vitamin C genes? And that they broke at some subsequent time? So how do you explain what would seem to be the odd coincidence of a subset of primates (including ourselves) having a broken version of that same gene? Why should exactly the same gene break in the same way in different lineages? On the other hand if primates have a common ancestor, and in one lineage, the GULO gene was broken, so that all descendents from that lineages inherited the same breakage, we have a neat explanation, even within Sanford's framework. The broken GULO gene is certainly not evidence in itself for evolutionary theory, but it is a powerful argument for common ancestry, is it not? Otherwise, how do you explain the distribution of the breakage across primate species? Elizabeth Liddle

Elizabeth asks; 'if common descent is false, how do you account for the Vitamin C pseudo gene?' If it is truly a broken gene, which I really don't have complete knowledge of, It is explained by Genetic Entropy, which happens to be the true principle governing all 'beneficial' biological adaptations; Is Antibiotic Resistance evidence for evolution? - 'The Fitness Test' - video http://www.metacafe.com/watch/3995248 The following study surveys four decades of experimental work, and solidly backs up the preceding conclusion that there has never been an observed violation of genetic entropy: “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain - Michael Behe - December 2010 Excerpt: In its most recent issue The Quarterly Review of Biology has published a review by myself of laboratory evolution experiments of microbes going back four decades.,,, The gist of the paper is that so far the overwhelming number of adaptive (that is, helpful) mutations seen in laboratory evolution experiments are either loss or modification of function. Of course we had already known that the great majority of mutations that have a visible effect on an organism are deleterious. Now, surprisingly, it seems that even the great majority of helpful mutations degrade the genome to a greater or lesser extent.,,, I dub it “The First Rule of Adaptive Evolution”: Break or blunt any functional coded element whose loss would yield a net fitness gain.(that is a net 'fitness gain' within a 'stressed' environment i.e. remove the stress from the environment and the parent strain is always more 'fit') http://behe.uncommondescent.com/2010/12/the-first-rule-of-adaptive-evolution/ Michael Behe talks about the preceding paper on this podcast: Michael Behe: Challenging Darwin, One Peer-Reviewed Paper at a Time - December 2010 http://intelligentdesign.podomatic.com/player/web/2010-12-23T11_53_46-08_00 Genetic Entropy, outlined by John Sanford in his book Genetic Entropy & the Mystery of the Genome, is when 'slightly detrimental' mutations, which are far below the power of natural selection to remove from a genome, slowly build up in a species/kind over long periods of time and lead to Genetic Meltdown. Evolution Vs Genetic Entropy - Andy McIntosh - video http://www.metacafe.com/watch/4028086 bornagain77

But what is the alternative explanation? Sure, evolutionary theory depends on more than "breaking things", but the question was just about common descent - if common descent is false, how do you account for the Vitamin C pseudo gene? I'm not saying you can't, but that that is the question :) Common descent explains it beautifully. Elizabeth Liddle

Whoa nellie- don't ya think that common descent requires more than breaking things? IOW just how does universal common descet explain it? It just does? Are you saying that an organism with a broken vitamin c gene is more viable than an organism with a functioning VC gene? Can you demonstrate such a thing? Joseph

Whoa, Nellie. What is the alternative explanation for the presence of the vitamin C pseudo-gene if not common descent? mike1962

At least he's reading the book. paragwinn

O/T: Darwin, Thomists, and secondary causality Mung

Larry Moran is very easy to explain. If he's wrong (which he is) he has squandered his life and career on a lie, and he knows it. It's just that simple. GilDodgen

This is classic Dr. Hunter: "Evolution and common descent have failed to explain how the original vitamin C gene could have arisen. In fact they fail to explain how any protein could have arisen. They have also failed to explain how all of biology could have arisen. This is not a good start." LOL,,, Definitely not a good start Dr. Hunter,, Not a good start at all! ==================== B. Reith Knockin On My Door - music video http://www.youtube.com/watch?v=_C4VzCpA19Y bornagain77

No prediction, no retrodiction, and no falsification. Evolution and common descent do not prediction the vitamin C pseudogene, and they are not harmed if there was no such thing. This in addition to the fact that evolution and common descent do not explain how the original gene could have arisen in the first place. Moran’s assertion that the vitamin C pseudogene is powerful evidence for his unlikely idea appears to be just that, an empty assertion.

It do appear that way. Funny that Moran would be discussing this already. I wonder what he's goingto do when he gets to the Appendix in Wells' book (Appendix: The Vitamin C Pseudogene). My guess, he'll disregard everything Wells writes about it in the Appendix, claiming he's already dealt with the topic. Mung