This article explains exactly what endogenous retroviruses are, the many distinctive features that leave no doubt as to their identity, and how they provide crushingly strong evidence for common ancestry. The argument from endogenous retroviruses to evolution in general, and to specific family trees, is to my mind one of the most immediately convincing (compare http://www.talkorigins.org/pdf/comdesc.pdf, 29+ Evidences for Macroevolution, Sec. 4.5).
As the article points out, the odds against any ERV occurring in the same place in humans and chimps is about 1 in 10^4; humans and chimps share 100,000 ERVs in the same locations, and the odds against this would then be 1 in 10^400,000. By my arithmetic, allowing for the 0.1% where there is no match changes this to 1 in 10^399,800, still a ridiculously vast number.
I would also have welcomed numbers showing where gorillas, for instance, fit into the picture, and numbers of ERVs specific to each species.
The final section of this post is addressed to those who, like the author, regard the Bible as divinely inspired but not as literally true. The argument goes back to Maimonides, if not Augustine, and here forms part of the ongoing civil war within the Abrahamic religions between Fundamentalists and Modernists. Not my battle.
Introduction to Endogenous Retroviruses
Advances in biochemical technology since 2000 have allowed us to determine the full DNA sequences for humans and other animals. This new information has illuminated our evolutionary history. A number of patterns in our DNA are consistent with a common ancestry of humans and other primates.
One such genetic feature is the distribution of endogenous retroviruses (ERVs) in our genomes. As most readers know, viruses work by introducing their RNA or DNA into a host cell, and hijacking the host cell’s genetic machinery to start making more copies of the virus. Some viruses, called “retroviruses”, do this by having their RNA transcribed into DNA, which then gets inserted into the cell’s DNA genome. (This is considered “retro”, because normally in a cell DNA is transcribed into RNA, not the other way around). The HIV virus that causes AIDS is an example of a retrovirus. Once the…
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I am posting this page from Jonathan Baker’s Age of Rocks here for several reasons. It is an extremely useful resource, well researched and well-written; the author addresses creationists with humanity and respect, even as he demolishes their position; and the author himself is a committed Christian (why that should matter to me, a free-thinking atheist, is something I explain below).
The evidence presented ranges from tree rings to topography to sedimentology to physical geography to archaeology and anthropology to geochemistry to the fossil record to radiometric dating to astrophysics. Many of these are topics I have touched on, for example in my discussions of the unconformity at Siccar Point, and the slowly cooled multiple lava flows and palaeosols of the Giants’ Causeway.
In each case, the reasoning is briefly described, with links to more detailed discussions, many framed specifically to refute creationist claims. By relegating those claims to second place, the author avoids the common mistake of teaching the very error that he is warning against. At the same time, he pays a respectful attention to his opponents, for reasons that he explains elsewhere in his blog, even as he dismantles their arguments.
Like the authors of EvoAnth and Leaving Fundamentalism, the author is at present a graduate student; welcome examples of how the web is democratising discourse, and how young scientists and educators are using the opportunity.
I commend this piece to all those who have to deal with creationism in schools and elsewhere, alongside such classics as 29+ Evidences for Macroevolution and Index to Creationist Claims, and hope that the author will continue to update and add to it as his own career progresses.
Like Dennis Venema at Biologos and Robert Wiens at Radiometric Dating – A Christian Perspective, the author is a committed Christian, thus helping to give the lie to the claim Read the rest of this entry
Until yesterday, it may just have been possible to accept the claim by Glasgow’s Centre for Intelligent Design (C4ID) that the view it promotes differs from old-fashioned creationism. Not any more. Dr Noble, the Director, writing for C4ID, has used a whole range of traditional creationist arguments in a full-blooded attack on the Scottish Secular Society’s petition, currently before the Scottish Parliament, in which the Society requests
official guidance to bar the presentation in Scottish publicly funded schools of separate creation and of Young Earth doctrines as viable alternatives to the established science of evolution, common descent, and deep time.
Predictably, the C4ID submission  attempts to disguise the fact that “Intelligent Design” is nothing more than a blend of creationism and obfuscation. This has famously been established in court (Kitzmiller vs Dover School Board), and elsewhere. Most relevant to the present petition is the statement to this effect from the Association for Science Education, the UK-wide association of science teachers at all levels, and the UK’s largest teaching subject organisation.
“Macro-evolution … unobserved and speculative”
More interestingly, the C4ID submission illustrates precisely the disinformation that we seek to guard our children against, by itself embracing creationism. It does this by driving a wedge between “micro-evolution” and “macro-evolution,” and admitting that the former of these occurs, while describing the latter. Such dismissal of macro-evolution can have only one implication, the separate creationism to which we are objecting, and the denial of the results of almost two centuries of careful scientific observation. As the submission puts it:
Few people, including the most ardent religious believers, deny that evolution in the form of adaptation is an empirically observed phenomenon. This can be described as ‘micro-evolution’ and it is the sort of variation, in, for example, the beak sizes of finches that Darwin observed in the Galapagos Islands. However, those findings say nothing about how finches arose in the first place. The speculation that evolutionary processes can explain the origin as opposed to the distribution of finches can be referred to as ‘macro-evolution’. This is an unobserved and speculative feature of the theory of evolution. It is therefore inaccurate and confusing to refer simply to ‘evolution’ without clarifying which aspect of the theory is being dealt with.
Some minor points: C4ID mention religion; we did not. C4ID, like all creationists, cannot resist referring back to Darwin, much as some demented opponent of atomic theory might keep on referring back to Dalton. But the main point regard evolution: if macro-evolution didn’t happen, the only alternative is separate creation.
As a commentator (David Bell at FB Secular Scotland) points out, Macro and Micro evolution are the ID version of Ken Ham’s “historical science” and “observable science”.
In a sense, of course, macro-evolution is unobserved, but only in much the sense that the Ice Ages are unobserved. Macro-evolution has not been directly observed over the 3000 or so years of recorded scientific observation because it takes more time than that, and the Ice Ages have not been directly observed by scientists because they happened too early, but in both these examples the evidence is incontrovertible.
Regarding the Ice Ages, we have evidence such as erratic boulders transported by glaciers, scratches on rocks, and massive moraines left behind, as far south as Lueneberg Heath in Germany and Minnesota in America. Regarding macro-evolution, we have, to choose just one well-explored example out of the enormous range available, the evolution of whales from terrestrial hoofed mammals. Here we have two completely independent lines of evidence ; a fossil record showing at least 10 well-defined intermediate forms, either on or close to the ancestral line leading to modern whales and porpoises, and molecular phylogenies (no different in principle from the DNA evidence used every day in our courts to establish family relationships) that show whales as first cousins to a hippopotamus and second cousins to a cow (for a general reader level open-access review, see here).
If the evolution of the blue whale, purely aquatic and the largest animal ever known on this planet, from a small terrestrial wader, does not count as macro-evolution, what does? If this kind of evidence does not remove macro-evolution from the domain of the “unobserved and speculative”, what would?
Or I could have chosen human evolution, where some 20 distinct hominin species have been identified, with steady progression in bipedality, cranial capacity, dentition, and all the other features that distinguish us from apes .
Or birds from non-avian dinosaurs, with the step-by-step evolution of feathers and then of flight. Or amphibia from lobefish. Or sheep and goats. Or dogs, bears, walrus and weasels from a common ancestral carnivore. All beautifully documented in the fossil record, and now supported by molecular phylogenies, along with numerous other examples. There is no lack of well written books explaining these things in highly accessible language , a major website has an entire section devoted to such transitions, and if C4ID are really ignorant of these evolutionary facts, the ignorance is self-imposed.
Having once placed C4ID in its rightful place in the evolution of delusion, their other arguments fall readily into place. We have the usual complaint that we want to put all talk of creationism off-limits, when we explicitly state that we intend no limitation on the discussion of ideas; merely on the misrepresentation of facts. We have the usual claim that an intelligence (or Intelligence) is required to generate new information, as if otherwise information were some kind of conserved entity like energy. We have the claim that all DNA has been shown to be functional – a travesty of even the most extravagant claims made in the current “junk DNA” controversy. We have the vulgar error that the forces driving evolution are random, whereas in fact organisms are sculpted by natural selection. We have the usual inversion of burden of proof, where the unexplained is deemed unexplainable, while those who seek natural explanations for what we do not yet understand are called closed minded. We have the argument that since natural selection sometimes works by elimination (and indeed it does), it can never really work by addition. We even have (was nothing learnt from the debacle at Dover?) irreducible complexity.
Since this is the high-class version of creationism, we also have the lofty argument that, in C4ID’s words,
The neo-Darwinian position that life and the universe, including conscious thought, are the result of blind and purposeless processes gives no reason to believe that our investigations and conclusions have any validity or truth. Students should be aware of this.
This is absurd, as I like many others have said before. If our investigations and conclusions had lacked validity or truth, we would simply not have survived. Indeed, there is now a flourishing if controversial subdiscipline that considers our minds, with both their strengths and weaknesses, as the products of natural selection. Given this, C4ID’s claim that “Students should be aware of this,” when “this” is a doctrine residing only on the philosophical fringe, is breathtaking in its arrogance. (There are of course environments, such as creationist universities and seminaries, where survival is more likely if one’s conclusions lack validity and truth, but the cradle of mankind was not one of them.)
Finally, the C4ID submission accuses the petition, which I helped draft, of making an unwarranted prior assumption of philosophical naturalism; here the author, Doctor Noble, is echoing the ideas of his mentor, Phillip Johnson. As it happens, my one and only contribution to professional-level discussions on the philosophy of science is to prove that in reality we neither need nor use any such assumption. Naturalistic explanations stand or fall in science, as in all human endeavours, on their merits; we use them because they work. Our reason for rejecting non-natural (supernatural? praeternatural? unnatural?) explanations is that they cut no ice. In every case studied, their predictions have turned out to be wrong, or unnecessary, or ambiguous to the point of utter uselessness, and the sorry history of Intelligent design research merely bears this out.
After C4ID, Answers in Genesis comes as comic relief, even if the gag lines are rather predictable. Evolution is a religion and an attack on Christianity (never mind that the spokesperson for BCSE, which supports the petition, is an Anglican priest; as far as AiG is concerned, he’s the wrong kind of Christian). Historical science is in a separate category because it deals with the past and is therefore not testable (what does AiG think geologists and palaeontologists do all day?) Evolutionary naturalism is atheism. Secularists (meaning, I imagine, everyone who does not use Genesis as a geology textbook) are in rebellion against God. Reaching these profound new conclusions the work of any one individual, butrequired the help of AiG‘s research team. And only one thing spoils the joke for me – the knowledge that People with a Mission Ministries, who promote AiG‘s materials, are made welcome in schools throughout Scotland.
Which is why the petition is needed in the first place.
 I have made these links “no-follow”, to avoid boosting the site’s ratings.
 Full text at http://www.scottish.parliament.uk/S4_PublicPetitionsCommittee/General%20Documents/PE1530_A_Centre_for_Intelligent_Design_UK_10.10.14.pdf (warning: extreme boredom alert).
 Some would say “other apes”, since if apes are a clade – a complete set of descendants from some common ancestor – then we are part of it.
 For the fossil record and its tie-in with phylogeny, my personal favourite here is Don Prothero’s Evolution: What the Fossils Say and Why It Matters.
 I refer of course to evolutionary psychology. Here my own position is that all psychology is evolutionary, since I have no other way of explaining the existence of our atavistic shortcomings.